PMID- 15101094 OWN - NLM STAT- in-data-review DA - 20040421 IS - 1009-3095 VI - 5 IP - 6 DP - 2004 Jun TI - A CHASE domain containing protein kinase OsCRL4, represents a new AtCRE1-like gene family in rice. PG - 629-33 AB - AtCRE1 is known to be a cytokinin receptor in Arabidopsis. The AtCRE1 protein contains CHASE domain at the N-terminal part, followed by a transmitter (histidine kinase) domain and two receiver domains. The N-terminal CHASE domain of AtCRE1 contains putative recognition sites for cytokinin. Five CHASE domains containing proteins were found in rice, OsCRL1a, OsCRL1b, OsCRL2, OsCRL3, and OsCRL4. OsCRL1a, OsCRL1b, OsCRL2 and OsCRL3 contain the four domains existing in CRE1, whereas OsCRL4 only contains the CHASE domain and a putative Ser/Thr protein kinase domain. The authors cloned the encoding gene OsCRL4 and found that it represents a new member of the cytokinin receptor protein in rice. AD - State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310029, China. FAU - Han, Qiu-Min AU - Han QM FAU - Jiang, Hua-Wu AU - Jiang HW FAU - Qi, Xiao-Peng AU - Qi XP FAU - Yu, Jie AU - Yu J FAU - Wu, Ping AU - Wu P LA - eng PT - Journal Article PL - China TA - J Zhejiang Univ Sci JID - 100954270 SB - IM EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 PST - ppublish SO - J Zhejiang Univ Sci 2004 Jun;5(6):629-33. PMID- 15100403 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - Genome-Wide Analysis of Spatial Gene Expression in Arabidopsis Flowers. AB - We have compared the gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous with that of wild-type plants using a flower-specific cDNA microarray and a whole genome oligonucleotide array. By combining the data sets from the individual mutant/wild type comparisons, we were able to identify a large number of genes that are, within flowers, predicted to be specifically or at least predominantly expressed in one type of floral organ. We have analyzed the expression patterns of several of these genes by in situ hybridization and found that they match the predictions that were made based on the microarray experiments. Moreover, genes with known floral organ-specific expression patterns were correctly assigned by our analysis. The vast majority of the identified transcripts are found in stamens or carpels, whereas few genes are predicted to be expressed specifically or predominantly in sepals or petals. These findings indicate that spatially limited expression of a large number of genes is part of flower development and that its extent differs significantly between the reproductive organs and the organs of the perianth. AD - California Institute of Technology, Division of Biology 156-29, Pasadena, California 91125. AU - Wellmer F AU - Riechmann JL AU - Alves-Ferreira M AU - Meyerowitz EM LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.021741 [doi] AID - tpc.021741 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100402 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - COTYLEDON VASCULAR PATTERN2-Mediated Inositol (1,4,5) Triphosphate Signal Transduction Is Essential for Closed Venation Patterns of Arabidopsis Foliar Organs. AB - Vein patterns in leaves and cotyledons form in a spatially regulated manner through the progressive recruitment of ground cells into vascular cell fate. To gain insight into venation patterning mechanisms, we have characterized the cotyledon vascular pattern2 (cvp2) mutants, which exhibit an increase in free vein endings and a resulting open vein network. We cloned CVP2 by a map-based cloning strategy and found that it encodes an inositol polyphosphate 5' phosphatase (5PTase). 5PTases regulate inositol (1,4,5) triphosphate (IP3) signal transduction by hydrolyzing IP3 and thus terminate IP3 signaling. CVP2 gene expression is initially broad and then gradually restricted to incipient vascular cells in several developing organs. Consistent with the inferred enzymatic activity of CVP2, IP3 levels are elevated in cvp2 mutants. In addition, cvp2 mutants exhibit hypersensitivity to the plant hormone abscisic acid. We propose that elevated IP3 levels in cvp2 mutants reduce ground cell recruitment into vascular cell fate, resulting in premature vein termination and, thus, in an open reticulum. AD - Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520-8104. AU - Carland FM AU - Nelson T LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.021030 [doi] AID - tpc.021030 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100401 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - Determinants of Plant U12-Dependent Intron Splicing Efficiency. AB - Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated. AD - Department of Gene Expression, Adam Mickiewicz University, Poznan 60-371, Poland. AU - Lewandowska D AU - Simpson CG AU - Clark GP AU - Jennings NS AU - Barciszewska-Pacak M AU - Lin CF AU - Makalowski W AU - Brown JW AU - Jarmolowski A LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.020743 [doi] AID - tpc.020743 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100400 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - P-Type ATPase Heavy Metal Transporters with Roles in Essential Zinc Homeostasis in Arabidopsis. AB - Arabidopsis thaliana has eight genes encoding members of the type 1B heavy metal-transporting subfamily of the P-type ATPases. Three of these transporters, HMA2, HMA3, and HMA4, are closely related to each other and are most similar in sequence to the divalent heavy metal cation transporters of prokaryotes. To determine the function of these transporters in metal homeostasis, we have identified and characterized mutants affected in each. Whereas the individual mutants exhibited no apparent phenotype, hma2 hma4 double mutants had a nutritional deficiency phenotype that could be compensated for by increasing the level of Zn, but not Cu or Co, in the growth medium. Levels of Zn, but not other essential elements, in the shoot tissues of a hma2 hma4 double mutant and, to a lesser extent, of a hma4 single mutant were decreased compared with the wild type. Together, these observations indicate a primary role for HMA2 and HMA4 in essential Zn homeostasis. HMA2promoter- and HMA4promoter-reporter gene constructs provide evidence that HMA2 and HMA4 expression is predominantly in the vascular tissues of roots, stems, and leaves. In addition, expression of the genes in developing anthers was confirmed by RT-PCR and was consistent with a male-sterile phenotype in the double mutant. HMA2 appears to be localized to the plasma membrane, as indicated by protein gel blot analysis of membrane fractions using isoform-specific antibodies and by the visualization of an HMA2-green fluorescent protein fusion by confocal microscopy. These observations are consistent with a role for HMA2 and HMA4 in Zn translocation. hma2 and hma4 mutations both conferred increased sensitivity to Cd in a phytochelatin-deficient mutant background, suggesting that they may also influence Cd detoxification. AD - Department of Genetics, University of Melbourne, Australia 3010. AU - Hussain D AU - Haydon MJ AU - Wang Y AU - Wong E AU - Sherson SM AU - Young J AU - Camakaris J AU - Harper JF AU - Cobbett CS LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.020487 [doi] AID - tpc.020487 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100399 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - The transparent testa4 Mutation Prevents Flavonoid Synthesis and Alters Auxin Transport and the Response of Arabidopsis Roots to Gravity and Light. AB - We examined whether flavonoids act as endogenous auxin transport regulators during gravity vector and light intensity changes in Arabidopsis thaliana roots. Flavonoid deficient transparent testa4 [tt4(2YY6)] seedlings had elevated root basipetal auxin transport compared with the wild type, consistent with the absence of a negative auxin transport regulator. The tt4(2YY6) roots had delayed gravitropism that was chemically complemented with a flavonoid intermediate. Flavonoid accumulation was found in wild-type columella cells, the site of gravity perception, and in epidermal and cortical cells, the site of differential growth, but flavonoid accumulation was absent in tt4(2YY6) roots. Flavonoid accumulation was higher in gravity-stimulated root tips as compared with vertical controls, with maximum differences coinciding with the timing of gravitropic bending, and was located in epidermal cells. Exogenous indole-3-acetic acid (IAA) also elevated flavonoid accumulation, suggesting that flavonoid changes in response to gravity might be partly as a result of changing IAA distribution. Acropetal IAA transport was also elevated in roots of tt4(2YY6). Flavonoid synthesis was repressed in the dark, as were differences in root acropetal transport in tt4(2YY6). These results are consistent with light- and gravity-induced flavonoid stimulation that alters auxin transport in roots and dependent physiological processes, including gravitropic bending and root development. AD - Department of Biology, Wake Forest University, Winston-Salem, North Carolina 27109. AU - Buer CS AU - Muday GK LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.020313 [doi] AID - tpc.020313 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100397 OWN - NLM STAT- publisher DA - 20040421 IS - 1040-4651 DP - 2004 Apr 20 TI - Viral Virulence Protein Suppresses RNA Silencing-Mediated Defense but Upregulates the Role of MicroRNA in Host Gene Expression. AB - Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are processed by the ribonuclease Dicer from distinct precursors, double-stranded RNA (dsRNA) and hairpin RNAs, respectively, although either may guide RNA silencing via a similar complex. The siRNA pathway is antiviral, whereas an emerging role for miRNAs is in the control of development. Here, we describe a virulence factor encoded by turnip yellow mosaic virus, p69, which suppresses the siRNA pathway but promotes the miRNA pathway in Arabidopsis thaliana. p69 suppression of the siRNA pathway is upstream of dsRNA and is as effective as genetic mutations in A. thaliana genes involved in dsRNA production. Possibly as a consequence of p69 suppression, p69-expressing plants contained elevated levels of a Dicer mRNA and of miRNAs as well as a correspondingly enhanced miRNA-guided cleavage of two host mRNAs. Because p69-expressing plants exhibited disease-like symptoms in the absence of viral infection, our findings suggest a novel mechanism for viral virulence by promoting the miRNA-guided inhibition of host gene expression. AD - Institute of Molecular and Cell Biology, National University of Singapore, Singapore 117609; Department of Biological Sciences, National University of Singapore, Singapore 117609. AU - Chen J AU - Li WX AU - Xie D AU - Peng JR AU - Ding SW LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1105/tpc.018986 [doi] AID - tpc.018986 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 20;. PMID- 15100247 OWN - NLM STAT- in-data-review DA - 20040421 IS - 0022-1554 VI - 52 IP - 5 DP - 2004 May TI - Uptake of a Fluorescent Dye as a Swift and Simple Indicator of Organelle Intactness: Import-competent Chloroplasts from Soil-grown Arabidopsis. PG - 701-4 AB - We developed a rapid and reliable technique for specifically staining intact chloroplasts using the fluorescent dye carboxyfluorescein diacetate. Intact, import-competent chloroplasts were isolated simply and rapidly from soil-grown Arabidopsis thaliana plants, with yields of 20 +/- 5 micro g chlorophyll per g FW, greater than previously reported yields from soil-grown ARABIDOPSIS: Traditional chloroplast isolation buffers sometimes contain low concentrations (<10 mM) sodium ascorbate as a general-purpose anti-oxidant, but we found that only Arabidopsis chloroplasts isolated in the presence of high concentrations (50-100 mM) of sodium ascorbate in the initial grinding buffer were import-competent. (J Histochem Cytochem 52:701-704, 2004) AD - Plant Biochemistry Laboratory (JK,HVS,AM) and Plant Anatomy and Physiology Laboratory (AS), The Royal Veterinary and Agricultural University, Copenhagen, Denmark. FAU - Schulz, Alexander AU - Schulz A FAU - Knoetzel, Jurgen AU - Knoetzel J FAU - Scheller, Henrik V AU - Scheller HV FAU - Mant, Alexandra AU - Mant A LA - eng PT - Journal Article PL - United States TA - J Histochem Cytochem JID - 9815334 SB - IM EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 PST - ppublish SO - J Histochem Cytochem 2004 May;52(5):701-4. PMID- 15100225 OWN - NLM STAT- publisher DA - 20040421 IS - 1083-351X DP - 2004 Apr 20 TI - Characterization of the heme environment in Arabidopsis thaliana fatty acid alpha-dioxygenase-18. AB - Plant alpha dioxygenases (PADOX) are hemoproteins in the myeloperoxidase family. We have used a variety of spectroscopic, mutagenesis and kinetic approaches to characterize the heme environment in Arabidopsis thaliana PADOX-1. Recombinant PADOX-1 purified to homogeneity contained one mol of heme bound tightly, but non-covalently, per protein monomer. Electronic absorbance, electron paramagnetic resonance and magnetic circular dichroism spectra showed a high-spin ferric heme that could be reduced to the ferrous state by dithionite. Cyanide bound relatively weakly in the ferric PADOX-1 heme vicinity (Kd ~ 10 mM) but did not shift the heme to the low-spin state. Cyanide was a very strong inhibitor of the fatty acid oxygenase activity (Ki ~ 5 M), and increased the Km value for oxygen but not that for fatty acid. Spectroscopic analyses indicated that carbon monoxide, azide, imidazole, and a variety of substituted imidazoles did not bind appreciably in the ferric PADOX-1 heme vicinity. Substitution of His163 and His389 with cysteine, glutamine, tyrosine, or methionine resulted in variable degrees of perturbation of the heme absorbance spectrum and oxygenase activity, consistent with His389 serving as the proximal heme ligand and indicating that the heme has a functional role in catalysis. Overall, A. thaliana PADOX-1 resembles a b-type cytochrome, though with much more restricted access to the distal face of the heme than seen in most other myeloperoxidase family members, explaining the previously puzzling lack of peroxidase activity in the plant protein. PADOX-1 is unusual in that it has a high-affinity, inhibitory, cyanide binding site distinct from the distal heme face and the fatty acid site.e AD - Univ of TX Hlth Sci Cent at Houston, Houston, TX 77030. AU - Liu W AU - Rogge CE AU - Bambai B AU - Palmer G AU - Tsai AL AU - Kulmacz RJ LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/04/22 05:00 MHDA- 2004/04/22 05:00 AID - 10.1074/jbc.M401779200 [doi] AID - M401779200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Apr 20;. PMID- 15098125 OWN - NLM STAT- publisher DA - 20040420 IS - 0032-0935 DP - 2004 Apr 20 TI - Light conditions influence specific defence responses in incompatible plant-pathogen interactions: uncoupling systemic resistance from salicylic acid and PR-1 accumulation. AB - In incompatible plant-pathogen interactions, disease resistance is generated by rapid activation of a multitude of plant defence reactions. Little is known about the dependency of these resistance responses on external factors. The plasticity of plant defence mechanisms in terms of light conditions is studied here. Interaction of Arabidopsis thaliana (L.) Heynh. with an avirulent strain of Pseudomonas syringae pv. maculicola in the dark resulted in increased apoplastic bacterial growth and therefore reduced local resistance as compared to an infection process in the presence of light. Several characteristic defence reactions, including activation of phenylalanine ammonia-lyase, accumulation of salicylic acid (SA), expression of the pathogenesis-related protein PR-1 and the development of a microscopically defined hypersensitive response, proved to be light dependent. In contrast, the extent of the oxidative burst, as estimated by induction of the protectant gene glutathione- S-transferase, was not weakened by the absence of light. Moreover, pathogen-induced accumulation of jasmonic acid, production of the phytoalexin camalexin and transcriptional induction of a pathogen-inducible myrosinase were even more pronounced in the dark. Apart from affecting local defence responses, light also influenced the establishment of systemic acquired resistance (SAR). SAR development in response to infection by avirulent bacteria was completely lost when the primary infection process occurred in the absence of light. SAR developed both under medium (70 micromol photons m(-2) s(-1)) and strong (500 micromol photons m(-2) s(-1)) light conditions but was in the latter case not associated with an accumulation of SA and PR-1 in systemic leaves, demonstrating that SAR can be executed independently from these molecular SAR markers. Our results are consistent with the notion that SA accumulation in infected primary leaves is necessary for induction of systemic resistance and indicate that defence mechanisms different from SA signalling and PR-protein action exist in systemic tissue to confer resistance during SAR. AD - Julius-von-Sachs-Institute of Biological Science, University of Wurzburg, Julius-von-Sachs-Platz 3, 97082, Wurzburg, Germany. AU - Zeier J AU - Pink B AU - Mueller MJ AU - Berger S LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/21 05:00 MHDA- 2004/04/21 05:00 AID - 10.1007/s00425-004-1272-z [doi] PST - aheadofprint SO - Planta 2004 Apr 20;. PMID- 15096616 OWN - NLM STAT- publisher DA - 20040420 IS - 0027-8424 DP - 2004 Apr 19 TI - Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae. AB - Viroids, subviral noncoding RNAs, replicate, move, and incite diseases in plants. Viroids replicate through a rolling-circle mechanism in which oligomeric RNAs of one or both polarities are cleaved and ligated into the circular monomers. Attempts to transmit viroids to Arabidopsis have failed for unknown reasons. To tackle this question, Arabidopsis was transformed with cDNAs expressing dimeric (+) transcripts of representative species of the families Pospiviroidae and Avsunviroidae, which replicate in the nucleus and the chloroplast, respectively. Correct processing to the circular (+) monomers was always observed, demonstrating that Arabidopsis has the appropriate RNase and RNA ligase. Northern blot hybridization also revealed the multimeric (-) RNAs of Citrus exocortis viroid and Hop stunt viroid (HSVd) of the family Pospiviroidae, but not of Avocado sunblotch viroid of the family Avsunviroidae, showing that the first RNA-RNA transcription of the rolling-circle mechanism occurs in Arabidopsis for the two nuclear viroids and that their multimeric (-) RNAs remain unprocessed as in typical hosts. Moreover, transgenic Arabidopsis expressing HSVd dimeric (-) transcripts accumulated the circular (+) monomers, although at low levels, together with the unprocessed primary transcript that served as the template for the second RNA-RNA transcription. Agroinoculation of Arabidopsis with the dimeric (+) Citrus exocortis viroid, HSVd, and Coleus blumei viroid 1 cDNAs showed that these viroids could not move to distal plant parts, in contrast with the situation observed in their experimental hosts. Therefore, deficiencies in movement or low replication appear to be the factors limiting infectivity of some viroids in Arabidopsis. AD - Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Universidad Politecnica de Valencia, Avenida de los Naranjos s/n, 46022 Valencia, Spain. AU - Daros JA AU - Flores R LA - ENG PT - JOURNAL ARTICLE TA - Proc Natl Acad Sci U S A JID - 7505876 EDAT- 2004/04/21 05:00 MHDA- 2004/04/21 05:00 AID - 10.1073/pnas.0401090101 [doi] AID - 0401090101 [pii] PST - aheadofprint SO - Proc Natl Acad Sci U S A 2004 Apr 19;. PMID- 15096600 OWN - NLM STAT- publisher DA - 20040420 IS - 0027-8424 DP - 2004 Apr 19 TI - Transgenic study of parallelism in plant morphological evolution. AB - Developmental constraint is indicated when one finds that similar genetic mechanisms are responsible for independent origins of the same derived phenotype. We studied three independent origins of rosette flowering within the mustard family and attempted to evaluate the extent to which the same mechanisms were involved in each transition from the ancestral phenotype, inflorescence flowering. We used transformation to move a candidate gene, LFY, and its cis-regulatory sequences from rosette-flowering species into an inflorescence-flowering recipient, Arabidopsis thaliana, in place of its endogenous LFY gene. The transgenic phenotypes of experimental and control lines (containing an A. thaliana LFY transgene) and the expression driven by the cis-regulatory sequences show that changes at the LFY locus might have contributed to the evolution of rosette flowering in two of the three lineages. In the third case, changes upstream of LFY are implicated. Our data suggest that changes in a single developmental regulatory program were involved in multiple origins of the same derived trait but that the specific genetic changes were different in each case. AD - Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706. AU - Yoon HS AU - Baum DA LA - ENG PT - JOURNAL ARTICLE TA - Proc Natl Acad Sci U S A JID - 7505876 EDAT- 2004/04/21 05:00 MHDA- 2004/04/21 05:00 AID - 10.1073/pnas.0401824101 [doi] AID - 0401824101 [pii] PST - aheadofprint SO - Proc Natl Acad Sci U S A 2004 Apr 19;. PMID- 15095151 OWN - NLM STAT- in-data-review DA - 20040419 IS - 0032-0943 VI - 70 IP - 4 DP - 2004 Apr TI - Studies on the Effects of fpf1 Gene on Artemisia annua Flowering Time and on the Linkage between Flowering and Artemisinin Biosynthesis. PG - 347-52 AB - The flowering promoting factor1 ( fpf1) from Arabidopsis thaliana was transferred into Artemisia annua L. via Agrobacterium tumefaciens. The fpf1 gene was firstly inserted in the binary vector pBI121 under the control of CaMV 35S promoter to construct the plant expression vector pBIfpf1, then leaf explants of A. annua were infected with A. tumefaciens LBA4404 containing pBIfpf1, and induced shoots. Transgenic plants were obtained through the selection with kanamycin. PCR, PCR-Southern and Southern blot analyses confirmed that the foreign fpf1 gene had been integrated into the A. annua genome. RT-PCR and RT-PCR-Southern analyses suggested that the foreign fpf1 gene had expressed at the transcriptional level. Under short-day conditions, the flowering time of fpf1 transgenic plants was about 20 days earlier than the non-transformed plants; however, no significant differences were detected in artemisinin content between the flowering transgenic plants and the non-flowering non-transgenic plants. These results showed that flowering is not a necessary factor for increasing the artemisinin content, furthermore, there may be no direct linkage between flowering and artemisinin biosynthesis. AD - Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China. FAU - Wang, Hong AU - Wang H FAU - Ge, Lei AU - Ge L FAU - Ye, He-Chun AU - Ye HC FAU - Chong, Kang AU - Chong K FAU - Liu, Ben-Ye AU - Liu BY FAU - Li, Guo-Feng AU - Li GF LA - eng PT - Journal Article PL - Germany TA - Planta Med JID - 0066751 SB - IM EDAT- 2004/04/20 05:00 MHDA- 2004/04/20 05:00 AID - 10.1055/s-2004-818947 [doi] PST - ppublish SO - Planta Med 2004 Apr;70(4):347-52. PMID- 15095092 OWN - NLM STAT- publisher DA - 20040419 IS - 0032-0935 DP - 2004 Apr 17 TI - Control of xyloglucan endotransglucosylase activity by salts and anionic polymers. AB - Crude extracts of cauliflower florets had high xyloglucan endotransglucosylase (XET) activity, but this was largely lost after partial purification and de-salting. Activity was restored (promoted up to 40-fold) by any of a wide variety of inorganic and organic salts. Optimum concentrations for Na(+), K(+) and NH(4)(+) salts were typically ~300 mM. The chlorides of Ca(2+), Mg(2+), Al(3+) and La(3+) were optimally active at lower concentrations (e.g. 0.1 mM LaCl(3)), but became inhibitory at higher concentrations (e.g. 5 mM LaCl(3)). Some anionic polysaccharides at 0.04-0.2% w/v (e.g. gum arabic, pectin and hypochlorite-oxidised xyloglucan) promoted the XET activity of de-salted enzyme, especially if a sub-optimal concentration of NaCl was also present; others (e.g. homogalacturonan, 4- O-methyl-glucuronoxylan and alginate) were inhibitory. Similar ionic effects were noted on the XET activity of the Arabidopsis protein XTH24 (heterologously expressed by insect cells); in this case carboxymethylcellulose was also stimulatory. To look for endogenous modulators of XET activity, we prepared a cold-water extract of cauliflower florets; after boiling and centrifugation, the supernatant [boiled cauliflower preparation (BCP)] promoted the XET activity of de-salted cauliflower enzyme and of XTH24. About half the activator present in BCP was an ethanol-precipitable, anionic polymer of apparent M(r) <5,000. After acid hydrolysis the polymer yielded much arabinose and galactose, and small amounts of galacturonic and glucuronic acids amino acids were also present. The polymer may thus contain arabinogalactan-proteins. We suggest that acidic polymers and/or other apoplastic ions are naturally occurring regulators of XET action in vivo, and may thus control cell wall assembly, loosening, and growth. AD - The Edinburgh Cell Wall Group, ICMB, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, EH9 3JH, Edinburgh, UK. AU - Takeda T AU - Fry SC LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/20 05:00 MHDA- 2004/04/20 05:00 AID - 10.1007/s00425-004-1267-9 [doi] PST - aheadofprint SO - Planta 2004 Apr 17;. PMID- 15090654 OWN - NLM STAT- publisher DA - 20040419 IS - 0027-8424 DP - 2004 Apr 16 TI - Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation. AB - Ubiquitination of various intracellular proteins by ubiquitin-protein ligases (or E3s) plays an essential role in eukaryotic cell regulation primarily through its ability to selectively target proteins for degradation by the 26S proteasome. Skp1, Cullin, F-box (SCF) complexes are one influential E3 class that use F-box proteins to deliver targets to a core ligase activity provided by the Skp1, Cullin, and Rbx1 subunits. Almost 700 F-box proteins can be found in Arabidopsis, indicating that SCF E3s likely play a pervasive role in plant physiology and development. Here, we describe the reverse genetic analysis of two F-box proteins, EBF1 and -2, that work coordinately in SCF complexes to repress ethylene action. Mutations in either gene cause hypersensitivity to exogenous ethylene and its precursor 1-aminocyclopropane-1-carboxylic acid. EBF1 and -2 interact directly with ethylene insensitive 3 (EIN3), a transcriptional regulator important for ethylene signaling. Levels of EIN3 are increased in mutants affecting either EBF1 or -2, suggesting that the corresponding SCF complexes work together in EIN3 breakdown. Surprisingly, double ebf1 ebf2 mutants display a substantial arrest of seedling growth and have elevated EIN3 levels, even in the absence of exogenous ethylene. Collectively, our results show that the SCF(EBF1/EBF2)-dependent ubiquitination and subsequent removal of EIN3 is critical not only for proper ethylene signaling but also for growth in plants. AD - *Department of Genetics, University of Wisconsin, Madison, WI 53706-1574; ()Department of Molecular Biology, Massachusetts General Hospital, and ()Department of Genetics, Harvard Medical School, Boston, MA 02114. AU - Gagne JM AU - Smalle J AU - Gingerich DJ AU - Walker JM AU - Yoo SD AU - Yanagisawa S AU - Vierstra RD LA - ENG PT - JOURNAL ARTICLE TA - Proc Natl Acad Sci U S A JID - 7505876 EDAT- 2004/04/20 05:00 MHDA- 2004/04/20 05:00 AID - 10.1073/pnas.0401698101 [doi] AID - 0401698101 [pii] PST - aheadofprint SO - Proc Natl Acad Sci U S A 2004 Apr 16;. PMID- 15090618 OWN - NLM STAT- publisher DA - 20040419 IS - 1059-1524 DP - 2004 Apr 16 TI - Members of the Toc159 import receptor family represent distinct pathways for protein targeting to plastids. AB - Plastids represent a diverse group of organelles that perform essential metabolic and signaling functions within all plant cells. The differentiation of specific plastid types relies on the import of selective sets of proteins from among the approximately 2500 nucleus-encoded plastid proteins. The Toc159 family of GTPases mediates the initial targeting of proteins to plastids. In Arabidopsis thaliana, the Toc159 family consists of four genes: atTOC159, atTOC132, atTOC120, and atTOC90. In vivo analysis of atToc159 function indicates that it is required specifically for the import of proteins necessary for chloroplast biogenesis (Bauer et al., 2000, Nature, 403:203-7). In this report, we demonstrate that atToc120 and atToc132 represent a structurally and functionally unique subclass of protein import receptors. Unlike atToc159, mutants lacking both atToc120 and atToc132 are inviable. Furthermore, atToc120 and atToc132 exhibit preprotein binding properties that are distinct from atToc159. These data indicate that the different members of the Toc159 family represent distinct pathways for protein targeting to plastids, and are consistent with the hypothesis that separate pathways have evolved to ensure balanced import of essential proteins during plastid development. AD - Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA. AU - Ivanova Y AU - Smith MD AU - Chen K AU - Schnell DJ LA - ENG PT - JOURNAL ARTICLE TA - Mol Biol Cell JID - 9201390 EDAT- 2004/04/20 05:00 MHDA- 2004/04/20 05:00 AID - 10.1091/mbc.E03-12-0923 [doi] AID - E03-12-0923 [pii] PST - aheadofprint SO - Mol Biol Cell 2004 Apr 16;. PMID- 15088401 OWN - NLM STAT- in-process DA - 20040419 IS - 0012-4966 VI - 394 DP - 2004 Jan-Feb TI - Localization and molecular analysis of the PXD gene encoding anionic peroxidase of Arabidopsis thaliana. PG - 41-3 AD - Department of Genetics, Biological Faculty, Moscow State University, Vorob'evy gory, Moscow, 119899 Russia. FAU - Lebedeva, O V AU - Lebedeva OV FAU - Ezhova, T A AU - Ezhova TA FAU - Shestakov, S V AU - Shestakov SV LA - eng PT - Journal Article PL - Russia TA - Dokl Biol Sci JID - 7505459 SB - IM EDAT- 2004/04/20 05:00 MHDA- 2004/04/20 05:00 PST - ppublish SO - Dokl Biol Sci 2004 Jan-Feb;394:41-3. PMID- 15088147 OWN - NLM STAT- publisher DA - 20040416 IS - 0032-0935 DP - 2004 Apr 16 TI - Cloning of a putative monogalactosyldiacylglycerol synthase gene from rice ( Oryza sativa L.) plants and its expression in response to submergence and other stresses. AB - Suppression subtractive hybridization was used to construct a subtractive cDNA library from plants of non-submerged and 7-day-submerged rice ( Oryza sativa L., FR13A, a submergence-tolerant cultivar). One clone of the subtractive cDNA library, S23, was expressed abundantly during submergence. The full length of S23 was amplified using 5'- and 3'-rapid amplification of cDNA ends, and found to consist of 1,671 bp with an open reading frame of 1,077 bp (181-1257) encoding 358 amino acids. Its deduced amino acid sequence showed a high homology with monogalactosyldiacylglycerol synthase (UDPgalactose: 1,2-diacylglycerol 3-beta- d-galactosyl transferase; EC 2.4.1.46, MGDG synthase) from Arabidopsis thaliana; therefore, we named the gene OsMGD. Time-course studies showed that the expression of OsMGD in the rice cultivars FR13A and IR42 (submergence-susceptive cultivar) during submergence was gradually increased and that expression in FR13A was higher than in IR42. The expression of OsMGD in FR13A was influenced by benzyladenine and illumination. The accumulation of OsMGD mRNA in both FR13A and IR42 was also increased by ethephon, gibberellin, drought and salt treatment, but cold stress had no effect on the expression of the gene. These results suggest that the expression of OsMGD mRNA requires benzyladenine or illumination, and that the process is also mediated by ethephon and gibberellin. Salt and drought stress have an effect similar to that of submergence. Furthermore, the enhanced expression of OsMGD may relate to photosynthesis, and play an important role during submergence. AD - Laboratory of Plant Biotechnology, Faculty of Agriculture, Tottori University, Koyama, 680-8553, Tottori, Japan. AU - Qi Y AU - Yamauchi Y AU - Ling J AU - Kawano N AU - Li D AU - Tanaka K LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1007/s00425-004-1245-2 [doi] PST - aheadofprint SO - Planta 2004 Apr 16;. PMID- 15088065 OWN - NLM STAT- publisher DA - 20040416 IS - 1469-221X DP - 2004 Apr 16 TI - gurke and pasticcino3 mutants affected in embryo development are impaired in acetyl-CoA carboxylase. AB - Normal embryo development is required for correct seedling formation. The Arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. We have recently identified lethal acc1 mutants affected in acetyl-CoA carboxylase 1 (ACCase 1) that display a similar embryo phenotype. A series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct sequencing of the ACC1 gene revealed point mutations in these new alleles. The isolation of leaky acc1 alleles demonstrated that ACCase 1 is essential for correct plant development and that mutations in ACCase affect cellular division in plants, as is the case in yeast. Interestingly, significant metabolic complementation of the mutant phenotype was obtained by exogenous supply of malonate, suggesting that the lack of cytosolic malonyl-CoA is likely to be the initial factor leading to abnormal development in the acc1 mutants. AD - Unite de Biologiedes Semences, INRA, RD10, 78026 Versailles, cedex, France. AU - Baud S AU - Bellec Y AU - Miquel M AU - Bellini C AU - Caboche M AU - Lepiniec L AU - Faure JD AU - Rochat C LA - ENG PT - JOURNAL ARTICLE DEP - 20040416 TA - EMBO Rep JID - 100963049 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 PHST- 2003/Oct/07 [received] PHST- 2004/Feb/11 [revised] PHST- 2004/Feb/13 [accepted] PHST- 2004/Apr/16 [aheadofprint] AID - 10.1038/sj.embor.7400124 [doi] AID - 7400124 [pii] PST - aheadofprint SO - EMBO Rep 2004 Apr 16;. PMID- 15087312 OWN - NLM STAT- publisher DA - 20040416 IS - 1367-4803 DP - 2004 Apr 15 TI - Metabolite fingerprinting: detecting biological features by independent component analysis. AB - MOTIVATION: Metabolite fingerprinting is a technology for providing information from spectra of total compositions of metabolites. Here, spectra acquisitions by microchip-based nanoflow-direct infusion QTOF mass spectrometry, a simple and high throughput technique, is tested for its informative power. As a simple test case we are using Arabidopsis thaliana crosses. The question is how metabolite fingerprinting reflects the biological background. In many applications the classical principal component analysis (PCA) is used for detecting relevant information. Here a modern alternative is introduced -- the independent component analysis (ICA). Due to its independence condition, ICA is more suitable for our questions than PCA. However, ICA has not been developed for a small number of high dimensional samples, therefore a strategy is needed to overcome this limitation. RESULTS: To apply ICA successfully it is essential first to reduce the high dimension of the data set, by using PCA. The number of principal components determines the quality of ICA significantly, therefore we propose a criterion for estimating the optimal dimension automatically. The kurtosis measure is used to order the extracted components to our interest. Applied to our Arabidopsis thaliana data, ICA detects three relevant factors, two biological and one technical, and clearly outperforms the PCA. AD - Max Planck Institute of Molecular Plant Physiology, 14424 Potsdam, Germany. AU - Scholz M AU - Gatzek S AU - Sterling A AU - Fiehn O AU - Selbig J LA - ENG PT - JOURNAL ARTICLE TA - Bioinformatics JID - 9808944 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1093/bioinformatics/bth270 [doi] AID - bth270 [pii] PST - aheadofprint SO - Bioinformatics 2004 Apr 15;. PMID- 15087121 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0378-1119 VI - 330 DP - 2004 Apr 14 TI - Genomic structure of a novel Arabidopsis clock-controlled gene, AtC401, which encodes a pentatricopeptide repeat protein. PG - 29-37 AB - We isolated and characterized AtC401, a novel Arabidopsis clock-controlled gene that encodes a protein containing the pentatricopeptide repeat (PPR) motif. AtC401 was isolated as an Arabidopsis homolog of Pharbitis nil C401 (PnC401), a gene that encodes a leaf protein closely related to the photoperiodic induction of flowering and displays a circadian rhythm at the transcriptional level. The AtC401 gene spans 5.6 kb and contains 12 exons. Comparisons of the sequences and genomic organization of AtC401 and PnC401 revealed that each has two exons near the 3'-end, which encode a highly conserved domain consisting of 12 repeats of the PPR motif. Phylogenetic analysis of at least 450 Arabidopsis proteins containing PPR motifs revealed that AtC401 and related proteins form a distinct group. Moreover, the position of the intron between the two exons that encode the PPR domain has been conserved exactly in other C401-like genes. Using a reporter assay, we found a fragment (-174 to +73) of AtC401 that was sufficient to regulate circadian rhythmic expression. These results suggest that the conserved domain of AtC401 has a function similar to that of PnC401, and that the expression of C401 genes according to a circadian rhythm is important for protein function. AD - Gene Research Center, Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nohdai, Tsukuba, Ibaraki 305-8572, Japan. FAU - Oguchi, Taichi AU - Oguchi T FAU - Sage-Ono, Kimiyo AU - Sage-Ono K FAU - Kamada, Hiroshi AU - Kamada H FAU - Ono, Michiyuki AU - Ono M LA - eng PT - Journal Article PL - Netherlands TA - Gene JID - 7706761 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 PHST- 2003/Aug/27 [received] PHST- 2003/Oct/16 [revised] PHST- 2003/Nov/14 [accepted] AID - 10.1016/j.gene.2003.11.012 [doi] AID - S0378111903010904 [pii] PST - ppublish SO - Gene 2004 Apr 14;330:29-37. PMID- 15086960 OWN - NLM STAT- publisher DA - 20040416 IS - 1471-2229 VI - 4 IP - 1 DP - 2004 Apr 15 TI - Synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit. PG - 5 AB - Background: Assembly of stable light-harvesting complexes (LHCs) in the chloroplast of green algae and plants requires synthesis of chlorophyll (Chl) b, a reaction that involves oxygenation of the 7-methyl group of Chl a to a formyl group. This reaction uses molecular oxygen and is catalyzed by chlorophyllide a oxygenase (CAO). The amino acid sequence of CAO predicts mononuclear iron and Rieske iron-sulfur centers in the protein. The mechanism of synthesis of Chl b and localization of this reaction in the chloroplast are essential steps toward understanding LHC assembly. Results: Fluorescence of a CAO-GFP fusion protein, transiently expressed in young pea leaves, was found at the periphery of mature chloroplasts and on thylakoid membranes by confocal fluorescence microscopy. However, when membranes from partially degreened cells of Chlamydomonas reinhardtii cw15 were resolved on sucrose gradients, full-length CAO was detected by immunoblot analysis only on the chloroplast envelope inner membrane. The electron paramagnetic resonance spectrum of CAO included a resonance at g = 4.3, assigned to the predicted mononuclear iron center. Instead of a spectrum of the predicted Rieske iron-sulfur center, a nearly symmetrical, approximately 100 Gauss peak-to-trough signal was observed at g = 2.057, with a sensitivity to temperature characteristic of an iron-sulfur center. A remarkably stable radical in the protein was revealed by an isotropic, 9 Gauss peak-to-trough signal at g = 2.0042. Fragmentation of the protein after incorporation of 125I- identified a conserved tyrosine residue (Tyr-422 in Chlamydomonas and Tyr-518 in Arabidopsis) as the radical species. The radical was quenched by chlorophyll a, an indication that it may be involved in the enzymatic reaction. Conclusion: CAO was found on the chloroplast envelope and thylakoid membranes in mature chloroplasts but only on the envelope inner membrane in dark-grown C. reinhardtii cells. Such localization provides further support for the envelope membranes as the initial site of Chl b synthesis and assembly of LHCs during chloroplast development. Identification of a tyrosine radical in the protein provides insight into the mechanism of Chl b synthesis. AU - Eggink LL AU - LoBrutto R AU - Brune DC AU - Brusslan J AU - Yamasato A AU - Tanaka A AU - Hoober JK LA - ENG PT - JOURNAL ARTICLE DEP - 20040415 TA - BMC Plant Biol JID - 100967807 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 PHST- 2003/Nov/07 [received] PHST- 2004/Apr/15 [accepted] PHST- 2004/Apr/15 [aheadofprint] AID - 10.1186/1471-2229-4-5 [doi] AID - 1471-2229-4-5 [pii] PST - aheadofprint SO - BMC Plant Biol 2004 Apr 15;4(1):5. PMID- 15086830 OWN - NLM STAT- publisher DA - 20040416 IS - 0031-9317 VI - 121 IP - 1 DP - 2004 May TI - Flowering genes in Metrosideros fit a broad herbaceous model encompassing Arabidopsis and Antirrhinum. PG - 163-173 AB - Molecular studies were conducted on Metrosideros excelsa to determine if the current genetic models for flowering with regard to inflorescence and floral meristem identity genes in annual plants were applicable to a woody perennial. MEL, MESAP1 and METFL1, the fragments of LEAFY (LFY), APETALA1 (AP1) and TERMINAL FLOWER1 (TFL1) equivalents, respectively, were isolated from M. excelsa. Temporal expression patterns showed that MEL and MESAP1 exhibited a bimodal pattern of expression. Expression exhibited during early floral initiation in autumn was followed by down-regulation during winter, and up-regulation in spring as floral organogenesis occurred. Spatial expression patterns of MEL showed that it had greater similarity to FLORICAULA (FLO) than to LFY, whereas MESAP1 was more similar to AP1 than SQUAMOSA. The interaction between MEL and METFL1 was more similar to the interaction between FLO and CENTRORADIALIS than that between LFY and TFL1. Consequently, the three genes from M. excelsa fit a broader herbaceous model encompassing Antirrhinum as well as Arabidopsis, but with differences, such as the bimodal pattern of expression seen with MEL and MESAP1. In mid-winter, at the time when both MEL and MESAP1 were down-regulated, GA(1) was below the level of detection in M. excelsa buds. Even though application of gibberellin inhibits flowering in members of the Myrtaceae, MEL was responsive to gibberellin with expression in juvenile plants up-regulated by GA(3). However, MESAP1 was not up-regulated indicating that meristem competence was also probably required to promote flowering in M. excelsa. AD - Institute of Molecular BioSciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand. AU - Sreekantan L AU - Clemens J AU - McKenzie MJ AU - Lenton JR AU - Croker SJ AU - Jameson PE LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0031-9317.2004.00304.x [doi] AID - PPL304 [pii] PST - ppublish SO - Physiol Plant 2004 May;121(1):163-173. PMID- 15086829 OWN - NLM STAT- publisher DA - 20040416 IS - 0031-9317 VI - 121 IP - 1 DP - 2004 May TI - Functional characterization of SEPALLATA3 and AGAMOUS orthologues in silver birch. PG - 149-162 AB - The development of flowers is regulated by a complex network of transcriptional activators and repressors, many of which belong to the MADS box gene family. In this study, we describe two MADS box genes of silver birch (Betula pendula Roth), BpMADS1 and BpMADS6, which are similar to SEPALLATA3 and AGAMOUS in Arabidopsis thaliana, respectively. In situ hybridization showed that BpMADS1 was expressed in the inflorescence meristem at a very early stage, but not later. Both genes were expressed in developing carpels, ovules and stamens but not in tepals or scales. Ectopic expression of BpMADS1 in Arabidopsis resulted in a reduced number of floral organs or whole whorls and in petaloid or carpelloid sepals, a phenotype reminiscent of that of fil mutants. 35S::BpMADS6 caused very early flowering in Arabidopsis. In tobacco, both 35S::BpMADS1 and 35S::BpMADS6 accelerated flowering and, in addition, 35S::BpMADS6 caused changes in sepals and petals. In some transgenic birch plants, 35S::BpMADS1 antisense resulted in the development of both male and female organs in the axil of a single bract and in a change of some inflorescences into vegetative shoots. In two plants, either 35S::BpMADS6 sense or antisense constructs resulted in an increase in the number of tepals and in complete lack of stamens in some male inflorescences. These results suggest that BpMADS1 participates both in inflorescence and in flower formation and BpMADS6 participates in flower formation and that they are functional homologues to SEPALLATA3 and AGAMOUS, respectively. AD - Department of Biology, University of Joensuu, P.O.Box 111, FIN-80101 Joensuu, Finland. AU - Lemmetyinen J AU - Hassinen M AU - Elo A AU - Porali I AU - Keinonen K AU - Makela H AU - Sopanen T LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0031-9317.2004.00303.x [doi] AID - PPL303 [pii] PST - ppublish SO - Physiol Plant 2004 May;121(1):149-162. PMID- 15086824 OWN - NLM STAT- publisher DA - 20040416 IS - 0031-9317 VI - 121 IP - 1 DP - 2004 May TI - Phloem specific expression driven by wheat dwarf geminivirus V-sense promoter in transgenic dicotyledonous species. PG - 108-116 AB - Wheat dwarf geminivirus (WDV) is a single-stranded DNA Mastrevirus. The large intergenic region (LIR) of WDV contains cis-acting elements essential for the replication of the genome as well as for the bidirectional transcription of virus genes. The LIR was fused to the GUS (uidA) reporter gene and the WDV viral sense (V-sense) promoter activity derived from the stable integration of that promoter was analysed in transgenic dicot plants. Various dicot species were tested, including Nicotiana tabacum, Nicotiana benthamiana, Arabidopsis thaliana and Cucumis melo. The GUS activity driven by the WDV promoter was also compared to that obtained in plants transformed with the GUS gene controlled by the CaMV 35S promoter as well as two phloem-specific promoters derived from the Arabidopsis thaliana AtSUC2 and AtAHA3 genes. Histochemistry showed that the WDV V-sense promoter consistently induced an expression pattern restricted to the vascular tissues, predominantly in the phloem of all organs. This promoter exhibited levels of GUS activity comparable to that driven by AtSUC2 and AtAHA3 promoters. A vascular expression pattern was observed in the four dicots tested. This was stable during plant development and was not altered following viral infection by an unrelated geminivirus. The uses of such a promoter are discussed regarding the targeting to the phloem of molecules active against vascular pests or pathogens. AD - Laboratoire de Biologie Cellulaire, INRA Route de St-Cyr 78026 Versailles, France. AU - Dinant S AU - Ripoll C AU - Pieper M AU - David C LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0031-9317.2004.00296.x [doi] AID - PPL296 [pii] PST - ppublish SO - Physiol Plant 2004 May;121(1):108-116. PMID- 15086823 OWN - NLM STAT- publisher DA - 20040416 IS - 0031-9317 VI - 121 IP - 1 DP - 2004 May TI - Effect of reduced arginine decarboxylase activity on salt tolerance and on polyamine formation during salt stress in Arabidopsis thaliana. PG - 101-107 AB - Polyamines have been suggested to play an important role in stress protection. However, attempts to determine the function of polyamines have been complicated by the fact that, dependent on the conditions, polyamine contents increase or decrease during stress. To determine the importance of polyamine formation during salt stress, we analysed polyamine contents and salt tolerance in two Arabidopsis thaliana mutants, spe1-1 and spe2-1 (Watson et al. Plant J 13: 231-239, 1998), with reduced activity of arginine decarboxylase (EC 4.1.1.19), an important enzyme in polyamine synthesis. Polyamines accumulated in wild-type plants (Col-0 and Ler-0) that were pre-treated with 100 mM NaCl before transfer to 125 mM NaCl, but not in plants that were directly transferred to 125 mM NaCl without prior treatment with 100 mM NaCl. This shows that polyamine accumulation depends on acclimation to salinity. The salt treatment that induced polyamine accumulation in wild-type plants did not lead to polyamine accumulation in the spe1-1 and spe2-1 mutants. Decreased fresh weight, chlorophyll content and photosynthetic efficiency indicated that the spe1-1 mutant was more severely affected by salt stress than its wild type, Col-0. In the spe2-1 mutant decreased salt tolerance compared to its wild type, Ler-0, became apparent as bleaching under severe salt stress. The present results demonstrate that decreased polyamine formation due to lower arginine decarboxylase activity leads to reduced salt tolerance. AD - Department of Biology, University College London, Gower Street, London WC1E 6BT, UK. AU - Kasinathan V AU - Wingler A LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0031-9317.2004.00309.x [doi] AID - PPL309 [pii] PST - ppublish SO - Physiol Plant 2004 May;121(1):101-107. PMID- 15086809 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. PG - 545-61 AB - Summary We describe the development of a high-density Arabidopsis'whole genome' oligonucleotide probe array for expression analysis (the Affymetrix ATH1 GeneChip((R)) probe array) that contains approximately 22 750 probe sets. Precedence on the array was given to genes for which either expression evidence or a credible database match existed. The remaining space was filled with 'hypothetical' genes. The new ATH1 array represents approximately 23 750 genes of which 60% were detected in RNA from cultured seedlings. Sensitivity of the array, determined using spiking controls, was approximately one transcript per cell. The array demonstrated high technical reproducibility and concordance with real-time PCR results. Indole-3 acetic acid (IAA)-induced changes in gene expression were used for biological validation of the array. A total of 222 genes were significantly upregulated and 103 significantly downregulated by exposure to IAA. Of the genes whose products could be functionally classified, the largest specific classes of upregulated genes were transcriptional regulators and protein kinases, many fewer of which were represented among the downregulated genes. Over one-third of the auxin-regulated genes have no known function, although many belong to gene families with members that have previously been shown to be auxin regulated. For the 6714 genes represented both on this and the earlier Arabidopsis Genome (AG) array, both signal intensities and gene expression ratios were very similar. Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes. AD - The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. FAU - Redman, Julia C AU - Redman JC FAU - Haas, Brian J AU - Haas BJ FAU - Tanimoto, Gene AU - Tanimoto G FAU - Town, Christopher D AU - Town CD LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02061.x [doi] AID - TPJ2061 [pii] PST - ppublish SO - Plant J 2004 May;38(3):545-61. PMID- 15086808 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - DISTORTED2 encodes an ARPC2 subunit of the putative Arabidopsis ARP2/3 complex. PG - 526-38 AB - Summary Arabidopsis trichomes are unicellular, branched structures that have highly constrained requirements for the cytoskeleton. The 'distorted group' genes function downstream from microtubule-based branch initiation, and are required during the actin-dependent phase of polarized stalk and branch expansion. Of the eight known 'distorted group' genes, a subset encode homologs of ARP2/3 complex subunits. In eukaryotic cells, the seven-protein ARP2/3 complex nucleates actin filament networks that push on the plasma membrane and organelles. In plants cells, the existence and function of an ARP2/3 complex is unclear. In this paper, we report that DISTORTED2 (DIS2) encodes a paralogue of the ARP2/3 complex subunit ARPC2. DIS2 has ARPC2 activity, based on its ability to rescue the growth defects of arpc2 (arc35Delta) null yeast cells. Like known ARPC2s, DIS2 physically interacts with ARPC4. Mutations in DIS2 cause a distorted trichome phenotype, defects in cell-cell adhesion, and a modest reduction in shoot FW. The actin cytoskeleton in dis2 trichomes is extensive, but developing branches fail to generate and maintain highly organized cytoplasmic actin bundles. AD - Agronomy Department, Purdue University, Lilly Hall, 915 West State Street, West Lafayette, IN 47907-2054, USA. FAU - El-Din El-Assal, Salah AU - El-Din El-Assal S FAU - Le, Jie AU - Le J FAU - Basu, Dipanwita AU - Basu D FAU - Mallery, Eileen L AU - Mallery EL FAU - Szymanski, Daniel B AU - Szymanski DB LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02065.x [doi] AID - TPJ2065 [pii] PST - ppublish SO - Plant J 2004 May;38(3):526-38. PMID- 15086807 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Induction of ASCORBATE PEROXIDASE 2 expression in wounded Arabidopsis leaves does not involve known wound-signalling pathways but is associated with changes in photosynthesis. PG - 499-511 AB - Summary ASCORBATE PEROXIDASE 2 (APX2) encodes a key enzyme of the antioxidant network. In excess light-stressed Arabidopsis leaves, photosynthetic electron transport (PET), hydrogen peroxide (H(2)O(2)) and abscisic acid (ABA) regulate APX2 expression. Wounded leaves showed low induction of APX2 expression, and when exposed to excess light, APX2 expression was increased synergistically. Signalling pathways dependent upon jasmonic acid (JA), chitosan and ABA were not involved in the wound-induced expression of APX2, but were shown to require PET and were preceded by a depressed rate of CO(2) fixation. This led to an accumulation of H(2)O(2) in veinal tissue. Diphenyl iodonium (DPI), which has been shown previously to be a potent inhibitor of H(2)O(2) accumulation in the veins of wounded leaves, prevented induction of APX2 expression probably by inhibition of PET. Thus, the weak induction of APX2 expression in wounded leaves may require H(2)O(2) and PET only. As in other environmental stresses, wounding of leaves resulted in decreased photosynthesis leading to increased reactive oxygen species (ROS) production. This may signal the induction of many 'wound-responsive' genes not regulated by JA-dependent or other known JA-independent pathways. AD - Department of Botany, Stockholm University, Frescati, SE-106 91 Stockholm, Sweden. FAU - Chang, Christine Chi-Chen AU - Chang CC FAU - Ball, Louise AU - Ball L FAU - Fryer, Michael J AU - Fryer MJ FAU - Baker, Neil R AU - Baker NR FAU - Karpinski, Stanislaw AU - Karpinski S FAU - Mullineaux, Philip M AU - Mullineaux PM LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02066.x [doi] AID - TPJ2066 [pii] PST - ppublish SO - Plant J 2004 May;38(3):499-511. PMID- 15086806 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - An Arabidopsis dynamin-related protein, DRP3A, controls both peroxisomal and mitochondrial division. PG - 487-98 AB - Summary Peroxisomes undergo dramatic changes in size, shape, number, and position within the cell, but the division process of peroxisomes has not been characterized. We screened a number of Arabidopsis mutants with aberrant peroxisome morphology (apm mutants). In one of these mutants, apm1, the peroxisomes are long and reduced in number, apparently as a result of inhibition of division. We showed that APM1 encodes dynamin-related protein 3A (DRP3A), and that mutations in APM1/DRP3A also caused aberrant morphology of mitochondria. The transient expression analysis showed that DRP3A is associated with the cytosolic side of peroxisomes. These findings indicate that the same dynamin molecule is involved in peroxisomal and mitochondrial division in higher plants. We also report that the growth of Arabidopsis, which requires the cooperation of various organelles, including peroxisomes and mitochondria, is repressed in apm1, indicating that the changes of morphology of peroxisomes and mitochondria reduce the efficiency of metabolism in these organelles. AD - Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan. FAU - Mano, Shoji AU - Mano S FAU - Nakamori, Chihiro AU - Nakamori C FAU - Kondo, Maki AU - Kondo M FAU - Hayashi, Makoto AU - Hayashi M FAU - Nishimura, Mikio AU - Nishimura M LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02063.x [doi] AID - TPJ2063 [pii] PST - ppublish SO - Plant J 2004 May;38(3):487-98. PMID- 15086805 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - A mutation of the CRUMPLED LEAF gene that encodes a protein localized in the outer envelope membrane of plastids affects the pattern of cell division, cell differentiation, and plastid division in Arabidopsis. PG - 448-59 AB - Summary We identified a novel mutation of a nuclear-encoded gene, designated as CRUMPLED LEAF (CRL), of Arabidopsis thaliana that affects the morphogenesis of all plant organs and division of plastids. Histological analysis revealed that planes of cell division were distorted in shoot apical meristems (SAMs), root tips, and embryos in plants that possess the crl mutation. Furthermore, we observed that differentiation patterns of cortex and endodermis cells in inflorescence stems and root endodermis cells were disturbed in the crl mutant. These results suggest that morphological abnormalities observed in the crl mutant were because of aberrant cell division and differentiation. In addition, cells of the crl mutant contained a reduced number of enlarged plastids, indicating that the division of plastids was inhibited in the crl. The CRL gene encodes a novel protein with a molecular mass of 30 kDa that is localized in the plastid envelope. The CRL protein is conserved in various plant species, including a fern, and in cyanobacteria, but not in other organisms. These data suggest that the CRL protein is required for plastid division, and it also plays an important role in cell differentiation and the regulation of the cell division plane in plants. A possible function of the CRL protein is discussed. AD - Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. FAU - Asano, Tomoya AU - Asano T FAU - Yoshioka, Yasushi AU - Yoshioka Y FAU - Kurei, Shunsuke AU - Kurei S FAU - Sakamoto, Wataru AU - Sakamoto W FAU - Machida, Yasunori AU - Machida Y CN - Sodmergen. LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02057.x [doi] AID - TPJ2057 [pii] PST - ppublish SO - Plant J 2004 May;38(3):448-59. PMID- 15086804 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Salicylic acid dependent signaling promotes basal thermotolerance but is not essential for acquired thermotolerance in Arabidopsis thaliana. PG - 432-47 AB - Summary Salicylic acid (SA) is reported to protect plants from heat shock (HS), but insufficient is known about its role in thermotolerance or how this relates to SA signaling in pathogen resistance. We tested thermotolerance and expression of pathogenesis-related (PR) and HS proteins (HSPs) in Arabidopsis thaliana genotypes with modified SA signaling: plants with the SA hydroxylase NahG transgene, the nonexpresser of PR proteins (npr1) mutant, and the constitutive expressers of PR proteins (cpr1 and cpr5) mutants. At all growth stages from seeds to 3-week-old plants, we found evidence for SA-dependent signaling in basal thermotolerance (i.e. tolerance of HS without prior heat acclimation). Endogenous SA correlated with basal thermotolerance, with the SA-deficient NahG and SA-accumulating cpr5 genotypes having lowest and highest thermotolerance, respectively. SA promoted thermotolerance during the HS itself and subsequent recovery. Recovery from HS apparently involved an NPR1-dependent pathway but thermotolerance during HS did not. SA reduced electrolyte leakage, indicating that it induced membrane thermoprotection. PR-1 and Hsp17.6 were induced by SA or HS, indicating common factors in pathogen and HS responses. SA-induced Hsp17.6 expression had a different dose-response to PR-1 expression. HS-induced Hsp17.6 protein appeared more slowly in NahG. However, SA only partially induced HSPs. Hsp17.6 induction by HS was more substantial than by SA, and we found no SA effect on Hsp101 expression. All genotypes, including NahG and npr1, were capable of expression of HSPs and acquisition of HS tolerance by prior heat acclimation. Although SA promotes basal thermotolerance, it is not essential for acquired thermotolerance. AD - Institute of Biological Sciences, University of Wales, Aberystwyth SY23 3DA, UK. FAU - Clarke, Shannon M AU - Clarke SM FAU - Mur, Luis A J AU - Mur LA FAU - Wood, Jacqueline E AU - Wood JE FAU - Scott, Ian M AU - Scott IM LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02054.x [doi] AID - TPJ2054 [pii] PST - ppublish SO - Plant J 2004 May;38(3):432-47. PMID- 15086802 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - A novel calmodulin-binding protein functions as a negative regulator of osmotic stress tolerance in Arabidopsis thaliana seedlings. PG - 410-20 AB - Summary A clone for a novel Arabidopsisthaliana calmodulin (CaM)-binding protein of 25 kDa (AtCaMBP25) has been isolated by using a radiolabelled CaM probe to screen a cDNA expression library derived from A. thaliana cell suspension cultures challenged with osmotic stress. The deduced amino acid sequence of AtCaMBP25 contains putative nuclear localization sequences and shares significant degree of similarity with hypothetical plant proteins only. Fusion of the AtCaMBP25 coding sequence to reporter genes targets the hybrid protein to the nucleus. Bacterially expressed AtCaMBP25 binds, in a calcium-dependent manner, to a canonical CaM but not to a less conserved isoform of the calcium sensor. AtCaMBP25 is encoded by a single-copy gene, whose expression is induced in Arabidopsis seedlings exposed to dehydration, low temperature or high salinity. Transgenic plants overexpressing AtCaMBP25 exhibits an increased sensitivity to both ionic (NaCl) and non-ionic (mannitol) osmotic stress during seed germination and seedling growth. By contrast, transgenic lines expressing antisense AtCaMBP25 are significantly more tolerant to mannitol and NaCl stresses than the wild type. Thus, the AtCaMBP25 gene functions as a negative effector of osmotic stress tolerance and likely participates in stress signal transduction pathways. AD - Surfaces cellulaires et signalisation chez les vegetaux, UMR 5546 CNRS/Universite Paul Sabatier, Pole de Biotechnologie Vegetale, BP 17 Auzeville, 31326 Castanet-Tolosan Cedex, France. FAU - Perruc, Elian AU - Perruc E FAU - Charpenteau, Martine AU - Charpenteau M FAU - Ramirez, Bertha Cecilia AU - Ramirez BC FAU - Jauneau, Alain AU - Jauneau A FAU - Galaud, Jean-Philippe AU - Galaud JP FAU - Ranjeva, Raoul AU - Ranjeva R FAU - Ranty, Benoit AU - Ranty B LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02062.x [doi] AID - TPJ2062 [pii] PST - ppublish SO - Plant J 2004 May;38(3):410-20. PMID- 15086800 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. PG - 381-95 AB - Summary Cyclic ADP-ribose (cADPR) was previously shown to activate transient expression of two abscisic acid (ABA)-responsive genes in tomato cells. Here, we show that the activity of the enzyme responsible for cADPR synthesis, ADP-ribosyl (ADPR) cyclase, is rapidly induced by ABA in both wild-type (WT) and abi1-1 mutant Arabidopsis plants in the absence of protein synthesis. Furthermore, in transgenic Arabidopsis plants, induced expression of the Aplysia ADPR cyclase gene resulted in an increase in ADPR cyclase activity and cADPR levels, as well as elevated expression of ABA-responsive genes KIN2, RD22, RD29a, and COR47 (although to a lesser extent than after ABA induction). Genome-wide profiling indicated that about 28% of all ABA-responsive genes in Arabidopsis are similarly up- and downregulated by cADPR and contributed to the identification of new ABA-responsive genes. Our results suggest that activation of ADPR cyclase is an early ABA-signaling event partially insensitive to the abi1-1 mutation and that an increase in cADPR plays an important role in downstream molecular and physiological ABA responses. AD - Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. FAU - Sanchez, Juan-Pablo AU - Sanchez JP FAU - Duque, Paula AU - Duque P FAU - Chua, Nam-Hai AU - Chua NH LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.1365-313X.2004.02055.x [doi] AID - TPJ2055 [pii] PST - ppublish SO - Plant J 2004 May;38(3):381-95. PMID- 15086798 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Salt stress-induced chloride flux: a study using transgenic Arabidopsis expressing a fluorescent anion probe. PG - 539-44 AB - Summary Salt stress leads to massive accumulation of toxic levels of Na(+) and Cl(-) ions in plants. By using the recombinant fluorescent probe CLOMELEON, we demonstrate passive anion flux under salt stress. Chloride influx is restricted in the presence of divalent cations like Mg(2+) and Ca(2+), and completely blocked by La(3+). The amount but not the rate of the reported chloride uptake is independent from the kind of corresponding permeable cation (K(+) versus Na(+)), external pH and magnitude of osmotic stress. Cl(-) efflux however seems to involve stretch-activated transport. From the influence of Ca(2+) on reported changes of cytosolic anion concentrations, we speculate that transport mechanisms of Cl(-) and Na(+) might be thermodynamically coupled under saline conditions. AD - Zentrum fur Biochemie und Molekularbiologie, Universitat Kiel, Am Botanischen Garten 9, 24118 Kiel, Germany. FAU - Lorenzen, Inken AU - Lorenzen I FAU - Aberle, Thomas AU - Aberle T FAU - Plieth, Christoph AU - Plieth C LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0960-7412.2004.02053.x [doi] AID - TPJ2053 [pii] PST - ppublish SO - Plant J 2004 May;38(3):539-44. PMID- 15086797 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Expression of rolB in tobacco flowers affects the coordinated processes of anther dehiscence and style elongation. PG - 512-25 AB - Summary The effect of auxin on stamen and pistil development in tobacco flowers was investigated by means of the localized expression of rolB (root loci B), an Agrobacterium oncogene that increases auxin sensitivity in a cell-autonomous fashion. When rolB is driven by the promoter of the meiosis-specific Arabidopsis gene DMC1 (disrupted meiotic cDNA 1), expression occurs earlier in male than in female developing organs, resulting in a delay in anther dehiscence with respect to normal timing of pistil development. As a consequence of this developmental uncoupling, self-pollination is prevented in pDMC1:rolB plants. Histological analysis of pDMC1:GFP plants indicates that in tobacco, this promoter is active not only in meiocytes but also in somatic tissues of the anther. In contrast, simultaneous expression of rolB in anther and pistil somatic tissues, achieved by expressing a construct containing rolB under the control of the promoter of the petunia gene FBP7 (floral binding protein 7), results in a concomitant delay of both anther dehiscence and pistil development without affecting self-pollination of the plants. Analysis of plants harboring the pFBP7:GUS construct shows that in tobacco, this promoter is active not only in the ovules, as described for petunia, but also in pistil and anther somatic tissues involved in the dehiscence program. The delay in anther dehiscence and pistil development could be phenocopied by exogenous application of auxin. Jasmonic acid (JA) could not rescue the delay in anther dehiscence. These results suggest that auxin plays a key role in the timing of anther dehiscence, the dehiscence program is controlled by the somatic tissues of the anther, and auxin also regulates pistil development. AD - Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Genetica e Biologia Molecolare, Universita La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy. FAU - Cecchetti, Valentina AU - Cecchetti V FAU - Pomponi, Mirella AU - Pomponi M FAU - Altamura, Maria Maddalena AU - Altamura MM FAU - Pezzotti, Mario AU - Pezzotti M FAU - Marsilio, Sonia AU - Marsilio S FAU - D'Angeli, Simone AU - D'Angeli S FAU - Tornielli, Giovanni Battista AU - Tornielli GB FAU - Costantino, Paolo AU - Costantino P FAU - Cardarelli, Maura AU - Cardarelli M LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0960-7412.2004.02064.x [doi] AID - TPJ2064 [pii] PST - ppublish SO - Plant J 2004 May;38(3):512-25. PMID- 15086796 OWN - NLM STAT- in-data-review DA - 20040416 IS - 0960-7412 VI - 38 IP - 3 DP - 2004 May TI - Identification of Botrytis cinerea susceptibility loci in Arabidopsis thaliana. PG - 473-86 AB - Summary Botrytis cinerea is a major pathogen of fruit and vegetable crops causing both pre- and post-harvest grey mould. We have analysed 16 Arabidopsis thaliana ecotypes for natural variation in B. cinerea susceptibility. Susceptibility was associated with lower camalexin accumulation, and three ecotypes (Cape Verdi Islands (Cvi-0), Slavice (Sav-0) and Kindalville (Kin-0)) showed differential susceptibility to the two B. cinerea isolates used. Subsequently, to better understand the genetic control of grey mould disease, we assayed the Arabidopsis Landsberg erecta (Ler) x Columbia (Col-0) recombinant inbred population with the two isolates, and identified multiple small-to-medium-effect quantitative trait loci (QTL) governing susceptibility. Interestingly, the QTL for each isolate are distinct, suggesting that different mechanisms govern defence against these two isolates. Two QTL for each isolate exhibited epistatic interactions with specific allele combinations generating heightened B. cinerea susceptibility. AD - Department of Molecular and Cell Biology, University of Cape Town, Private Bag Rondebosch 7700, South Africa. FAU - Denby, Katherine J AU - Denby KJ FAU - Kumar, Pavan AU - Kumar P FAU - Kliebenstein, Daniel J AU - Kliebenstein DJ LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 AID - 10.1111/j.0960-7412.2004.02059.x [doi] AID - TPJ2059 [pii] PST - ppublish SO - Plant J 2004 May;38(3):473-86. PMID- 15085933 OWN - NLM STAT- in-process DA - 20040416 IS - 1521-6543 VI - 56 IP - 2 DP - 2004 Feb TI - Structural aspects of microRNA biogenesis. PG - 95-100 AB - One of the biggest surprises at the beginning of the 'post-genome era' was the discovery of numerous genes encoding microRNAs. They were found in genomes of such diverse organisms as Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and Homo sapiens which implies their important role in multicellular life evolution. The number of microRNA genes is estimated to be nearly 1% of that of protein-coding genes. Their products, tiny RNAs, are thought to regulate gene expression during development, organogenesis, and very likely during many other processes, by hybridizing to their target mRNAs. The cellular functions of mRNAs that are regulated by microRNAs are only beginning to be revealed, and details of this regulation mechanism are still poorly understood. In this article we discuss the possible mechanisms of microRNA biogenesis with special emphasis on their structural aspects. We have focused on the factors and effects that may be responsible for the existing length differences between different microRNAs, and for the observed length heterogeneity within some individual microRNA species. AD - Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14., 61-704 Poznan, Poland. FAU - Krol, Jacek AU - Krol J FAU - Krzyzosiak, Wlodzimierz J AU - Krzyzosiak WJ LA - eng PT - Journal Article PL - England TA - IUBMB Life JID - 100888706 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 PST - ppublish SO - IUBMB Life 2004 Feb;56(2):95-100. PMID- 15085802 OWN - NLM STAT- in-process DA - 20040415 IS - 1087-0156 VI - 22 IP - 4 DP - 2004 Apr TI - A conditional marker gene allowing both positive and negative selection in plants. PG - 455-8 AB - Selectable markers enable transgenic plants or cells to be identified after transformation. They can be divided into positive and negative markers conferring a selective advantage or disadvantage, respectively. We present a marker gene, dao1, encoding D-amino acid oxidase (DAAO, EC 1.4.3.3) that can be used for either positive or negative selection, depending on the substrate. DAAO catalyzes the oxidative deamination of a range of D-amino acids. Selection is based on differences in the toxicity of different D-amino acids and their metabolites to plants. Thus, D-alanine and D-serine are toxic to plants, but are metabolized by DAAO into nontoxic products, whereas D-isoleucine and D-valine have low toxicity, but are metabolized by DAAO into the toxic keto acids 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate, respectively. Hence, both positive and negative selection is possible with the same marker gene. The marker has been successfully established in Arabidopsis thaliana, and proven to be versatile, rapidly yielding unambiguous results, and allowing selection immediately after germination. FAU - Erikson, Oskar AU - Erikson O FAU - Hertzberg, Magnus AU - Hertzberg M FAU - Nasholm, Torgny AU - Nasholm T LA - eng PT - Letter PL - United States TA - Nat Biotechnol JID - 9604648 SB - IM EDAT- 2004/04/17 05:00 MHDA- 2004/04/17 05:00 PST - ppublish SO - Nat Biotechnol 2004 Apr;22(4):455-8. PMID- 15085429 OWN - NLM STAT- publisher DA - 20040415 IS - 0032-0935 DP - 2004 Apr 15 TI - Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits. AB - Embryos express several unique differentiation characteristics, including the accumulation of a number of metabolites that are generally considered to be unique to seeds. PICKLE ( PKL) codes for a CHD3-chromatin remodeling factor that is necessary for repression of embryonic traits in seedlings of Arabidopsis thaliana (L.) Heynh. In pkl mutants, primary roots are capable of expressing many embryonic traits after germination and are referred to as "pickle roots". In an attempt to examine the breadth of PKL-dependent repression of embryo-specific differentiation pathways, we determined the extent to which a variety of embryo-specific compounds accumulate in pickle roots. We found that pickle roots accumulate triacylglycerol with a fatty acid composition that is similar to that found in seeds. The major seed storage proteins are also present in pickle roots. In addition to these two well-characterized seed storage compounds, we observed that pickle roots accumulate phytate, a form of stored phosphate that is preferentially accumulated in seeds. Seeds of members of the Brassicaceae also accumulate a variety of unique secondary metabolites, including sinapate esters and glucosinolates. Surprisingly, the levels of secondary metabolites in pickle roots were not suggestive of an embryonic differentiation state, but did reveal that a mutation in PKL results in substantial changes in root secondary metabolism. Taken together, these data suggest that PKL is responsible for regulating some but not all aspects of the embryonic program as it relates to the accumulation of embryo-specific metabolites. AD - Department of Biochemistry, Purdue University, 175 S. University Street, IN 47907-2063, West Lafayette, USA. AU - Rider SD Jr AU - Hemm MR AU - Hostetler HA AU - Li HC AU - Chapple C AU - Ogas J LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1007/s00425-004-1254-1 [doi] PST - aheadofprint SO - Planta 2004 Apr 15;. PMID- 15085136 OWN - NLM STAT- in-process DA - 20040415 IS - 1476-4687 VI - 428 IP - 6984 DP - 2004 Apr 15 TI - Bacterial disease resistance in Arabidopsis through flagellin perception. PG - 764-7 AB - Plants and animals recognize microbial invaders by detecting pathogen-associated molecular patterns (PAMPs) such as flagellin. However, the importance of flagellin perception for disease resistance has, until now, not been demonstrated. Here we show that treatment of plants with flg22, a peptide representing the elicitor-active epitope of flagellin, induces the expression of numerous defence-related genes and triggers resistance to pathogenic bacteria in wild-type plants, but not in plants carrying mutations in the flagellin receptor gene FLS2. This induced resistance seems to be independent of salicylic acid, jasmonic acid and ethylene signalling. Wild-type and fls2 mutants both display enhanced resistance when treated with crude bacterial extracts, even devoid of elicitor-active flagellin, indicating the existence of functional perception systems for PAMPs other than flagellin. Although fls2 mutant plants are as susceptible as the wild type when bacteria are infiltrated into leaves, they are more susceptible to the pathogen Pseudomonas syringae pv. tomato DC3000 when it is sprayed on the leaf surface. Thus, flagellin perception restricts bacterial invasion, probably at an early step, and contributes to the plant's disease resistance. AD - Friedrich Miescher Institute for Biomedical Research, PO Box 2543, CH-4002 Basel, Switzerland. FAU - Zipfel, Cyril AU - Zipfel C FAU - Robatzek, Silke AU - Robatzek S FAU - Navarro, Lionel AU - Navarro L FAU - Oakeley, Edward J AU - Oakeley EJ FAU - Jones, Jonathan D G AU - Jones JD FAU - Felix, Georg AU - Felix G FAU - Boller, Thomas AU - Boller T LA - eng PT - Journal Article PL - England TA - Nature JID - 0410462 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 PHST- 2003/Dec/24 [received] PHST- 2004/Mar/11 [accepted] AID - 10.1038/nature02485 [doi] AID - nature02485 [pii] PST - ppublish SO - Nature 2004 Apr 15;428(6984):764-7. PMID- 15084749 OWN - NLM STAT- publisher DA - 20040415 IS - 0027-8424 DP - 2004 Apr 14 TI - The Arabidopsis repressor of light signaling, COP1, is regulated by nuclear exclusion: Mutational analysis by bioluminescence resonance energy transfer. AB - Bioluminescence resonance energy transfer (BRET) between Renilla luciferase and yellow fluorescent protein has been adapted to serve as a real-time reporter on protein-protein interactions in live plant cells by using the Arabidopsis Constitutive photomorphogenesis 1 (COP1) protein as a model system. COP1 is a repressor of light signal transduction that functions as part of a nuclear E3 ubiquitin ligase. COP1 possesses a leucine-rich nuclear-exclusion signal that resides in a domain implicated in COP1 dimerization. BRET was applied in conjunction with site-directed mutagenesis to explore the respective contributions of the nuclear-exclusion and dimerization motifs to the regulation of COP1 activity in vivo. One specific mutant protein, COP1(L105A), showed increased nuclear accumulation but retained the ability to dimerize, as monitored by BRET, whereas other mutations inhibited both nuclear exclusion and COP1 dimerization. Mutant rescue and overexpression experiments indicated that nuclear exclusion of COP1 protein is a rate-limiting step in light signal transduction. AD - *Department of Botany, University of Tennessee, Knoxville, TN 37996-1100. AU - Subramanian C AU - Kim BH AU - Lyssenko NN AU - Xu X AU - Johnson CH AU - Von Arnim AG LA - ENG PT - JOURNAL ARTICLE TA - Proc Natl Acad Sci U S A JID - 7505876 EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1073/pnas.0307964101 [doi] AID - 0307964101 [pii] PST - aheadofprint SO - Proc Natl Acad Sci U S A 2004 Apr 14;. PMID- 15084732 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The GATA Family of Transcription Factors in Arabidopsis and Rice. PG - 1718-32 AB - GATA transcription factors are a group of DNA binding proteins broadly distributed in eukaryotes. The GATA factors DNA binding domain is a class IV zinc finger motif in the form CX(2)CX(17-20)CX(2)C followed by a basic region. In plants, GATA DNA motifs have been implicated in light-dependent and nitrate-dependent control of transcription. Herein, we show that the Arabidopsis and the rice (Oryza sativa) genomes present 29 and 28 loci, respectively, that encode for putative GATA factors. A phylogenetic analysis of the 57 GATA factors encoding genes, as well as the study of their intron-exon structure, indicates the existence of seven subfamilies of GATA genes. Some of these subfamilies are represented in both species but others are exclusive for one of them. In addition to the GATA zinc finger motif, polypeptides of the different subfamilies are characterized by the presence of additional domains such as an acidic domain, a CCT (CONSTANS, CO-like, and TOC1) domain, or a transposase-like domain also found in FAR1 and FHY3. Subfamily VI comprises genes that encode putative bi-zinc finger polypeptides, also found in metazoan and fungi, and a tri-zinc finger protein which has not been previously reported in eukaryotes. The phylogeny of the GATA zinc finger motif, excluding flanking regions, evidenced the existence of four classes of GATA zinc fingers, three of them containing 18 residues in the zinc finger loop and one containing a 20-residue loop. Our results support multiple models of evolution of the GATA gene family in plants including gene duplication and exon shuffling. AD - Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas, Universidad de Seville, Americo Vespucio s/n, E-41092 Seville, Spain. FAU - Reyes, Jose C AU - Reyes JC FAU - Muro-Pastor, M Isabel AU - Muro-Pastor MI FAU - Florencio, Francisco J AU - Florencio FJ LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1104/pp.103.037788 [doi] AID - 134/4/1718 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1718-32. PMID- 15084729 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase. PG - 1388-400 AB - The transformation of 4-hydroxyphenylpyruvate to homogentisate, catalyzed by 4-hydroxyphenylpyruvate dioxygenase (HPPD), plays an important role in degrading aromatic amino acids. As the reaction product homogentisate serves as aromatic precursor for prenylquinone synthesis in plants, the enzyme is an interesting target for herbicides. In this study we report the first x-ray structures of the plant HPPDs of Zea mays and Arabidopsis in their substrate-free form at 2.0 A and 3.0 A resolution, respectively. Previous biochemical characterizations have demonstrated that eukaryotic enzymes behave as homodimers in contrast to prokaryotic HPPDs, which are homotetramers. Plant and bacterial enzymes share the overall fold but use orthogonal surfaces for oligomerization. In addition, comparison of both structures provides direct evidence that the C-terminal helix gates substrate access to the active site around a nonheme ferrous iron center. In the Z. mays HPPD structure this helix packs into the active site, sequestering it completely from the solvent. In contrast, in the Arabidopsis structure this helix tilted by about 60 degrees into the solvent and leaves the active site fully accessible. By elucidating the structure of plant HPPD enzymes we aim to provide a structural basis for the development of new herbicides. AD - Max-Planck-Institut fur Biochemie, Abteilung fur Strukturforschung, 82152 Martinsried, Germany. FAU - Fritze, Iris M AU - Fritze IM FAU - Linden, Lars AU - Linden L FAU - Freigang, Jorg AU - Freigang J FAU - Auerbach, Gunter AU - Auerbach G FAU - Huber, Robert AU - Huber R FAU - Steinbacher, Stefan AU - Steinbacher S LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1104/pp.103.034082 [doi] AID - 134/4/1388 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1388-400. PMID- 15084723 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Arabidopsis AtCYP20-2 Is a Light-Regulated Cyclophilin-Type Peptidyl-Prolyl cis-trans Isomerase Associated with the Photosynthetic Membranes. PG - 1244-7 AD - Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom. FAU - Romano, Patrick G N AU - Romano PG FAU - Edvardsson, Anna AU - Edvardsson A FAU - Ruban, Alexander V AU - Ruban AV FAU - Andersson, Bertil AU - Andersson B FAU - Vener, Alexander V AU - Vener AV FAU - Gray, Julie E AU - Gray JE FAU - Horton, Peter AU - Horton P LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1104/pp.104.041186 [doi] AID - 134/4/1244 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1244-7. PMID- 15084721 OWN - NLM STAT- publisher DA - 20040415 IS - 1040-4651 DP - 2004 Apr 14 TI - The Embryo MADS Domain Protein AGAMOUS-Like 15 Directly Regulates Expression of a Gene Encoding an Enzyme Involved in Gibberellin Metabolism. AB - AGL15 (for AGAMOUS-Like 15) is a member of the MADS domain family of DNA binding transcriptional regulators that accumulates to its highest amounts during embryo development. To better understand how AGL15 functions, a chromatin immunoprecipitation approach was used to identify directly regulated genes. One DNA fragment that coprecipitated with AGL15 corresponded to a portion of the regulatory region of a gene named DTA1 (for Downstream Target of AGL15-1). The expression of DTA1 was positively correlated with AGL15 abundance during embryogenesis. In this report, a cis element for response to AGL15 was identified, and the activity of DTA1 as a gibberellin (GA) 2-oxidase was confirmed. DTA1 corresponds to AtGA2ox6 and was renamed to indicate this identity. Further experiments related the function of AtGA2ox6 to regulation by AGL15. Constitutive expression of AGL15 and of AtGA2ox6 altered endogenous GA amounts and caused GA-deficient phenotypes in Arabidopsis thaliana that could be at least partially rescued by application of biologically active GA. The phenotype of plants with decreased expression of AtGA2ox6 was the converse of plants overexpressing AtGA2ox6 in terms of seed germination attributes and effects on somatic embryo production. AD - Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546-0312. AU - Wang H AU - Caruso LV AU - Downie AB AU - Perry SE LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1105/tpc.021261 [doi] AID - tpc.021261 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 14;. PMID- 15084720 OWN - NLM STAT- publisher DA - 20040415 IS - 1040-4651 DP - 2004 Apr 14 TI - SPIRAL1 Encodes a Plant-Specific Microtubule-Localized Protein Required for Directional Control of Rapidly Expanding Arabidopsis Cells. AB - Highly organized interphase cortical microtubule (MT) arrays are essential for anisotropic growth of plant cells, yet little is known about the molecular mechanisms that establish and maintain the order of these arrays. The Arabidopsis thaliana spiral1 (spr1) mutant shows right-handed helical growth in roots and etiolated hypocotyls. Characterization of the mutant phenotypes suggested that SPR1 may control anisotropic cell expansion through MT-dependent processes. SPR1 was identified by map-based cloning and found to encode a small protein with unknown function. Proteins homologous to SPR1 occur specifically and ubiquitously in plants. Genetic complementation with green fluorescent protein fusion proteins indicated that the SPR1 protein colocalizes with cortical MTs and that both MT localization and cell expansion control are conferred by the conserved N- and C-terminal regions. Strong SPR1 expression was found in tissues undergoing rapid cell elongation. Plants overexpressing SPR1 showed enhanced resistance to an MT drug and increased hypocotyl elongation. These observations suggest that SPR1 is a plant-specific MT-localized protein required for the maintenance of growth anisotropy in rapidly elongating cells. AD - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan. AU - Nakajima K AU - Furutani I AU - Tachimoto H AU - Matsubara H AU - Hashimoto T LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1105/tpc.017830 [doi] AID - tpc.017830 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 14;. PMID- 15084715 OWN - NLM STAT- publisher DA - 20040415 IS - 1040-4651 DP - 2004 Apr 14 TI - Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing. AB - In plants, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are effectors of RNA silencing, a process involved in defense through RNA interference (RNAi) and in development. Plant viruses are natural targets of RNA silencing, and as a counterdefensive strategy, they have evolved highly diverse silencing suppressor proteins. Although viral suppressors are usually thought to act at distinct steps of the silencing machinery, there had been no consensus system so far that allowed a strict side-by-side analysis of those factors. We have set up such a system in Arabidopsis thaliana and used it to compare the effects of five unrelated viral silencing suppressors on the siRNA and miRNA pathways. Although all the suppressors inhibited RNAi, only three of them induced developmental defects, indicating that the two pathways are only partially overlapping. These developmental defects were remarkably similar, and their penetrance correlated with inhibition of miRNA-guided cleavage of endogenous transcripts and not with altered miRNA accumulation per se. Among the suppressors investigated, the tombusviral P19 protein coimmunoprecipitated with siRNA duplexes and miRNA duplexes corresponding to the primary cleavage products of miRNA precursors. Thus, it is likely that P19 prevents RNA silencing by sequestering both classes of small RNAs. Moreover, the finding here that P19 binds siRNAs and suppresses RNAi in Hela cells also suggests that this factor may be useful to dissect the RNA silencing pathways in animals. Finally, the differential effects of the silencing suppressors tested here upon other types of Arabidopsis silencing-related small RNAs revealed a surprising variety of biosynthetic and, presumably, functional pathways for those molecules. Therefore, silencing suppressors are valuable probes of the complexity of RNA silencing. AD - Institut de Biologie Moleculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France. AU - Dunoyer P AU - Lecellier CH AU - Parizotto EA AU - Himber C AU - Voinnet O LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1105/tpc.020719 [doi] AID - tpc.020719 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 14;. PMID- 15084303 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0960-9822 VI - 14 IP - 8 DP - 2004 Apr 20 TI - Organellar proteomics: chloroplasts in the spotlight. PG - R317-9 AB - The post-genomic era of biology has seen a significant shift in focus, from the genes themselves to the proteins they encode. New studies on the Arabidopsis chloroplast proteome have raised interesting questions about the biogenesis, evolution and functions of chloroplasts. AD - Department of Biology, University of Leicester, Leicester, LE1 7RH, UK. FAU - Jarvis, Paul AU - Jarvis P LA - eng PT - Journal Article PL - England TA - Curr Biol JID - 9107782 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 AID - 10.1016/j.cub.2004.03.054 [doi] AID - S0960982204002313 [pii] PST - ppublish SO - Curr Biol 2004 Apr 20;14(8):R317-9. PMID- 15083810 OWN - NLM STAT- in-process DA - 20040414 IS - 1469-221X VI - 5 IP - 3 DP - 2004 Mar TI - Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. PG - 297-303 AB - The structure of the DNA-binding NAC domain of Arabidopsis ANAC (abscisic-acid-responsive NAC) has been determined by X-ray crystallography to 1.9A resolution (Protein Data Bank codes 1UT4 and 1UT7). This is the first structure determined for a member of the NAC family of plant-specific transcriptional regulators. NAC proteins are characterized by their conserved N-terminal NAC domains that can bind both DNA and other proteins. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain does not possess a classical helix-turn-helix motif; instead it reveals a new transcription factor fold consisting of a twisted beta-sheet surrounded by a few helical elements. The functional dimer formed by the NAC domain was identified in the structure, which will serve as a structural template for understanding NAC protein function at the molecular level. AD - Department of Chemistry, Centre for Crystallographic Studies, University of Copenhagen O, Denmark. FAU - Ernst, Heidi A AU - Ernst HA FAU - Olsen, Addie Nina AU - Olsen AN FAU - Larsen, Sine AU - Larsen S FAU - Lo Leggio, Leila AU - Lo Leggio L LA - eng PT - Journal Article PL - England TA - EMBO Rep JID - 100963049 SB - IM EDAT- 2004/04/16 05:00 MHDA- 2004/04/16 05:00 PST - ppublish SO - EMBO Rep 2004 Mar;5(3):297-303. PMID- 15082929 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0167-4412 VI - 53 IP - 6 DP - 2003 Dec TI - L-Gulono-1,4-lactone oxidase expression rescues vitamin C-deficient Arabidopsis ( vtc ) mutants. PG - 837-44 AB - Vitamin C (L-ascorbic acid) has important antioxidant and metabolic functions in both plants and animals, humans have lost the ability to synthesize it. Fresh produce is the major source of vitamin C in the human diet yet only limited information is available concerning its route(s) of synthesis in plants. In contrast, the animal vitamin C biosynthetic pathway has been elucidated since the 1960s. Two biosynthetic pathways for vitamin C in plants are presently known. The D-mannose pathway appears to be predominant in leaf tissue, but a D-galacturonic acid pathway operates in developing fruits. Our group has previously shown that transforming lettuce and tobacco with a cDNA encoding the terminal enzyme of the animal pathway, L-gulono-1,4-lactone oxidase (GLOase, EC 1.1.3.8), increased the vitamin C leaf content between 4- and 7-fold. Additionally, we found that wild-type (wt) tobacco plants had elevated vitamin C levels when fed L-gulono-1,4-lactone, the animal precursor. These data suggest that at least part of the animal pathway may be present in plants. To further investigate this possibility, wild-type and vitamin-C-deficient Arabidopsis thaliana (L.) Heynh ( vtc ) plants were transformed with a 35S: GLOase construct, homozygous lines were developed, and vitamin C levels were compared to those in untransformed controls. Wild-type plants transformed with the construct showed up to a 2-fold increase in vitamin C leaf content compared to controls. All five vtc mutant lines expressing GLOase had a rescued vitamin C leaf content equal or higher (up to 3-fold) than wt leaves. These data and the current knowledge about the identity of genes mutated in the vtc lines suggest that an alternative pathway is present in plants, which can bypass the deficiency of GDP-mannose production of the vtc1-1 mutant and possibly circumvent other steps in the D-mannose pathway to synthesize vitamin C. AD - Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, 413 Price Hall, Blacksburg, VA 24061-0331, USA. FAU - Radzio, Jessica A AU - Radzio JA FAU - Lorence, Argelia AU - Lorence A FAU - Chevone, Boris I AU - Chevone BI FAU - Nessler, Craig L AU - Nessler CL LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1023/B:PLAN.0000023671.99451.1d [doi] AID - 5265269 [pii] PST - ppublish SO - Plant Mol Biol 2003 Dec;53(6):837-44. PMID- 15082928 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0167-4412 VI - 53 IP - 6 DP - 2003 Dec TI - ZmEBE genes show a novel, continuous expression pattern in the central cell before fertilization and in specific domains of the resulting endosperm after fertilization. PG - 821-36 AB - Two novel maize genes expressed specifically in the central cell of the female gametophyte and in two compartments of the endosperm (the basal endosperm transfer layer and the embryo surrounding region) were characterized. The ZmEBE (embryo sac/basal endosperm transfer layer/embryo surrounding region) genes were isolated by a differential display between the upper and the lower half of the kernel at 7 days after pollination (DAP). Sequence analysis revealed ORFs coding for two closely related proteins of 304 amino acids (ZmEBE-1) and 286 amino acids (ZmEBE-2). This size difference was due to differences in the splicing of the two genes. Both protein sequences showed significant similarity to the DUF239 family of Arabidopsis, a group of 22 proteins of unknown function, a small number of which are putative peptidases. ZmEBE genes had a novel cell type-specific expression pattern in the central cell before and the resulting endosperm after fertilization. RT-PCR analysis showed that the expression of both genes started before pollination in the central cell and continued in the kernel up to 20 DAP with a peak at 7 DAP. In situ hybridization revealed that the expression in the kernel was restricted to the basal transfer cell layer and the embryo surrounding region of the endosperm. The expression of ZmEBE-1 was at least 10 times lower than that of ZmEBE-2. Similarly to other genes expressed in the endosperm, ZmEBE-1 expression was subject to a parent-of-origin effect, while no such effect was detected in ZmEBE-2. Sequence analysis of upstream regions revealed a potential cis element of 33 bp repeated 7 times in ZmEBE-1 and ZmEBE-2 between positions -900 and -100. The 1.6 kb ZmEBE-2 upstream sequence containing the seven R7 elements was able to confer expression in the basal endosperm to a Gus reporter gene. These data indicate that ZmEBE is potentially involved in the early development of specialized domains of the endosperm and that this process is possibly already initiated in the central cell, which is at the origin of the endosperm. AD - RDP, UMR 5667 INRA-CNRS-ENSL-UCBL, ENS-Lyon, 46 Allee d'Italie, 69364 Lyon Cedex 07, France. FAU - Magnard, Jean-Louis AU - Magnard JL FAU - Lehouque, Gaelle AU - Lehouque G FAU - Massonneau, Agnes AU - Massonneau A FAU - Frangne, Nathalie AU - Frangne N FAU - Heckel, Thierry AU - Heckel T FAU - Gutierrez-Marcos, Jose F AU - Gutierrez-Marcos JF FAU - Perez, Pascual AU - Perez P FAU - Dumas, Christian AU - Dumas C FAU - Rogowsky, Peter M AU - Rogowsky PM LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1023/B:PLAN.0000023672.37089.00 [doi] AID - 5265270 [pii] PST - ppublish SO - Plant Mol Biol 2003 Dec;53(6):821-36. PMID- 15082927 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0167-4412 VI - 53 IP - 6 DP - 2003 Dec TI - Changes in gene expression in response to altered SHL transcript levels. PG - 805-20 AB - The nuclear SHL protein is composed of a N-terminal BAH domain and a C-terminal PHD finger. Both domains are found in transcriptional regulators and chromatin-modifying proteins. Arabidopsis plants over-expressing SHL showed earlier flowering and senescence phenotype. To identify SHL regulated genes, expression profiles of 35S::SHL plants were established with Affymetrix ATH1 microarrays. About 130 genes showed reduced transcript levels, and about 45 genes showed increased transcript levels in 35S::SHL plants. The up-regulated genes included AGL20 and AGL9, which most likely cause the early flowering phenotype of 35S::SHL plants. Late-flowering SHL-antisense lines showed reduced AGL20 mRNA levels, suggesting that AGL20 gene expression depends on the SHL protein. The stronger expression of senescence- and defence-related genes (such as DIN2, DIN11 and PR-1 ) is in line with the early senescence phenotype of SHL- over-expressing plants. SHL-down-regulated genes included stress response genes and the PSR3.2 gene (encoding a beta-glucosidase). SHL over-expression did not alter the tissue specificity of PSR3.2 gene expression, but resulted in reduced transcript levels in both shoots and roots. Plants with glucocorticoid-inducible SHL over-expression were established and used for expression profiling as well. A subset of genes was identified, which showed consistent changes in the inducible system and in plants with constitutive SHL over-expression. AD - Universitat Potsdam - Genetik, c/o MPI fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Golm, Germany e-mail muessig@mpimp-golm.mpg.de FAU - Mussig, Carsten AU - Mussig C FAU - Altmann, Thomas AU - Altmann T LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1023/B:PLAN.0000023661.65248.4b [doi] AID - 5264593 [pii] PST - ppublish SO - Plant Mol Biol 2003 Dec;53(6):805-20. PMID- 15082924 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0167-4412 VI - 53 IP - 6 DP - 2003 Dec TI - Fertilization induces strong accumulation of a histone deacetylase (HD2) and of other chromatin-remodeling proteins in restricted areas of the ovules. PG - 759-69 AB - Fertilization triggers a unique and complex developmental program leading to embryogenesis and seed set. Recently, mutations affecting chromatin-remodeling enzymes in plants have shown their key roles in development as demonstrated before in animal cells. Using a negative selection screen to isolate genes expressed in ovary tissues upon fertilization, we have identified a histone deacetylase gene (named ScHD2a ) of the plant-specific HD2 family, which is predominantly expressed in ovaries of the self-incompatible species Solanum chacoense. The ScHD2a is the probable orthologue of the Arabidopsis thaliana AtHD2a gene, which upon antisense suppression leads to aborted seeds formation. Transcription of the ScHD2a gene is strongly triggered by fertilization and transcripts accumulate predominantly in the micropylar region of the ovule's integument. Interestingly, this fertilization-induced accumulation pattern was also observed for other genes involved in transcriptional repression but not for a MYST-family histone acetyltransferase. The strong increase in ScHD2a mRNA levels in ovules after fertilization suggests an important and localized role for transcriptional repression in seed development, and indicates why silencing of the AtHD2a gene leads to aborted seed formation. AD - Institut de Recherche en Biologie Vegetale, Departement de Sciences Biologiques, Universite de Montreal, 4101 Sherbrooke est, Montreal, Quebec, Canada H1X 2B2. FAU - Lagace, Marie AU - Lagace M FAU - Chantha, Sier-Ching AU - Chantha SC FAU - Major, Genevieve AU - Major G FAU - Matton, Daniel P AU - Matton DP LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1023/B:PLAN.0000023665.36676.89 [doi] AID - 5264879 [pii] PST - ppublish SO - Plant Mol Biol 2003 Dec;53(6):759-69. PMID- 15082565 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0016-6731 VI - 166 IP - 3 DP - 2004 Mar TI - The Maintenance of Extreme Amino Acid Diversity at the Disease Resistance Gene, RPP13, in Arabidopsis thaliana. PG - 1517-27 AB - We have used the naturally occurring plant-parasite system of Arabidopsis thaliana and its common parasite Peronospora parasitica (downy mildew) to study the evolution of resistance specificity in the host population. DNA sequence of the resistance gene, RPP13, from 24 accessions, including 20 from the United Kingdom, revealed amino acid sequence diversity higher than that of any protein coding gene reported so far in A. thaliana. A significant excess of amino acid polymorphism segregating within this species is localized within the leucine-rich repeat (LRR) domain of RPP13. These results indicate that single alleles of the gene have not swept through the population, but instead, a diverse collection of alleles have been maintained. Transgenic complementation experiments demonstrate functional differences among alleles in their resistance to various pathogen isolates, suggesting that the extreme amino acid polymorphism in RPP13 is maintained through continual reciprocal selection between host and pathogen. AD - Center for Population Biology, University of California, Davis, California 95616. FAU - Rose, Laura E AU - Rose LE FAU - Bittner-Eddy, Peter D AU - Bittner-Eddy PD FAU - Langley, Charles H AU - Langley CH FAU - Holub, Eric B AU - Holub EB FAU - Michelmore, Richard W AU - Michelmore RW FAU - Beynon, Jim L AU - Beynon JL LA - eng PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 166/3/1517 [pii] PST - ppublish SO - Genetics 2004 Mar;166(3):1517-27. PMID- 15082560 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0016-6731 VI - 166 IP - 3 DP - 2004 Mar TI - Functional Divergence in Tandemly Duplicated Arabidopsis thaliana Trypsin Inhibitor Genes. PG - 1419-36 AB - In multigene families, variation among loci and alleles can contribute to trait evolution. We explored patterns of functional and genetic variation in six duplicated Arabidopsis thaliana trypsin inhibitor (ATTI) loci. We demonstrate significant variation in constitutive and herbivore-induced transcription among ATTI loci that show, on average, 65% sequence divergence. Significant variation in ATTI expression was also found between two molecularly defined haplotype classes. Population genetic analyses for 17 accessions of A. thaliana showed that six ATTI loci arranged in tandem within 10 kb varied 10-fold in nucleotide diversity, from 0.0009 to 0.0110, and identified a minimum of six recombination events throughout the tandem array. We observed a significant peak in nucleotide and indel polymorphism spanning ATTI loci in the interior of the array, due primarily to divergence between the two haplotype classes. Significant deviation from the neutral equilibrium model for individual genes was interpreted within the context of intergene linkage disequilibrium and correlated patterns of functional differentiation. In contrast to the outcrosser Arabidopsis lyrata for which recombination is observed even within ATTI loci, our data suggest that response to selection was slowed in the inbreeding, annual A. thaliana because of interference among functionally divergent ATTI loci. AD - Department of Genetics and Evolution, Max Planck Institute of Chemical Ecology, 07745 Jena, Germany. FAU - Clauss, M J AU - Clauss MJ FAU - Mitchell-Olds, T AU - Mitchell-Olds T LA - eng PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 166/3/1419 [pii] PST - ppublish SO - Genetics 2004 Mar;166(3):1419-36. PMID- 15082530 OWN - NLM STAT- in-process DA - 20040414 IS - 0890-9369 VI - 18 IP - 7 DP - 2004 Apr 1 TI - BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. PG - 782-93 AB - DNA repair associated with DNA replication is important for the conservation of genomic sequence information, whereas reconstitution of chromatin after replication sustains epigenetic information. We have isolated and characterized mutations in the BRU1 gene of Arabidopsis that suggest a novel link between these underlying maintenance mechanisms. Bru1 plants are highly sensitive to genotoxic stress and show stochastic release of transcriptional gene silencing. They also show increased intrachromosomal homologous recombination and constitutively activated expression of poly (ADP-ribose) polymerase-2 (AtPARP-2), the induction of which is associated with elevated DNA damage. Bru1 mutations affect the stability of heterochromatin organization but do not interfere with genome-wide DNA methylation. BRU1 encodes a novel nuclear protein with two predicted protein-protein interaction domains. The developmental abnormalities characteristic of bru1 mutant plants resemble those triggered by mutations in genes encoding subunits of chromatin assembly factor (CAF-1), the condensin complex, or MRE11. Comparison of bru1 with these mutants indicates cooperative roles in the replication and stabilization of chromatin structure, providing a novel link between chromatin replication, epigenetic inheritance, S-phase DNA damage checkpoints, and the regulation of meristem development. AD - Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland. shin.takeda@bioveg.unige.ch FAU - Takeda, Shin AU - Takeda S FAU - Tadele, Zerihun AU - Tadele Z FAU - Hofmann, Ingo AU - Hofmann I FAU - Probst, Aline V AU - Probst AV FAU - Angelis, Karel J AU - Angelis KJ FAU - Kaya, Hidetaka AU - Kaya H FAU - Araki, Takashi AU - Araki T FAU - Mengiste, Tesfaye AU - Mengiste T FAU - Scheid, Ortrun Mittelsten AU - Scheid OM FAU - Shibahara, Kei-ichi AU - Shibahara K FAU - Scheel, Dierk AU - Scheel D FAU - Paszkowski, Jerzy AU - Paszkowski J LA - eng PT - Journal Article PL - United States TA - Genes Dev JID - 8711660 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1101/gad.295404 [doi] AID - 18/7/782 [pii] PST - ppublish SO - Genes Dev 2004 Apr 1;18(7):782-93. PMID- 15081890 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0003-9861 VI - 425 IP - 1 DP - 2004 May 1 TI - Examination of the role of Gln-158 in the mechanism of CO [Formula: see text] hydration catalyzed by beta-carbonic anhydrase from Arabidopsis thaliana. PG - 25-32 AB - We have cloned and overexpressed a variant of Arabidopsis thaliana beta-carbonic anhydrase (Q158A) that deletes the functional equivalent of the backbone amide NH of Thr-199 in human alpha-carbonic anhydrase II. The latter residue is hypothesized to be important in catalyzing the rate of CO [Formula: see text] -HCO [Formula: see text] (-) interconversion in alpha-carbonic anhydrase but this hypothesis is not directly testable in that enzyme. Kinetic studies of a variant of the functionally equivalent residue in A. thaliana beta-carbonic anhydrase provide direct evidence for the role of this residue in beta-carbonic anhydrase. Namely, the mutation of Gln-158 to Ala results in a significant decrease in the maximal [Formula: see text] (33% of wild type) at steady state and the maximal rate of CO [Formula: see text] -HCO [Formula: see text] (-) exchange at chemical equilibrium as measured by [Formula: see text] (7% of wild type), while leaving the maximal rate of H(+) transfer, as measured by [Formula: see text] at steady state, or [Formula: see text] at chemical equilibrium, largely unaffected. AD - Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA. FAU - Rowlett, Roger S AU - Rowlett RS FAU - Tu, Chingkuang AU - Tu C FAU - Murray, Paul S AU - Murray PS FAU - Chamberlin, Joy E AU - Chamberlin JE LA - eng PT - Journal Article PL - United States TA - Arch Biochem Biophys JID - 0372430 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 PHST- 2004/Feb/05 [received] PHST- 2004/Feb/16 [revised] AID - 10.1016/j.abb.2004.02.033 [doi] AID - S0003986104001213 [pii] PST - ppublish SO - Arch Biochem Biophys 2004 May 1;425(1):25-32. PMID- 15081049 OWN - NLM STAT- in-data-review DA - 20040414 IS - 0958-1669 VI - 15 IP - 2 DP - 2004 Apr TI - Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. PG - 120-5 AB - The importance of angiosperms to sustaining humanity by providing a wide range of 'ecosystem services' warrants increased exploration of their genomic diversity. The nearly completed sequences for two species representing the major angiosperm subclasses, specifically the dicot Arabidopsis thaliana and the monocot Oryza sativa, provide a foundation for comparative analysis across the angiosperms. The angiosperms also exemplify some challenges to be faced as genomics makes new inroads into describing biotic diversity, in particular polyploidy (genome-wide chromatin duplication), and much larger genome sizes than have been studied to date. AD - Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA. FAU - Paterson, Andrew H AU - Paterson AH FAU - Bowers, John E AU - Bowers JE FAU - Chapman, Brad A AU - Chapman BA FAU - Peterson, Daniel G AU - Peterson DG FAU - Rong, Junkang AU - Rong J FAU - Wicker, Thomas M AU - Wicker TM LA - eng PT - Journal Article PL - England TA - Curr Opin Biotechnol JID - 9100492 SB - IM EDAT- 2004/04/15 05:00 MHDA- 2004/04/15 05:00 AID - 10.1016/j.copbio.2004.03.001 [doi] AID - S0958166904000308 [pii] PST - ppublish SO - Curr Opin Biotechnol 2004 Apr;15(2):120-5. PMID- 15079801 OWN - NLM STAT- in-data-review DA - 20040413 IS - 1003-9406 VI - 21 IP - 2 DP - 2004 Apr TI - [Advances in the molecular mechanism of RNA interference] PG - 161-5 AB - This paper reviews the latest development of RNA interference(RNAi). RNA interference is the process of sequence-specific degradation of homologous mRNA triggered by double-stranded RNA. As a technically simple and an effective genetic tool which can exert effect on the expression of gene and substitute for gene knock-out technique in some degree, RNAi phenomena have been broadly validated in diverse model organisms such as Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana and Neurospora crassa. Simultaneously, study on molecular mechanism of RNAi, which might be involved in the level of post-transcription, translation, genome methylation or conduction of silencing signals, is now making unceasing progress. Clear elucidation of the molecular mechanism could provide important theoretical references and powerful tools for the practical application in this field where RNAi may be put into the use of systematic gene screening, the discovery of new genes and the gene therapy for human tumor or other refractory human diseases. AD - Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041 P.R.China.szzhang@mcwcums.com FAU - He, Guoping AU - He G FAU - Zhang, Sizhong AU - Zhang S LA - chi PT - Journal Article PL - China TA - Zhonghua Yi Xue Yi Chuan Xue Za Zhi JID - 9425197 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 940621037 [pii] PST - ppublish SO - Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2004 Apr;21(2):161-5. PMID- 15078816 OWN - NLM STAT- publisher DA - 20040413 IS - 0890-9369 DP - 2004 Apr 12 TI - Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. AB - Two evolutionarily distant plant species, rice (Oryza sativa L.), a short-day (SD) plant, and Arabidopsis thaliana, a long-day plant, share a conserved genetic network controlling photoperiodic flowering. The orthologous floral regulators-rice Heading date 1 (Hd1/BI) and Arabidopsis CONSTANS (CO)-integrate circadian clock and external light signals into mRNA expression of the FLOWERING LOCUS T (FT) group floral inducer. Here, we report that the rice Early heading date 1 (Ehd1) gene, which confers SD promotion of flowering in the absence of a functional allele of Hd1, encodes a B-type response regulator that might not have an ortholog in the Arabidopsis genome. Ehd1 mRNA was induced by 1-wk SD treatment, and Ehd1 may promote flowering by inducing FT-like gene expression only under SD conditions. Microarray analysis further revealed a few MADS box genes downstream of Ehd1. Our results indicate that a novel two-component signaling cascade is integrated into the conserved pathway in the photoperiodic control of flowering in rice. AD - Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan. AU - Doi K AU - Izawa T AU - Fuse T AU - Yamanouchi U AU - Kubo T AU - Shimatani Z AU - Yano M AU - Yoshimura A LA - ENG PT - JOURNAL ARTICLE TA - Genes Dev JID - 8711660 EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1101/gad.1189604 [doi] AID - 1189604 [pii] PST - aheadofprint SO - Genes Dev 2004 Apr 12;. PMID- 15078338 OWN - NLM STAT- in-data-review DA - 20040413 IS - 0960-7412 VI - 38 IP - 2 DP - 2004 Apr TI - Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. PG - 366-79 AB - Summary To overcome the detection limits inherent to DNA array-based methods of transcriptome analysis, we developed a real-time reverse transcription (RT)-PCR-based resource for quantitative measurement of transcripts for 1465 Arabidopsis transcription factors (TFs). Using closely spaced gene-specific primer pairs and SYBR((R)) Green to monitor amplification of double-stranded DNA (dsDNA), transcript levels of 83% of all target genes could be measured in roots or shoots of young Arabidopsis wild-type plants. Only 4% of reactions produced non-specific PCR products. The amplification efficiency of each PCR was determined from the log slope of SYBR((R)) Green fluorescence versus cycle number in the exponential phase, and was used to correct the readout for each primer pair and run. Measurements of transcript abundance were quantitative over six orders of magnitude, with a detection limit equivalent to one transcript molecule in 1000 cells. Transcript levels for different TF genes ranged between 0.001 and 100 copies per cell. Only 13% of TF transcripts were undetectable in these organs. For comparison, 22K Arabidopsis Affymetrix chips detected less than 55% of TF transcripts in the same samples, the range of transcript levels was compressed by a factor more than 100, and the data were less accurate especially in the lower part of the response range. Real-time RT-PCR revealed 35 root-specific and 52 shoot-specific TF genes, most of which have not been identified as organ-specific previously. Finally, many of the TF transcripts detected by RT-PCR are not represented in Arabidopsis EST (expressed sequence tag) or Massively Parallel Signature Sequencing (MPSS) databases. These genes can now be annotated as expressed. AD - Max-Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Golm, Germany. FAU - Czechowski, Tomasz AU - Czechowski T FAU - Bari, Rajendra P AU - Bari RP FAU - Stitt, Mark AU - Stitt M FAU - Scheible, Wolf-Rudiger AU - Scheible WR FAU - Udvardi, Michael K AU - Udvardi MK LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1111/j.1365-313X.2004.02051.x [doi] AID - TPJ2051 [pii] PST - ppublish SO - Plant J 2004 Apr;38(2):366-79. PMID- 15078337 OWN - NLM STAT- in-data-review DA - 20040413 IS - 0960-7412 VI - 38 IP - 2 DP - 2004 Apr TI - Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis. PG - 358-65 AB - Summary Many mutants have been isolated from the model plant Arabidopsis thaliana, and recent important genetic resources, such as T-DNA knockout lines, facilitate the speed of identifying new mutants. However, present phenotypic analysis of mutant screens depends mainly on qualitative descriptions after visual observation of morphological traits. We propose a novel method of phenotypic analysis based on precise three-dimensional (3D) measurement by a laser range finder (LRF) and automatic data processing. We measured the 3D surfaces of young plants of two Arabidopsis ecotypes and successfully defined two new traits, the direction of the blade surface and epinasty of the blade, quantitatively. The proposed method enables us to obtain quantitative and precise descriptions of plant morphologies compared to conventional 2D measurement. The method will open a way to find new traits from mutant pools or natural ecotypes based on 3D data. AD - Genomic Knowledge Base Research Team, Bioinformatics Group, RIKEN Yokohama Institute, Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. FAU - Kaminuma, Eli AU - Kaminuma E FAU - Heida, Naohiko AU - Heida N FAU - Tsumoto, Yuko AU - Tsumoto Y FAU - Yamamoto, Naoki AU - Yamamoto N FAU - Goto, Nobuharu AU - Goto N FAU - Okamoto, Naoki AU - Okamoto N FAU - Konagaya, Akihiko AU - Konagaya A FAU - Matsui, Minami AU - Matsui M FAU - Toyoda, Tetsuro AU - Toyoda T LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1111/j.1365-313X.2004.02042.x [doi] AID - TPJ2042 [pii] PST - ppublish SO - Plant J 2004 Apr;38(2):358-65. PMID- 15078335 OWN - NLM STAT- in-data-review DA - 20040413 IS - 0960-7412 VI - 38 IP - 2 DP - 2004 Apr TI - The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways. PG - 332-47 AB - Summary The role of the Arabidopsis transcription factor LONG HYPOCOTYL 5 (HY5) in promoting photomorphogenic development has been extensively characterized. Although the current model for HY5 action largely explains its role in this process, it does not adequately address the root phenotype observed in hy5 mutants. In our search for common mechanisms underlying all hy5 traits, we found that they are partly the result of an altered balance of signaling through the plant hormones auxin and cytokinin. hy5 mutants are resistant to cytokinin application, and double mutant analyses indicate that a decrease in auxin signaling moderates hy5 phenotypes. Microarray analyses and semiquantitative RT-PCR indicate that two negative regulators of auxin signaling, AUXIN RESISTANT 2 (AXR2)/INDOLE ACETIC ACID 7 (IAA7) and SOLITARY ROOT (SLR)/IAA14, are underexpressed in hy5 mutants. The promoters of these genes contain a putative HY5 binding site, and in line with this observation, HY5 can bind to the promoter of AXR2 in vitro. Increased AXR2 expression in a hy5 background partially rescues the elongated hypocotyl phenotype. In summary, it appears that auxin signaling is elevated in hy5 mutants because HY5 promotes the expression of negative regulators of auxin signaling, thereby linking hormone and light signaling pathways. AD - Biology Department, McGill University, 1205 Docteur Penfield Avenue, Montreal, Quebec, Canada H3A 1B1. FAU - Cluis, Corinne P AU - Cluis CP FAU - Mouchel, Celine F AU - Mouchel CF FAU - Hardtke, Christian S AU - Hardtke CS LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1111/j.1365-313X.2004.02052.x [doi] AID - TPJ2052 [pii] PST - ppublish SO - Plant J 2004 Apr;38(2):332-47. PMID- 15078327 OWN - NLM STAT- in-data-review DA - 20040413 IS - 0960-7412 VI - 38 IP - 2 DP - 2004 Apr TI - A link between sterol biosynthesis, the cell wall, and cellulose in Arabidopsis. PG - 227-43 AB - Summary A crucial role for sterols in plant growth and development is underscored by the identification of three Arabidopsis sterol biosynthesis mutants that exhibit embryonic defects: fackel (fk), hydra1 (hyd1), and sterol methyltransferase 1/cephalopod (smt1/cph). We have taken a dual approach of sterol profiling and ultrastructural analysis to investigate the primary defects underlying the mutant phenotypes. Comprehensive gas chromatography (GC)-MS analysis of hyd1 in comparison to fk reveals an abnormal accumulation of unique sterol intermediates in each case. Sterol profiling of the fk hyd1 double mutant provides genetic evidence that FK C-14 reductase acts upstream of HYD1 C-8,7 isomerase. Despite distinct differences in sterol profiles, fk and hyd1 as well as smt1/cph share ultrastructural features such as incomplete cell walls and aberrant cell wall thickenings in embryonic and post-embryonic tissues. The common defects are coupled with ectopic callose and lignin deposits. We show that all three mutants exhibit a deficiency in cellulose, but are not reduced in pectin and sugars of the cell wall and cytosol. The sterol biosynthesis inhibitors 15-azasterol and fenpropimorph also cause cell wall gaps in dividing root cells and a reduction in bulk cellulose, corroborating that the cell wall abnormalities are due to altered sterol composition. Our results demonstrate that sterols are crucial for cellulose synthesis in the building of the plant cell wall. AD - Department of Developmental Genetics, ZMBP (Center for Plant Molecular Biology), University of Tubingen, 72076 Tubingen, Germany. FAU - Schrick, Kathrin AU - Schrick K FAU - Fujioka, Shozo AU - Fujioka S FAU - Takatsuto, Suguru AU - Takatsuto S FAU - Stierhof, York-Dieter AU - Stierhof YD FAU - Stransky, Harald AU - Stransky H FAU - Yoshida, Shigeo AU - Yoshida S FAU - Jurgens, Gerd AU - Jurgens G LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1111/j.1365-313X.2004.02039.x [doi] AID - TPJ2039 [pii] PST - ppublish SO - Plant J 2004 Apr;38(2):227-43. PMID- 15078325 OWN - NLM STAT- in-data-review DA - 20040413 IS - 0960-7412 VI - 38 IP - 2 DP - 2004 Apr TI - Cytokinins play opposite roles in lateral root formation, and nematode and Rhizobial symbioses. PG - 203-14 AB - Summary We used the cytokinin-responsive Arabidopsis response regulator (ARR)5 gene promoter fused to a beta-glucuronidase (GUS) reporter gene, and cytokinin oxidase (CKX) genes from Arabidopsis thaliana (AtCKX3) and maize (ZmCKX1) to investigate the roles of cytokinins in lateral root formation and symbiosis in Lotus japonicus. ARR5 expression was undetectable in the dividing initial cells at early stages of lateral root formation, but later we observed high expression in the base of the lateral root primordium. The root tip continues to express ARR5 during subsequent development of the lateral root. These results suggest a dynamic role for cytokinin in lateral root development. We observed ARR5 expression in curled/deformed root hairs, and also in nodule primordia in response to Rhizobial inoculation. This expression declined once the nodule emerged from the parent root. Root penetration and migration of root-knot nematode (RKN) second-stage larvae (L2) did not elevate ARR5 expression, but a high level of expression was induced when L2 reached the differentiating vascular bundle and during early stages of the nematode-plant interaction. ARR5 expression was specifically absent in mature giant cells (GCs), although dividing cells around the GCs continued to express this reporter. The same pattern was observed using a green fluorescent protein (GFP) reporter driven by the ARR5 promoter in tomato. Overexpression of CKX genes rendered the transgenic hairy roots resistant to exogenous application of the cytokinin [N(6)-(Delta(2) isopentenyl) adenine riboside] (iPR). CKX roots have significantly more lateral roots, but fewer nodules and nematode-induced root galls per plant, than control hairy roots. AD - Center for the Biology of Nematode Parasitism, North Carolina State University, Campus Box 7253, Raleigh, NC 27695-7253, USA. FAU - Lohar, Dasharath Prasad AU - Lohar DP FAU - Schaff, Jennifer E AU - Schaff JE FAU - Laskey, James G AU - Laskey JG FAU - Kieber, Joseph J AU - Kieber JJ FAU - Bilyeu, Kristin D AU - Bilyeu KD FAU - Bird, David McK AU - Bird DM LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 AID - 10.1111/j.1365-313X.2004.02038.x [doi] AID - TPJ2038 [pii] PST - ppublish SO - Plant J 2004 Apr;38(2):203-14. PMID- 15077668 OWN - NLM STAT- in-process DA - 20040413 IS - 0894-0282 VI - 17 IP - 4 DP - 2004 Apr TI - Feedback control of the Arabidopsis hypersensitive response. PG - 357-65 AB - The plant hypersensitive response (HR) to avirulent bacterial pathogens results from programmed cell death of plant cells in the infected region. Ion leakage and changes in signaling components associated with HR progression were measured. These studies compared Arabidopsis mutants affecting feedback loops with wild-type plants, with timepoints taken hourly. In response to Pseudomonas syringae pv. tomato DC3000 x avrB, npr1-2 mutant plants showed increased ion leakage relative to wild-type plants. Hydrogen peroxide accumulation was similar to that in wild type, but salicylic acid accumulation was reduced at some timepoints. With DC3000 x avrRpt2, similar trends were seen. In response to DC3000 x avrB, ndr1-1 mutant plants showed more ion leakage than wild-type or npr1-2 plants. Hydrogen peroxide accumulation was delayed by approximately 1 h and reached half the level seen with wild-type plants. Salicylic acid accumulation was similar to npr1-2 mutant plants. With DC3000 x avrRpt2, ndr1-1 mutant plants showed no ion leakage, no hydrogen peroxide accumulation, and minimal salicylic acid accumulation. Results with a ndr1-1 and npr1-2 double mutant were similar to ndr1-1. A model consistent with these data is presented, in which one positive and two negative regulatory circuits control HR progression. Understanding this circuitry will facilitate HR manipulation for enhanced disease resistance. AD - Department of Plant and Soil Sciences, Delaware Agricultural Experiment Station, College of Agriculture and Natural Resources, University of Delaware, Newark, DE 19716-2170, USA. FAU - Zhang, Chu AU - Zhang C FAU - Gutsche, Annie Tang AU - Gutsche AT FAU - Shapiro, Allan D AU - Shapiro AD LA - eng PT - Journal Article PL - United States TA - Mol Plant Microbe Interact JID - 9107902 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 PST - ppublish SO - Mol Plant Microbe Interact 2004 Apr;17(4):357-65. PMID- 15077666 OWN - NLM STAT- in-process DA - 20040413 IS - 0894-0282 VI - 17 IP - 4 DP - 2004 Apr TI - Proline accumulation and AtP5CS2 gene activation are induced by plant-pathogen incompatible interactions in Arabidopsis. PG - 343-50 AB - Accumulation of free L-proline (Pro) is a typical stress response incited by osmotic injuries in plants and microorganisms. Although the protective role of Pro in osmotic stress is not well understood, it is thought to function as compatible osmolyte or as a scavenger of reactive oxygen species (ROS). Here we show that, in Arabidopsis thaliana, Pro biosynthesis can be activated by incompatible plant-pathogen interactions triggering a hypersensitive response (HR). Pro accumulates in leaf tissues treated with Pseudomonas syringae pv. tomato avirulent strains (avrRpt2 and avrRpm1) but remains unchanged in leaves infected with isogenic virulent bacteria. Incompatible interactions lead to transcriptional activation of AtP5CS2, but not AtP5CS1, encoding the rate limiting enzyme in Pro biosynthesis pyrroline-5-carboxylate synthase (P5CS). AtP5CS2:GUS and AtP5CS2:LUC transgenes were induced inside and around the HR lesions produced by avirulent Pseudomonas spp. in transgenic plants. Pro accumulation was faster and stronger when stimulated by avrRpm1 than by avrRpt2, and was compromised in the low-salicylic acid plants NahG and eds5 when signaled through the RPS2-dependent pathway. In addition, Pro content and AtP5CS2 expression were enhanced by ROS in wild-type plants, suggesting that ROS may function as an intermediate signal in AtP5CS2-mediated Pro accumulation. AD - CIQUIBIC-CONICET, Departamento de Quimica Biologica, Facultad de Ciencias Quimicas Universidad Nacional de Cordoba, 5000 Cordoba, Argentina. FAU - Fabro, Georgina AU - Fabro G FAU - Kovacs, Izabella AU - Kovacs I FAU - Pavet, Valeria AU - Pavet V FAU - Szabados, Laszlo AU - Szabados L FAU - Alvarez, Maria E AU - Alvarez ME LA - eng PT - Journal Article PL - United States TA - Mol Plant Microbe Interact JID - 9107902 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 PST - ppublish SO - Mol Plant Microbe Interact 2004 Apr;17(4):343-50. PMID- 15077624 OWN - NLM STAT- in-process DA - 20040413 IS - 0176-1617 VI - 161 IP - 3 DP - 2004 Mar TI - Phytochrome regulation of pea phototropin. PG - 265-70 AB - Type 1 phototropin, one of the blue light receptors responsible for phototropism, is encoded in peas by at least two genes, PsPHOT1A and PsPHOT1B (formerly PsPK4 and PsPK5), both of which are more similar to Arabidopsis PHOT1 than to Arabidopsis PHOT2. We show here that PsPHOT1B encodes a full-length phototropin, whose expression pattern suggests that Psphot1b is the predominant phot1-type phototropin in etiolated seedlings. The gene encoding the other type 1 phototropin, PsPHOT1A, is expressed at low levels, with its highest levels in the leaves and stems of more mature, light-grown plants. Studies with phyA, phyB and the phyAphyB double mutants show that phyA and phyB have partially redundant roles in the reduction of PsPHOT1B expression under red light. AD - School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia. Robert.Elliott@utas.edu.au FAU - Elliott, Robert C AU - Elliott RC FAU - Platten, J Damien AU - Platten JD FAU - Watson, John C AU - Watson JC FAU - Reid, James B AU - Reid JB LA - eng PT - Journal Article PL - Germany TA - J Plant Physiol JID - 9882059 SB - IM EDAT- 2004/04/14 05:00 MHDA- 2004/04/14 05:00 PST - ppublish SO - J Plant Physiol 2004 Mar;161(3):265-70. PMID- 15075400 OWN - NLM STAT- publisher DA - 20040412 IS - 1040-4651 DP - 2004 Apr 9 TI - COS1: An Arabidopsis coronatine insensitive1 Suppressor Essential for Regulation of Jasmonate-Mediated Plant Defense and Senescence. AB - The Arabidopsis thaliana CORONATINE INSENSITIVE1 (COI1) gene encodes an F-box protein to assemble SCF(COI1) complexes essential for response to jasmonates (JAs), which are a family of plant signaling molecules required for many essential functions, including plant defense and reproduction. To better understand the molecular basis of JA action, we screened for suppressors of coi1 and isolated a coi1 suppressor1 (cos1) mutant. The cos1 mutation restores the coi1-related phenotypes, including defects in JA sensitivity, senescence, and plant defense responses. The COS1 gene was cloned through a map-based approach and found to encode lumazine synthase, a key component in the riboflavin pathway that is essential for diverse yet critical cellular processes. We demonstrated a novel function for the riboflavin pathway that acts downstream of COI1 in the JA signaling pathway and is required for suppression of the COI1-mediated root growth, senescence, and plant defense. AD - Laboratory of Plant Signal Transduction, Institute of Molecular and Cell Biology, National University of Singapore, 117604 Republic of Singapore; School of Plant Protection, Hunan Agricultural University, Changsha, 410128 China. AU - Xiao S AU - Dai L AU - Liu F AU - Wang Z AU - Peng W AU - Xie D LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/13 05:00 MHDA- 2004/04/13 05:00 AID - 10.1105/tpc.020370 [doi] AID - tpc.020370 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 9;. PMID- 15075398 OWN - NLM STAT- publisher DA - 20040412 IS - 1040-4651 DP - 2004 Apr 9 TI - Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion. AB - The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit). Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements. AD - Waksman Institute, Rutgers University, Piscataway, New Jersey 08855; Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901. AU - Xu Z AU - Yan X AU - Maurais S AU - Fu H AU - O'Brien DG AU - Mottinger J AU - Dooner HK LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/13 05:00 MHDA- 2004/04/13 05:00 AID - 10.1105/tpc.019802 [doi] AID - tpc.019802 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 9;. PMID- 15075397 OWN - NLM STAT- publisher DA - 20040412 IS - 1040-4651 DP - 2004 Apr 9 TI - ATR Regulates a G2-Phase Cell-Cycle Checkpoint in Arabidopsis thaliana. AB - Ataxia telangiectasia-mutated and Rad3-related (ATR) plays a central role in cell-cycle regulation, transmitting DNA damage signals to downstream effectors of cell-cycle progression. In animals, ATR is an essential gene. Here, we find that Arabidopsis (Arabidopsis thaliana) atr-/- mutants were viable, fertile, and phenotypically wild-type in the absence of exogenous DNA damaging agents but exhibit altered expression of AtRNR1 (ribonucleotide reductase large subunit) and alteration of some damage-induced cell-cycle checkpoints. atr mutants were hypersensitive to hydroxyurea (HU), aphidicolin, and UV-B light but only mildly sensitive to gamma-radiation. G2 arrest was observed in response to gamma-irradiation in both wild-type and atr plants, albeit with slightly different kinetics, suggesting that ATR plays a secondary role in response to double-strand breaks. G2 arrest also was observed in wild-type plants in response to aphidicolin but was defective in atr mutants, resulting in compaction of nuclei and subsequent cell death. By contrast, HU-treated wild-type and atr plants arrested in G1 and showed no obvious signs of cell death. We propose that, in plants, HU invokes a novel checkpoint responsive to low levels of deoxynucleotide triphosphates. These results demonstrate the important role of cell-cycle checkpoints in the ability of plant cells to sense and cope with problems associated with DNA replication. AD - Section of Plant Biology, University of California, Davis, California 95616. AU - Culligan K AU - Tissier A AU - Britt A LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/04/13 05:00 MHDA- 2004/04/13 05:00 AID - 10.1105/tpc.018903 [doi] AID - tpc.018903 [pii] PST - aheadofprint SO - Plant Cell 2004 Apr 9;. PMID- 15075394 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - An overview of gibberellin metabolism enzyme genes and their related mutants in rice. PG - 1642-53 AB - To enhance our understanding of GA metabolism in rice (Oryza sativa), we intensively screened and identified 29 candidate genes encoding the following GA metabolic enzymes using all available rice DNA databases: ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox). In contrast to the Arabidopsis genome, multiple CPS-like, KS-like, and KO-like genes were identified in the rice genome, most of which are contiguously arranged. We also identified 18 GA-deficient rice mutants at six different loci from rice mutant collections. Based on the mutant and expression analyses, we demonstrated that the enzymes catalyzing the early steps in the GA biosynthetic pathway (i.e. CPS, KS, KO, and KAO) are mainly encoded by single genes, while those for later steps (i.e. GA20ox, GA3ox, and GA2ox) are encoded by gene families. The remaining CPS-like, KS-like, and KO-like genes were likely to be involved in the biosynthesis of diterpene phytoalexins rather than GAs because the expression of two CPS-like and three KS-like genes (OsCPS2, OsCPS4, OsKS4, OsKS7, and OsKS8) were increased by UV irradiation, and four of these genes (OsCPS2, OsCPS4, OsKS4, and OsKS7) were also induced by an elicitor treatment. AD - Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188-0002, Japan. FAU - Sakamoto, Tomoaki AU - Sakamoto T FAU - Miura, Koutarou AU - Miura K FAU - Itoh, Hironori AU - Itoh H FAU - Tatsumi, Tomoko AU - Tatsumi T FAU - Ueguchi-Tanaka, Miyako AU - Ueguchi-Tanaka M FAU - Ishiyama, Kanako AU - Ishiyama K FAU - Kobayashi, Masatomo AU - Kobayashi M FAU - Agrawal, Ganesh K AU - Agrawal GK FAU - Takeda, Shin AU - Takeda S FAU - Abe, Kiyomi AU - Abe K FAU - Miyao, Akio AU - Miyao A FAU - Hirochika, Hirohiko AU - Hirochika H FAU - Kitano, Hidemi AU - Kitano H FAU - Ashikari, Motoyuki AU - Ashikari M FAU - Matsuoka, Makoto AU - Matsuoka M LA - eng PT - Journal Article DEP - 20040409 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/13 05:00 MHDA- 2004/04/13 05:00 PHST- 2004/Apr/09 [aheadofprint] AID - 10.1104/pp.103.033696 [doi] AID - pp.103.033696 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1642-53. Epub 2004 Apr 9. PMID- 15073273 OWN - NLM STAT- publisher DA - 20040409 IS - 1535-9476 DP - 2004 Apr 7 TI - Identification of the linker-SH2 domain of STAT as the origin of the SH2domain using two dimensional structural alignment. AB - The availability of large volumes of genome sequence presents an unprecedented challenge for proteomics to characterize various protein motifs in order to determine their structure and function. Primary sequence alignment is often unable to accurately identify a given motif due to sequence divergence. However, with the aid of secondary structural prediction for analysis, it is feasible to explore protein motifs on a proteome-wide scale. Here we report the use of secondary structural alignment to characterize the SH2 domains of both conventional and divergent sequences and divide them into two groups, Src type and STAT type. In addition to the basic abbba structure, the Src type SH2 domain contains an extra b-strand, i.e., the bE or bE-bF motif. Whereas, the linker domain conjugated SH2 domain in STAT contains the aB motif instead. We combined the bB core motif sequence BLAST with secondary structural alignment to screen for SH2 domains in various eukaryotic model systems including Arabidopsis, Dictyostelium and Saccharomyces. Two novel genes carrying the linker-SH2 domain of STAT were discovered and subsequently cloned from Arabidopsis. These genes, designated as STAT-like factors (STATL), exist widely in vascular and nonvascular plants suggesting that STATs linker-SH2 domain was not acquired accidentally by Arabidopsis, rather that they co-evolved prior to the divergence of plants and animals. Using this approach, we expanded the number of putative SH2 domain-bearing genes in Dictyostelium and comparatively studied the secondary structural profiles of both typical and atypical SH2 domains. Our results indicate that the linker-SH2 domain of the transcription factor STAT is one of the most ancient and fully developed functional domains, which may have served as a template for the continuing evolution of the SH2 domain essential for phosphotyrosine signal transduction. AD - Pathology Laboratory Medicine and Surgery Sci, Brown University, Providence, Rhode Island 02903. AU - Gao Q AU - Hua J AU - Kimura R AU - Headd JJ AU - Fu XY AU - Chin YE LA - ENG PT - JOURNAL ARTICLE TA - Mol Cell Proteomics JID - 101125647 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1074/mcp.M300131-MCP200 [doi] AID - M300131-MCP200 [pii] PST - aheadofprint SO - Mol Cell Proteomics 2004 Apr 7;. PMID- 15073219 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - Why hypocotyl extension mutants need to be characterized at the cell level: a case study of axr3-1. AB - Since the discovery of auxin, a debate has taken place as to whether the auxin distribution in elongating organs can account for the distinctive cell elongation profiles that have been found. In an attempt to address this important issue, the elongation profiles of cells have been compared in the hypocotyls of wild-type and auxin-hypersensitive axr3-1 Arabidopsis Columbia ecotype seedlings. Clear differences in cell elongation profiles were found in the two types of seedling, whether they were light- or dark-grown. However, it was not possible unambiguously to ascribe the cell elongation profile differences to the proposition that the axr3-1 mutation causes the hypocotyl to be hypersensitive to auxin. The possibility that the abnormal hypocotyl elongation profile of the mutant was a secondary effect, consequent on a more fundamental effect of the axr3-1 mutation, is considered. It is clear from this study that cell elongation and its control needs to be studied at the cell, and not the organ, level. To characterize a mutant as having a short, or long, hypocotyl is inadequate. To determine which factors control the timing and the magnitude of cell elongation requires the demonstration of correlations between the growth rate of cells and their content of regulating substances or their sensitivity to that substance. Studies of the cell elongation profiles of the many hypocotyl length mutants could also be a very effective means of probing the co-ordination of root and shoot elongation. AD - Department of Biology, Plant Laboratory, University of York, Heslington, York YO10 5YW, UK. AU - Barley K LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh115 [doi] AID - erh115 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073217 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - RNA interference in Agrobacterium rhizogenes-transformed roots of Arabidopsis and Medicago truncatula. AB - RNA interference (RNAi) is a powerful reverse genetic tool to study gene function. The data presented here show that Agrobacterium rhizogenes-mediated RNAi is a fast and effective tool to study genes involved in root biology. The Arabidopsis gene KOJAK, involved in root hair development, was efficiently knocked down. A. rhizogenes-mediated root transformation is a fast method to generate adventitious, genetically transformed roots. In order to select for co-transformed roots a binary vector was developed that enables selection based on DsRED1 expression, with the additional benefit that chimaeric roots can be discriminated. The identification of chimaeric roots provided the opportunity to examine the extent of systemic spread of the silencing signal in the composite plants of both Arabidopsis and Medicago truncatula. It is shown that RNA silencing does not spread systemically to non-co-transformed (lateral) roots and only inefficiently to the non-transgenic shoot. Furthermore, evidence is presented which shows that RNAi is cell autonomous in the root epidermis. AD - Laboratory of Molecular Biology, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands. AU - Limpens E AU - Ramos J AU - Franken C AU - Raz V AU - Compaan B AU - Franssen H AU - Bisseling T AU - Geurts R LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh122 [doi] AID - erh122 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073215 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - Involvement of polyamines in the interacting effects of low temperature and mineral supply on Pringlea antiscorbutica (Kerguelen cabbage) seedlings. AB - Pringlea antiscorbutica, which is the sole endemic crucifer in the subantarctic zone, undergoes seedling development in a harsh and cold environment. Since, at the mature stage, this species exhibits several adaptations linked to cold tolerance such as high polyamine levels, potential adaptations and polyamine response were investigated in seedlings. In order to assess the specificity of responses, P. antiscorbutica was compared with Arabidopsis thaliana, which is characterized by a life cycle preventing cold exposure at seedling stage. P. antiscorbutica and A. thaliana seedlings were found to have strikingly contrasted responses to temperature changes and to mineral nutrition. Whereas A. thaliana seedlings showed the typical growth arrest of chilling-sensitive plants, P. antiscorbutica seedlings showed optimal root growth at low temperature (5/10 degrees C) and temperate conditions caused the early arrest of root growth. Cold tolerance was associated with increased levels of polyamines or with maintenance of high levels of polyamines. Comparison of both species showed that polyamine levels could be a significant marker of chilling tolerance in seedlings. Treatments with varying mineral supply showed a positive relationship between root growth rate and variations of agmatine and putrescine endogenous contents in roots of P. antiscorbutica. This may be the first demonstration that, even under conditions of accumulation induced by environmental stress, polyamine levels can still be correlated with developmental processes. Com parison of mineral supply and temperature effects strongly indicated a trade-off of polyamine involvement between development and response to stress. AD - Centre National de la Recherche Scientifique, Universite de Rennes 1, UMR 6553 ECOBIO, Campus de Beaulieu, batiment 14A, 263 avenue du General Leclerc, F-35042 Rennes Cedex, France. AU - Hummel I AU - El Amrani A AU - Gouesbet G AU - Hennion F AU - Couee I LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh126 [doi] AID - erh126 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073212 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - An {alpha}-crystallin gene, ACD31.2 from Arabidopsis is negatively regulated by FPF1 overexpression, floral induction, gibberellins, and long days. AB - A gene sequence was isolated from a differential display experiment to find transcripts altered in expression by overexpression of FLORAL PROMOTING FACTOR 1 (FPF1) in Arabidopsis thaliana. The gene, ACD31.2, encodes an alpha-crystallin domain containing protein with homology to small heat shock proteins. In addition to down-regulation by FPF1 overexpression, the ACD31.2 transcript is also down-regulated by long days, floral induction, and by gibberellin in wild-type plants. Expression is highest in leaves and stems. AD - Institute of Developmental Biology, University of Cologne, Gyrhofstrasse 17, D-50923 Cologne, Germany. AU - Chandler JW AU - Melzer S LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh131 [doi] AID - erh131 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073209 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - Seeing 'cool' and 'hot'--infrared thermography as a tool for non-invasive, high-throughput screening of Arabidopsis guard cell signalling mutants. AB - The use of Arabidopsis mutants defective in abscisic acid (ABA) perception has been instrumental in the understanding of stomatal function, in particular, ABA signalling in guard cells. The considerable attention devoted to ABA signalling in guard cells is due in part to (1) the fundamental role of ABA in drought stress and (2) the use of a screening protocol based on the sensitivity of seed germination to ABA. Such a screen has facilitated the isolation of ABA signalling mutants with genetic lesions that exert pleiotropic effects at the whole plant level. As such, there is a requirement for new approaches to complement the seed germination screen. The recent advances made in the use of infrared thermography as a non-invasive, high-throughput tool are reviewed here and the versatility of this technique for screening Arabidopsis defective in stomatal regulation is highlighted. AD - Department of Biological Sciences, Institute of Environmental and Natural Sciences, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. AU - Wang Y AU - Holroyd G AU - Hetherington AM AU - Ng CK LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh135 [doi] AID - erh135 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073208 OWN - NLM STAT- publisher DA - 20040409 IS - 0022-0957 DP - 2004 Apr 8 TI - Isolation of cDNAs encoding typical and novel types of phosphoinositide-specific phospholipase C from the moss Physcomitrella patens. AB - Two cDNAs encoding proteins, PpPLC1 and PpPLC2, with catalytic and C2 domains conserved in plant phosphoinositide-specific phospholipase C (PI-PLC) were isolated from Physcomitrella patens. The N domain, which has been identified in Arabidopsis PI-PLCs as an EF hand-like domain, was found in both isoforms, although that in PpPLC2 was a split type. At micromolar Ca(2+) concentrations, PpPLC1 preferentially hydrolysed phosphatidylinositol-4,5-bisphosphate, while PpPLC2 showed no specificity. Furthermore, at millimolar Ca(2+), phosphatidylinositol was hydrolysed by PpPLC2, but not by PpPLC1. Thus, PpPLC1 and PpPLC2 are typical and novel types of plant PI-PLC, respectively. AD - National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan. AU - Mikami K AU - Repp A AU - Graebe-Abts E AU - Hartmann E LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1093/jxb/erh140 [doi] AID - erh140 [pii] PST - aheadofprint SO - J Exp Bot 2004 Apr 8;. PMID- 15073153 OWN - NLM STAT- publisher DA - 20040409 IS - 0950-1991 DP - 2004 Apr 8 TI - The HALTED ROOT gene encoding the 26S proteasome subunit RPT2a is essential for the maintenance of Arabidopsis meristems. AB - In higher plants, post-embryonic development is dependent on the activity of the root and shoot apical meristem (RAM and SAM). The quiescent center (QC) in the RAM and the organizing center (OC) in the SAM are known to be essential for the maintenance of meristematic activity. To understand the mechanism that maintains post-embryonic meristems, we isolated an Arabidopsis mutant, halted root (hlr). In this mutant, the cellular organization was disrupted in post-embryonic meristems both in the root and in the shoot, and their meristematic activity was reduced or became abnormal. We showed that the mutant RAM lost its QC identity after germination, which was specified during embryogenesis, whereas the identity of differentiated tissues was maintained. In the post-embryonic SAM, the expression pattern of a typical OC marker gene, WUSCHEL, was disturbed in the mutant. These observations indicate that the HLR gene is essential to maintain the cellular organization and normal nature of the RAM and SAM. The HLR gene encodes RPT2a, which is a subunit of the 26S proteasome that degrades key proteins in diverse cellular processes. We showed that the HLR gene was expressed both in the RAM and in the SAM, including in the QC and the OC, respectively, and that the activity of proteasomes were reduced in the mutant. We propose that proteasome-dependent programmed proteolysis is required to maintain the meristem integrity both in the shoot and in the root. AU - Ueda M AU - Matsui K AU - Ishiguro S AU - Sano R AU - Wada T AU - Paponov I AU - Palme K AU - Okada K LA - ENG PT - JOURNAL ARTICLE TA - Development JID - 8701744 EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 AID - 10.1242/dev.01096 [doi] AID - dev.01096 [pii] PST - aheadofprint SO - Development 2004 Apr 8;. PMID- 15071894 OWN - NLM STAT- in-process DA - 20040409 IS - 0039-9450 VI - 49 IP - 5 DP - 2004 Apr TI - [Epigenetics in Arabidopsis thaliana] PG - 634-41 AD - hsaze@lab.nig.ac.jp FAU - Saze, Hidetoshi AU - Saze H FAU - Kakutani, Tetsuji AU - Kakutani T LA - jpn PT - Journal Article PL - Japan TA - Tanpakushitsu Kakusan Koso JID - 0413762 SB - IM EDAT- 2004/04/10 05:00 MHDA- 2004/04/10 05:00 PST - ppublish SO - Tanpakushitsu Kakusan Koso 2004 Apr;49(5):634-41. PMID- 15071729 OWN - NLM STAT- publisher DA - 20040408 IS - 0040-5752 DP - 2004 Apr 8 TI - Arabidopsis thaliana chromosome III restores fertility in a cytoplasmic male-sterile Brassica napus line with A. thaliana mitochondrial DNA. AB - Somatic Brassica napus (+) Arabidopsis thaliana hybrids with a cytoplasmic male sterility (CMS)-inducing cytoplasm were screened for fertility-restored plants. One line was selected and recurrently backcrossed with the maintainer line, B. napus, resulting in fertile/sterile segregating populations. Restriction fragment length polymorphism mapping showed the co-segregation of A. thaliana chromosome (chr) III markers with the fertility trait. As it was not possible to stabilise the fertility trait via selfings, a dihaploidisation strategy was assessed. Ninety haploid plants were regenerated and analysed with numerous simple sequence length polymorphism (SSLP) markers. Markers covering both arms of A. thaliana chr III were present in two plants, whereas no A. thaliana DNA could be detected in the other plants. Following colchicine-induced chromosome doubling only these two plants with A. thaliana DNA produced fertile offspring. In one of the two lines, however, the A. thaliana-specific DNA markers and fertility were lost in subsequent generations. The other line remained fertile after repeated selfings. Using genomic in situ hybridisation (GISH) we were able to demonstrate that this latter line possessed a disomic addition of the A. thaliana chromosome. The restored line was comparable to the maintainer line with respect to flower morphology, but the petals and stamens were slightly reduced in size. The homeotic conversion of stamens to pistil-like structures, which is typical for the CMS line, was reversed, and stamens with a normal appearance with viable pollen appeared. Flowering time was as in the CMS line-in both lines it was delayed in comparison to the maintainer line. The introgressed chromosome also contributes to several pleiotropic effects, such as reduced leaf crinkling and shorter stems. The ability to restore fertility through the introgression of nuclear genes from the main cytoplasmic donor species indicates that the CMS trait in this system mainly is due to B. napus/ A. thaliana alloplasmic incompatibility and not mitochondrial DNA rearrangements. Further exploitation of the material is discussed. AD - Department of Plant Biology and Forest Genetics, Swedish University for Agricultural Sciences, Box 7080, 750 07, Uppsala, Sweden. AU - Leino M AU - Thyselius S AU - Landgren M AU - Glimelius K LA - ENG PT - JOURNAL ARTICLE TA - Theor Appl Genet JID - 0145600 EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 AID - 10.1007/s00122-004-1644-6 [doi] PST - aheadofprint SO - Theor Appl Genet 2004 Apr 8;. PMID- 15070894 OWN - NLM STAT- publisher DA - 20040408 IS - 1083-351X DP - 2004 Apr 7 TI - Progression and specificity of protein oxidation in the life cycle of Arabidopsis thaliana. AB - Protein carbonylation is an irreversible oxidative process leading to a loss of function of the modified proteins and in a variety of model systems, including worms, flies, and mammals, carbonyl levels gradually increase with age. In contrast, we report here that in Arabidopsis thaliana an initial increase in protein oxidation during the first 20 days of the plants life cycle is followed by a drastic reduction in protein carbonyls prior to bolting and flower development. Protein carbonylation prior to the transition to flowering targets specific proteins such as Hsp70, ATP synthases, the large subunit of Rubisco, and proteins involved in light harvesting/energy transfer and the C2 oxidative photosynthetic carbon cycle. The precipitous fall in protein carbonyl levels is due to the specific reduction in the levels of oxidized proteins rather than an overall loss of chlorophyll and Rubisco associated with the senescence syndrome. The results are discussed in light of contemporary theories of aging in animals. AD - Department of Cell and Molecular Biology, Institution of Microbiology, Gteborg University, Gteborg 40530. AU - Johansson EC AU - Olsson O AU - Nystrom T LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 AID - 10.1074/jbc.M402652200 [doi] AID - M402652200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Apr 7;. PMID- 15070783 OWN - NLM STAT- in-process DA - 20040408 IS - 0027-8424 VI - 101 IP - 13 DP - 2004 Mar 30 TI - A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. PG - 4712-7 AB - A latitudinal cline in flowering time in accessions of Arabidopsis thaliana has been widely predicted because the environmental cues that promote flowering vary systematically with latitude, but evidence for such clines has been lacking. Here, we report evidence of a significant latitudinal cline in flowering time among 70 Northern European and Mediterranean ecotypes when grown under ecologically realistic conditions in a common garden environment. The detected cline, however, is found only in ecotypes with alleles of the flowering time gene FRIGIDA (FRI) that lack major deletions that would disrupt protein function, whereas there is no relationship between flowering time and latitude of origin among accessions with FRI alleles containing such deletions. Analysis of climatological data suggests that late flowering in accessions with putatively functional FRI was associated with reduced January precipitation at the site of origin, consistent with previous reports of a positive genetic correlation between water use efficiency and flowering time in Arabidopsis, and the pleiotropic effects of FRI of increasing water use efficiency. In accessions collected from Southern latitudes, we detected that putatively functional FRI alleles were associated with accelerated flowering relative to accessions with nonfunctional FRI under the winter conditions of our experiment. These results suggest that the ecological function of the vernalization requirement conferred by FRI differs across latitudes. More generally, our results indicate that by combining ecological and molecular genetic data, it is possible to understand the forces acting on life history transitions at the level of specific loci. AD - Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA. john_stinchcombe@brown.edu FAU - Stinchcombe, John R AU - Stinchcombe JR FAU - Weinig, Cynthia AU - Weinig C FAU - Ungerer, Mark AU - Ungerer M FAU - Olsen, Kenneth M AU - Olsen KM FAU - Mays, Charlotte AU - Mays C FAU - Halldorsdottir, Solveig S AU - Halldorsdottir SS FAU - Purugganan, Michael D AU - Purugganan MD FAU - Schmitt, Johanna AU - Schmitt J LA - eng PT - Journal Article DEP - 20040319 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 PHST- 2004/Mar/19 [aheadofprint] AID - 10.1073/pnas.0306401101 [doi] AID - 0306401101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Mar 30;101(13):4712-7. Epub 2004 Mar 19. PMID- 15070782 OWN - NLM STAT- in-process DA - 20040408 IS - 0027-8424 VI - 101 IP - 13 DP - 2004 Mar 30 TI - WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis. PG - 4706-11 AB - Epicuticular wax forms a layer of hydrophobic material on plant aerial organs, which constitutes a protective barrier between the plant and its environment. We report here the identification of WIN1, an Arabidopsis thaliana ethylene response factor-type transcription factor, which can activate wax deposition in overexpressing plants. We constitutively expressed WIN1 in transgenic Arabidopsis plants, and found that leaf epidermal wax accumulation was up to 4.5-fold higher in these plants than in control plants. A significant increase was also found in stems. Interestingly, approximately 50% of the additional wax could only be released by complete lipid extractions, suggesting that not all of the wax is superficial. Gene expression analysis indicated that a number of genes, such as CER1, KCS1, and CER2, which are known to be involved in wax biosynthesis, were induced in WIN1 overexpressors. This observation indicates that induction of wax accumulation in transgenic plants is probably mediated through an increase in the expression of genes encoding enzymes of the wax biosynthesis pathway. AD - Mendel Biotechnology, 21375 Cabot Boulevard, Hayward, CA 94545, USA. pb22@york.ac.uk FAU - Broun, Pierre AU - Broun P FAU - Poindexter, Patricia AU - Poindexter P FAU - Osborne, Erin AU - Osborne E FAU - Jiang, Cai-Zhong AU - Jiang CZ FAU - Riechmann, Jose Luis AU - Riechmann JL LA - eng SI - GENBANK/AY378101 PT - Journal Article DEP - 20040322 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 PHST- 2004/Mar/22 [aheadofprint] AID - 10.1073/pnas.0305574101 [doi] AID - 0305574101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Mar 30;101(13):4706-11. Epub 2004 Mar 22. PMID- 15070781 OWN - NLM STAT- in-process DA - 20040408 IS - 0027-8424 VI - 101 IP - 13 DP - 2004 Mar 30 TI - A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. PG - 4701-5 AB - In the establishment of the legume-rhizobial symbiosis, bacterial lipochitooligosaccharide signaling molecules termed Nod factors activate the formation of a novel root organ, the nodule. Nod factors elicit several responses in plant root hair cells, including oscillations in cytoplasmic calcium levels (termed calcium spiking) and alterations in root hair growth. A number of plant mutants with defects in the Nod factor signaling pathway have been identified. One such Medicago truncatula mutant, dmi3, exhibits calcium spiking and root hair swelling in response to Nod factor, but fails to initiate symbiotic gene expression or cell divisions for nodule formation. On the basis of these data, it is thought that the dmi3 mutant perceives Nod factor but fails to transduce the signal downstream of calcium spiking. Additionally, the dmi3 mutant is defective in the symbiosis with mycorrhizal fungi, indicating the importance of the encoded protein in multiple symbioses. We report the identification of the DMI3 gene, using a gene cloning method based on transcript abundance. We show that transcript-based cloning is a valid approach for cloning genes in barley, indicating the value of this technology in crop plants. DMI3 encodes a calcium/calmodulin-dependent protein kinase. Mutants in pea sym9 have phenotypes similar to dmi3 and have alterations in this gene. The DMI3 class of proteins is well conserved among plants that interact with mycorrhizal fungi, but it is less conserved in Arabidopsis thaliana, which does not participate in the mycorrhizal symbiosis. AD - Department of Biological Sciences, 371 Serra Mall, Stanford University, Stanford, CA 94305-5020, USA. FAU - Mitra, Raka M AU - Mitra RM FAU - Gleason, Cynthia A AU - Gleason CA FAU - Edwards, Anne AU - Edwards A FAU - Hadfield, James AU - Hadfield J FAU - Downie, J Allan AU - Downie JA FAU - Oldroyd, Giles E D AU - Oldroyd GE FAU - Long, Sharon R AU - Long SR LA - eng SI - GENBANK/AJ621916 SI - GENBANK/AY496049 PT - Journal Article DEP - 20040301 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 PHST- 2004/Mar/01 [aheadofprint] AID - 10.1073/pnas.0400595101 [doi] AID - 0400595101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Mar 30;101(13):4701-5. Epub 2004 Mar 1. PMID- 15070437 OWN - NLM STAT- in-data-review DA - 20040408 IS - 0029-6651 VI - 63 IP - 1 DP - 2004 Feb TI - Intestinal and placental zinc transport pathways. PG - 21-9 AB - Mammalian members of the cation diffusion facilitator (CDF) and zrt-, irt-like protein (ZIP) families of Zn transporters, initially identified in Saccharomyces cerevisiae and Arabidopsis thalania spp., have been cloned during the last 8 years and have been classified as families SLC30 and SLC39 respectively. The cloning of human Zn transporters ZnT-like transporter 1 (hZTL1)/ZnT5 (SLC30A5) and hZIP4 (SLC39A4) were major advances in the understanding of the molecular mechanisms of dietary Zn absorption. Both transporters are localised at the enterocyte apical membrane and are, therefore, potentially of fundamental importance in dietary Zn uptake. hZTL1 mediates Zn uptake when expressed in Xenopus laevis oocytes and hZIP4 is mutated in most cases of the inherited Zn deficiency disease acrodermatitis enteropathica. Localisation of hZTL1/ZnT5 at the apical membrane of the placental syncytiotrophoblast indicates a fundamental role in the transfer of Slc30 Zn to the foetus. Observations in rodent models indicate that in the intestine increased Zn availability increases expression of Zn transporters. Human intestinal Caco-2 cells show a similar response to increasing the Zn(2+) concentration of the nutrient medium in relation to the expression of mRNA corresponding to several Zn transporters and that of ZnT1 (SLC30A1) and hZTL1/ZnT5 proteins. In the human placental cell line JAR, however, expression at the mRNA level of a number of Zn transporters is not modified by Zn availability, whilst ZnT1 and hZTL1/ZnT5 proteins are reduced under Zn-supplemented conditions. These differences between Caco-2 and JAR cells in Zn transporter gene responses to Zn supply may reflect the different extracellular Zn concentrations encountered by the corresponding cell types in vitro. AD - School of Cell and Molecular Biosciences, Agriculture Building, University of Newcastle, Kings Road, Newcastle upon Tyne NE1 7RU, UK. FAU - Ford, Dianne AU - Ford D LA - eng PT - Journal Article PL - England TA - Proc Nutr Soc JID - 7505881 SB - IM EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 AID - 10.1079/PNS2003320 [doi] PST - ppublish SO - Proc Nutr Soc 2004 Feb;63(1):21-9. PMID- 15070431 OWN - NLM STAT- publisher DA - 20040408 IS - 1471-2199 VI - 5 IP - 1 DP - 2004 Apr 7 TI - Translation of the radioresistance kinase TLK1B is induced by gamma irradiation through activation of mTOR and phosphorylation of 4E-BP1. PG - 1 AB - Background: The mammalian protein kinase TLK1 is a homologue of Tousled, a gene involved in flower development in Arabidopsis thaliana. The function of TLK1 is not well known, although knockout of the gene in Drosophila or expression of a dominant negative mutant in mouse cells causes loss of nuclear divisions and missegregation chromosome probably due to alterations in chromatin remodeling capacity. Overexpression of TLK1B, a spliced variant of the TLK1 mRNA, in a model mouse cell line increases their resistance to ionizing radiation, also likely due to through changes in chromatin remodeling. The TLK1B mRNA is translationally repressed by its 5'UTR and is regulated by the availability of eIF4E. We now report that radiation or doxorubicin result in an increase in the translation of TLK1B, and we have uncovered the likely mechanism for this effect. Results: Radiation causes a shift in the polysomal distribution of TLK1B mRNA, from the untranslated region and small polysomes to the large polysomes, concomitant with an increase in the expression of TLK1B protein. This change is preceded by an increase in phosphorylation of the eIF4E inhibitory protein 4E-BP1, which release eIF4E when it is phosphorylated. The phosphorylation of 4E-BP1 depends on mTOR, since rapamycin blocked the increase in phosphorylation induced by radiation, and prevented the increase in TLK1B protein expression. The activation of mTOR was likely due to the rapid activation of Akt following radiation. The activation of Akt could be inhibited with wortmannin, an inhibitor of PI3 kinase, hence placing PI3 kinase upstream of Akt as a very early event following radiation. Conclusions: The translational upregulation of TLK1B elicited by DNA double strand breaks represents an interesting mechanism of translational regulation of a protein involved in radioprotection and highlights a novel mechanism of the stress response following radiation. AU - Sunavala-Dossabhoy GN AU - Fowler M AU - De Benedetti A LA - ENG PT - JOURNAL ARTICLE DEP - 20040407 TA - BMC Mol Biol JID - 100966983 EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 PHST- 2003/Dec/16 [received] PHST- 2004/Apr/07 [accepted] PHST- 2004/Apr/07 [aheadofprint] AID - 10.1186/1471-2199-5-1 [doi] AID - 1471-2199-5-1 [pii] PST - aheadofprint SO - BMC Mol Biol 2004 Apr 7;5(1):1. PMID- 15070398 OWN - NLM STAT- publisher DA - 20040408 IS - 0264-6021 VI - Pt DP - 2004 Apr 7 TI - Functional and biochemical characterization of a recombinant Arabidopsis thaliana 3-deoxy-D-manno-octulosonic 8-phosphate synthase. AB - An open reading frame, encoding for 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDOPS), from Arabidopsis thaliana was cloned into a T7-driven expression vector. The protein was overexpressed in Escherichia coli and purified to homogeneity. Recombinant A. thaliana KDOPS, in solution, displays an apparent molecular weight of 76 kDa and a subunit molecular weight of 31,519. Unlike previously studied bacterial KDOPSs which are tetrameric, A. thaliana KDOPS appears to be a dimer in solution. The temperature optimum of the enzyme is 65 degrees C and the pH optimum is 7.5 with a broad peak between pH 6.5 and 9.5 showing 90% of maximum activity. The enzyme cannot be inactivated by EDTA or dipicolinic acid treatment, nor activated by a series of divalent metal ions, suggesting that it is a non-metallo enzyme as opposed to the initial prediction that it would be a metallo enzyme. Kinetic studies showed that the enzyme follows a sequential mechanism with K m PEP = 3.6 micro M, K m A5P = 3.8 micro M, and k cat = 5.9 s -1 at 37 degrees C. Based on the characterization of A. thaliana KDOPS and phylogenetic analysis, plant KDOPSs may represent a new distinct class of KDOPSs. AU - Wu J AU - Patel MA AU - Sundaram AK AU - Woodard RW LA - ENG PT - JOURNAL ARTICLE TA - Biochem J JID - 2984726R EDAT- 2004/04/09 05:00 MHDA- 2004/04/09 05:00 PHST- 2004/Feb/06 [received] PHST- 2004/Mar/31 [revised] PHST- 2004/Apr/07 [accepted] AID - 10.1042/BJ20040207 [doi] AID - BJ20040207 [pii] PST - aheadofprint SO - Biochem J 2004 Apr 7;Pt. PMID- 15069639 OWN - NLM STAT- publisher DA - 20040407 IS - 1617-4615 DP - 2004 Apr 7 TI - Organisation and structural evolution of the rice glutathione S-transferase gene family. AB - Glutathione S-transferases (GSTs) comprise a large family of key defence enzymes against xenobiotic toxicity. Here we describe the comprehensive characterisation of this important multigene family in the model monocot species rice [ Oryza sativa(L.)]. Furthermore, we investigate the molecular evolution of the family based on the analysis of (1) the patterns of within-genome duplication, and (2) the phylogenetic relationships and evolutionary divergence among rice, Arabidopsis, maize and soybean GSTs. By in-silico screening of the EST and genome divisions of the Genbank/EMBL/DDBJ database we have isolated 59 putative genes and two pseudogenes, making this the largest plant GST family characterised to date. Of these, 38 (62%) are represented by genomic and EST sequences and 23 (38%) are known only from their genomic sequences. A preliminary survey of EST collections shows a large degree of variability in gene expression between different tissues and environmental conditions, with a small number of genes (13) accounting for 80% of all ESTs. Rice GSTs are organised in four main phylogenetic classes, with 91% of all rice genes belonging to the two plant-specific classes Tau (40 genes) and Phi (16 genes). Pairwise identity scores range between 17 and 98% for proteins of the same class, and 7 and 21% for interclass comparisons. Rapid evolution by gene duplication is suggested by the discovery of two large clusters of 7 and 23 closely related genes on chromosomes 1 and 10, respectively. A comparison of the complete GST families in two monocot and two dicot species suggests a monophyletic origin for all Theta and Zeta GSTs, and no more than three common ancestors for all Phi and Tau genes. AD - Department of Biomolecular Sciences and Biotechnology, University of Milan, Via Celoria 26, 20133, Milano, Italy. AU - Soranzo N AU - Sari Gorla M AU - Mizzi L AU - De Toma G AU - Frova C LA - ENG PT - JOURNAL ARTICLE TA - Mol Genet Genomics JID - 101093320 EDAT- 2004/04/08 05:00 MHDA- 2004/04/08 05:00 AID - 10.1007/s00438-004-1006-8 [doi] PST - aheadofprint SO - Mol Genet Genomics 2004 Apr 7;. PMID- 15069083 OWN - NLM STAT- publisher DA - 20040407 IS - 1083-351X DP - 2004 Apr 6 TI - Proteomic analysis of arabidopsis glutathione S-transferases from Benoxacor- and copper-treated seedlings. AB - Glutathione S-transferases (GSTs) are involved in many stress responses in plants, participating in the detoxification of xenobiotics and limiting oxidative damage. Studies examining the regulation of this gene family in diverse plant species have focused primarily on RNA expression. A proteomics method was developed to identify GSTs expressed in Arabidopsis seedlings and to determine how the abundance of these proteins changed in response to copper, a promoter of oxidative stress, and benoxacor, a herbicide safener. A total of eight GSTs were identified in seedlings grown under control conditions and only one of these, AtGSTU19, was induced by benoxacor. In contrast, four GSTs were significantly more abundant in copper-treated seedlings, AtGSTF2, AtGSTF6, AtGSTF7, AtGSTU19. The different responses to these treatments may reflect the potential for copper to impact many more aspects of plant growth and physiology compared to a herbicide safener. Differences between RNA and protein expression of GSTs indicate that both transcriptional and translational mechanisms are involved in regulation of GSTs under these conditions. AD - Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907-2010. AU - Smith AP AU - DeRidder BP AU - Guo WJ AU - Seeley EH AU - Regnier FE AU - Goldsbrough PB LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/04/08 05:00 MHDA- 2004/04/08 05:00 AID - 10.1074/jbc.M402807200 [doi] AID - M402807200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Apr 6;. PMID- 15067523 OWN - NLM STAT- publisher DA - 20040406 IS - 0949-8257 DP - 2004 Apr 6 TI - The binding of iron and zinc to glyoxalase II occurs exclusively as di-metal centers and is unique within the metallo-beta-lactamase family. AB - Cytosolic glyoxalase 2 (GLX2-2) from Arabidopsis thaliana is a metalloenzyme that has been shown to bind a mixture of Zn, Fe, or Mn when produced in cells grown in rich media. In an effort to prepare metal-enriched samples, GLX2-2 was over-expressed in minimal media containing either Zn, Fe, or Mn. The resulting enzymes bound an average of 1 equivalent of metal ion and were partially enriched with a specific metal ion. The enzymes produced in minimal media were active towards the substrate S- d-lactoylglutathione, yielding k(cat)/ K(m) values similar to those of rich media GLX2-2. EPR studies on minimal media GLX2-2 samples revealed spectra which were identical to those over-expressed in rich media that contained nearly 2 equivalents of metal. The EPR spectra showed the presence of antiferromagnetically and ferromagnetically coupled, dinuclear metal centers. EXAFS spectra on the minimal media GLX2-2 samples over-expressed in the presence of Fe or Zn were also very similar to those of the rich media GLX2-2 samples, indicating the presence of dinuclear metal centers. The EXAFS studies also demonstrate that Zn(II) and Fe (in the Fe-enriched sample) are distributed in the dinuclear site. These data indicate that the minimal media GLX2-2 samples are a mixture of fully loaded, dinuclear metal-containing enzyme and metal-free enzyme. This characteristic of A. thaliana GLX2-2 makes it unique among the other members of the metallo-beta-lactamase family in that it does not ever appear to exist as a mononuclear metal ion containing enzyme and that it exhibits positive cooperativity in metal binding. AD - Department of Chemistry and Biochemistry, Miami University, 112 Hughes Hall, OH 45056, Oxford, USA. AU - Wenzel NF AU - Carenbauer AL AU - Pfiester MP AU - Schilling O AU - Meyer-Klaucke W AU - Makaroff CA AU - Crowder MW LA - ENG PT - JOURNAL ARTICLE TA - J Biol Inorg Chem JID - 9616326 EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 AID - 10.1007/s00775-004-0535-2 [doi] PST - aheadofprint SO - J Biol Inorg Chem 2004 Apr 6;. PMID- 15067507 OWN - NLM STAT- publisher DA - 20040406 IS - 0040-5752 DP - 2004 Apr 6 TI - A salt-responsive receptor-like kinase gene regulated by the ethylene signaling pathway encodes a plasma membrane serine/threonine kinase. AB - NTHK1 is a salt-inducible ethylene receptor gene in tobacco. Transgenic tobacco plants for this gene show reduced ethylene sensitivity. Using cDNA microarray analysis, we were able to identify those genes that have different expression levels between NTHK1 transgenic plants and wild-type plants under salt stress conditions. One of these, AtLecRK2, which encodes a receptor-like kinase with an extracellular lectin-like domain, was characterized in detail in the present study. AtLecRK2 contains a signal peptide, an extracellular lectin-like domain, a single transmembrane domain and a cytoplasmic protein kinase domain. AtLecRK2 is transcribed in the root, flower and leaf but not in the stem. In wild-type Arabidopsis, salt stress induced the transcription level of AtLecRK2, whereas in the transgenic NTHK1 Arabidopsis induction of the AtLecRK2 transcript was inhibited and retarded. AtLecRK2 was constitutively overexpressed in the ethylene-overproducer mutant, eto1-1, and could be induced by ethylene. However, in the ethylene-insensitive mutant, ein2-1, the salt-induced expression pattern of AtLecRK2 was the same as that in wild-type plants. The results demonstrate that the induction of AtLecRK2 in response to salt stress is regulated by the ethylene signaling pathway. The induction was inhibited by the ethylene receptor, NTHK1, while it was independent of EIN2. The kinase activity of AtLecRK2 was also studied. We found that that AtLecRK2 can be autophosphorylated and has serine/threonine kinase activities. The subcellular localization of AtLecRK2-GFP in onion epidermal cells indicates that AtLecRK2 is localized on the plasma membrane. AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, PR China. AU - He XJ AU - Zhang ZG AU - Yan DQ AU - Zhang JS AU - Chen SY LA - ENG PT - JOURNAL ARTICLE TA - Theor Appl Genet JID - 0145600 EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 AID - 10.1007/s00122-004-1641-9 [doi] PST - aheadofprint SO - Theor Appl Genet 2004 Apr 6;. PMID- 15067390 OWN - NLM STAT- in-data-review DA - 20040408 IS - 0040-5752 VI - 108 IP - 6 DP - 2004 Apr TI - Identification and mapping of resistance gene analogs and a white rust resistance locus in Brassica rapa ssp. oleifera. PG - 1039-46 AB - The objective of this investigation was to tag a locus for white rust resistance in a Brassica rapa ssp. oleifera F(2) population segregating for this trait, using bulked segregant analysis with random amplified polymorphic DNA (RAPD) markers, linkage mapping and a candidate gene approach based on resistance gene analogs (RGAs). The resistance source was the Finnish line Bor4109. The reaction against white rust races 7a and 7v was scored in 20 seedlings from each self-pollinated F(2 )individual. The proportion of resistant plants among these F(3) families varied from 0 to 67%. Bulked segregant analysis did not reveal any markers linked with resistance and, therefore, a linkage map with 81 markers was created. A locus that accounted for 18.4% of the variation in resistance to white rust was mapped to linkage group (LG) 2 near the RAPD marker Z19a. During the study, a bacterial resistance gene homologous to Arabidopsis RPS2 and six different RGAs were sequenced. RPS2 and five of the RGAs were mapped to linkage groups LG1, LG4 and LG9. Unfortunately, none of the RGAs could be shown to be associated with white rust resistance. AD - Crops and Biotechnology, Plant Production Research, MTT/Agrifood Research Finland, 31600, Jokioinen, Finland, pirjo.tanhuanpaa@mtt.fi FAU - Tanhuanpaa, P AU - Tanhuanpaa P LA - eng PT - Journal Article DEP - 20031205 PL - Germany TA - Theor Appl Genet JID - 0145600 SB - IM EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 PHST- 2003/Apr/04 [received] PHST- 2003/Oct/19 [accepted] PHST- 2003/Dec/05 [aheadofprint] AID - 10.1007/s00122-003-1525-4 [doi] PST - ppublish SO - Theor Appl Genet 2004 Apr;108(6):1039-46. Epub 2003 Dec 5. PMID- 15067383 OWN - NLM STAT- in-data-review DA - 20040408 IS - 0040-5752 VI - 108 IP - 6 DP - 2004 Apr TI - Organization of repetitive DNAs and the genomic regions carrying ribosomal RNA, cob, and atp9 genes in the cucurbit mitochondrial genomes. PG - 982-92 AB - Plants in the genus Cucumis (cucumber and melon) have the largest mitochondrial genomes known among all plants, due in part to the accumulation of repetitive DNAs of varying complexities. Recombination among these repetitive DNAs should produce highly rearranged mitochondrial genomes relative to the smaller mitochondrial genomes of related plants. We cloned and sequenced mitochondrial genomic regions near the rRNA, atp9 and cob genes from cucumber, melon, squash and watermelon (all members of the Cucurbitaceae family), and compared to the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugar beet to study the distribution and arrangement of coding and repetitive DNAs. Cucumber and melon had regions of concentrated repetitive DNAs spread throughout the sequenced regions; few repetitive DNAs were revealed in the mitochondrial genomes of A. thaliana, sugar beet, squash and watermelon. Recombination among these repetitive DNAs most likely produced unique arrangements of the rrn18 and rrn5 genes in the genus Cucumis. Cucumber mitochondrial DNA had more pockets of dispersed direct and inverted repeats than melon and the other plants, and we did not reveal repetitive sequences significantly contributing to mitochondrial genome expansion in both cucumber and melon. AD - Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA. FAU - Bartoszewski, Grzegorz AU - Bartoszewski G FAU - Katzir, Nurit AU - Katzir N FAU - Havey, Michael J AU - Havey MJ LA - eng PT - Journal Article DEP - 20031127 PL - Germany TA - Theor Appl Genet JID - 0145600 SB - IM EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 PHST- 2003/Aug/26 [received] PHST- 2003/Sep/25 [accepted] PHST- 2003/Nov/27 [aheadofprint] AID - 10.1007/s00122-003-1516-5 [doi] PST - ppublish SO - Theor Appl Genet 2004 Apr;108(6):982-92. Epub 2003 Nov 27. PMID- 15066586 OWN - NLM STAT- in-data-review DA - 20040406 IS - 0027-5107 VI - 559 IP - 1-2 DP - 2004 Apr 11 TI - Luciferase-based transgenic recombination assay is more sensitive than beta-glucoronidase-based. PG - 189-97 AB - Study of the DNA repair and genome stability in plants is directly dependent on the availability of an easy, inexpensive, and reliable assay. Marker gene-based homologous recombination (HR) assays were introduced more than a decade ago and have been intensively used ever since. Here, we compared several transgenic Arabidopsis and tobacco lines that carried in their genome the luciferase (LUC) or the beta-glucoronidase (uidA or GUS) substrates for HR. The average recombination frequency detected with the luciferase transgene was nearly 9.0-fold higher in Arabidopsis and 12.4-fold higher in tobacco plants. Importantly, both transgenes were under the control of 35S promoter and had similar expression levels throughout the plants. Irradiation with UVC increased the HR frequency similarly in both transgenes. The actual difference in the frequency of HR in Arabidopsis and tobacco possibly results from differing sensitivity to detection of transgene activity. Thus, we could suggest that luciferase recombination assay, due to its higher sensitivity, should be the assay of choice when plant genome stability is studied. AD - Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, Alta., Canada T1K 3M4. FAU - Ilnytskyy, Yaroslav AU - Ilnytskyy Y FAU - Boyko, Alexander AU - Boyko A FAU - Kovalchuk, Igor AU - Kovalchuk I LA - eng PT - Journal Article PL - Netherlands TA - Mutat Res JID - 0400763 SB - IM EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 PHST- 2003/Nov/14 [received] PHST- 2004/Jan/30 [revised] PHST- 2004/Feb/05 [accepted] AID - 10.1016/j.mrgentox.2004.02.001 [doi] AID - S1383571804000336 [pii] PST - ppublish SO - Mutat Res 2004 Apr 11;559(1-2):189-97. PMID- 15066372 OWN - NLM STAT- in-data-review DA - 20040406 IS - 0074-7696 VI - 234 DP - 2004 TI - Leucine-rich repeat receptor kinases in plants: structure, function, and signal transduction pathways. PG - 1-46 AB - Leucine-rich repeat receptor kinases (LRR-RKs) comprise the largest subfamily of transmembrane receptor-like kinases in plants, with over 200 members in Arabidopsis. LRR-RKs regulate a wide variety of developmental and defense-related processes including cell proliferation, stem cell maintenance, hormone perception, host-specific as well as non-host-specific defense response, wounding response, and symbiosis. Several studies indicate that LRR-RKs act as dimers, and some may form a receptor complex with leucine-rich repeat receptor-like proteins (LRR-RPs) that lack a cytoplasmic kinase domain. Despite the fact that structural features of LRR-RKs are fairy similar, five available ligand molecules for LRR-RKs are structurally diverse, from steroids (brassinolides) to peptides (phytosulfokine and systemin) and secreted proteins (CLV3). Precise ligand-binding sites of LRR-RKs are not understood. However, the extracellular "island" domain that intercepts the LRR domain in some LRR-RKs may play an important role in ligand binding. Advances in unveiling components of three LRR-RK signaling pathways, namely BRI1 in steroid signaling, CLV1 in meristem maintenance, and FLS2 in bacterial elicitor perception, revealed an intriguing link between plant LRR-RK and animal receptor signaling pathways. Finally, rapid progress made in LRR-RK research beyond the model system Arabidopsis has provided exciting, novel insights into the evolution of the LRR-RK signaling system in plants, such as BRI1 utilized in the wound-responsive signaling pathway in Solanaceae plants and recruitment of CLV1 in nodule development in leguminous plants. AD - Department of Biology, University of Washington, Seattle, Washington 98195; and CREST Japan Science and Technology Corporations, Saitama 332-0012, Japan. FAU - Torii, Keiko U AU - Torii KU LA - eng PT - Journal Article PL - United States TA - Int Rev Cytol JID - 2985180R SB - IM EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 AID - 10.1016/S0074-7696(04)34001-5 [doi] AID - S0074769604340015 [pii] PST - ppublish SO - Int Rev Cytol 2004;234:1-46. PMID- 15065439 OWN - NLM STAT- in-process DA - 20040406 IS - 0016-6758 VI - 40 IP - 2 DP - 2004 Feb TI - [In Process Citation] PG - 282-5 AB - The antisense suppressor was constructed for proline dehydrogenase gene (PDH; a fragment of PDH from Arabidopsis in antisense orientation and under the control of 35S promoter of cauliflower mosaic virus, CMV). In Nicotiana tabacum SR1 tobacco transformants bearing antisense suppressor for PDH, the proline content and the cytoplasm osmotic pressure were increased. The proline content in these transformants varied, whereas cytoplasm osmotic pressure was stable, which seems to reflect complicated relationships between these characteristics of the plant cell. AD - Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090 Russia. LA - rus PT - Journal Article PL - Russia TA - Genetika JID - 0047354 SB - IM EDAT- 2004/04/07 05:00 MHDA- 2004/04/07 05:00 PST - ppublish SO - Genetika 2004 Feb;40(2):282-5. PMID- 15064405 OWN - NLM STAT- in-process DA - 20040414 IS - 0027-8424 VI - 101 IP - 15 DP - 2004 Apr 13 TI - Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. PG - 5589-94 AB - Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea ( approximately 600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana. AD - Department of Plant Biology, University of Georgia, Athens, GA 30602, USA. FAU - Zhang, Xiaoyu AU - Zhang X FAU - Wessler, Susan R AU - Wessler SR LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1073/pnas.0401243101 [doi] AID - 0401243101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Apr 13;101(15):5589-94. Epub 2004 Apr 2. PMID- 15064386 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The Timing of Senescence and Response to Pathogens Is Altered in the Ascorbate-Deficient Arabidopsis Mutant vitamin c-1. PG - 1784-92 AB - The ozone-sensitive Arabidopsis mutant vitamin c-1 (vtc1) is deficient in l-ascorbic acid (AsA) due to a mutation in GDP-Man pyrophosphorylase (Conklin et al., 1999), an enzyme involved in the AsA biosynthetic pathway (Smirnoff et al., 2001). In this study, the physiology of this AsA deficiency was initially investigated in response to biotic (virulent pathogens) stress and subsequently with regards to the onset of senescence. Infection with either virulent Pseudomonas syringae or Peronospora parasitica resulted in largely reduced bacterial and hyphal growth in the vtc1 mutant in comparison to the wild type. When vitamin c-2 (vtc2), another AsA-deficient mutant, was challenged with P. parasitica, growth of the fungus was also reduced, indicating that the two AsA-deficient mutants are more resistant to these pathogens. Induction of pathogenesis-related proteins PR-1 and PR-5 is significantly higher in vtc1 than in the wild type when challenged with virulent P. syringae. In addition, the vtc1 mutant exhibits elevated levels of some senescence-associated gene (SAG) transcripts as well as heightened salicylic acid levels. Presumably, therefore, low AsA is causing vtc1 to enter at least some stage(s) of senescence prematurely with an accompanying increase in salicylic acid levels that results in a faster induction of defense responses. AD - Boyce Thompson Institute for Plant Research, Ithaca, New York 14853. FAU - Barth, Carina AU - Barth C FAU - Moeder, Wolfgang AU - Moeder W FAU - Klessig, Daniel F AU - Klessig DF FAU - Conklin, Patricia L AU - Conklin PL LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.032185 [doi] AID - pp.103.032185 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1784-92. Epub 2004 Apr 2. PMID- 15064385 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Cytoplasmic Alkalization Precedes Reactive Oxygen Species Production during Methyl Jasmonate- and Abscisic Acid-Induced Stomatal Closure. PG - 1536-45 AB - Signaling events during abscisic acid (ABA) or methyl jasmonate (MJ)-induced stomatal closure were examined in Arabidopsis wild type, ABA-insensitive (ost1-2), and MJ-insensitive mutants (jar1-1) in order to examine a crosstalk between ABA and MJ signal transduction. Some of the experiments were performed on epidermal strips of Pisum sativum. Stomata of jar1-1 mutant plants are insensitive to MJ but are able to close in response to ABA. However, their sensitivity to ABA is less than that of wild-type plants. Reciprocally, the stomata of ost1-2 are insensitive to ABA but are able to close in response to MJ to a lesser extent compared to wild-type plants. Both MJ and ABA promote H(2)O(2) production in wild-type guard cells, while exogenous application of diphenylene iodonium (DPI) chloride, an inhibitor of NAD(P)H oxidases, results in the suppression of ABA- and MJ-induced stomatal closure. ABA elevates H(2)O(2) production in wild-type and jar1-1 guard cells but not in ost1-2, whereas MJ induces H(2)O(2) production in both wild-type and ost1-2 guard cells, but not in jar1-1. MJ-induced stomatal closing is suppressed in the NAD(P)H oxidase double mutant atrbohD/F and in the outward potassium channel mutant gork1. Furthermore, MJ induces alkalization in guard cell cytosol, and MJ-induced stomatal closing is inhibited by butyrate. Analyses of the kinetics of cytosolic pH changes and reactive oxygen species (ROS) production show that the alkalization of cytoplasm precedes ROS production during the stomatal response to both ABA and MJ. Our results further indicate that JAR1, as OST1, functions upstream of ROS produced by NAD(P)H oxidases and that the cytoplasmic alkalization precedes ROS production during MJ or ABA signal transduction in guard cells. AD - CEA/Cadarache-DSV-DEVM, Laboratoire des Echanges Membranaires et Signalisation, UMR 163 CNRS-CEA, Universite de la Mediterranee, 13108 St Paul lez Durance cedex, France. FAU - Suhita, Dontamala AU - Suhita D FAU - Raghavendra, Agepati S AU - Raghavendra AS FAU - Kwak, June M AU - Kwak JM FAU - Vavasseur, Alain AU - Vavasseur A LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.032250 [doi] AID - pp.103.032250 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1536-45. Epub 2004 Apr 2. PMID- 15064384 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Heterosis of Biomass Production in Arabidopsis. Establishment during Early Development. PG - 1813-23 AB - Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F(1) hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51% to 66% mid-parent-heterosis at low and intermediate light intensities (60 and 120 micromol m(-2) s(-1)), and 161% at high light intensity (240 micromol m(-2) s(-1)). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0-15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics. AD - Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany. FAU - Meyer, Rhonda C AU - Meyer RC FAU - Torjek, Otto AU - Torjek O FAU - Becher, Martina AU - Becher M FAU - Altmann, Thomas AU - Altmann T LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.033001 [doi] AID - pp.103.033001 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1813-23. Epub 2004 Apr 2. PMID- 15064382 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Ethylene Insensitivity Does Not Increase Leaf Area or Relative Growth Rate in Arabidopsis, Nicotiana tabacum, and Petunia x hybrida. PG - 1803-12 AB - The plant hormone ethylene plays a role in various growth related processes. In this detailed study of the vegetative growth of Arabidopsis, Nicotiana tabacum, and Petunia x hybrida plants, we show that ethylene insensitivity does not result in an increased total leaf area or relative growth rate (RGR) under optimal growth conditions. When grown in semiclosed containers, leaf area of ethylene-insensitive plants was larger compared to the wild type. This effect was caused by a buildup of ethylene inside these containers, which inhibited the growth of wild-type plants. Ethylene-insensitive Arabidopsis and N. tabacum plants had a lower biomass, which was mainly the result of a smaller seed mass. RGR of vegetative plants was not affected by ethylene insensitivity, but the underlying components of RGR differed; specific leaf area (leaf area per unit leaf mass) was higher, and unit leaf rate (growth rate per unit leaf area) was lower. The latter was a result of a slower rate of photosynthesis per unit leaf area in the ethylene-insensitive plants. AD - Plant Ecophysiology, Utrecht University, 3584 CA Utrecht, The Netherlands. FAU - Tholen, Danny AU - Tholen D FAU - Voesenek, Laurentius A C J AU - Voesenek LA FAU - Poorter, Hendrik AU - Poorter H LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.034389 [doi] AID - pp.103.034389 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1803-12. Epub 2004 Apr 2. PMID- 15064379 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Phytohormones participate in an s6 kinase signal transduction pathway in Arabidopsis. PG - 1527-35 AB - Addition of fresh medium to stationary cells of Arabidopsis suspension culture induces increased phosphorylation of the S6 ribosomal protein and activation of its cognate kinase, AtS6k. Analysis of the activation response revealed that medium constituents required for S6 kinase activation were the phytohormones 1-naphthylacetic acid (auxin) and kinetin. Pretreatment of cells with anti-auxin or PI3-kinase drugs inhibited this response. Consistent with these findings, LY294002, a PI3-kinase inhibitor, efficiently suppressed phytohormone-induced S6 phosphorylation and translational up-regulation of ribosomal protein S6 and S18A mRNAs without affecting global translation. These data indicate that (1) activation of AtS6k is regulated by phytohormones, at least in part, via a lipid kinase-dependent pathway, that (2) the translational regulation of ribosomal proteins appears to be conserved throughout the plant and animal kingdom, and that (3) these events are hallmarks of a growth-related signal transduction pathway novel in plants. AD - Friedrich Miescher Institute, CH-4002 Basel, Switzerland. FAU - Turck, Franziska AU - Turck F FAU - Zilbermann, Frederic AU - Zilbermann F FAU - Kozma, Sara C AU - Kozma SC FAU - Thomas, George AU - Thomas G FAU - Nagy, Ferenc AU - Nagy F LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.035873 [doi] AID - pp.103.035873 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1527-35. Epub 2004 Apr 2. PMID- 15064378 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Identification and Characterization of Four Chrysanthemum MADS-Box Genes, Belonging to the APETALA1/FRUITFULL and SEPALLATA3 Subfamilies. PG - 1632-41 AB - Four full-length MADS-box cDNAs from chrysanthemum, designated Chrysanthemum Dendrathema grandiflorum MADS (CDM) 8, CDM41, CDM111, and CDM44, have been isolated and further functionally characterized. Protein sequence alignment and expression patterns of the corresponding genes suggest that CDM8 and CDM41 belong to the FRUITFULL (FUL) clade, CDM111 is a member of the APETALA1 (AP1) subfamily, and CDM44 is a member of the SEPALLATA3 (SEP3) subfamily of MADS-box transcription factors. Overexpression of CDM111 in Arabidopsis plants resulted in an aberrant phenotype that is reminiscent of the phenotype obtained by ectopic expression of the AP1 gene. In addition, CDM111 was able to partially complement the ap1-1 mutant from Arabidopsis, illustrating that CDM111 is the functional equivalent to AP1. Yeast two- and three-hybrid studies were performed to investigate the potential protein interactions and complexes in which these chrysanthemum MADS-box proteins are involved. Based on these studies, we conclude that CDM44 is most likely the SEP3 functional equivalent, because the CDM44 protein interacts with CDM proteins of the AP1/FUL and AG subfamilies, and as a higher order complex with the heterodimer between the presumed B-type CDM proteins. AD - Plant Research International, Business Unit Bioscience, Wageningen, The Netherlands. FAU - Shchennikova, Anna V AU - Shchennikova AV FAU - Shulga, Olga A AU - Shulga OA FAU - Immink, Richard AU - Immink R FAU - Skryabin, Konstantin G AU - Skryabin KG FAU - Angenent, Gerco C AU - Angenent GC LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.036665 [doi] AID - pp.103.036665 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1632-41. Epub 2004 Apr 2. PMID- 15064376 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Tissue-Specific Localization of an Abscisic Acid Biosynthetic Enzyme, AAO3, in Arabidopsis. PG - 1697-707 AB - Arabidopsis aldehyde oxidase 3 (AAO3) is an enzyme involved in abscisic acid (ABA) biosynthesis in response to drought stress. Since the enzyme catalyzes the last step of the pathway, ABA production sites may be determined by the presence of AAO3. Here, AAO3 localization was investigated using AAO3 promoter:AAO3-GFP transgenic plants and by an immunohistochemical technique. AAO3-GFP protein exhibited an activity to produce ABA from abscisic aldehyde, and the transgene restored the wilty phenotype of the aao3 mutant. GFP-fluorescence was detected in the root tips, vascular bundles of roots, hypocotyls and inflorescence stems, and along the leaf veins. Intense immunofluorescence signals were localized in phloem companion cells and xylem parenchyma cells. Faint but significant GFP- and immuno-fluorescence signals were observed in the leaf guard cells. In situ hybridization with antisense AAO3 mRNA showed AAO3 mRNA expression in the guard cells of dehydrated leaves. These results indicate that the ABA synthesized in vascular systems is transported to various target tissues and cells, and also that the guard cells themselves are able to synthesize ABA. AD - Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan. FAU - Koiwai, Hanae AU - Koiwai H FAU - Nakaminami, Kentaro AU - Nakaminami K FAU - Seo, Mitsunori AU - Seo M FAU - Mitsuhashi, Wataru AU - Mitsuhashi W FAU - Toyomasu, Tomonobu AU - Toyomasu T FAU - Koshiba, Tomokazu AU - Koshiba T LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.036970 [doi] AID - pp.103.036970 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1697-707. Epub 2004 Apr 2. PMID- 15064375 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Molecular Characterization of Cytokinin-Responsive Histidine Kinases in Maize. Differential Ligand Preferences and Response to cis-Zeatin. PG - 1654-61 AB - Genes for cytokinin-responsive His-protein kinases (ZmHK1, ZmHK2, and ZmHK3a) were isolated from maize (Zea mays). Heterologous expression of each of the ZmHKs in Escherichia coli having the DeltarcsC and cpslacZ genetic background conferred cytokinin-inducibility of lacZ expression on the bacteria. In the recombinant E. coli system, ZmHK1 and ZmHK3a were more sensitive to free-base cytokinins than to the corresponding nucleosides; isopentenyladenine was most effective for ZmHK1, while ZmHK2 tended to be most sensitive to trans-zeatin and the riboside. In contrast to a known cytokinin receptor of Arabidopsis (AHK4/CRE1/WOL), all ZmHKs responded to cis-zeatin (cZ), which generally is believed to be inactive or only weakly active. In cultured maize cells, expression of ZmRR1, a cytokinin-inducible response regulator, was induced by cZ as well as by trans-zeatin. These results strongly suggest that maize cytokinin receptors differ in ligand preference, and that cZ is an active cytokinin at least in maize. AD - Plant Science Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama 230-0045, Japan. FAU - Yonekura-Sakakibara, Keiko AU - Yonekura-Sakakibara K FAU - Kojima, Mikiko AU - Kojima M FAU - Yamaya, Tomoyuki AU - Yamaya T FAU - Sakakibara, Hitoshi AU - Sakakibara H LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.037176 [doi] AID - pp.103.037176 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1654-61. Epub 2004 Apr 2. PMID- 15064374 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Arabidopsis CYP707As Encode (+)-Abscisic Acid 8'-Hydroxylase, a Key Enzyme in the Oxidative Catabolism of Abscisic Acid. PG - 1439-49 AB - Abscisic acid (ABA) is involved in a number of critical processes in normal growth and development as well as in adaptive responses to environmental stresses. For correct and accurate actions, a physiologically active ABA level is controlled through fine-tuning of de novo biosynthesis and catabolism. The hydroxylation at the 8'-position of ABA is known as the key step of ABA catabolism, and this reaction is catalyzed by ABA 8'-hydroxylase, a cytochrome P450. Here, we demonstrate CYP707As as the P450 responsible for the 8'-hydroxylation of (+)-ABA. First, all four CYP707A cDNAs were cloned from Arabidopsis and used for the production of the recombinant proteins in insect cells using a baculovirus system. The insect cells expressing CYP707A3 efficiently metabolized (+)-ABA to yield phaseic acid, the isomerized form of 8'-hydroxy-ABA. The microsomes from the insect cells exhibited very strong activity of 8'-hydroxylation of (+)-ABA (K(m) = 1.3 microm and k(cat) = 15 min(-1)). The solubilized CYP707A3 protein bound (+)-ABA with the binding constant K(s) = 3.5 microm, but did not bind (-)-ABA. Detailed analyses of the reaction products confirmed that CYP707A3 does not have the isomerization activity of 8'-hydroxy-ABA to phaseic acid. Further experiments revealed that Arabidopsis CYP707A1 and CYP707A4 also encode ABA 8'-hydroxylase. The transcripts of the CYP707A genes increased in response to salt, osmotic, and dehydration stresses as well as ABA. These results establish that the CYP707A family plays a key role in regulating the ABA level through the 8'-hydroxylation of (+)-ABA. AD - Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. FAU - Saito, Shigeki AU - Saito S FAU - Hirai, Nobuhiro AU - Hirai N FAU - Matsumoto, Chiaki AU - Matsumoto C FAU - Ohigashi, Hajime AU - Ohigashi H FAU - Ohta, Daisaku AU - Ohta D FAU - Sakata, Kanzo AU - Sakata K FAU - Mizutani, Masaharu AU - Mizutani M LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.037614 [doi] AID - pp.103.037614 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1439-49. Epub 2004 Apr 2. PMID- 15064372 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Molecular Analyses of the Arabidopsis TUBBY-Like Protein Gene Family. PG - 1586-97 AB - In mammals, TUBBY-like proteins play an important role in maintenance and function of neuronal cells during postdifferentiation and development. We have identified a TUBBY-like protein gene family with 11 members in Arabidopsis, named AtTLP1-11. Although seven of the AtTLP genes are located on chromosome I, no local tandem repeats or gene clusters are identified. Except for AtTLP4, reverse transcription-PCR analysis indicates that all these genes are expressed in various organs in 6-week-old Arabidopsis. AtTLP1, 2, 3, 6, 7, 9, 10, and 11 are expressed ubiquitously in all the organs tested, but the expression of AtTLP5 and 8 shows dramatic organ specificity. These 11 family members share 30% to 80% amino acid similarities across their conserved C-terminal tubby domains. Unlike the highly diverse N-terminal region of animal TUBBY-like proteins, all AtTLP members except AtTLP8 contain a conserved F-box domain (51-57 residues). The interaction between AtTLP9 and ASK1 (Arabidopsis Skp1-like 1) is confirmed via yeast (Saccharomyces cerevisiae) two-hybrid assays. Abscisic acid (ABA)-insensitive phenotypes are observed for two independent AtTLP9 mutant lines, whereas transgenic plants overexpressing AtTLP9 are hypersensitive to ABA. These results suggest that AtTLP9 may participate in the ABA signaling pathway. AD - Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 106, Taiwan. FAU - Lai, Chia-Ping AU - Lai CP FAU - Lee, Chang-Lung AU - Lee CL FAU - Chen, Po-Hsuan AU - Chen PH FAU - Wu, Shu-Hsing AU - Wu SH FAU - Yang, Chien-Chih AU - Yang CC FAU - Shaw, Jei-Fu AU - Shaw JF LA - eng PT - Journal Article DEP - 20040402 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2004/Apr/02 [aheadofprint] AID - 10.1104/pp.103.037820 [doi] AID - pp.103.037820 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1586-97. Epub 2004 Apr 2. PMID- 15063866 OWN - NLM STAT- in-data-review DA - 20040405 IS - 1360-1385 VI - 9 IP - 4 DP - 2004 Apr TI - Towards a comprehensive integration of morphological and genetic studies of floral development. PG - 164-73 AB - Floral developmental genetics has exploded as a discipline. In addition to the rich genetic database for well-established models (Arabidopsis, Antirrhinum, Zea), numerous species have become the focus of floral genomic and genetic initiatives. Extensive documentation of the developmental morphology of Arabidopsis flowers has facilitated the linkage of genes and morphology. Complete developmental series also need to be assembled for emerging systems of molecular studies of floral genes. We address issues of homology assessment in floral structures, emphasize the need for assembling a complete floral developmental series for each species studied molecularly and genetically, stress the importance of a common set of terminology, and suggest a set of 'landmarks' to designate major events in floral development. We compare the floral developmental series of three species with different floral morphologies and propose a consensus of developmental stages to facilitate comparison of gene expression patterns. Taxa occupying key phylogenetic positions offer great potential for generating hypotheses about the regulation of floral development. AD - Department of Botany and the Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-8526, USA. FAU - Buzgo, Matyas AU - Buzgo M FAU - Soltis, Douglas E AU - Soltis DE FAU - Soltis, Pamela S AU - Soltis PS FAU - Ma, Hong AU - Ma H LA - eng PT - Journal Article PL - England TA - Trends Plant Sci JID - 9890299 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 AID - 10.1016/j.tplants.2004.02.003 [doi] AID - S1360138504000494 [pii] PST - ppublish SO - Trends Plant Sci 2004 Apr;9(4):164-73. PMID- 15063738 OWN - NLM STAT- in-process DA - 20040405 IS - 0014-5793 VI - 563 IP - 1-3 DP - 2004 Apr 9 TI - TGA5 acts as a positive and TGA4 acts as a negative regulator of ocs element activity in Arabidopsis roots in response to defence signals. PG - 141-5 AB - TGA/OBF family members are bZIP transcription factors that bind to the octopine synthase (ocs) element, a plant promoter sequence that has been strongly linked to defence/stress responses. Intron-containing hairpin (ihp) constructs were used to generate Arabidopsis lines with reduced expression of TGA4 and TGA5. No visible phenotypic differences were observed between ihpTGA and wild-type (WT) plants. However, the ihpTGA4 and ihpTGA5 plants had opposite affects on ocs element activity, with the ihpTGA4 lines enhancing, and the ihpTGA5 lines reducing, the response of an ocs element construct to the key defence signals, salicylic acid (SA) and H(2)O(2), in roots. AD - CSIRO Plant Industry, Private Bag No.5, Wembley, WA 6913, Australia. FAU - Foley, Rhonda C AU - Foley RC FAU - Singh, Karam B AU - Singh KB LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2003/Dec/22 [received] PHST- 2004/Feb/19 [revised] PHST- 2004/Mar/04 [accepted] AID - 10.1016/S0014-5793(04)00288-1 [doi] AID - S0014579304002881 [pii] PST - ppublish SO - FEBS Lett 2004 Apr 9;563(1-3):141-5. PMID- 15063185 OWN - NLM STAT- in-data-review DA - 20040405 IS - 0012-1606 VI - 268 IP - 2 DP - 2004 Apr 15 TI - The ENHANCER OF TRY AND CPC1 gene acts redundantly with TRIPTYCHON and CAPRICE in trichome and root hair cell patterning in Arabidopsis. PG - 506-13 AB - The development of trichomes and root hairs in Arabidopsis provide useful models for the study of cell fate determination in plants. A common network of putative transcriptional regulators, including the small MYB proteins TRIPTYCHON (TRY) and CAPRICE (CPC), is known to influence the patterning of both cell types. Here, we used an activation tagging strategy to identify a new regulator, ENHANCER OF TRY AND CPC 1 (ETC1). The ETC1 sequence is similar to TRY and CPC, and ETC1 overexpression causes a reduction in trichome formation and excessive root hair production. The etc1 single mutant has no significant phenotype, but it enhances the effect of cpc and try on trichome and root hair development, which shows that ETC1 function is partially redundant with TRY and CPC. In addition, the etc1 try cpc triple mutant has novel phenotypes, revealing previously unrecognized roles for these regulators in epidermis development. An ETC1 promoter-reporter gene fusion is expressed in the developing trichome and non-hair cells, similar to the expression of TRY and CPC. These results suggest that ETC1, TRY, and CPC act in concert to repress the trichome cell fate in the shoot epidermis and the non-hair cell fate in the root epidermis. AD - Botanical Institute, University of Koeln, Gyrhofstrasse, Koeln, Germany. FAU - Kirik, Victor AU - Kirik V FAU - Simon, Marissa AU - Simon M FAU - Huelskamp, Martin AU - Huelskamp M FAU - Schiefelbein, John AU - Schiefelbein J LA - eng PT - Journal Article PL - United States TA - Dev Biol JID - 0372762 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2003/Nov/07 [received] PHST- 2003/Dec/24 [revised] PHST- 2003/Dec/30 [accepted] AID - 10.1016/j.ydbio.2003.12.037 [doi] AID - S0012160604000430 [pii] PST - ppublish SO - Dev Biol 2004 Apr 15;268(2):506-13. PMID- 15062783 OWN - NLM STAT- in-data-review DA - 20040405 IS - 1055-7903 VI - 31 IP - 2 DP - 2004 May TI - The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny. PG - 403-15 AB - We used RT-PCR to sequence approximately 3kb of the gene coding for the largest subunit of RNA polymerase II (rpb1) from nine land plants. Our results show that plant rpb1 genes all have a similar GC-content and that their amino acid sequences evolve at a similar rate in most species we examined, except for the Arabidopsis thaliana and rice sequences which evolve faster. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve the evolutionary relationships among seed plants. Protein maximum parsimony, as well as neighbor-joining and maximum likelihood analyses of DNA and protein sequences, all generated identical tree topologies with similar strong support values at each node. The angiosperms are a clade comprising Amborella as a sister group to all other angiosperms, followed by Nymphaea, Magnolia, Arabidopsis, and a monocot clade containing maize and rice. The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycas and Zamia clade. These findings concur with recent studies that refute the Anthophyte Hypothesis and place Amborella at the base of the angiosperm tree. These rpb1 sequences also give a more consistent picture of seed plant relationships than similar analyses performed on data sets made of 18S rDNA, atpB, and rbcL sequences from the same species. These sequences therefore show great promise to help further resolve the phylogenetic relationships of seed plants. AD - Departement de biologie, Universite d'Ottawa, 30 Marie Curie, Ottawa, Ont., Canada K1N 6N5. FAU - Nickerson, Jennifer AU - Nickerson J FAU - Drouin, Guy AU - Drouin G LA - eng PT - Journal Article PL - United States TA - Mol Phylogenet Evol JID - 9304400 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PHST- 2002/Jun/07 [received] PHST- 2003/Aug/05 [revised] AID - 10.1016/j.ympev.2003.08.013 [doi] AID - S1055790303003312 [pii] PST - ppublish SO - Mol Phylogenet Evol 2004 May;31(2):403-15. PMID- 15061088 OWN - NLM STAT- in-process DA - 20040405 IS - 0981-9428 VI - 42 IP - 1 DP - 2004 Jan TI - Sucrose increases pathogenesis-related PR-2 gene expression in Arabidopsis thaliana through an SA-dependent but NPR1-independent signaling pathway. PG - 81-8 AB - Pathogenesis-related (PR) protein-coding gene expression was studied in Arabidopsis thaliana grown in liquid medium in the presence of sugars (sucrose or glucose). PR protein transcripts accumulated in the presence of sugar in the medium. A potential effect linked to osmolarity changes induced by sugar addition in the medium was ruled out using osmotica (NaCl or polyethylene glycol). Two major proteins were purified from the culture medium and found to be homologous to A. thaliana PR-2 (acidic form of beta-1, 3-glucanase) and PR-5 (thaumatin-like PR-protein). The expression of the corresponding genes was increased in the presence of sucrose and was detected exclusively in the green parts of the plant. The use of mutants and transgenic plants of A. thaliana indicated that salicylic acid (SA) was involved in the sugar-dependent activation of these PR protein-coding genes. Activation of the PR-2-coding gene was demonstrated not to be hexokinase-dependent and to be linked to a sugar metabolite acting as an internal signal as shown with non-metabolizable sugars, which were inefficient for the induction of the PR-2-coding gene. Moreover, the activation of this gene occurred in the npr1 mutant suggesting that the sugar signal acts either downstream or independently of NPR1. AD - Laboratoire de Biologie du Developpement des Plantes, CEA Cadarache, DSV DEVM/LBDP, Universite Mediterranee (CNRS-CEA, UMR 163), 13108 Saint Paul, Les Durance, France. mcthibaud@cea.fr FAU - Thibaud, Marie-Christine AU - Thibaud MC FAU - Gineste, Sandrine AU - Gineste S FAU - Nussaume, Laurent AU - Nussaume L FAU - Robaglia, Christophe AU - Robaglia C LA - eng PT - Journal Article PL - France TA - Plant Physiol Biochem JID - 9882449 SB - IM EDAT- 2004/04/06 05:00 MHDA- 2004/04/06 05:00 PST - ppublish SO - Plant Physiol Biochem 2004 Jan;42(1):81-8. PMID- 15060827 OWN - NLM STAT- publisher DA - 20040402 IS - 0032-0935 DP - 2004 Apr 2 TI - Changes in endogenous abscisic acid levels during dormancy release and maintenance of mature seeds: studies with the Cape Verde Islands ecotype, the dormant model of Arabidopsis thaliana. AB - Mature seeds of the Cape Verde Islands (Cvi) ecotype of Arabidopsis thaliana (L.) Heynh. show a very marked dormancy. Dormant (D) seeds completely fail to germinate in conditions that are favourable for germination whereas non-dormant (ND) seeds germinate easily. Cvi seed dormancy is alleviated by after-ripening, stratification, and also by nitrate or fluridone treatment. Addition of gibberellins to D seeds does not suppress dormancy efficiently, suggesting that gibberellins are not directly involved in the breaking of dormancy. Dormancy expression of Cvi seeds is strongly dependent on temperature: D seeds do not germinate at warm temperatures (20-27 degrees C) but do so easily at a low temperature (13 degrees C) or when a fluridone treatment is given to D seeds sown at high temperature. To investigate the role of abscisic acid (ABA) in dormancy release and maintenance, we measured the ABA content in both ND and D seeds imbibed using various dormancy-breaking conditions. It was found that dry D seeds contained higher amounts of ABA than dry ND after-ripened seeds. During early imbibition in standard conditions, there was a decrease in ABA content in both seeds, the rate of which was slower in D seeds. Three days after sowing, the ABA content in D seeds increased specifically and then remained at a high level. When imbibed with fluridone, nitrate or stratified, the ABA content of D seeds decreased and reached a level very near to that of ND seeds. In contrast, gibberellic acid (GA(3)) treatment caused a transient increase in ABA content. When D seeds were sown at low optimal temperature their ABA content also decreased to the level observed in ND seeds. The present study indicates that Cvi D and ND seeds can be easily distinguished by their ability to synthesize ABA following imbibition. Treatments used here to break dormancy reduced the ABA level in imbibed D seeds to the level observed in ND seeds, with the exception of GA(3) treatment, which was active in promoting germination only when ABA synthesis was inhibited. AD - UER de Physiologie Vegetale, INA-PG, UMR INRA-INAPG Biologie des Semences, 16 rue Claude Bernard, 75231, Paris Cedex 05, France. AU - Ali-Rachedi S AU - Bouinot D AU - Wagner MH AU - Bonnet M AU - Sotta B AU - Grappin P AU - Jullien M LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1007/s00425-004-1251-4 [doi] PST - aheadofprint SO - Planta 2004 Apr 2;. PMID- 15060611 OWN - NLM STAT- in-process DA - 20040402 IS - 0831-2796 VI - 47 IP - 1 DP - 2004 Feb TI - Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. PG - 141-55 AB - To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications. AD - Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA. FAU - Yan, H H AU - Yan HH FAU - Mudge, J AU - Mudge J FAU - Kim, D-J AU - Kim DJ FAU - Shoemaker, R C AU - Shoemaker RC FAU - Cook, D R AU - Cook DR FAU - Young, N D AU - Young ND LA - eng PT - Journal Article PL - Canada TA - Genome JID - 8704544 SB - IM EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1139/g03-106 [doi] AID - g03-106 [pii] PST - ppublish SO - Genome 2004 Feb;47(1):141-55. PMID- 15060594 OWN - NLM STAT- publisher DA - 20040402 IS - 0831-2796 VI - 47 IP - 2 DP - 2004 Apr TI - Soybean FGAM synthase promoters direct ectopic nematode feeding site activity. PG - 404-413 AB - Soybean cyst nematode (SCN) resistance in soybean is a complex oligogenic trait. One of the most important nematode resistance genes, rhg1, has been mapped to a distal region of molecular linkage group G in soybean. A simplified genetic system to identify soybean genes with modified expression in response to SCN led to the identification of several genes within the nematode feeding sites. The genes were mapped to reveal their linkage relationship to known QTLs associated with soybean cyst nematode (SCN) resistance. One candidate, a phosphoribosyl formyl glycinamidine (FGAM) synthase (EC 6.3.5.3) gene, mapped to the same genomic interval as the major SCN resistance gene rhg1 within linkage group G. Isolation of FGAM synthase from a soybean bacterial artificial chromosome (BAC) library revealed two highly homologous paralogs. The genes appeared to be well conserved between bacteria and humans. Promoter analysis of the two soybean homologs was carried out with the Arabidopsis thaliana – Heterodera schachtii system to investigate gene response to nematode feeding. The two promoters and their derived deletion constructions effected green fluorescent protein (GFP) expression within nematode feeding sites. The 1.0-kb promoter sequence immediately adjacent to the translation start site was sufficient to direct expression of GFP within syncytia. A wound-inducible element and a floral organ expression sequence were also identified within these promoters. Although a nematode-responsive element could not be identified, the observed expression of GFP within feeding sites supports the hypothesis that plant gene expression is redirected within feeding sites to benefit the parasite. AU - Vaghchhipawala ZE AU - Schlueter JA AU - Shoemaker RC AU - Mackenzie SA LA - ENG PT - JOURNAL ARTICLE TA - Genome JID - 8704544 EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1139/g03-110 [doi] AID - g03-110 [pii] PST - ppublish SO - Genome 2004 Apr;47(2):404-413. PMID- 15060584 OWN - NLM STAT- in-data-review DA - 20040402 IS - 0831-2796 VI - 47 IP - 2 DP - 2004 Apr TI - Characterization of two Arabidopsis thaliana myb-like proteins showing affinity to telomeric DNA sequence. PG - 316-24 AB - Telomere-binding proteins participate in forming a functional nucleoprotein structure at chromosome ends. Using a genomic approach, two Arabidopsis thaliana genes coding for candidate Myb-like telomere binding proteins were cloned and expressed in E. coli. Both proteins, termed AtTBP2 (accession Nos. T46051 (protein database) and GI:638639 (nucleotide database); 295 amino acids, 32 kDa, pI 9.53) and AtTBP3 (BAB08466, GI:9757879; 299 amino acids, 33 kDa, pI 9.88), contain a single Myb-like DNA-binding domain at the N-terminus, and a histone H1/H5-like DNA-binding domain in the middle of the protein sequence. Both proteins are expressed in various A. thaliana tissues. Using the two-hybrid system interaction between the proteins AtTBP2 and AtTBP3 and self interactions of each of the proteins were detected. Gel-retardation assays revealed that each of the two proteins is able to bind the G-rich strand and double-stranded DNA of plant telomeric sequence with an affinity proportional to a number of telomeric repeats. Substrates bearing a non-telomeric DNA sequence positioned between two telomeric repeats were bound with an efficiency depending on the length of interrupting sequence. The ability to bind variant telomere sequences decreased with sequence divergence from the A. thaliana telomeric DNA. None of the proteins alone or their mixture affects telo merase activity in vitro. Correspondingly, no interaction was observed between any of two proteins and the Arabidopsis telo merase reverse transcriptase catalytic subunit TERT (accession No. AF172097) using two-hybrid assay. FAU - Schrumpfova, Petra AU - Schrumpfova P FAU - Kuchar, Milan AU - Kuchar M FAU - Mikova, Gabriela AU - Mikova G FAU - Skrisovska, Lenka AU - Skrisovska L FAU - Kubicarova, Tatiana AU - Kubicarova T FAU - Fajkus, Jiri AU - Fajkus J LA - eng PT - Journal Article PL - Canada TA - Genome JID - 8704544 SB - IM EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1139/g03-136 [doi] AID - g03-136 [pii] PST - ppublish SO - Genome 2004 Apr;47(2):316-24. PMID- 15060130 OWN - NLM STAT- publisher DA - 20040402 IS - 1535-9476 DP - 2004 Apr 1 TI - Identification of new intrinsic proteins in arabidopsis plasma membrane proteome. AB - Identification and characterization of anion channel genes in plants represent a goal for a better understanding of their central role in cell signaling, osmoregulation, nutrition and metabolism. Though channel activities have been well characterized in plasma membrane by electrophysiology, the corresponding molecular entities are little documented. Indeed, the hydrophobic protein equipment of plant plasma membrane still remains largely unknown though several proteomic approaches have been reported. To identify new putative transport systems, we developed a new proteomic strategy based on mass spectrometry analyses of a plasma membrane fraction enriched in hydrophobic proteins. We produced from Arabidopsis cell suspensions a highly purified plasma membrane fraction, and characterized it in detail by immunological and enzymatic tests. Using complementary methods for the extraction of hydrophobic proteins and mass spectrometry analyses on mono-dimensional gels, about one hundred proteins have been identified, 95% of which had never been found in previous proteomic studies. The inventory of the plasma membrane proteome generated by this approach contains numerous plasma membrane integral proteins, one third displaying at least 4 trans-membrane segments. The plasma membrane localization was confirmed for several proteins, therefore validating such proteomic strategy. An in silico analysis shows a correlation between the putative functions of the identified proteins and the expected roles for plasma membrane in transport, signaling, cellular traffic and metabolism. This analysis also reveals ten proteins which display structural properties compatible with transport functions, and will constitute interesting targets for further functional studies. AD - Institut des Sciences du Vegetal, CNRS, Gif sur Yvette 91190. AU - Marmagne A AU - Rouet MA AU - Ferro M AU - Rolland N AU - Alcon C AU - Joyard J AU - Garin J AU - Barbier-Brygoo H AU - Ephritikhine G LA - ENG PT - JOURNAL ARTICLE TA - Mol Cell Proteomics JID - 101125647 EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1074/mcp.M400001-MCP200 [doi] AID - M400001-MCP200 [pii] PST - aheadofprint SO - Mol Cell Proteomics 2004 Apr 1;. PMID- 15059816 OWN - NLM STAT- publisher DA - 20040402 IS - 1367-4803 DP - 2004 Apr 1 TI - Spot shape modelling and data transformations for microarrays. AB - MOTIVATION: To study lowly expressed genes in microarray experiments it is useful to increase the photometric gain in the scanning. However, a large gain may cause some pixels for highly expressed genes to become saturated. Spatial statistical models that model spot shapes on the pixel level may be used to infer information about the saturated pixel intensities. Other possible applications for spot shape models include data quality control and accurate determination of spot centres and spot diameters. RESULTS: Spatial statistical models for spotted microarrays are studied including pixel level transformations and spot shape models. The models are applied to a dataset from 50-mer oligonucleotide microarrays with 452 selected Arabidopsis genes. Logarithmic, Box-Cox and inverse hyperbolic sine transformations are compared in combination with four spot shape models: a cylindric plateau shape, an isotropic Gaussian distribution and a difference of two scaled Gaussian distribution suggested in the literature, as well as a proposed new polynomial-hyperbolic spot shape model. A substantial improvement is obtained for the dataset studied by the polynomial-hyperbolic spot shape model in combination with the Box-Cox transformation. The spatial statistical models are used to correct spot measurements with saturation by extrapolating the censored data. AVAILABILITY: Source code for R are available at http://www.matfys.kvl.dk/~ekstrom/spotshapes/ AD - Dept. of Mathematics and Physics, The Royal Veterinary and Agricultural University, Thorvaldsensvej 40, DK-1871 Frederiksberg C., Denmark. AU - Ekstrom CT AU - Bak S AU - Kristensen C AU - Rudemo M LA - ENG PT - JOURNAL ARTICLE TA - Bioinformatics JID - 9808944 EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1093/bioinformatics/bth237 [doi] AID - bth237 [pii] PST - aheadofprint SO - Bioinformatics 2004 Apr 1;. PMID- 15058987 OWN - NLM STAT- in-data-review DA - 20040402 IS - 8756-7938 VI - 20 IP - 2 DP - 2004 Mar-Apr TI - A dynamic mathematical model to clarify signaling circuitry underlying programmed cell death control in Arabidopsis disease resistance. PG - 426-42 AB - Plant cells undergo programmed cell death in response to invading pathogens. This cell death limits the spread of the infection and triggers whole plant antimicrobial and immune responses. The signaling network connecting molecular recognition of pathogens to these responses is a prime target for manipulation in genetic engineering strategies designed to improve crop plant disease resistance. Moreover, as alterations to metabolism can be misinterpreted as pathogen infection, successful plant metabolic engineering will ultimately depend on controlling these signaling pathways to avoid inadvertent activation of cell death. Programmed cell death resulting from infection of Arabidopsis thaliana with Pseudomonas syringae bacterial pathogens was chosen as a model system. Signaling circuitry hypotheses in this model system were tested by construction of a differential-equations-based mathematical model. Model-based simulations of time evolution of signaling components matched experimental measurements of programmed cell death and associated signaling components obtained in a companion study. Simulation of systems-level consequences of mutations used in laboratory studies led to two major improvements in understanding of signaling circuitry: (1) Simulations supported experimental evidence that a negative feedback loop in salicylic acid biosynthesis postulated by others does not exist. (2) Simulations showed that a second negative regulatory circuit for which there was strong experimental support did not affect one of two pathways leading to programmed cell death. Simulations also generated testable predictions to guide future experiments. Additional testable hypotheses were generated by results of individually varying each model parameter over 2 orders of magnitude that predicted biologically important changes to system dynamics. These predictions will be tested in future laboratory studies designed to further elucidate the signaling network control structure. AD - Department of Plant and Soil Sciences, Delaware Agricultural Experiment Station, College of Agriculture and Natural Resources, and Department of Chemical Engineering, College of Engineering, University of Delaware, Newark, Delaware 19716. FAU - Agrawal, Vikas AU - Agrawal V FAU - Zhang, Chu AU - Zhang C FAU - Shapiro, Allan D AU - Shapiro AD FAU - Dhurjati, Prasad S AU - Dhurjati PS LA - eng PT - Journal Article PL - United States TA - Biotechnol Prog JID - 8506292 SB - IM EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 AID - 10.1021/bp034226s [doi] PST - ppublish SO - Biotechnol Prog 2004 Mar-Apr;20(2):426-42. PMID- 15058443 OWN - NLM STAT- in-process DA - 20040402 IS - 0962-8452 VI - 271 IP - 1536 DP - 2004 Feb 7 TI - The phenotype of Arabidopsis ovule mutants mimics the morphology of primitive seed plants. PG - 311-6 AB - In seed plants, the ovule is the female reproductive structure, which surrounds and nourishes the gametophyte and embryo. This investigation describes the PRETTY FEW SEEDS2 (PFS2) locus, which regulates ovule patterning. The pfs2 mutant exhibited developmental defects in the maternal integuments and gametophyte. This mutation was inherited as a maternal trait, indicating that gametophyte defects resulted from ovule patterning aberrations. Specifically, the boundary between the chalaza and the nucellus, two regions of the ovule primordia, shifted towards the distal end of pfs2 ovule primordia. Results indicated that the PFS2 locus could: (i) be involved in the development of either the nucellus or the chalaza; or (ii) establish a boundary between these two regions. Examination of genetic interactions of the pfs2 mutation with other well-characterized ovule loci indicates that this locus affects integument morphogenesis. Interestingly, the pfs2 inner no outer and pfs2 strubbelig double mutants had inner integuments that appeared similar to their ancestral precursor. The fossil record indicates that the inner integument evolved by fusion of sterilized sporangia or branches around a central megasporangium. The question of whether the structures observed in these double mutants are homologous or merely analogous to the ancestral precursors of the inner integument is discussed. AD - Department of Botany, University of Florida, Gainesville 32611-8526, USA. FAU - Park, Sung Ok AU - Park SO FAU - Hwang, Soon AU - Hwang S FAU - Hauser, Bernard A AU - Hauser BA LA - eng PT - Journal Article PL - England TA - Proc R Soc Lond B Biol Sci JID - 7505889 SB - IM EDAT- 2004/04/03 05:00 MHDA- 2004/04/03 05:00 PST - ppublish SO - Proc R Soc Lond B Biol Sci 2004 Feb 7;271(1536):311-6. PMID- 15057934 OWN - NLM STAT- in-process DA - 20040401 IS - 0265-9247 VI - 26 IP - 4 DP - 2004 Apr TI - It's time to flower: the genetic control of flowering time. PG - 363-73 AB - In plants, successful sexual reproduction and the ensuing development of seeds and fruits depend on flowering at the right time. This involves coordinating flowering with the appropriate season and with the developmental history of the plant. Genetic and molecular analysis in the small cruciform weed, Arabidopsis, has revealed distinct but linked pathways that are responsible for detecting the major seasonal cues of day length and cold temperature, as well as other local environmental and internal signals. The balance of signals from these pathways is integrated by a common set of genes to determine when flowering occurs. Excitingly, it has been discovered that many of these same genes regulate flowering in other plants, such as rice. This review focuses on recent advances in how three of the signalling pathways (the day-length, vernalisation and autonomous pathways) function to control flowering. CI - Copyright 2004 Wiley-Liss, Inc. AD - School of Biological Sciences, University of Auckland, Auckland, New Zealand. J.Putterill@auckland.ac.nz FAU - Putterill, Jo AU - Putterill J FAU - Laurie, Rebecca AU - Laurie R FAU - Macknight, Richard AU - Macknight R LA - eng PT - Journal Article PL - United States TA - Bioessays JID - 8510851 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 AID - 10.1002/bies.20021 [doi] PST - ppublish SO - Bioessays 2004 Apr;26(4):363-73. PMID- 15057819 OWN - NLM STAT- completed DA - 20040401 DCOM- 20040414 IS - 1476-4687 VI - 428 IP - 6982 DP - 2004 Apr 1 TI - Gene regulation: ancient microRNA target sequences in plants. PG - 485-6 AB - MicroRNAs are an abundant class of small RNAs that are thought to regulate the expression of protein-coding genes in plants and animals. Here we show that the target sequence of two microRNAs, known to regulate genes in the class-III homeodomain-leucine zipper (HD-Zip) gene family of the flowering plant Arabidopsis, is conserved in homologous sequences from all lineages of land plants, including bryophytes, lycopods, ferns and seed plants. We also find that the messenger RNAs from these genes are cleaved within the same microRNA-binding site in representatives of each land-plant group, as they are in Arabidopsis. Our results indicate not only that microRNAs mediate gene regulation in non-flowering as well as flowering plants, but also that the regulation of this class of plant genes dates back more than 400 million years. AD - Section of Plant Biology, University of California, Davis, California 95616, USA. FAU - Floyd, Sandra K AU - Floyd SK FAU - Bowman, John L AU - Bowman JL LA - eng PT - Journal Article PL - England TA - Nature JID - 0410462 RN - 0 (MicroRNAs) SB - IM MH - Base Sequence MH - *Gene Expression Regulation, Plant MH - Genes, Plant/*genetics MH - MicroRNAs/genetics/*metabolism MH - Phylogeny MH - Plants/classification/*genetics MH - Substrate Specificity EDAT- 2004/04/02 05:00 MHDA- 2004/04/15 05:00 AID - 10.1038/428485a [doi] AID - 428485a [pii] PST - ppublish SO - Nature 2004 Apr 1;428(6982):485-6. PMID- 15056905 OWN - NLM STAT- in-data-review DA - 20040401 IS - 0916-8451 VI - 68 IP - 3 DP - 2004 Mar TI - DNA Microarray Analysis of Plastid Gene Expression in an Arabidopsis Mutant Deficient in a Plastid Transcription Factor Sigma, SIG2. PG - 694-704 AB - The plastid genome of higher plants contains more than one hundred genes for photosynthesis, gene expression, and other processes. Plastid transcription is done by two types of RNA polymerase, PEP and NEP. PEP is a eubacteria-type RNA polymerase that is essential for chloroplast development. In Arabidopsis thaliana, six sigma factors (SIG1-6) are encoded by the nuclear genome, and postulated to determine the transcription specificity of PEP. In this study, we constructed a DNA microarray for all of the plastid protein-coding genes, and analyzed the effects of the sig2 lesion on the global plastid gene expression. Of the 79 plastid protein genes, it was found that only the psaJ transcript was decreased in the mutant, whereas transcripts of 47 genes were rather increased. Since many of the up-regulated genes are under the control of NEP, it was suggested that the NEP activity was increased in the sig2-1 mutant. AD - Laboratory of Molecular Genetics, Department of Molecular Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo. FAU - Nagashima, Akitomo AU - Nagashima A FAU - Hanaoka, Mitsumasa AU - Hanaoka M FAU - Motohashi, Reiko AU - Motohashi R FAU - Seki, Motoaki AU - Seki M FAU - Shinozaki, Kazuo AU - Shinozaki K FAU - Kanamaru, Kengo AU - Kanamaru K FAU - Takahashi, Hideo AU - Takahashi H FAU - Tanaka, Kan AU - Tanaka K LA - eng PT - Journal Article PL - Japan TA - Biosci Biotechnol Biochem JID - 9205717 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Biosci Biotechnol Biochem 2004 Mar;68(3):694-704. PMID- 15056893 OWN - NLM STAT- in-data-review DA - 20040401 IS - 0916-8451 VI - 68 IP - 3 DP - 2004 Mar TI - Differential Expression of Acid Invertase Genes during Seed Germination in Arabidopsis thaliana. PG - 602-8 AB - In Arabidopsis thaliana (L.) Heynh ecotype Landsberg, levels of soluble acid invertase activity are closely related to the progress of seed germination. To study the mechanism(s) of the development of these enzymes, two cDNA clones that encode putative vacuolar acid invertases were isolated from germinating seeds and very young seedlings using reverse-transcription polymerase chain reactions with degenerate primers. These fragments corresponded to the genes Atbetafruct3 and Atbetafruct4 from the Columbia ecotype. An apoplasmic invertase gene corresponding to Atbetafruct1/ATCWINV1 was also isolated from these samples. Northern blot analyses showed that Atbetafruct3 and Atbetafruc4 are expressed concomitantly with germination and the subsequent seedling growth. In contrast, the Atbetafruct1/AtcwINV1 mRNA is translated before germination. These expression patterns are regulated by phytochrome, which perceives red light and in turn triggers de novo synthesis of gibberellin, initiating Arabidopsis seed germination. To test the effects of gibberellin on the expression of these genes, seed were treated with a gibberellin biosynthesis inhibitor, uniconazole or prohexadione. These chemicals inhibited both seed germination and expression of the above genes, but subsequently applied GA(4), an active gibberellin, reversed the inhibition. These results suggest that the transcription of genes encoding the vacuolar invertases, Atbetafruct3 and Atbetafruct4 and a gene encoding the apoplasmic invertase, Atbetafruct1/AtcwINV1, are induced by gibberellin synthesized de novo following irradiation with red light. AD - Department of Bioresource Engineering, Faculty of Agriculture, Yamagata University. FAU - Mitsuhashi, Wataru AU - Mitsuhashi W FAU - Sasaki, Shigekazu AU - Sasaki S FAU - Kanazawa, Akihiko AU - Kanazawa A FAU - Yang, Young-Yell AU - Yang YY FAU - Kamiya, Yuji AU - Kamiya Y FAU - Toyomasu, Tomonobu AU - Toyomasu T LA - eng PT - Journal Article PL - Japan TA - Biosci Biotechnol Biochem JID - 9205717 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Biosci Biotechnol Biochem 2004 Mar;68(3):602-8. PMID- 15056652 OWN - NLM STAT- publisher DA - 20040401 IS - 1083-351X DP - 2004 Mar 31 TI - Endogenous superoxide production and the nitrite/nitrate ratio control the concentration of bioavailable free nitric oxide in leaves. AB - We have quanititatively measured nitric oxide production in leaves of Arabidopsis thaliana and Vicia faba by adapting ferrous dithiocarbamate spin tapping methods previously used in animal systems. Hydrophobic diethyldithiocarbamate complexes were used to measure NO interacting with membranes and hydrophilic N-methyl-D-glucamine dithiocarbamate was used to measure NO released into the external solution. Both complexes were able to trap levels of NO, readily detectable by EPR spectroscopy. Basal rates of NO production (in the order of 1 nmol g(-1) h(-1)) agreed with previous studies. However, use of methodologies that corrected for the removal of free NO by endogenously produced superoxide, resulted in a significant increase in the trapped NO (up to 18 nmol g(-1) h(-1)). Basal NO production in leaves is therefore much higher than previously thought, but this is masked by significant superoxide production. The effects of nitrite (increased rate) and nitrate (decreased rate) are consistent with a role for nitrate reductase as the source of this basal NO production. However, rates under physiologically achievable nitrite concentrations never approach that reported following pathogen induction of plant nitric oxide synthase. In Hibiscus rosa sinensis, the addition of exogenous nitrite generated sufficient NO such that EPR could be used to detect its production using endogenous spin traps (forming paramagnetic dinitrosyl iron complexes). Indeed the levels of this nitrosylated iron pool are sufficiently high that they may represent a method of maintaining bioavailable iron levels under conditions of iron starvation, thus explaining the previously observed role of NO in preventing chlorosis under these conditions. AD - Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ. AU - Vanin AF AU - Svistunenko DA AU - Mikoyan VD AU - Serezhenkov VA AU - Fryer MJ AU - Baker NR AU - Cooper CE LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 AID - 10.1074/jbc.M312601200 [doi] AID - M312601200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 31;. PMID- 15055537 OWN - NLM STAT- in-process DA - 20040401 IS - 1016-8478 VI - 17 IP - 1 DP - 2004 Feb 29 TI - Altered cell shapes, hyperplasia, and secondary growth in Arabidopsis caused by beet curly top geminivirus infection. PG - 117-24 AB - Arabidopsis Sei-O ecotype was found to be hypersusceptible to the BCTV-Logan strain in that it developed very severe symptoms, including severely deformed inflorescences with the callus-like structure, and accumulated high level of viral DNA. Microscopic studies of the BCTV-induced cell divisions demonstrated that the activation of cell divisions was preceded by the phloem disruption and the callus-like structure seemed to be originated from the cortex nearby disrupted phloem. We have further defined the callus-like structure formed by BCTV infection using molecular and histochemical analyses. Results indicate that BCTV infection causes the phloem disruption, following by cell enlargement and elongation in cortex and even epidermis. Finally, BCTV induced symptomatic secondary growth in cortex by de novo anticlinal and periclinal cell divisions. Expression of cdc2 and saur from BCTV-infected Arabidopsis correlates with symptom development. These results suggest a critical role of auxin in symptom development in the interactions between Arabidopsis and BCTV. AD - Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746, Korea. FAU - Park, Jongbum AU - Park J FAU - Hwang, Hyunsik AU - Hwang H FAU - Shim, Haekyung AU - Shim H FAU - Im, Kyunghoan AU - Im K FAU - Auh, Chung-Kyoon AU - Auh CK FAU - Lee, Sukchan AU - Lee S FAU - Davis, Keith R AU - Davis KR LA - eng PT - Journal Article PL - Korea (South) TA - Mol Cells JID - 9610936 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Mol Cells 2004 Feb 29;17(1):117-24. PMID- 15055534 OWN - NLM STAT- in-process DA - 20040401 IS - 1016-8478 VI - 17 IP - 1 DP - 2004 Feb 29 TI - Acceleration of flowering by overexpression of MFT (MOTHER OF FT AND TFL1). PG - 95-101 AB - MFT (MOTHER OF FT AND TFL1) is a member of a gene family that includes two important regulators, FT (FLOWERING LOCUS T) and TFL1 (TERMINAL FLOWER 1), in determination of flowering time in Arabidopsis. Although the functions of FT and TFL1 are assigned in the family, the roles of other members are largely unknown. Especially the sequence of MFT is homologous to both FT and TFL1, which act as a floral promoter and an inhibitor, respectively, making it difficult to predict the role of MFT. We performed genetic analyses of MFT to understand its role in floral development. Constitutive expression of MFT led to slightly early flowering under long days. However, a T-DNA insertion allele of MFT did not show obvious phenotype. Further genetic analyses with the loss-of-function alleles of FT, TFL1, and ATC (Arabidopsis Thaliana CENTRORADIALIS homologue) showed that a decrease of MFT activity did not enhance the phenotypes of the single mutants. Taken together, we suggest that MFT functions as a floral inducer and that it may act redundantly in determination of flowering time in Arabidopsis. AD - Plant Signaling Network Research Center, School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea. FAU - Yoo, So Yeon AU - Yoo SY FAU - Kardailsky, Igor AU - Kardailsky I FAU - Lee, Jong Seob AU - Lee JS FAU - Weigel, Detlef AU - Weigel D FAU - Ahn, Ji Hoon AU - Ahn JH LA - eng PT - Journal Article PL - Korea (South) TA - Mol Cells JID - 9610936 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Mol Cells 2004 Feb 29;17(1):95-101. PMID- 15055533 OWN - NLM STAT- in-process DA - 20040401 IS - 1016-8478 VI - 17 IP - 1 DP - 2004 Feb 29 TI - Molecular cloning and characterization of nucleoside diphosphate (NDP) kinases from Chinese cabbage (Brassica campestris). PG - 86-94 AB - Nucleoside diphosphate kinases (NDPKs) are key metabolic enzymes that catalyze the synthesis of non-adenosine nucleoside triphosphates (NTP) by transfer of the terminal phosphate between NDP and NTP. Recently we isolated three NDPK cDNAs from Chinese cabbage cDNA library. BcNDK1 has 636 bp and encodes a putative 17.4 kDa protein, BcNDK2 has 854 bp and encodes a putative 25.5 kDa protein, and BcNDK3 is 986 bp long and encodes a putative 25.7 kDa protein. The precursor proteins of BcNDK2 and BcNDK3 have long N-terminal extensions containing putative chloroplast or mitochondrial targeting sequences. A phylogenic tree showed that the 3 BcNDKs are highly homologous to other plant NDPK genes, especially those of Arabidopsis. Expression of the BcNDK genes depended on the developmental stage and the conditions of seed germination. Most notably, expression of BcNDK2 increased dramatically in seedlings transferred to the light after germinating in the dark. In addition, BcNDK3 differed from BcNDK1 in being highly expressed in the hooks and cotyledons of seedlings. Although all BcNDKs were highly expressed in petals, BcNDK1 was also expressed in pistils. Expression of each of the BcNDKs increased as the flower bud matured. These results indicate that NDPKs are involved in physiological pathways activated by a variety of environmental conditions and at different developmental stages. AD - Division of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea. FAU - Shin, Dong Ho AU - Shin DH FAU - In, Jun Gyo AU - In JG FAU - Lim, Yong Pyo AU - Lim YP FAU - Hasunuma, Kohji AU - Hasunuma K FAU - Choi, Kwan Sam AU - Choi KS LA - eng PT - Journal Article PL - Korea (South) TA - Mol Cells JID - 9610936 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Mol Cells 2004 Feb 29;17(1):86-94. PMID- 15055520 OWN - NLM STAT- in-process DA - 20040401 IS - 1016-8478 VI - 17 IP - 1 DP - 2004 Feb 29 TI - Circadian regulation of rice (Oryza sativa L.) CONSTANS-like gene transcripts. PG - 10-6 AB - We identified three rice cDNA clones showing amino acid similarity to the Arabidopsis CONSTANS-like proteins from a database search (S12569, S3574, and C60910), to examine if their transcript abundances were under circadian control. Unlike the other two proteins, the protein encoded by the S12569 cDNA contains only one CONSTANS-like zinc finger B box, and a CCT region. We found that the transcript levels of these rice CONSTANS-like (COL) genes were under circadian control. The oscillation phase of the S12569 gene transcript was more or less opposite to those of OsGI (rice GIGANTEA homolog) and Hd1 (rice COSTANS homolog), whereas the phases of the other two gene transcripts were similar to that of the Hd1 transcript. S12569 mRNA started to increase about 3 h after the onset of the dark period, with a peak about 3 h after its end. The S3574 and C60910 genes were expressed to similar extents during the vegetative and reproductive phases, like OsGI. Higher levels of S12569 transcripts, however, like those of Hd1, were detected in the earlier stages of panicle development. Unlike Hd1 transcripts, S12569, S3574, and C60910 transcripts were present at similar levels in the aerial parts of plants and in their roots during the vegetative phase. In conclusion, the rice COL genes showed distinctive expression patterns from the CO and COL genes, as well as Hd1, a rice CO homolog. AD - School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea. FAU - Shin, Bong-Soo AU - Shin BS FAU - Lee, Jeong-Hyun AU - Lee JH FAU - Lee, Jeong-Hwan AU - Lee JH FAU - Jeong, Hyun-Joo AU - Jeong HJ FAU - Yun, Choong-Hyo AU - Yun CH FAU - Kim, Jeong-Kook AU - Kim JK LA - eng PT - Journal Article PL - Korea (South) TA - Mol Cells JID - 9610936 SB - IM EDAT- 2004/04/02 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - Mol Cells 2004 Feb 29;17(1):10-6. PMID- 15054659 OWN - NLM STAT- publisher DA - 20040331 IS - 0032-0935 DP - 2004 Mar 31 TI - Overexpression of a cyanobacterial phospho enolpyruvate carboxylase with diminished sensitivity to feedback inhibition in Arabidopsis changes amino acid metabolism. AB - Phospho enolpyruvate carboxylase (EC 4.1.1.31) from Synechococcus vulcanus (SvPEPC) is a unique enzyme, being almost insensitive to feedback inhibition at neutral pH. In order to assess its usefulness in metabolic engineering of plants, SvPEPC was expressed in Arabidopsis thaliana (L.) Heynh. under the control of the cauliflower mosaic virus 35S promoter. About one-third of the transformants of the T1 generation showed severe visible phenotypes such as leaf bleaching and were infertile when grown on soil. However, no such phenotype was observed with Arabidopsis transformed with Zea mays L. PEPC (ZmPEPC) for C4 photosynthesis, which is normally sensitive to a feedback inhibitor, l-malate. For the SvPEPC transformants of the T2 generation, which had been derived from fertile T1 transformants, three kinds of phenotype were observed when plants were grown on an agar medium containing sucrose: Type-I plants showed poor growth and a block in true leaf development; Type-II plants produced a few true leaves, which were partially bleached; Type-III plants were apparently normal. In Type-I plants, total PEPC activity was increased about 2-fold over the control plant but there was no such increase in Type-III plants. The phenotypes of Type-I plants were rescued when the sucrose-containing agar medium was supplemented with aromatic amino acids. Measurement of the free amino acid content in whole seedlings of Type-I transformants revealed that the levels of the aromatic amino acids Phe and Tyr were lowered significantly as compared with the control plants. In contrast, the levels of several amino acids of the aspartic and glutamic families, such as Asn, Gln and Arg, were markedly enhanced (4- to 8-fold per plant fresh weight). However, when the medium was supplemented with aromatic amino acids, the levels of Asn, Gln, and Arg decreased to levels slightly higher than those of control plants, accompanied by growth recovery. Taken together, it can be envisaged that SvPEPC is capable of efficiently exerting its activity in the plant cell environment so as to cause imbalance between aromatic and non-aromatic amino acid syntheses. The growth inhibition of Type-I plants was presumed to be primarily due to a decreased availability of phospho enolpyruvate, one of the precursors for the shikimate pathway for the synthesis of aromatic amino acids and phenylpropanoids. The possible usefulness of SvPEPC as one of the key components for installing the C(4)-like pathway is proposed. AD - Laboratory of Plant Physiology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, 606-8502, Kyoto, Japan. AU - Chen LM AU - Li KZ AU - Miwa T AU - Izui K LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1007/s00425-004-1244-3 [doi] PST - aheadofprint SO - Planta 2004 Mar 31;. PMID- 15054111 OWN - NLM STAT- publisher DA - 20040419 IS - 0021-9533 VI - 117 IP - Pt 10 DP - 2004 Apr 15 TI - Identification and functional characterization of Arabidopsis AP180, a binding partner of plant {alpha}C-adaptin. PG - 2051-2062 AB - Clathrin-mediated endocytosis is a well-studied uptake mechanism for nutrients and signalling receptors in mammalian cells that depends on the coordinated interaction of coat proteins and endocytic network proteins to perform the internalization. In this process AP180 promotes the assembly of clathrin triskelia into coated membrane patches at the plasma membrane, while alpha-adaptin interacts with various network proteins that are in turn required for the budding of the coated pits. The process of clathrin-mediated endocytosis in plants has not been dissected at the molecular level, nor have the members of an analogous uptake machinery been functionally described. In this respect, we have investigated the AP180 and alpha-adaptin orthologs from Arabidopsis thaliana: At-AP180 and At-alphaC-Ad. Both plant proteins display the same structural features as their mammalian counterparts and fulfill the same basic functions. To identify their interacting partners, the ear region of At-alphaC-Ad and the C-terminal region of At-AP180 were used as fusion proteins in pull-down experiments and plasmon-resonance measurements. At-alphaC-Ad binds several mammalian endocytic proteins, and its interaction with At-AP180 requires the DPF motif. At-AP180 functions as a clathrin assembly protein that promotes the formation of cages with an almost uniform size distribution. Deletion of the single DLL motif abolished the assembly activity of At-AP180 almost completely, but did not affect its binding to triskelia, suggesting the existence of additional binding determinants. AD - University of Heidelberg, Department of Cell Biology, Heidelberg Institute for Plant Sciences, 69120 Heidelberg, Im Neuenheimer Feld 230, Germany. AU - Barth M AU - Holstein SE LA - ENG PT - JOURNAL ARTICLE DEP - 20040330 TA - J Cell Sci JID - 0052457 EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 PHST- 2004/Mar/30 [aheadofprint] AID - 10.1242/jcs.01062 [doi] AID - jcs.01062 [pii] PST - ppublish SO - J Cell Sci 2004 Apr 15;117(Pt 10):2051-2062. Epub 2004 Mar 30. PMID- 15053772 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - Nested core collections maximizing genetic diversity in Arabidopsis thaliana. PG - 193-202 AB - Summary The successful exploitation of natural genetic diversity requires a basic knowledge of the extent of the variation present in a species. To study natural variation in Arabidopsis thaliana, we defined nested core collections maximizing the diversity present among a worldwide set of 265 accessions. The core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity. The core collections are available to the scientific community and thus provide an important resource for the study of genetic variation and its functional consequences in Arabidopsis. Moreover, this strategy can be used in other species to provide a rational framework for undertaking diversity surveys, including single nucleotide polymorphism (SNP) discovery and phenotyping, allowing the utilization of genetic variation for the study of complex traits. AD - Centre National de Genotypage, 2 rue Gaston Cremieux, 91057 Evry Cedex, France. FAU - McKhann, Heather I AU - McKhann HI FAU - Camilleri, Christine AU - Camilleri C FAU - Berard, Aurelie AU - Berard A FAU - Bataillon, Thomas AU - Bataillon T FAU - David, Jacques L AU - David JL FAU - Reboud, Xavier AU - Reboud X FAU - Le Corre, Valerie AU - Le Corre V FAU - Caloustian, Christophe AU - Caloustian C FAU - Gut, Ivo G AU - Gut IG FAU - Brunel, Dominique AU - Brunel D LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02034.x [doi] AID - TPJ2034 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):193-202. PMID- 15053771 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - High-resolution boundary analysis during Arabidopsis thaliana flower development. PG - 182-92 AB - Summary We report a comparative analysis of cell proliferation patterns during Arabidopsis flower development. Cell division was evaluated by a direct method, i.e. the 5-bromo-2'-deoxyuridine (BrdU) incorporation/immunodetection procedure. BrdU patterns in wild-type plants were correlated with the expression profiles of both several cell cycle genes involved in the control of the G(1)/S transition and cell cycle-related repressor genes, MSI4 and MSI5, encoding WD-repeat proteins. To evaluate how proliferation patterns arise with respect to boundaries and vice versa, the expression of a boundary gene, CUP SHAPED COTYLEDON (CUC)2, was determined. Combining these approaches, we demonstrate that boundaries between inflorescence and floral meristems and between floral whorls are narrow bands of non-dividing cells. In addition, we show that negative and positive regulators of cell proliferation are simultaneously and continuously expressed in dividing meristematic domains, being excluded from boundary cells. Finally, BrdU incorporation and CUC2 in situ hybridisation patterns were analysed in two mutant backgrounds, agamous (ag)-1 and superman (sup)-1, in order to assess changes in boundary establishment and different levels of indeterminacy under conditions of altered proliferation at the floral meristem centre. AD - Laboratoire Reproduction et Developpement des Plantes, UMR 5667, Ecole Normale Superieure de Lyon, 46 Allee d'Italie, F-69364 Lyon Cedex 07, France. FAU - Breuil-Broyer, Stephanie AU - Breuil-Broyer S FAU - Morel, Patrice AU - Morel P FAU - De Almeida-Engler, Janice AU - De Almeida-Engler J FAU - Coustham, Vincent AU - Coustham V FAU - Negrutiu, Ioan AU - Negrutiu I FAU - Trehin, Christophe AU - Trehin C LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02026.x [doi] AID - TPJ2026 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):182-92. PMID- 15053769 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - Temporally and spatially controlled induction of gene expression in Arabidopsis thaliana. PG - 164-71 AB - Summary Temporally and spatially regulated induction of gene expression is an important tool of genetic analysis. In plants, several systems are available for spatially unregulated induction of gene expression, or for spatially regulated expression. Here, we describe a new system that provides both temporal and spatial control for transgene expression. It combines the advantages of its two constituent components: temporally regulated activity of the ethanol-dependent AlcR transcription factor, and tissue specificity of a plant promoter. As a proof of principle, transgenic lines were developed in which the promoter of the meristem identity gene LEAFY (LFY) provided flower-specific expression of the AlcR activator. Tissue-specific activity of AlcR was confirmed with a responder in which the beta-glucuronidase (GUS) reporter was under the control of the alcA response element. As expected, reporter activity in a pattern typical for the LFY promoter was ethanol dependent. Next, we placed the LFY coding sequenced under control of the AlcA response element. In a strong lfy-12 background, this construct in combination with the LFY:AlcR driver provided complete, ethanol-dependent rescue of the lfy phenotype, including restoration of fertility. Apart from facilitating the investigation of temporal and spatial requirements of gene activity, this technology will permit new types of genetic modifier screens starting with mutations that otherwise confer lethality or sterility. AD - Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, D-72076 Tubingen, Germany. FAU - Maizel, Alexis AU - Maizel A FAU - Weigel, Detlef AU - Weigel D LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02027.x [doi] AID - TPJ2027 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):164-71. PMID- 15053768 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis. PG - 152-63 AB - Summary Plastid gene expression is regulated by a variety of nuclear genes. We have isolated Arabidopsis thaliana proton gradient regulation 3 (pgr3) mutants, which display aberrant chlorophyll fluorescence because of defects in chloroplast gene expression. High chlorophyll fluorescence (HCF) because of a reduced level of the cytochrome b(6)/f complex was observed in two alleles, pgr3-1 and pgr3-2 but not in pgr3-3. In contrast, a transient increase in fluorescence after turning off the actinic light, which was ascribed to chloroplast NAD(P)H dehydrogenase (NDH) activity, was impaired in pgr3-1 and pgr3-3 but not in pgr3-2. Both phenotypes were complemented by the introduction of a single gene, PGR3, encoding a protein containing 27 pentatrico-peptide repeat (PPR) motifs. PPR motifs are present in proteins functioning in the post-transcriptional regulation of organellar gene expression. The conserved threonine in the motif was substituted by isoleucine in the 15th and 12th PPR motifs in pgr3-1 and pgr3-2, respectively, and the conserved leucine by phenylalanine in the final incomplete motif of pgr3-3. We consider that the different domains of the PPR repeats in PGR3 might have different functions in conferring RNA stability and probably allowing translation as well as recognizing at least two distinct target RNAs. AD - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan. FAU - Yamazaki, Hiroyuki AU - Yamazaki H FAU - Tasaka, Masao AU - Tasaka M FAU - Shikanai, Toshiharu AU - Shikanai T LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02035.x [doi] AID - TPJ2035 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):152-63. PMID- 15053765 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - beta-amino-butyric acid-induced resistance against necrotrophic pathogens is based on ABA-dependent priming for callose. PG - 119-30 AB - Summary The non-protein amino acid beta-amino-butyric acid (BABA) protects plants against a wide range of pathogens. We have examined the effectiveness and mode of action of BABA on resistance against two necrotrophic pathogens. Treatment of Arabidopsis with BABA induced resistance against Alternaria brassicicola and Plectosphaerella cucumerina to a similar level by jasmonic acid (JA). Conversely, treatment with benzothiadiazole (BTH), a functional analogue of salicylic acid (SA), had no significant effect on the resistance against both pathogens. BABA-induced resistance against A. brassicicola and P. cucumerina was unaffected in the JA-insensitive mutant coi1-1 and the camalexin-deficient mutant pad3-1. Moreover, the expression of BABA-induced resistance was not associated with enhanced accumulation of camalexin or enhanced transcription of the JA-inducible PDF1.2 gene. The expression of BABA-induced resistance against P. cucumerina was unaffected in mutants impaired in ethylene (ET) and SA signalling, but was blocked in the abscisic acid (ABA)-deficient mutant aba1-5, the ABA-insensitive mutant abi4-1 and the callose-deficient mutant pmr4-1. Upon infection by both pathogens, BABA-treated plants showed an earlier and more pronounced accumulation of callose. Treatment with the callose-inhibitor 2-deoxy-D-glucose (2-DDG) reversed the BABA-induced resistance against A. brassicicola. Furthermore, primed callose deposition was absent in BABA-treated abi4-1 and pmr4-1 plants upon infection by P. cucumerina. Although the expression of BABA-induced resistance was not associated with enhanced transcription of the ABA-inducible RAB18 gene, application of ABA mimicked the effect of BABA on the level of callose accumulation and resistance. Hence, BABA-induced resistance against necrotrophic pathogens is based on primed callose accumulation, which is controlled by an ABA-dependent defence pathway. AD - Laboratory of Biochemistry and Molecular Biology, Department of Science, Institute of Botany, University of Neuchatel, Rue Emile-Argand 9, PO Box 2, CH-2007 Neuchatel, Switzerland. FAU - Ton, Jurriaan AU - Ton J FAU - Mauch-Mani, Brigitte AU - Mauch-Mani B LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02028.x [doi] AID - TPJ2028 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):119-30. PMID- 15053763 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis. PG - 93-106 AB - Summary Translocon at the outer envelope membrane of chloroplasts, 34 kDa (Toc34) is a GTP-binding component of the protein import apparatus within the outer envelope membrane of plastids. The Arabidopsis genome encodes two homologues of Toc34, designated atToc33 and atToc34. In this report, we describe the identification and characterization of two atToc34 knockout mutants, plastid protein import 3-1 (ppi3-1) and ppi3-2. Aerial tissues of the ppi3 mutants appeared similar to the wild type throughout development, and contained structurally normal chloroplasts that were able to efficiently import the Rubisco small subunit precursor (prSS) in vitro. The absence of an obvious ppi3 phenotype in green tissues presumably reflects the ability of atToc33 to substitute for atToc34 in the mutant, and the relatively high level of expression of the atTOC33 gene in these tissues. In the roots, where atTOC33 is expressed at a much lower level, significant growth defects were observed in both mutants: ppi3 roots were approximately 20-30% shorter than wild-type roots. Attempts to identify a double homozygote lacking atToc34 and atToc33 (by crossing the ppi3 mutants with ppi1, an atToc33 knockout mutant) were unsuccessful, indicating that the function provided by atToc33/atToc34 is essential during early development. Plants that were homozygous for ppi1 and heterozygous for ppi3 displayed a chlorotic phenotype much more severe than that of the ppi1 single mutant. Furthermore, the siliques of these plants contained approximately 25% aborted seeds, indicating that the double homozygous mutation is embryo lethal. The data demonstrate that atToc33/atToc34 performs a central and essential role during plastid protein import, and indicate that the atToc34 isoform is relatively more important for plastid biogenesis in roots. AD - MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. FAU - Constan, Diane AU - Constan D FAU - Patel, Ramesh AU - Patel R FAU - Keegstra, Kenneth AU - Keegstra K FAU - Jarvis, Paul AU - Jarvis P LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02024.x [doi] AID - TPJ2024 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):93-106. PMID- 15053761 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - Interallelic complementation at the Arabidopsis CRE1 locus uncovers independent pathways for the proliferation of vascular initials and canonical cytokinin signalling. PG - 70-9 AB - Summary The differentiation of vascular tissue plays a central role in root architecture and its functionality. Regardless of its importance, the molecular mechanisms involved in the inception of vascular morphogenesis and their interaction with hormones are only now beginning to be understood. The characterisation of the WOODEN LEG (wol/cre1 mutant), impaired in procambial cell proliferation and the identification of WOL/CRE1 as a cytokinin receptor, provided the first genetic evidence pointing to a role of cytokinins in the formation of vascular initials. However, the striking wol phenotype in vascular differentiation is unique among all the available cre1 alleles collection. In this work, we identified a mutant with identical deficiencies in vascular differentiation as wol. Complementation analysis revealed that this mutant rescued the wol short-root phenotype. However, genetic characterisation of the mutant showed that the mutation was located at the CRE1 locus, indicating that both alleles displayed interallelic complementation. Trans-heterozygotes characterisation showed that these plants fully restored the deficiency in vascular differentiation but not the canonical cytokinin signalling. Furthermore, we show that, as measured in root growth inhibition, calli regeneration assays and northern analysis, the original wol allele is in fact more sensitive to cytokinins than the trans-heterozygous plants, or some cre1 alleles showing wild-type vascular morphogenesis. Thus, there is no strict correlation between the phenotype in vascular differentiation displayed by the cre1/wol alleles and canonical cytokinin signalling. These results indicate that at least partially independent regulatory circuits may operate in procambial cell proliferation and in cytokinin responsiveness exerted through the CRE1 receptor. AD - Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia, Campus de la Universidad Autonoma de Madrid Cantoblanco, 28049 Madrid, Spain. FAU - De Leon, Berenice Garcia-Ponce AU - De Leon BG FAU - Zorrilla, Jose Manuel Franco AU - Zorrilla JM FAU - Rubio, Vicente AU - Rubio V FAU - Dahiya, Preeti AU - Dahiya P FAU - Paz-Ares, Javier AU - Paz-Ares J FAU - Leyva, Antonio AU - Leyva A LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02023.x [doi] AID - TPJ2023 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):70-9. PMID- 15053760 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - Genome stability of vtc1, tt4, and tt5 Arabidopsis thaliana mutants impaired in protection against oxidative stress. PG - 60-9 AB - Summary Reactive oxygen species (ROS) are formed upon normal cellular metabolism or influence of environmental factors and, at normal levels, they play an important physiological role. However, at elevated levels, radicals are toxic and extremely dangerous to all cellular components, including DNA. To efficiently protect themselves, plants have developed sophisticated mechanisms for radical screening and scavenging. In this paper, we analyzed the genome stability of several plant mutants impaired in the protection against free radicals. We crossed the well-known uidA recombination reporter line 651 to flavonoid (tt4 and tt5) and Vitamin C (vtc1)-deficient plants. We found that in all lines tested, both spontaneous and induced (UVC and Rose Bengal (RB)) recombination was higher than in the original 651 parental line. The mRNA expression levels of various DNA repair (RAD1, RAD54-like, MSH3) as well as radical scavenging genes (GPx1, CAT, FSD3) exhibited substantial differences in both control and induced conditions. Our data show that plants impaired in certain aspects of the protection against elevated levels of free radicals induce the production of scavenging enzymes earlier than wild-type (wt) plants, and the higher level of radical species results in the increased incidence of spontaneous double-strand breaks resulting in a higher expression of DNA repair genes. AD - Department of Biological Sciences, University of Lethbridge, Lethbridge, Alta, Canada T1K 3M4. FAU - Filkowski, Jody AU - Filkowski J FAU - Kovalchuk, Olga AU - Kovalchuk O FAU - Kovalchuk, Igor AU - Kovalchuk I LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02020.x [doi] AID - TPJ2020 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):60-9. PMID- 15053758 OWN - NLM STAT- in-data-review DA - 20040331 IS - 0960-7412 VI - 38 IP - 1 DP - 2004 Apr TI - Organellar gene transcription and early seedling development are affected in the rpoT;2 mutant of Arabidopsis. PG - 38-48 AB - Summary An Arabidopsis mutant that exhibited reduced root length was isolated from a population of activation-tagged T-DNA insertion lines in a screen for aberrant root growth. This mutant also exhibited reduced hypocotyl length as well as a delay in greening and altered leaf shape. Molecular genetic analysis of the mutant indicated a single T-DNA insertion in the gene RpoT;2 encoding a homolog of the phage-type RNA polymerase (RNAP), that is targeted to both mitochondria and plastids. A second T-DNA-tagged allele also showed a similar phenotype. The mutation in RpoT;2 affected the light-induced accumulation of several plastid mRNAs and proteins and resulted in a lower photosynthetic efficiency. In contrast to the alterations in the plastid gene expression, no major effect of the rpoT;2 mutation on the accumulation of examined mitochondrial gene transcripts and proteins was observed. The rpoT;2 mutant exhibited tissue-specific alterations in the transcript levels of two other organelle-directed nuclear-encoded RNAPs, RpoT;1 and RpoT;3. This suggests the existence of cross-talk between the regulatory pathways of the three RNAPs through organelle to nucleus communication. These data provide an important information on a role of RpoT;2 in plastid gene expression and early plant development. AD - Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden. FAU - Baba, Kyoko AU - Baba K FAU - Schmidt, Julien AU - Schmidt J FAU - Espinosa-Ruiz, Ana AU - Espinosa-Ruiz A FAU - Villarejo, Arsenio AU - Villarejo A FAU - Shiina, Takashi AU - Shiina T FAU - Gardestrom, Per AU - Gardestrom P FAU - Sane, Aniruddha P AU - Sane AP FAU - Bhalerao, Rishikesh P AU - Bhalerao RP LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/04/01 05:00 MHDA- 2004/04/01 05:00 AID - 10.1111/j.1365-313X.2004.02022.x [doi] AID - TPJ2022 [pii] PST - ppublish SO - Plant J 2004 Apr;38(1):38-48. PMID- 15052571 OWN - NLM STAT- in-process DA - 20040330 IS - 0951-4198 VI - 18 IP - 6 DP - 2004 TI - Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins. PG - 643-50 AB - Recently, multidimensional shotgun proteomics has proven to be an alternative technology able to identify hundreds of proteins from single samples. Two major limitations of the technology are the presence of high abundance proteins (e.g. RUBISCO in plant leaf tissue) and the enormous number of co-eluting peptides that overstrain the loading and resolving capacity of conventional particle-packed columns as well as the capacity of electrospray ionisation due to ion suppression. Here, the coupling of fast performance liquid chromatography (FPLC) pre-fractionation of an Arabidopsis leaf protein extract and subsequent two-dimensional liquid chromatography/mass spectrometry with improved resolution using a monolithic silica C18 capillary column allowed the identification of 1032 unique proteins in a single 4 mg total protein plant leaf tissue sample. The reassignment of peptide IDs to distinct FPLC protein fractions enhances the identification procedure, especially in the case of present protein isoforms. The proposed strategy is useful to detect proteins otherwise not seen in conventional multidimensional chromatography/mass spectrometry approaches. CI - Copyright 2004 John Wiley & Sons, Ltd. AD - Max-Planck-Institut fur Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany. FAU - Wienkoop, Stefanie AU - Wienkoop S FAU - Glinski, Mirko AU - Glinski M FAU - Tanaka, Nobuo AU - Tanaka N FAU - Tolstikov, Vladimir AU - Tolstikov V FAU - Fiehn, Oliver AU - Fiehn O FAU - Weckwerth, Wolfram AU - Weckwerth W LA - eng PT - Journal Article PL - England TA - Rapid Commun Mass Spectrom JID - 8802365 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 AID - 10.1002/rcm.1376 [doi] PST - ppublish SO - Rapid Commun Mass Spectrom 2004;18(6):643-50. PMID- 15052565 OWN - NLM STAT- in-process DA - 20040330 IS - 0951-4198 VI - 18 IP - 7 DP - 2004 TI - Determination of brassinosteroids in the sub-femtomolar range using dansyl-3-aminophenylboronate derivatization and electrospray mass spectrometry. PG - 816-21 AB - A selective and sensitive electrospray ionization (ESI) mass spectrometry based method for detection of brassinosteroids (BS) in plant samples was developed. The limit of detection (LOD) was dramatically reduced over existing analytical methods using a microbore (1.00 mm) C18 column and chemical derivatization of free BS to dansyl-3-aminophenylboronates. The LOD in the selected-ion monitoring (SIM) mode for derivatized BS was 125 attomole (signal-to-noise ratio 3). The practical utility of the method is documented in Arabidopsis thaliana plant transformation of castasterone to brassinolide using a deuterium-labeled precursor. The method could be very useful for the detection of native BS in plant tissue and biosynthetic studies. CI - Copyright 2004 John Wiley & Sons, Ltd. AD - Max-Planck-Institute for Chemical Ecology, Hans-Knoll-Str. 8, D-07745 Jena, Germany. svatos@ice.mpg.de FAU - Svatos, Ales AU - Svatos A FAU - Antonchick, Andrey AU - Antonchick A FAU - Schneider, Bernd AU - Schneider B LA - eng PT - Journal Article PL - England TA - Rapid Commun Mass Spectrom JID - 8802365 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 AID - 10.1002/rcm.1413 [doi] PST - ppublish SO - Rapid Commun Mass Spectrom 2004;18(7):816-21. PMID- 15051881 OWN - NLM STAT- in-data-review DA - 20040407 IS - 0027-8424 VI - 101 IP - 14 DP - 2004 Apr 6 TI - Transcript profiling of early lateral root initiation. PG - 5146-51 AB - At the onset of lateral root initiation in Arabidopsis thaliana, the phytohormone auxin activates xylem pole pericycle cells for asymmetric cell division. However, the molecular events leading from auxin to lateral root initiation are poorly understood, in part because the few responsive cells in the process are embedded in the root and are thus difficult to access. A lateral root induction system, in which most xylem pole pericycle cells were synchronously activated by auxin transport inhibition followed by auxin application, was used for microarray transcript profiling. Of 4,600 genes analyzed, 906 significantly differentially regulated genes were identified that could be grouped into six major clusters. Basically, three major patterns were discerned representing induced, repressed, and transiently expressed genes. Analysis of the coregulated genes, which were specific for each time point, provided new insight into the molecular regulation and signal transduction preceding lateral root initiation in Arabidopsis. The reproducible expression profiles during a time course allowed us to define four stages that precede the cell division in the pericycle. These early stages were characterized by G(1) cell cycle block, auxin perception, and signal transduction, followed by progression over G(1)/S transition and G(2)/M transition. All these processes took place within 6 h after transfer from N-1-naphthylphthalamic acid to 1-naphthalene acetic acid. These results indicate that this lateral root induction system represents a unique synchronized system that allows the systematic study of the developmental program upstream of the cell cycle activation during lateral root initiation. AD - Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Ghent, Belgium. FAU - Himanen, Kristiina AU - Himanen K FAU - Vuylsteke, Marnik AU - Vuylsteke M FAU - Vanneste, Steffen AU - Vanneste S FAU - Vercruysse, Steven AU - Vercruysse S FAU - Boucheron, Elodie AU - Boucheron E FAU - Alard, Philippe AU - Alard P FAU - Chriqui, Dominique AU - Chriqui D FAU - Van Montagu, Marc AU - Van Montagu M FAU - Inze, Dirk AU - Inze D FAU - Beeckman, Tom AU - Beeckman T LA - eng PT - Journal Article DEP - 20040329 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2004/Mar/29 [aheadofprint] AID - 10.1073/pnas.0308702101 [doi] AID - 0308702101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Apr 6;101(14):5146-51. Epub 2004 Mar 29. PMID- 15051864 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The Arabidopsis cyclophilin gene family. PG - 1268-82 AB - Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness. AD - Robert Hill Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom. FAU - Romano, Patrick G N AU - Romano PG FAU - Horton, Peter AU - Horton P FAU - Gray, Julie E AU - Gray JE LA - eng PT - Journal Article DEP - 20040329 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2004/Mar/29 [aheadofprint] AID - 10.1104/pp.103.022160 [doi] AID - pp.103.022160 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1268-82. Epub 2004 Mar 29. PMID- 15051861 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Differential Expression of Vacuolar H+-ATPase Subunit c Genes in Tissues Active in Membrane Trafficking and Their Roles in Plant Growth as Revealed by RNAi. PG - 1514-26 AB - Acidification of intracellular compartments by the vacuolar-type H(+)-ATPases (VHA) is known to energize ion and metabolite transport, though cellular processes influenced by this activity are poorly understood. At least 26 VHA genes encode 12 subunits of the V(1)V(o)-ATPase complex in Arabidopsis, and how the expression, assembly, and activity of the pump are integrated into signaling networks that govern growth and adaptation are largely unknown. The role of multiple VHA-c genes encoding the 16-kD subunit of the membrane V(o) sector was investigated. Expression of VHA-c1, monitored by promoter-driven beta-glucuronidase (GUS) activity was responsive to light or dark in an organ-specific manner. VHA-c1 expression in expanding cotyledons, hypocotyls of etiolated seedlings, and elongation zone of roots supported a role for V-ATPase in cell enlargement. Mutants reduced in VHA-c1 transcript using dsRNA-mediated interference showed reduction in root growth relative to wild-type seedlings. In contrast, VHA-c3 promoter::GUS expression was undetectable in most organs of seedlings, but strong in the root cap. Interestingly, dsRNA-mediated mutants of vha-c3 also showed reduced root length and decreased tolerance to moderate salt stress. The results suggest that V-ATPase functions in the root cap influenced root growth. Expression of VHA-c1 and VHA-c3 in tissues with active membrane flow, including root cap, vascular strands, and floral style would support a model for participation of the V(o) sector and V(1)V(o)-ATPase in membrane trafficking and fusion. Two VHA-c genes are thus differentially expressed to support growth in expanding cells and to supply increased demand for V-ATPase in cells with active exocytosis. AD - Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742. FAU - Padmanaban, Senthilkumar AU - Padmanaban S FAU - Lin, Xiaoying AU - Lin X FAU - Perera, Imara AU - Perera I FAU - Kawamura, Yukio AU - Kawamura Y FAU - Sze, Heven AU - Sze H LA - eng PT - Journal Article DEP - 20040329 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2004/Mar/29 [aheadofprint] AID - 10.1104/pp.103.034025 [doi] AID - pp.103.034025 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1514-26. Epub 2004 Mar 29. PMID- 15051048 OWN - NLM STAT- in-data-review DA - 20040330 IS - 0981-9428 VI - 42 IP - 3 DP - 2004 Mar TI - Strong expression of the rice catalase gene CatB promoter in protoplasts and roots of both a monocot and dicots. PG - 241-9 AB - The rice (Oryza sativa L.) catalase (EC 1.11.1.6) gene CatB is expressed in roots and cultured cells. We examined the promoter activity of its 5'-flanking region in a monocot and in two dicots. Transient expression assays in rice Oc and tobacco BY-2 suspension cell protoplasts showed that CatB's 5'-flanking DNA fragments (nucleotides -1066 to +298) had about 20 and 3-4 times as much promoter activity, respectively, as the CaMV 35S promoter. Serial deletion analyses of the CatB promoter region revealed that the shortest fragment (-56 to +298) still had about 10 times as much promoter activity as the CaMV 35S promoter in rice protoplasts. In tobacco protoplasts, the activity of the fragment (-56 to +298) was about half of the CaMV 35S promoter. Transgenic rice and Arabidopsis plants carrying GUS genes driven by the 5'-truncated CatB promoters were generated and their GUS activity was examined. The region ranging from -329 to +298 showed preferential expression in the roots of rice and Arabidopsis, and in the shoot apical meristems of Arabidopsis. In situ hybridization revealed that CatB was highly expressed in branch root primordia and root apices of rice. Fusion of the GUS gene to the region (-329 to +298) conferred strong expression in these same areas, indicating that the presence of this region was sufficient to express CatB specifically in the roots. There may be new regulatory element(s) in this region, because it contained no previously known cis-regulatory elements specific for gene expression in roots. AD - Genome and Biodiversity Research Center, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan. FAU - Iwamoto, Masao AU - Iwamoto M FAU - Higo, Hiromi AU - Higo H FAU - Higo, Kenichi AU - Higo K LA - eng PT - Journal Article PL - France TA - Plant Physiol Biochem JID - 9882449 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2003/Jul/11 [received] PHST- 2004/Jan/30 [accepted] AID - 10.1016/j.plaphy.2004.01.008 [doi] AID - S098194280400018X [pii] PST - ppublish SO - Plant Physiol Biochem 2004 Mar;42(3):241-9. PMID- 15051046 OWN - NLM STAT- in-data-review DA - 20040330 IS - 0981-9428 VI - 42 IP - 3 DP - 2004 Mar TI - Effect of chlorophyll reduction in Arabidopsis thaliana by methyl jasmonate or norflurazon on antioxidant systems. PG - 225-31 AB - Methyl jasmonate (MeJA) and norflurazon (NF) treatments resulted in a substantial decrease in photosynthetic activities and chlorophylls (Chls) in Arabidopsis thaliana plants, causing a senescence-like yellowing and a bleaching in MeJA- and NF-treated plants, respectively. Non-radiative energy dissipation through q(N) and non-photochemical quenching increased greatly in NF-treated plants in concomitance with an increase in photoprotectants antheraxanthin and zeaxanthin from interconversion of violaxanthin, although they were not changed in MeJA-treated plants. A significant accumulation of anthocyanin was observed only in MeJA-treated plants, not in NF-treated plants. Total activities of catalase (CAT, EC 1.11.1.6), peroxidase (POD, EC 1.11.1.7), superoxide dismutase (EC 1.15.1.1) and glutathione reductase (EC 1.6.4.2) increased greatly in response to MeJA, particularly a 100-fold increase in POD activity 7 days after MeJA treatment. NF application to plants exhibited less increase in antioxidant enzymes than MeJA-treated plants. NF-treated young leaves had a greater decline in Chls and CAT activity, and less zeaxanthin accumulation compared to NF-treated mature leaves, indicating that NF-treated young leaves are more susceptible to excess light exposure and a possible photooxidative stress. Both MeJA- and NF-treated Arabidopsis plants suffered destruction of Chls, however, they developed differential antioxidant responses during the stress, in large part by an increased anthocyanin level in the epidermis and enzymatic antioxidants in MeJA-treated plants and by accumulation of antheraxanthin and zeaxanthin, and enhanced energy dissipation in NF-treated plants. AD - Department of Biotechnology, Biotechnology Research Institute, Chonnam National University, 300 Yongbong-dong, Puk-gu, Gwangju, 500-757, Republic of Korea. FAU - Jung, S AU - Jung S LA - eng PT - Journal Article PL - France TA - Plant Physiol Biochem JID - 9882449 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2003/Aug/07 [received] PHST- 2004/Jan/12 [accepted] AID - 10.1016/j.plaphy.2004.01.001 [doi] AID - S098194280400004X [pii] PST - ppublish SO - Plant Physiol Biochem 2004 Mar;42(3):225-31. PMID- 15051045 OWN - NLM STAT- in-data-review DA - 20040330 IS - 0981-9428 VI - 42 IP - 3 DP - 2004 Mar TI - Isolation of the gene encoding Carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis. PG - 215-23 AB - The Arabidopsis thaliana LEC1 gene regulates embryo morphology and seed maturation. For a better understanding of its function, we isolated a carrot (Daucus carota L. cv. US-Harumakigosun) counterpart of this gene, C-LEC1, from a cDNA library of carrot somatic embryos, since carrot is a better model plant for preparing large quantities of somatic embryos at the same developmental stage. The predicted amino acid sequence of C-LEC1 is similar to that of LEC1 and contains regions that are conserved in the heme-activated protein 3 (HAP3) subunit of plants, animals and microorganisms. C-LEC1 expression was detected in embryogenic cells, somatic embryos, and developing seeds. In situ hybridization analysis revealed C-LEC1 expression in the peripheral region of the embryos but not in the endosperm. Expression of C-LEC1 driven by Arabidopsis LEC1 promoter was able to complement the defects of the Arabidopsis lec1-1 mutant. These results suggest that C-LEC1 is a functional homolog of Arabidopsis LEC1, an important regulator of zygotic and somatic embryo development. AD - Gene Research Center, Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan. FAU - Yazawa, Katsumi AU - Yazawa K FAU - Takahata, Kiminori AU - Takahata K FAU - Kamada, Hiroshi AU - Kamada H LA - eng PT - Journal Article PL - France TA - Plant Physiol Biochem JID - 9882449 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2003/Sep/20 [received] PHST- 2003/Dec/10 [accepted] AID - 10.1016/j.plaphy.2003.12.003 [doi] AID - S0981942803002134 [pii] PST - ppublish SO - Plant Physiol Biochem 2004 Mar;42(3):215-23. PMID- 15051040 OWN - NLM STAT- in-data-review DA - 20040330 IS - 0981-9428 VI - 42 IP - 3 DP - 2004 Mar TI - A reciprocal translocation, induced by a canonical integration of a single T-DNA, interrupts the HMG-I/Y Arabidopsis thaliana gene. PG - 171-9 AB - Major chromosomal rearrangements occur during Arabidopsis thaliana T-DNA transformation. They generally result from interactions between multiple T-DNA copies during the integration process or from aborted integration events. We report here a reciprocal translocation associated with the integration of a single T-DNA which otherwise shows all the characteristic features of a canonical integration event. The exchanged fragments roughly correspond to half of the left arm of chromosome 1 and to two thirds of the right arm of chromosome 2. The chromosome 1 breakpoint maps close to position 23.6 cM and interrupts the coding sequence of the HMG-I/Y gene, which is present at a single copy in the Arabidopsis genome and encodes a non-histone chromosomal protein putatively involved in regulation of gene expression. The chromosome 2 breakpoint maps close to position 33.6 cM, and is located 419 bp upstream of a gene encoding a putative homeodomain transcription factor. Homozygotes for the translocation display a severe phenotype with major developmental abnormalities and total sterility, while heterozygotes are fertile, most of them showing a wild-type phenotype. Among the six possible unbalanced genotypic classes, four are entirely lethal while only a few individuals from the two others survive. Analysis of relations between phenotypes and genotypes strongly suggests that the major phenotypic alterations observed do not result from inactivation of the HMG-I/Y gene. AD - GEEM-BIOMOVE, Universite Blaise-Pascal, CNRS UMR 6547, 24, avenue des Landais, 63177 Aubiere cedex, France. FAU - Lafleuriel, Jacqueline AU - Lafleuriel J FAU - Degroote, Fabienne AU - Degroote F FAU - Depeiges, Annie AU - Depeiges A FAU - Picard, Georges AU - Picard G LA - eng PT - Journal Article PL - France TA - Plant Physiol Biochem JID - 9882449 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PHST- 2003/Oct/14 [received] PHST- 2004/Jan/19 [accepted] AID - 10.1016/j.plaphy.2004.01.003 [doi] AID - S0981942804000142 [pii] PST - ppublish SO - Plant Physiol Biochem 2004 Mar;42(3):171-9. PMID- 15049302 OWN - NLM STAT- in-process DA - 20040329 IS - 0168-9525 VI - 20 IP - 3 DP - 2004 Mar TI - Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene. PG - 116-22 AB - NBS-LRR genes are the major class of disease resistance genes in flowering plants, and are arranged as single genes and as clustered loci. The evolution of these genes has been investigated in Arabidopsis thaliana by combining data on their genomic organisation and position in phylogenetic trees. Tandem and segmental duplications distribute and separate NBS-LRR genes in the genome. It is, however, unclear by which mechanism(s) NBS-LRR genes from different clades are sampled into heterogeneous clusters. Once physically removed from their closest relatives, the NBS-LRR genes might adopt and preserve new specificities because they are less prone to sequence homogenization. AD - Abteilung fur Pflanzezuchtung und Ertragsphysiologie, Max-Planck-Instutut fur Zuchtungsforschung, Koln, Germany. leister@mpiz-koeln.mpg.de FAU - Leister, Dario AU - Leister D LA - eng PT - Journal Article PL - England TA - Trends Genet JID - 8507085 SB - IM EDAT- 2004/03/31 05:00 MHDA- 2004/03/31 05:00 PST - ppublish SO - Trends Genet 2004 Mar;20(3):116-22. PMID- 15048833 OWN - NLM STAT- in-process DA - 20040329 IS - 1097-0134 VI - 55 IP - 2 DP - 2004 May 1 TI - Characterization of Arabidopsis thaliana stellacyanin: a comparison with umecyanin. PG - 426-35 AB - The cupredoxin domain of a putative type 1 blue copper protein (BCB) from Arabidopsis thaliana was overexpressed and purified. A recursive polymerase chain reaction method was used to synthesize an artificial coding region for the cupredoxin domain of horseradish stellacyanin (commonly known as umecyanin), prior to overexpression and purification. The recombinant proteins were refolded from inclusion bodies and reconstituted with copper, and their in vitro characteristics were studied. Recombinant umecyanin, which is nonglycosylated, has identical spectroscopic and redox properties to the native protein. The UV/Vis and EPR spectra of recombinant BCB and umecyanin demonstrate that they have comparable axial type 1 copper binding sites. Paramagnetic (1)H NMR spectroscopy highlights the similarity between the active site architectures of BCB and umecyanin. The reduction potential of recombinant BCB is 252 mV, compared to 293 mV for recombinant umecyanin. Identical pK(a) values of 9.7 are obtained for the alkaline transitions in both proteins. This study demonstrates that BCB is the A. thaliana stellacyanin and the results form the biochemical basis for a discussion of BCB function in the model vascular plant. CI - Copyright 2004 Wiley-Liss, Inc. AD - School of Natural Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom. FAU - Harrison, Mark D AU - Harrison MD FAU - Dennison, Christopher AU - Dennison C LA - eng PT - Journal Article PL - United States TA - Proteins JID - 8700181 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 AID - 10.1002/prot.20017 [doi] PST - ppublish SO - Proteins 2004 May 1;55(2):426-35. PMID- 15047905 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis. PG - 1248-67 AB - Immunophilins are defined as receptors for immunosuppressive drugs including cyclosporin A, FK506, and rapamycin. The cyclosporin A receptors are referred to as cyclophilins (CYPs) and FK506- and rapamycin-binding proteins are abbreviated as FKBPs. These two groups of proteins (collectively called immunophilins) share little sequence homology, but both have peptidyl prolyl cis/trans isomerase (PPIase) activity that is involved in protein folding processes. Studies have identified immunophilins in all organisms examined including bacteria, fungi, animals, and plants. Nevertheless, the physiological function of immunophilins is poorly understood in any organism. In this study, we have surveyed the genes encoding immunophilins in Arabidopsis genome. A total of 52 genes have been found to encode putative immunophilins, among which 23 are putative FKBPs and 29 are putative CYPs. This is by far the largest immunophilin family identified in any organism. Both FKBPs and CYPs can be classified into single domain and multiple domain members. The single domain members contain a basic catalytic domain and some of them have signal sequences for targeting to a specific organelle. The multiple domain members contain not only the catalytic domain but also defined modules that are involved in protein-protein interaction or other functions. A striking feature of immunophilins in Arabidopsis is that a large fraction of FKBPs and CYPs are localized in the chloroplast, a possible explanation for why plants have a larger immunophilin family than animals. Parvulins represent another family of PPIases that are unrelated to immunophilins in protein sequences and drug binding properties. Three parvulin genes were found in Arabidopsis genome. The expression of many immunophilin and parvulin genes is ubiquitous except for those encoding chloroplast members that are often detected only in the green tissues. The large number of genes and diversity of structure domains and cellular localization make PPIases a versatile superfamily of proteins that clearly function in many cellular processes in plants. AD - Department of Plant and Microbial Biology, University of California, Berkeley, California 94720. FAU - He, Zengyong AU - He Z FAU - Li, Legong AU - Li L FAU - Luan, Sheng AU - Luan S LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.031005 [doi] AID - pp.103.031005 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1248-67. Epub 2004 Mar 26. PMID- 15047903 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Regulation of Flower Development in Arabidopsis by SCF Complexes. PG - 1574-85 AB - SCF complexes are the largest and best studied family of E3 ubiquitin protein ligases that facilitate the ubiquitylation of proteins targeted for degradation. The SCF core components Skp1, Cul1, and Rbx1 serve in multiple SCF complexes involving different substrate-specific F-box proteins that are involved in diverse processes including cell cycle and development. In Arabidopsis, mutations in the F-box gene UNUSUAL FLORAL ORGANS (UFO) result in a number of defects in flower development. However, functions of the core components Cul1 and Rbx1 in flower development are poorly understood. In this study we analyzed floral phenotypes caused by altering function of Cul1 or Rbx1, as well as the effects of mutations in ASK1 and ASK2. Plants homozygous for a point mutation in the AtCUL1 gene showed reduced floral organ number and several defects in each of the four whorls. Similarly, plants with reduced AtRbx1 expression due to RNA interference also exhibited floral morphological defects. In addition, compared to the ask1 mutant, plants homozygous for ask1 and heterozygous for ask2 displayed enhanced reduction of B function, as well as other novel defects of flower development, including carpelloid sepals and an inhibition of petal development. Genetic analyses demonstrate that AGAMOUS (AG) is required for the novel phenotypes observed in the first and second whorls. Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes. These results suggest that SCF complexes regulate several aspects of floral development in Arabidopsis. AD - Department of Biology and the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802. FAU - Ni, Weimin AU - Ni W FAU - Xie, Daoxin AU - Xie D FAU - Hobbie, Lawrence AU - Hobbie L FAU - Feng, Baomin AU - Feng B FAU - Zhao, Dazhong AU - Zhao D FAU - Akkara, Joseph AU - Akkara J FAU - Ma, Hong AU - Ma H LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.031971 [doi] AID - pp.103.031971 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1574-85. Epub 2004 Mar 26. PMID- 15047901 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. PG - 1683-96 AB - Within their natural habitat, plants are subjected to a combination of abiotic conditions that include stresses such as drought and heat. Drought and heat stress have been extensively studied; however, little is known about how their combination impacts plants. The response of Arabidopsis plants to a combination of drought and heat stress was found to be distinct from that of plants subjected to drought or heat stress. Transcriptome analysis of Arabidopsis plants subjected to a combination of drought and heat stress revealed a new pattern of defense response in plants that includes a partial combination of two multigene defense pathways (i.e. drought and heat stress), as well as 454 transcripts that are specifically expressed in plants during a combination of drought and heat stress. Metabolic profiling of plants subjected to drought, heat stress, or a combination of drought and heat stress revealed that plants subject to a combination of drought and heat stress accumulated sucrose and other sugars such as maltose and gulose. In contrast, Pro that accumulated in plants subjected to drought did not accumulate in plants during a combination of drought and heat stress. Heat stress was found to ameliorate the toxicity of Pro to cells, suggesting that during a combination of drought and heat stress sucrose replaces Pro in plants as the major osmoprotectant. Our results highlight the plasticity of the plant genome and demonstrate its ability to respond to complex environmental conditions that occur in the field. AD - Department of Biology, Technion, Israel Institute of Technology, Technion City, Haifa 32000, Israel. FAU - Rizhsky, Ludmila AU - Rizhsky L FAU - Liang, Hongjian AU - Liang H FAU - Shuman, Joel AU - Shuman J FAU - Shulaev, Vladimir AU - Shulaev V FAU - Davletova, Sholpan AU - Davletova S FAU - Mittler, Ron AU - Mittler R LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.033431 [doi] AID - pp.103.033431 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1683-96. Epub 2004 Mar 26. PMID- 15047898 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. PG - 1555-73 AB - Although numerous physiological studies have addressed the interactions between brassinosteroids and auxins, little is known about the underlying molecular mechanisms. Using an Affymetrix GeneChip representing approximately 8,300 Arabidopsis genes, we studied comprehensive transcript profiles over 24 h in response to indole-3-acetic acid (IAA) and brassinolide (BL). We identified 409 genes as BL inducible, 276 genes as IAA inducible, and 637 genes in total. These two hormones regulated only 48 genes in common, suggesting that most of the actions of each hormone are mediated by gene expression that is unique to each. IAA-up-regulated genes were enriched in genes regulated in common. They were induced quickly by IAA and more slowly by BL, suggesting divergent physiological roles. Many were early auxin-inducible genes and their homologs, namely SAUR, GH3, and IAA. The comprehensive comparison also identified IAA- and BL-specific genes, which should help to elucidate the specific actions of each hormone. The identified genes were classified using hierarchical clustering based on the similarity of their responses to the two hormones. Gene classification also allowed us to analyze the frequency of cis-elements. The TGTCTC element, a core element of the previously reported auxin response element, was not enriched in genes specifically regulated by IAA but was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL. Such gene classification should be useful for predicting the functions of unknown genes, to understand the roles of these two hormones, and the promoter analysis should provide insight into the interaction of transcriptional regulation by the two hormones. AD - Plant Science Center, RIKEN, Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan. FAU - Goda, Hideki AU - Goda H FAU - Sawa, Shinichiro AU - Sawa S FAU - Asami, Tadao AU - Asami T FAU - Fujioka, Shozo AU - Fujioka S FAU - Shimada, Yukihisa AU - Shimada Y FAU - Yoshida, Shigeo AU - Yoshida S LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.034736 [doi] AID - pp.103.034736 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1555-73. Epub 2004 Mar 26. PMID- 15047896 OWN - NLM STAT- publisher DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The Effect of {alpha}-Amanitin on the Arabidopsis Seed Proteome Highlights the Distinct Roles of Stored and Neosynthesized mRNAs during Germination. PG - 1598-1613 AB - To investigate the role of stored and neosynthesized mRNAs in seed germination, we examined the effect of alpha-amanitin, a transcriptional inhibitor targeting RNA polymerase II, on the germination of nondormant Arabidopsis seeds. We used transparent testa mutants, of which seed coat is highly permeable, to better ascertain that the drug can reach the embryo during seed imbibition. Even with the most permeable mutant (tt2-1), germination (radicle protrusion) occurred in the absence of transcription, while subsequent seedling growth was blocked. In contrast, germination was abolished in the presence of the translational inhibitor cycloheximide. Taken together, the results highlight the role of stored proteins and mRNAs for germination in Arabidopsis and show that in this species the potential for germination is largely programmed during the seed maturation process. The alpha-amanitin-resistant germination exhibited characteristic features. First, this germination was strongly slowed down, indicating that de novo transcription normally allows the synthesis of factor(s) activating the germination rate. Second, the sensitivity of germination to gibberellic acid was reduced 15-fold, confirming the role of this phytohormone in germination. Third, de novo synthesis of enzymes involved in reserve mobilization and resumption of metabolic activity was repressed, thus accounting for the failure in seedling establishment. Fourth, germinating seeds can recapitulate at least part of the seed maturation program, being capable of using mRNAs stored during development. Thus, commitment to germination and plant growth requires transcription of genes allowing the imbibed seed to discriminate between mRNAs to be utilized in germination and those to be destroyed. AD - Laboratoire Mixte Centre National de la Recherche Scientifique-Bayer CropScience, Bayer CropScience, F-69263 Lyon, France. AU - Rajjou L AU - Gallardo K AU - Debeaujon I AU - Vandekerckhove J AU - Job C AU - Job D LA - ENG PT - JOURNAL ARTICLE DEP - 20040326 TA - Plant Physiol JID - 0401224 EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.036293 [doi] AID - pp.103.036293 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1598-1613. Epub 2004 Mar 26. PMID- 15047895 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Brassinosteroids interact with auxin to promote lateral root development in Arabidopsis. PG - 1624-31 AB - Plant hormone brassinosteroids (BRs) and auxin exert some similar physiological effects likely through their functional interaction, but the mechanism for this interaction is unknown. In this study, we show that BRs are required for lateral root development in Arabidopsis and that BRs act synergistically with auxin to promte lateral root formation. BR perception is required for the transgenic expression of the beta-glucuronidase gene fused to a synthetic auxin-inducible promoter (DR5::GUS) in root tips, while exogenous BR promotes DR5::GUS expression in the root tips and the stele region proximal to the root tip. BR induction of both lateral root formation and DR5::GUS expression is suppressed by the auxin transport inhibitor N-(1-naphthyl) phthalamic acid. Importantly, BRs promote acropetal auxin transport (from the base to the tip) in the root. Our observations indicate that BRs regulate auxin transport, providing a novel mechanism for hormonal interactions in plants and supporting the hypothesis that BRs promote lateral root development by increasing acropetal auxin transport. AD - Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, California 92521. FAU - Bao, Fang AU - Bao F FAU - Shen, Junjiang AU - Shen J FAU - Brady, Shari R AU - Brady SR FAU - Muday, Gloria K AU - Muday GK FAU - Asami, Tadao AU - Asami T FAU - Yang, Zhenbiao AU - Yang Z LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.036897 [doi] AID - pp.103.036897 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1624-31. Epub 2004 Mar 26. PMID- 15047894 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - Mechanism of Gene Expression of Arabidopsis Glutathione S-Transferase, AtGST1, and AtGST11 in Response to Aluminum Stress. PG - 1672-82 AB - The gene expression of two Al-induced Arabidopsis glutathione S-transferase genes, AtGST1 and AtGST11, was analyzed to investigate the mechanism underlying the response to Al stress. An approximately 1-kb DNA fragment of the 5'-upstream region of each gene was fused to a beta-glucuronidase (GUS) reporter gene (pAtGST1::GUS and pAtGST11::GUS) and introduced into Arabidopsis ecotype Landsberg erecta. The constructed transgenic lines showed a time-dependent gene expression to a different degree in the root and/or leaf by Al stress. The pAtGST1::GUS gene was induced after a short Al treatment (maximum expression after a 2-h exposure), while the pAtGST11::GUS gene was induced by a longer Al treatment (approximately 8 h for maximum expression). Since the gene expression was observed in the leaf when only the root was exposed to Al stress, a signaling system between the root and shoot was suggested in Al stress. A GUS staining experiment using an adult transgenic line carrying the pAtGST11::GUS gene supported this suggestion. Furthermore, Al treatment simultaneously with various Ca depleted conditions in root region enhanced the gene expression of the pAtGST11::GUS in the shoot region. This result suggested that the degree of Al toxicity in the root reflects the gene response of pAtGST11::GUS in the shoot via the deduced signaling system. Both transgenic lines also showed an increase of GUS activity after cold stress, heat stress, metal toxicity, and oxidative damages, suggesting a common induction mechanism in response to the tested stresses including Al stress. AD - Research Institute for Bioresources, Okayama University, 2-20-1, Chuou, Kurashiki, Okayama 710-0046, Japan. FAU - Ezaki, Bunichi AU - Ezaki B FAU - Suzuki, Masakatsu AU - Suzuki M FAU - Motoda, Hirotoshi AU - Motoda H FAU - Kawamura, Masako AU - Kawamura M FAU - Nakashima, Susumu AU - Nakashima S FAU - Matsumoto, Hideaki AU - Matsumoto H LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.037135 [doi] AID - pp.103.037135 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1672-82. Epub 2004 Mar 26. PMID- 15047893 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - TOUSLED Kinase Activity Oscillates during the Cell Cycle and Interacts with Chromatin Regulators. PG - 1488-99 AB - The TOUSLED (TSL)-like nuclear protein kinase family is highly conserved in plants and animals. tsl loss of function mutations cause pleiotropic defects in both leaf and flower development, and growth and initiation of floral organ primordia is abnormal, suggesting that basic cellular processes are affected. TSL is more highly expressed in exponentially growing Arabidopsis culture cells than in stationary, nondividing cells. While its expression remains constant throughout the cell cycle in dividing cells, TSL kinase activity is higher in enriched late G2/M-phase and G1-phase populations of Arabidopsis suspension culture cells compared to those in S-phase. tsl mutants also display an aberrant pattern and increased expression levels of the mitotic cyclin gene CycB1;1, suggesting that TSL represses CycB1;1 expression at certain times during development or that cells are delayed in mitosis. TSL interacts with and phosphorylates one of two Arabidopsis homologs of the nucleosome assembly/silencing protein Asf1 and histone H3, as in humans, and a novel plant SANT/myb-domain protein, TKI1, suggesting that TSL plays a role in chromatin metabolism. AD - Program in Molecular, Cellular, and Developmental Biology, Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901. FAU - Ehsan, Hashimul AU - Ehsan H FAU - Reichheld, Jean-Philippe AU - Reichheld JP FAU - Durfee, Tim AU - Durfee T FAU - Roe, Judith L AU - Roe JL LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.038117 [doi] AID - pp.103.038117 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1488-99. Epub 2004 Mar 26. PMID- 15047892 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - The Immunophilin-Interacting Protein AtFIP37 from Arabidopsis Is Essential for Plant Development and Is Involved in Trichome Endoreduplication. PG - 1283-92 AB - The FKBP12 (FK506-binding protein 12 kD) immunophilin interacts with several protein partners in mammals and is a physiological regulator of the cell cycle. In Arabidopsis, only one specific partner of AtFKBP12, namely AtFIP37 (FKBP12 interacting protein 37 kD), has been identified but its function in plant development is not known. We present here the functional analysis of AtFIP37 in Arabidopsis. Knockout mutants of AtFIP37 show an embryo-lethal phenotype that is caused by a strong delay in endosperm development and embryo arrest. AtFIP37 promoter::beta-glucuronidase reporter gene constructs show that the gene is expressed during embryogenesis and throughout plant development, in undifferentiating cells such as meristem or embryonic cells as well as highly differentiating cells such as trichomes. A translational fusion with the enhanced yellow fluorescent protein indicates that AtFIP37 is a nuclear protein localized in multiple subnuclear foci that show a speckled distribution pattern. Overexpression of AtFIP37 in transgenic lines induces the formation of large trichome cells with up to six branches. These large trichomes have a DNA content up to 256C, implying that these cells have undergone extra rounds of endoreduplication. Altogether, these data show that AtFIP37 is critical for life in Arabidopsis and implies a role for AtFIP37 in the regulation of the cell cycle as shown for FKBP12 and TOR (target of rapamycin) in mammals. AD - Laboratoire Plastes et Differenciation Cellulaire, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5575, Universite Joseph Fourier, F-38041 Grenoble cedex 9, France. FAU - Vespa, Laurent AU - Vespa L FAU - Vachon, Gilles AU - Vachon G FAU - Berger, Frederic AU - Berger F FAU - Perazza, Daniel AU - Perazza D FAU - Faure, Jean-Denis AU - Faure JD FAU - Herzog, Michel AU - Herzog M LA - eng PT - Journal Article DEP - 20040326 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/26 [aheadofprint] AID - 10.1104/pp.103.028050 [doi] AID - pp.103.028050 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1283-92. Epub 2004 Mar 26. PMID- 15047884 OWN - NLM STAT- publisher DA - 20040329 IS - 0032-0781 VI - 45 IP - 3 DP - 2004 Mar 15 TI - A Combination of the Arabidopsis DREB1A Gene and Stress-Inducible rd29A Promoter Improved Drought- and Low-Temperature Stress Tolerance in Tobacco by Gene Transfer. PG - 346-350 AB - The transcription factor DREB1A/CBF3 specifically interacts with the dehydration responsive element (DRE/CRT) and induces expression of genes involved in environmental stress tolerance in ARABIDOPSIS: Overexpression of DREB1A improved drought- and low-temperature stress tolerance in tobacco. The stress-inducible rd29A promoter minimized the negative effects on the plant growth in tobacco. Furthermore, we detected overexpression of stress-inducible target genes of DREB1A in tobacco. These results indicate that a combination of the rd29A promoter and DREB1A is useful for improvement of various kinds of transgenic plants that are tolerant to environmental stress. AD - Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686 Japan Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Japan. AU - Kasuga M AU - Miura S AU - Shinozaki K AU - Yamaguchi-Shinozaki K LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell Physiol JID - 9430925 EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Mar 15;45(3):346-350. PMID- 15047883 OWN - NLM STAT- in-data-review DA - 20040329 IS - 0032-0781 VI - 45 IP - 3 DP - 2004 Mar TI - Induction of SULTR1;1 Sulfate Transporter in Arabidopsis Roots Involves Protein Phosphorylation/Dephosphorylation Circuit for Transcriptional Regulation. PG - 340-5 AB - SULTR1;1 high-affinity sulfate transporter is highly regulated by sulfur deficiency (-S) in the epidermis and cortex of Arabidopsis roots. The regulatory mechanism of SULTR1;1 expression was studied using inhibitors for transcription, translation, protein phosphorylation and dephosphorylation. The induction of SULTR1;1 mRNA during -S was blocked by the addition of actinomycin D in the medium, suggesting that SULTR1;1 is transcriptionally regulated. Cycloheximide repressed the -S induction of SULTR1;1, but enhanced the basal mRNA level of SULTR1;1 under sulfur replete (+S) condition. In addition, the induction of SULTR1;1 by -S was significantly blocked by okadaic acid (OKA) and calyculin A (CalyA). Regulation of SULTR1;1 was further confirmed in transgenic plants expressing green fluorescent protein (GFP) under the control of SULTR1;1 promoter. Accumulation of GFP during -S was dependent to SULTR1;1 promoter, and the effects of OKA and CalyA were reproducible in the SULTR1;1 promoter-GFP plants. These results suggested that the up-regulation of SULTR1;1 by -S requires protein phosphatase as an upstream regulatory factor. AD - RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan. FAU - Maruyama-Nakashita, Akiko AU - Maruyama-Nakashita A FAU - Nakamura, Yumiko AU - Nakamura Y FAU - Watanabe-Takahashi, Akiko AU - Watanabe-Takahashi A FAU - Yamaya, Tomoyuki AU - Yamaya T FAU - Takahashi, Hideki AU - Takahashi H LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Mar;45(3):340-5. PMID- 15047879 OWN - NLM STAT- publisher DA - 20040329 IS - 0032-0781 VI - 45 IP - 3 DP - 2004 Mar 15 TI - A Novel Subgroup of bZIP Proteins Functions as Transcriptional Activators in Hypoosmolarity-Responsive Expression of the ProDH Gene in Arabidopsis. PG - 309-317 AB - A 6-bp sequence, ACTCAT, acts as a cis-acting element involved in hypoosmolarity- and proline-responsive expression of an Arabidopsis proline dehydrogenase (ProDH) gene. Search of the database for plant cis-acting elements revealed that the ACTCAT sequence is similar to the GCN4 motif [ATGA(C/G)TCAT] that is recognized by bZIP transcription factors. To identify transcription factor(s) for regulation of ProDH, we examined whether Arabidopsis bZIPs function as transcription factors for the ACTCAT sequence. Transient expression analysis revealed that the four proteins in Group S bZIPs, AtbZIP11/ATB2, AtbZIP44, AtbZIP2/GBF5 and AtbZIP53, formed an ATB2 subgroup that activated expression of the GUS reporter gene driven by the ACTCAT sequence while other bZIPs and different families of plant transcription factors did not. The transactivation activity of the ATB2 subgroup was enhanced in a hypoosmotic condition. In a gel mobility shift assay, the recombinant proteins of the ATB2 subgroup specifically bound to the ACTCAT sequence. RNA gel blot analysis indicated that the expression of AtbZIP2/GBF5 and AtbZIP53, as well as that of ProDH, is induced by hypoosmolarity. Moreover, we showed that the sGFP::AtbZIP11/ATB2 fusion protein is localized in the nucleus. These results suggest that the ATB2 subgroup functions as a transcriptional activator for hypoosmolarity-inducible ProDH in ARABIDOPSIS: AD - Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686 Japan Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572 Japan Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan Plant Functional Genomics Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Japan. AU - Satoh R AU - Fujita Y AU - Nakashima K AU - Shinozaki K AU - Yamaguchi-Shinozaki K LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell Physiol JID - 9430925 EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Mar 15;45(3):309-317. PMID- 15047876 OWN - NLM STAT- publisher DA - 20040329 IS - 0032-0781 VI - 45 IP - 3 DP - 2004 Mar 15 TI - OsEIN2 is a Positive Component in Ethylene Signaling in Rice. PG - 281-289 AB - EIN2 is a central signal transducer in the ethylene-signaling pathway, and a unique membrane-anchored protein. By screening a cDNA library, we have isolated a cDNA clone (OsEIN2) that encodes the rice EIN2 homolog. The full-length ORF clone was obtained by reverse transcriptase-polymerase chain reaction. OsEIN2 shares significant amino acid sequence similarity with Arabidopsis EIN2 (57% similarity and 42% identity). Both the numbers and positions of introns and exons in the OsEIN2 and AtEIN2 coding regions are also conserved. To address whether this structural similarity is indicative of functional conservation of the corresponding proteins, we also generated transgenic lines expressing the antisense construct of OsEIN2. Those plants were stunted and shoot elongation was severely inhibited. Their phenotypes were similar to that found with wild-type rice seedlings that were treated with AgNO(3), an ethylene signal inhibitor. In the OsEIN2 antisense plants, the expression levels of two ethylene-responsive genes, SC129 and SC255, were decreased compared with the wild types. These results suggest that OsEIN2 is a positive component of the ethylene-signaling pathway in rice, just as AtEIN2 is in ARABIDOPSIS: Our antisense transgenic plants produced approximately 3.5 times more ethylene than the wild-type plants. Expression analysis of rice ACS and ACO genes showed that the transcript levels of OsACS1 and OsACO1 were elevated in the transgenic plants. AD - National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Korea Department of Biology, College of Science, Yonsei University, Seoul, 120-749 Korea. AU - Jun SH AU - Han MJ AU - Lee S AU - Seo YS AU - Kim WT AU - An G LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell Physiol JID - 9430925 EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Mar 15;45(3):281-289. PMID- 15047697 OWN - NLM STAT- publisher DA - 20040329 IS - 1083-351X DP - 2004 Mar 26 TI - Characterization of the yam tuber storage proteins from Dioscorea batatas exhibiting unique lectin activities. AB - Four major proteins designated DB1, DB2, DB3 and DB4 were isolated and characterized from the yam tubers, Dioscorea batatas. The ratios of their yields were 20:50:20:10. DB1 was a mannose-binding lectin (20 kDa) consisting of 10 kDa subunits. DB2 accounting for 50% of the total protein was the storage protein, commonly called dioscorins consisting of a 31 kDa subunit. DB3 was a maltose-binding lectin, having an apparent molecular mass of 120 kDa and composed of a 66 kDa subunit and two 31 kDa subuits (DB3S). The 66 kDa subunit was further composed of two 31 kDa subunits (DB3L) cross-linked by disulfide bonds. DB3L and DB3S (242 and 241 amino acid residues, respectively) were homologous with each other with 72% sequence identity. They showed a sequence homology to carbonic anhydrase from Arabidopsis thaliana with about 45% identity. DB3S had one intrachain disulfide bond located as Cys28-Cys187, whereas DB3L had one interchain disulfide bond (Cys40-Cys40 ) in addition to the intrachain disulfide bond (Cys28-Cys188) to form a 66 kDa subunit. DB1 and DB3 agglutinated rabbit erythrocytes at 2.7 ug/ml and 3.9 ug/ml, respectively. The 66 kDa subunit itself revealed the full hemagglutinating activity of DB3, indicating that DB3L but not DB3S was responsible for the activity. The hemagglutinatng activity of DB3 required Ca2+ ions and was exclusively inhibited by maltose and oligomaltoses, but not by D-glucose. DB3 could not be classified into none of known plant lectin families. DB4 was a chitinase. DB1, DB2, and DB3 did not show any carbonic anhydrase, amylase, or trypsin inhibitor activity. These results show that two of the four major proteins isolated from the yam tubers,Dioscorea batatas, have uniquelectin activities. AD - Graduate School of Life Sciences, Department of Biomolecular Science, Tohoku University, Sendai, Miyagi 981-8555. AU - Gaidamashvili M AU - Ohizumi Y AU - Iijima S AU - Takayama T AU - Ogawa T AU - Muramoto K LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 AID - 10.1074/jbc.M402139200 [doi] AID - M402139200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 26;. PMID- 15047186 OWN - NLM STAT- in-data-review DA - 20040329 IS - 0003-9861 VI - 424 IP - 2 DP - 2004 Apr 15 TI - Co-incorporation of heterologously expressed Arabidopsis cytochrome P450 and P450 reductase into soluble nanoscale lipid bilayers. PG - 141-53 AB - Heterologous expression of CYP73A5, an Arabidopsis cytochrome P450 monooxygenase, in baculovirus-infected insect cells yields correctly configured P450 detectable by reduced CO spectral analysis in microsomes and cell lysates. Co-expression of a housefly NADPH P450 reductase substantially increases the ability of this P450 to hydroxylate trans-cinnamic acid, its natural phenylpropanoid substrate. For development of high-throughput P450 substrate profiling procedures, membrane proteins derived from cells overexpressing CYP73A5 and/or NADPH P450 reductase were incorporated into soluble His(6)-tagged nanoscale lipid bilayers (Nanodiscs) using a simple self-assembly process. Biochemical characterizations of nickel affinity-purified and size-fractionated Nanodiscs indicate that CYP73A5 protein assembled into Nanodiscs in the absence of NADPH P450 reductase maintains its ability to bind its [Formula: see text] -cinnamic acid substrate. CYP73A5 protein co-assembled with P450 reductase into Nanodiscs hydroxylates [Formula: see text] -cinnamic acid using reduced pyridine nucleotide as an electron source. These data indicate that baculovirus-expressed P450s assembled in Nanodiscs can be used to define the chemical binding profiles and enzymatic activities of these monooxygenases. AD - Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. FAU - Duan, Hui AU - Duan H FAU - Civjan, Natanya R AU - Civjan NR FAU - Sligar, Stephen G AU - Sligar SG FAU - Schuler, Mary A AU - Schuler MA LA - eng PT - Journal Article PL - United States TA - Arch Biochem Biophys JID - 0372430 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2003/Dec/17 [received] PHST- 2004/Feb/03 [revised] AID - 10.1016/j.abb.2004.02.010 [doi] AID - S0003986104000633 [pii] PST - ppublish SO - Arch Biochem Biophys 2004 Apr 15;424(2):141-53. PMID- 15047141 OWN - NLM STAT- in-process DA - 20040329 IS - 0006-291X VI - 317 IP - 1 DP - 2004 Apr 23 TI - Rice octadecanoid pathway. PG - 1-15 AB - Plant jasmonic acid (JA) and structurally similar animal prostaglandins play pivotal roles in regulating cellular responses against environmental cues, including the innate immune response(s). In plants, JA and its immediate precursor 12-oxo-phytodienoic acid (OPDA) are synthesized by the octadecanoid pathway, which employs at least five enzymes (lipase, lipoxygenase, allene oxide synthase and cyclase, and OPDA reductase), in addition to the enzymes involved in the beta-oxidation steps. Genetic, molecular, and biochemical analyses have led to the identification of almost all the genes of the octadecanoid pathway in Arabidopsis--a model dicotyledonous plant. In this regard, rice (Oryza sativa L.)--an important socio-economic monocotyledonous model research plant--remains poorly characterized. Until now, no gene has been specifically associated with this pathway. It is therefore of utmost importance to identify, characterize, and assign the pathway specific genes in rice. In this review, we have surveyed the rice genome, extracted a large number of putative genes of the octadecanoid pathway, and discussed their relationship with the known pathway genes from other plant species. Moreover, the achievements made so far on the rice octadecanoid pathway have also been summarized to reflect the contribution of rice towards extending our knowledge on this critical pathway in plants. AD - Research Laboratory for Agricultural Biotechnology and Biochemistry, Kathmandu, Nepal. gkagrawal@onebox.com FAU - Agrawal, Ganesh K AU - Agrawal GK FAU - Tamogami, Shigeru AU - Tamogami S FAU - Han, Oksoo AU - Han O FAU - Iwahashi, Hitoshi AU - Iwahashi H FAU - Rakwal, Randeep AU - Rakwal R LA - eng PT - Journal Article PL - United States TA - Biochem Biophys Res Commun JID - 0372516 SB - IM EDAT- 2004/03/30 05:00 MHDA- 2004/03/30 05:00 PHST- 2004/Mar/01 [received] AID - 10.1016/j.bbrc.2004.03.020 [doi] AID - S0006291X04004917 [pii] PST - ppublish SO - Biochem Biophys Res Commun 2004 Apr 23;317(1):1-15. PMID- 15045671 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1435-8603 VI - 6 IP - 2 DP - 2004 Mar TI - Involvement of the Plasma Membrane Ca2+-ATPase in the Short-Term Response of Arabidopsis thaliana Cultured Cells to Oligogalacturonides. PG - 192-200 AB - Treatment of Arabidopsis thaliana cells with oligogalacturonides (OG) initiates a transient production of reactive oxygen species (ROS), the concentration of which in the medium peaks after about 20 min of treatment. The analysis of OG effects on Ca (2+) fluxes shows that OG influence both Ca (2+) influx and Ca (2+) efflux (measured as (45)Ca (2+) fluxes) in a complex way. During the first 10 - 15 min, OG stimulate Ca (2+) influx and decrease its efflux, while at successive times of treatment, OG cause an increase of Ca (2+) efflux and a slight decrease of its influx. Treatment with sub- micro M concentrations of eosin yellow (EY), which selectively inhibits the Ca (2+)-ATPase of plasma membrane (PM), completely prevents the OG-induced increase in Ca (2+) efflux. EY also suppresses the transient feature of OG-induced ROS accumulation, keeping the level of ROS in the medium high. The biochemical analysis of PM purified from OG-treated cells indicates that treatment with OG for 15 to 45 min induces a significant decrease in Ca (2+)-ATPase activation by exogenous calmodulin (CaM), and markedly increases the amount of CaM associated with the PM. During the same time span, OG do not influence the expression of At-ACA8, the main isoform of PM Ca (2+)-ATPase in suspension-cultured A. thaliana cells, and of CaM genes. Overall, the reported results demonstrate that the PM Ca (2+)-ATPase is involved in the response of plant cells to OG and is essential in regulation of the oxidative burst. AD - Istituto di Biofisica del CNR-Sezione di Milano, Dipartimento di Biologia, Universita degli Studi di Milano, Milano, Italy. giulia.romani@unimi.it FAU - Romani, G AU - Romani G FAU - Bonza, M C AU - Bonza MC FAU - Filippini, I AU - Filippini I FAU - Cerana, M AU - Cerana M FAU - Beffagna, N AU - Beffagna N FAU - De Michelis, M I AU - De Michelis MI LA - eng PT - Journal Article PL - Germany TA - Plant Biol (Stuttg) JID - 101148926 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 AID - 10.1055/s-2004-817848 [doi] PST - ppublish SO - Plant Biol (Stuttg) 2004 Mar;6(2):192-200. PMID- 15045669 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1435-8603 VI - 6 IP - 2 DP - 2004 Mar TI - Senescence-Related Gene Expression Profiles of Rosette Leaves of Arabidopsis thaliana: Leaf Age Versus Plant Age. PG - 178-83 AB - Senescence is a form of programmed cell death (PCD) which leads to the death of whole organs, e.g., leaves or flowers, and eventually to the death of entire plants. Like all forms of PCD, senescence is a highly regulated and energy consuming process. Senescence parameters, like protein content, chlorophyll content, expression of photosynthesis-associated genes or senescence-associated genes (SAGs), reveal that senescence occurs in old leaves derived from young plants (6 week old) as well as in young leaves derived from older plants (8 week old), indicating that it is governed by the actual age of the leaves. In order to analyse the differential gene expression profiles during leaf senescence, hybridizations of high-density genome arrays were performed with: i) individual leaves within the rosette of a 6-week-old plant and ii) leaves of the same position within the rosette but harvested from plants of different ages, ranging from 5 to 8 weeks. Cluster and genetree analyses, according to the expression pattern revealed that genes which are up-regulated with respect to the age of the entire plant, showed completely different expression profiles with respect to the age of the individual leaves within one rosette. This was observed even though the actual difference in leaf age was approximately the same. This indicates that gene expression appears to be governed by different parameters: i) the age of the individual leaf and ii) the age and developmental stage of the entire plant. AD - Centre of Molecular Biolology of Plants (ZMBP), University of Tubingen, Tubingen, Germany. ulrike.zentgraf@uni-tuebingen.de FAU - Zentgraf, U AU - Zentgraf U FAU - Jobst, J AU - Jobst J FAU - Kolb, D AU - Kolb D FAU - Rentsch, D AU - Rentsch D LA - eng PT - Journal Article PL - Germany TA - Plant Biol (Stuttg) JID - 101148926 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 AID - 10.1055/s-2004-815735 [doi] PST - ppublish SO - Plant Biol (Stuttg) 2004 Mar;6(2):178-83. PMID- 15045663 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1435-8603 VI - 6 IP - 2 DP - 2004 Mar TI - Geographic Distribution and Recombination of Genomic Fragments on the Short Arm of Chromosome 2 of Arabidopsis thaliana. PG - 128-39 AB - Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene ( approximately 1500 bp) and a non-coding region ( approximately 500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, pi, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform "Asian" and a more variable "European" haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between "Asian" and "European" haplotypes occurs where they meet. Especially in the "European" haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern. AD - Department of Taxonomy, Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany. schmuths@ipk-gatersleben.de FAU - Schmuths, H AU - Schmuths H FAU - Hoffmann, M H AU - Hoffmann MH FAU - Bachmann, K AU - Bachmann K LA - eng PT - Journal Article PL - Germany TA - Plant Biol (Stuttg) JID - 101148926 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 AID - 10.1055/s-2004-817837 [doi] PST - ppublish SO - Plant Biol (Stuttg) 2004 Mar;6(2):128-39. PMID- 15045661 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1435-8603 VI - 6 IP - 2 DP - 2004 Mar TI - Molecular evolution of the s locus controlling mating in the brassicaceae. PG - 109-18 AB - Flowering plants possess self-incompatibility (SI) mechanisms that promote outbreeding and thereby increase their genetic diversity. In the self-incompatible Brassicaceae, recognition and rejection of self-pollen is based on a receptor-ligand interaction between male and female SI determinants. A transmembrane receptor kinase ( S locus Receptor Kinase, SRK) determines the SI specificity in stigmatic cells, whereas a pollen coat-localized ligand ( S locus Cysteine-Rich, SCR) determines the SI specificity in pollen. During recent years, major advances have been made in the understanding of the molecular basis of self-pollen recognition by stigmatic cells. In this review, we will focus on evolutionary aspects of the SI system in Brassicaceae. We will describe how the study of the molecular aspect of SI, not only in the historical Brassica model but also in Arabidopsis species, has contributed to highlight certain aspects of evolution of SI in the Brassicaceae. AD - Reproduction et Developpement des Plantes, Ecole Normale Superieure de Lyon, UMR 5667 CNRS-INRA-ENSL-UCBI Lyon, Lyon, France. FAU - Fobis-Loisy, I AU - Fobis-Loisy I FAU - Miege, C AU - Miege C FAU - Gaude, T AU - Gaude T LA - eng PT - Journal Article PL - Germany TA - Plant Biol (Stuttg) JID - 101148926 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 AID - 10.1055/s-2004-817804 [doi] PST - ppublish SO - Plant Biol (Stuttg) 2004 Mar;6(2):109-18. PMID- 15044947 OWN - NLM STAT- in-data-review DA - 20040407 IS - 0261-4189 VI - 23 IP - 7 DP - 2004 Apr 7 TI - The Arabidopsis cytochrome P450 CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism. PG - 1647-56 AB - The hormonal action of abscisic acid (ABA) in plants is controlled by the precise balance between its biosynthesis and catabolism. In plants, ABA 8'-hydroxylation is thought to play a predominant role in ABA catabolism. ABA 8'-hydroxylase was shown to be a cytochrome P450 (P450); however, its corresponding gene had not been identified. Through phylogenetic and DNA microarray analyses during seed imbibition, the candidate genes for this enzyme were narrowed down from 272 Arabidopsis P450 genes. These candidate genes were functionally expressed in yeast to reveal that members of the CYP707A family, CYP707A1-CYP707A4, encode ABA 8'-hydroxylases. Expression analyses revealed that CYP707A2 is responsible for the rapid decrease in ABA level during seed imbibition. During drought stress conditions, all CYP707A genes were upregulated, and upon rehydration a significant increase in mRNA level was observed. Consistent with the expression analyses, cyp707a2 mutants exhibited hyperdormancy in seeds and accumulated six-fold greater ABA content than wild type. These results demonstrate that CYP707A family genes play a major regulatory role in controlling the level of ABA in plants. AD - Plant Science Center, RIKEN, Yokohama, Japan. FAU - Kushiro, Tetsuo AU - Kushiro T FAU - Okamoto, Masanori AU - Okamoto M FAU - Nakabayashi, Kazumi AU - Nakabayashi K FAU - Yamagishi, Kazutoshi AU - Yamagishi K FAU - Kitamura, Sayaka AU - Kitamura S FAU - Asami, Tadao AU - Asami T FAU - Hirai, Nobuhiro AU - Hirai N FAU - Koshiba, Tomokazu AU - Koshiba T FAU - Kamiya, Yuji AU - Kamiya Y FAU - Nambara, Eiji AU - Nambara E LA - eng PT - Journal Article DEP - 20040325 PL - England TA - EMBO J JID - 8208664 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2003/Sep/30 [received] PHST- 2004/Jan/09 [accepted] PHST- 2004/Mar/25 [aheadofprint] AID - 10.1038/sj.emboj.7600121 [doi] AID - 7600121 [pii] PST - ppublish SO - EMBO J 2004 Apr 7;23(7):1647-56. Epub 2004 Mar 25. PMID- 15044825 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1464-1801 VI - 6 IP - 2 DP - 2003 TI - [In Process Citation] PG - 67-75 AB - All the members of pyridoxal-5'-phosphate-dependent enzymes are involved in the metabolism of amino acids. The sequence homology studies further divide this family into three distinct groups. A fine scrutiny of the reactions catalyzed by these enzymes shows their regio specificity; they have been considered as the largest group of enzymes having tendency to affect the valency of the same carbon atom that carries the amino group forming an amine linkage with the coenzyme. Thus, this group was named 'alpha-class of enzymes'. Serine hydroxymethyltransferase (SHMT) is a member of this alpha-class; it reversibly catalyses the conversion of serine into glycine while the hydroxymethyl group is transferred to 5,6,7,8-tetrahydrofolate. The resultant compound is the sole precursor of purine biosynthesis. Henceforth, this enzyme greatly affects nucleic acid biosynthesis in all the organisms. It is obvious that SHMT plays an indispensable role in nucleic acid biosynthesis; therefore, designing and developing a repressor/inhibitor of the SHMT gene/protein may resolve the problem of drug resistance to cancer chemotherapy. SHMT has been widely studied in many living systems (e.g. Escherichia coli, humans, sheep, rabbits, Trypanosoma,Arabidopsis, peas, tobacco) in terms of its structure, cloning, expression, purification and folding patterns. Such studies have enabled one to assess the pattern of overall kinetic and activity behaviour of the enzyme, which may further help in developing a suitable cancer therapeutic molecule. CI - Copyright 2003 S. Karger AG, Basel AD - Department of Biotechnology, Institute of Engineering and Technology, Lucknow, India. FAU - Agrawal, Shipra AU - Agrawal S FAU - Kumar, Ajay AU - Kumar A FAU - Srivastava, Vivek AU - Srivastava V FAU - Mishra, B N AU - Mishra BN LA - eng PT - Journal Article PL - Switzerland TA - J Mol Microbiol Biotechnol JID - 100892561 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 AID - 10.1159/000076737 [doi] AID - MMB2003006002067 [pii] PST - ppublish SO - J Mol Microbiol Biotechnol 2003;6(2):67-75. PMID- 15044700 OWN - NLM STAT- in-data-review DA - 20040407 IS - 0027-8424 VI - 101 IP - 14 DP - 2004 Apr 6 TI - Oleic acid levels regulated by glycerolipid metabolism modulate defense gene expression in Arabidopsis. PG - 5152-7 AB - Stearoyl-acyl-carrier-protein-desaturase-mediated conversion of stearic acid (18:0) to oleic acid (18:1) is a key step, which regulates levels of unsaturated fatty acids in cells. We previously showed that stearoyl-acyl-carrier-protein-desaturase mutants ssi2/fab2 carrying a loss-of-function mutation in the plastidial glycerol-3-phosphate (G3P) acyltransferase (act1) have elevated 18:1 levels and are restored in their altered defense signaling. Because G3P is required for the acylation of 18:1 by G3P acyltransferase, it was predicted that reduction of G3P levels should increase 18:1 levels and thereby revert ssi2-triggered phenotypes. Here we show that a mutation in G3P dehydrogenase restores both salicylic acid- and jasmonic acid-mediated phenotypes of ssi2 plants. The G3P dehydrogenase gene was identified by map-based cloning of the ssi2 suppressor mutant rdc8 (gly1-3) and confirmed by epistatic analysis of ssi2 with gly1-1. Restoration of ssi2-triggered phenotypes by the gly1-3 mutation was age-dependent and correlated with the levels of 18:1. Regeneration of G3P pools by glycerol application in ssi2 and ssi2 gly1-3 plants caused a marked reduction in the 18:1 levels, which rendered these plants hypersensitive to glycerol. This hypersensitivity in ssi2 was rescued by the act1 mutation. Furthermore, overexpression of the ACT1 gene resulted in enhanced sensitivity to glycerol. Glycerol application also lowered the 18:1 content in SSI2 plants and converted these into ssi2-mimics. Our results show that 18:1 levels in plastids are regulated by means of acylation with G3P, and a balance between G3P and 18:1 is critical for the regulation of salicylic acid- and jasmonic acid-mediated signaling pathways. AD - Departments of Plant Pathology and Agronomy and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546. FAU - Kachroo, Aardra AU - Kachroo A FAU - Venugopal, Srivathsa C AU - Venugopal SC FAU - Lapchyk, Ludmila AU - Lapchyk L FAU - Falcone, Deane AU - Falcone D FAU - Hildebrand, David AU - Hildebrand D FAU - Kachroo, Pradeep AU - Kachroo P LA - eng PT - Journal Article DEP - 20040325 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2004/Mar/25 [aheadofprint] AID - 10.1073/pnas.0401315101 [doi] AID - 0401315101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Apr 6;101(14):5152-7. Epub 2004 Mar 25. PMID- 15044686 OWN - NLM STAT- in-data-review DA - 20040407 IS - 0027-8424 VI - 101 IP - 14 DP - 2004 Apr 6 TI - Enhancement of folates in plants through metabolic engineering. PG - 5158-63 AB - Humans depend on plants as a major source of dietary folates. Inadequate dietary levels of the vitamin folate can lead to megaloblastic anemia, birth defects, impaired cognitive development, and increased risk of cardiovascular disease and cancer. The biofortification of folate levels in food crops is a target for metabolic engineering. Folates are synthesized de novo from pterins and para-amino benzoic acid, which are subsequently combined to form dihydropteroate, the direct precursor to dihydrofolate. We postulated that GTP cyclohydrolase-1, which catalyzes the first committed step in pterin biosynthesis, was a rate-limiting step in pterin synthesis in plants and, therefore, in folate synthesis. On this basis, we proposed that the expression of an unregulated bacterial GTP cyclohydrolase-1 in plants would increase pterin biosynthesis with a concomitant enhancement of folate levels. The folE gene encoding GTP cyclohydrolase-1 was cloned from Escherichia coli and introduced into Arabidopsis thaliana through plant transformation. The expression of bacterial GTP cyclohydrolase-1 in transgenic Arabidopsis resulted in a 1,250-fold and 2- to 4-fold enhancement of pterins and folates, respectively. These results helped to identify other potential factors regulating folate synthesis, suggesting ways to further enhance folate levels in food crops. AD - Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132. FAU - Hossain, Tahzeeba AU - Hossain T FAU - Rosenberg, Irwin AU - Rosenberg I FAU - Selhub, Jacob AU - Selhub J FAU - Kishore, Ganesh AU - Kishore G FAU - Beachy, Roger AU - Beachy R FAU - Schubert, Karel AU - Schubert K LA - eng PT - Journal Article DEP - 20040324 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2004/Mar/24 [aheadofprint] AID - 10.1073/pnas.0401342101 [doi] AID - 0401342101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Apr 6;101(14):5158-63. Epub 2004 Mar 24. PMID- 15044023 OWN - NLM STAT- in-process DA - 20040326 IS - 0014-5793 VI - 562 IP - 1-3 DP - 2004 Mar 26 TI - Effect of salt and osmotic stress upon expression of the ethylene receptor ETR1 in Arabidopsis thaliana. PG - 189-92 AB - In hormone perception, varying the concentrations of hormone, receptor, or downstream signaling elements can modulate signal transduction. Previous research has demonstrated that ethylene biosynthesis in plants is regulated by abiotic factors. Here we report that exposure of Arabidopsis plants to NaCl reduced expression of the ethylene receptor ETR1. The change in gene expression was reflected at the protein level based on immunoblot analysis. Further analysis supports a general effect of osmotic stress upon the expression level of ETR1. The reduction in ETR1 levels should cause increased sensitivity of the plant to ethylene. These results suggest that plant responses to abiotic stress are modulated by changes in the expression level of ethylene receptors. AD - Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, NH 03824, USA. FAU - Zhao, Xue-Chu AU - Zhao XC FAU - Schaller, G Eric AU - Schaller GE LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2004/Jan/27 [received] PHST- 2004/Feb/26 [revised] PHST- 2004/Feb/26 [accepted] AID - 10.1016/S0014-5793(04)00238-8 [doi] AID - S0014579304002388 [pii] PST - ppublish SO - FEBS Lett 2004 Mar 26;562(1-3):189-92. PMID- 15044016 OWN - NLM STAT- in-process DA - 20040326 IS - 0014-5793 VI - 562 IP - 1-3 DP - 2004 Mar 26 TI - Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis. PG - 147-54 AB - Trihelix DNA-binding factors (or GT factors) bind to GT elements found in the promoters of many plant genes. Although the binding specificity and the transcriptional activity of some members (e.g. GT-1 and GT-2) have been studied, the regulatory function of this family of transcription factors remains largely unknown. In this work, we have characterised a new GT factor, namely GT-3a, and a closely related member, GT-3b. We show that (1) they can form either homo- or heterodimers but do not interact with GT-1; (2) they are predominantly expressed in floral buds and roots; (3) GT-3a cannot bind to the binding sites of GT-1 or GT-2, but binds to the cab2 and rbcS-1A gene promoters via the 5'-GTTAC sequence, which has been previously shown to be the core of the Site 1 type of GT elements. These results suggest that GT-3a and GT-3b belong to a distinct subgroup of GT factors and that each subgroup of GT factors binds to a functionally distinct type of cis-acting GT elements. AD - Faculte des Sciences, Universite de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens, France. FAU - Ayadi, Mira AU - Ayadi M FAU - Delaporte, Virginie AU - Delaporte V FAU - Li, You-Fang AU - Li YF FAU - Zhou, Dao-Xiu AU - Zhou DX LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2004/Feb/04 [received] PHST- 2004/Feb/23 [revised] PHST- 2004/Feb/23 [accepted] AID - 10.1016/S0014-5793(04)00222-4 [doi] AID - S0014579304002224 [pii] PST - ppublish SO - FEBS Lett 2004 Mar 26;562(1-3):147-54. PMID- 15043846 OWN - NLM STAT- in-data-review DA - 20040326 IS - 1011-1344 VI - 74 IP - 1 DP - 2004 Mar 19 TI - Up-regulation by phytochrome A of the active protochlorophyllide, Pchlide(655), biosynthesis in dicots under far-red light. PG - 47-54 AB - It is well-documented that phytochrome A (phyA) down-regulates the synthesis of NADPH:protochlorophyllide (Pchlide) oxidoreductase and active Pchlide(655) under far-red light (FR). In this work, we demonstrate that phyA can up-regulate the synthesis of Pchlide(655) under FR as well and that its sign and extent depend on plant species and tissue. With the use of fluorescence spectroscopy, it was found that [Pchlide(655)] in the upper stems of FR-grown seedlings of pea and tobacco increased #10878;10-fold and much lower in cotyledons or leaves as compared with the dark-grown. In the upper stems of Arabidopsis and tomato, the positive effect of FR was low, 1.2- to 1.5-fold, and the negative effect of FR was seen in cotyledons. In stems of wild-type (WT) tobacco and its line overexpressing full-length oat phyA (FL), we observed gross stimulating effect of FR while in its line overexpressing N-terminally truncated (Delta7-69) oat phyA (NA) it was low. Because WT and FL comprise both native phyA forms, phyA [Formula: see text] and phyA [Formula: see text], while NA, only phyA [Formula: see text], the regulation under FR can be associated with phyA [Formula: see text], while phyA [Formula: see text] inhibits the action of phyA [Formula: see text]. In etiolated seedlings of the NA line, [Pchlide(655)] was much higher than in those of WT and FL suggesting that phyA [Formula: see text] may have relation to this enhancement. The regulation of Pchlide(633) in contrast to Pchlide(655) was positive independent of the plant species and tissue. AD - Biology Department of the M.V. Lomonosov Moscow State University, Moscow 119899, Russia. FAU - Sineshchekov, V AU - Sineshchekov V FAU - Belyaeva, O AU - Belyaeva O FAU - Sudnitsin, A AU - Sudnitsin A LA - eng PT - Journal Article PL - Switzerland TA - J Photochem Photobiol B JID - 8804966 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2003/Dec/01 [received] PHST- 2004/Feb/01 [revised] PHST- 2004/Feb/04 [accepted] AID - 10.1016/j.jphotobiol.2004.02.001 [doi] AID - S1011134404000211 [pii] PST - ppublish SO - J Photochem Photobiol B 2004 Mar 19;74(1):47-54. PMID- 15043816 OWN - NLM STAT- in-process DA - 20040326 IS - 0960-9822 VI - 14 IP - 6 DP - 2004 Mar 23 TI - Exon junction sequences as cryptic splice sites: implications for intron origin. PG - 505-9 AB - Introns are flanked by a partially conserved coding sequence that forms the immediate exon junction sequence following intron removal from pre-mRNA. Phylogenetic evidence indicates that these sequences have been targeted by numerous intron insertions during evolution, but little is known about this process. Here, we test the prediction that exon junction sequences were functional splice sites that existed in the coding sequence of genes prior to the insertion of introns. To do this, we experimentally identified nine cryptic splice sites within the coding sequence of actin genes from humans, Arabidopsis, and Physarum by inactivating their normal intron splice sites. We found that seven of these cryptic splice sites correspond exactly to the positions of exon junctions in actin genes from other species. Because actin genes are highly conserved, we could conclude that at least seven actin introns are flanked by cryptic splice sites, and from the phylogenetic evidence, we could also conclude that actin introns were inserted into these cryptic splice sites during evolution. Furthermore, our results indicate that these insertion events were dependent upon the splicing machinery. Because most introns are flanked by similar sequences, our results are likely to be of general relevance. AD - Institute of Reproductive and Developmental Biology, Hammersmith Campus, Imperial College London, London W12 ONN, England. FAU - Sadusky, Terrie AU - Sadusky T FAU - Newman, Andrew J AU - Newman AJ FAU - Dibb, Nicholas J AU - Dibb NJ LA - eng PT - Journal Article PL - England TA - Curr Biol JID - 9107782 SB - IM EDAT- 2004/03/27 05:00 MHDA- 2004/03/27 05:00 PHST- 2003/Dec/16 [received] PHST- 2004/Feb/02 [revised] PHST- 2004/Feb/02 [accepted] AID - 10.1016/j.cub.2004.02.063 [doi] AID - S0960982204001538 [pii] PST - ppublish SO - Curr Biol 2004 Mar 23;14(6):505-9. PMID- 15042411 OWN - NLM STAT- publisher DA - 20040325 IS - 0721-7714 DP - 2004 Mar 24 TI - A new tool for plant cell biology: in vivo antibody uptake in plant protoplasts. AB - We report on the in vivo uptake of antibodies into plant protoplasts. When protoplasts of sunflower, Arabidopsis or tobacco were incubated in vivo with an antibody, this antibody was detected by immunofluorescence in the cytoplasm and/or the nucleus, depending on the location of the target protein. Furthermore, when protoplasts were cultured in the presence of antibodies, specific effects were observed. Incubation with antibodies raised against p34(cdc2) led to a strong inhibition of the division rate, and a decrease in the average DNA content of protoplasts. With antibodies against HaWLIM1, a LIM domain protein of the CRP type, a negative effect on actin organisation was observed. We conclude that antibodies can penetrate plant protoplasts in vivo, and thus may be used as powerful tools for the study of protein function. AD - UMR CNRS/UPS 5546, BP 17 Auzeville, 31326, Castanet-Tolosan, France. AU - Briere C AU - Barthou H AU - Petitprez M LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell Rep JID - 9880970 EDAT- 2004/03/26 05:00 MHDA- 2004/03/26 05:00 AID - 10.1007/s00299-004-0788-9 [doi] PST - aheadofprint SO - Plant Cell Rep 2004 Mar 24;. PMID- 15040888 OWN - NLM STAT- in-process DA - 20040325 IS - 1001-0602 VI - 14 IP - 1 DP - 2004 Feb TI - DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments. PG - 34-45 AB - The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses. Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK), phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms. In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf, stem and flower tissues, and leaves from plants treated with various hormones (auxin, cytokinin, gibberellin, abscisic acid and brassinosteroid) or environmental factors (temperature, calcium, sodium, drought, salicylic acid and jasmonic acid). Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions. In particular, the different isoforms of each family were specifically expressed in many cases, suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses. AD - National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, China. FAU - Lin, Wen Hui AU - Lin WH FAU - Ye, Rui AU - Ye R FAU - Ma, Hui AU - Ma H FAU - Xu, Zhi Hong AU - Xu ZH FAU - Xue, Hong Wei AU - Xue HW LA - eng PT - Journal Article PL - China TA - Cell Res JID - 9425763 SB - IM EDAT- 2004/03/26 05:00 MHDA- 2004/03/26 05:00 PST - ppublish SO - Cell Res 2004 Feb;14(1):34-45. PMID- 15040885 OWN - NLM STAT- in-process DA - 20040325 IS - 1001-0602 VI - 14 IP - 1 DP - 2004 Feb TI - Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. PG - 8-15 AB - RAV1 is a novel DNA-binding protein with two distinct DNA-binding domains unique in higher plants, but its role in plant growth and development remains unknown. Using cDNA array, we found that transcription of RAV1 is down-regulated by epibrassinolide (epiBL) in Arabidopsis suspension cells. RNA gel blot analysis revealed that epiBL-regulated RAV1 transcription involves neither protein phosphorylation/dephosphorylation nor newly synthesized protein, and does not require the functional BRI1, suggesting that this regulation might be through a new BR signaling pathway. Overexpressing RAV1 in Arabidopsis results in a retardation of lateral root and rosette leaf development, and the underexpression causes an earlier flowering phenotype, implying that RAV1 may function as a negative regulatory component of growth and development. AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. FAU - Hu, Yu Xin AU - Hu YX FAU - Wang, Yong Xong AU - Wang YX FAU - Liu, Xin Fang AU - Liu XF FAU - Li, Jia Yang AU - Li JY LA - eng PT - Journal Article PL - China TA - Cell Res JID - 9425763 SB - IM EDAT- 2004/03/26 05:00 MHDA- 2004/03/26 05:00 PST - ppublish SO - Cell Res 2004 Feb;14(1):8-15. PMID- 15040446 OWN - NLM STAT- completed DA - 20040325 DCOM- 20040407 IS - 1471-0072 VI - 5 IP - 2 DP - 2004 Feb TI - The dynamin superfamily: universal membrane tubulation and fission molecules? PG - 133-47 AB - Dynamins are large GTPases that belong to a protein superfamily that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins. They are involved in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. With sequenced genomes from Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, yeast species and Arabidopsis thaliana, we now have a complete picture of the members of the dynamin superfamily from different organisms. Here, we review the superfamily of dynamins and their related proteins, and propose that a common mechanism leading to membrane tubulation and/or fission could encompass their many varied functions. AD - Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. gerrit@mrc-lmb.cam.ac.uk FAU - Praefcke, Gerrit J K AU - Praefcke GJ FAU - McMahon, Harvey T AU - McMahon HT LA - eng PT - Journal Article PT - Review PT - Review, Tutorial PL - England TA - Nat Rev Mol Cell Biol JID - 100962782 RN - 0 (Fungal Proteins) RN - 0 (Lipids) RN - 0 (Plant Proteins) RN - EC 3.6.1.50 (Dynamins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Membrane/*metabolism MH - Dynamins/classification/genetics/*metabolism MH - Fungal Proteins/genetics/metabolism MH - Human MH - Lipids/chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Multigene Family MH - Phylogeny MH - Plant Proteins/genetics/metabolism MH - Protein Conformation MH - Sequence Alignment RF - 145 EDAT- 2004/03/26 05:00 MHDA- 2004/04/08 05:00 PST - ppublish SO - Nat Rev Mol Cell Biol 2004 Feb;5(2):133-47. PMID- 15040443 OWN - NLM STAT- completed DA - 20040325 DCOM- 20040407 IS - 1471-0072 VI - 5 IP - 2 DP - 2004 Feb TI - Traffic jams affect plant development and signal transduction. PG - 100-9 AB - Analysis of the Arabidopsis thaliana endomembrane system has shown that plant cell viability depends on a properly functioning vacuole and intact vesicular trafficking. The endomembrane system is also essential for various aspects of plant development and signal transduction. In this review, we discuss examples of these newly discovered roles for the endomembrane system in plants, and new experimental approaches and technologies that are based on high-throughput screens, which combine chemical genetics and automated confocal microscopy. AD - Center for Plant Cell Biology, University of California, Riverside, California 92521, USA. msurpin@pop.ucr.edu FAU - Surpin, Marci AU - Surpin M FAU - Raikhel, Natasha AU - Raikhel N LA - eng PT - Journal Article PT - Review PT - Review, Tutorial PL - England TA - Nat Rev Mol Cell Biol JID - 100962782 RN - 0 (Auxins) RN - 0 (Membrane Proteins) RN - 0 (SNAP receptor) RN - 21293-29-8 (Abscisic Acid) SB - IM MH - Abscisic Acid/metabolism MH - Arabidopsis/*cytology/genetics/*growth & development MH - Autophagocytosis/physiology MH - Auxins/metabolism MH - Cell Division/physiology MH - Gravitropism/physiology MH - Immunity, Natural/physiology MH - Intracellular Membranes/*metabolism MH - Membrane Proteins/metabolism MH - Morphogenesis/genetics/physiology MH - Signal Transduction/*physiology MH - Support, U.S. Gov't, Non-P.H.S. MH - Transport Vesicles/metabolism MH - Vacuoles/metabolism RF - 106 EDAT- 2004/03/26 05:00 MHDA- 2004/04/08 05:00 PST - ppublish SO - Nat Rev Mol Cell Biol 2004 Feb;5(2):100-9. PMID- 15038836 OWN - NLM STAT- in-process DA - 20040416 IS - 1471-2148 VI - 4 IP - 1 DP - 2004 Mar 24 TI - A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry. PG - 10 AB - BACKGROUND: Plant natriuretic peptides (PNPs) are systemically mobile molecules that regulate homeostasis at nanomolar concentrations. PNPs are up-regulated under conditions of osmotic stress and PNP-dependent processes include changes in ion transport and increases of H2O uptake into protoplasts and whole tissue. PRESENTATION OF THE HYPOTHESIS: The bacterial citrus pathogen Xanthomonas axonopodis pv. Citri str. 306 contains a gene encoding a PNP-like protein. We hypothesise that this bacterial protein can alter plant cell homeostasis and thus is likely to represent an example of molecular mimicry that enables the pathogen to manipulate plant responses in order to bring about conditions favourable to the pathogen such as the induced plant tissue hyper-hydration seen in the wet edged lesions associated with Xanthomonas axonopodis infection. TESTING THE HYPOTHESIS: We found a Xanthomonas axonopodis PNP-like protein that shares significant sequence similarity and identical domain organisation with PNPs. We also observed a significant excess of conserved residues between the two proteins within the domain previously identified as being sufficient to induce biological activity. Structural modelling predicts identical six stranded double-psi beta barrel folds for both proteins thus supporting the hypothesis of similar modes of action. No significant similarity between the Xanthomonas axonopodis protein and other bacterial proteins from GenBank was found. Sequence similarity of the Xanthomonas axonopodis PNP-like protein with the Arabidopsis thaliana PNP (AtPNP-A), shared domain organisation and incongruent phylogeny suggest that the PNP-gene may have been acquired by the bacteria in an ancient lateral gene transfer event. Finally, activity of a recombinant Xanthomonas axonopodis protein in plant tissue and changes in symptoms induced by a Xanthomonas axonopodis mutant with a knocked-out PNP-like gene will be experimental proof of molecular mimicry. IMPLICATION OF THE HYPOTHESIS: If the hypothesis is true, it could at least in part explain why the citrus pathogen Xanthomonas campestris that does not contain a PNP-like gene produces dry corky lesions while the closely related Xanthomonas axonopodis forms lesions with wet edges. It also suggests that genes typically found in the host, horizontally transferred or heterologous, can help to explain aspects of the physiology of the host-pathogen interactions. AD - South African National Bioinformatics Institute, Private Bag X17, Bellville, 7535, South Africa. victoria@sanbi.ac.za FAU - Nembaware, Victoria AU - Nembaware V FAU - Seoighe, Cathal AU - Seoighe C FAU - Sayed, Muhammed AU - Sayed M FAU - Gehring, Chris AU - Gehring C LA - eng PT - Journal Article DEP - 20040324 PL - England TA - BMC Evol Biol JID - 100966975 SB - IM EDAT- 2004/03/25 05:00 MHDA- 2004/03/25 05:00 PHST- 2004/Jan/08 [received] PHST- 2004/Mar/24 [accepted] PHST- 2004/Mar/24 [aheadofprint] AID - 10.1186/1471-2148-4-10 [doi] AID - 1471-2148-4-10 [pii] PST - epublish SO - BMC Evol Biol 2004 Mar 24;4(1):10. PMID- 15037732 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. PG - 1021-34 AB - Histone acetylation and deacetylation are connected with transcriptional activation and silencing in many eukaryotic organisms. Gene families for enzymes that accomplish these modifications show a surprising multiplicity in sequence and expression levels, suggesting a high specificity for different targets. We show that mutations in Arabidopsis (Arabidopsis thaliana) HDA6, a putative class I histone deacetylase gene, result in loss of transcriptional silencing from several repetitive transgenic and endogenous templates. Surprisingly, total levels of histone H4 acetylation are only slightly affected, whereas significant hyperacetylation is restricted to the nucleolus organizer regions that contain the rDNA repeats. This switch coincides with an increase of histone 3 methylation at Lys residue 4, a modified DNA methylation pattern, and a concomitant decondensation of the chromatin. These results indicate that HDA6 might play a role in regulating activity of rRNA genes, and this control might be functionally linked to silencing of other repetitive templates and to its previously assigned role in RNA-directed DNA methylation. AD - Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland. aline.probst@bioveg.unige.ch FAU - Probst, Aline V AU - Probst AV FAU - Fagard, Mathilde AU - Fagard M FAU - Proux, Florence AU - Proux F FAU - Mourrain, Philippe AU - Mourrain P FAU - Boutet, Stephanie AU - Boutet S FAU - Earley, Keith AU - Earley K FAU - Lawrence, Richard J AU - Lawrence RJ FAU - Pikaard, Craig S AU - Pikaard CS FAU - Murfett, Jane AU - Murfett J FAU - Furner, Ian AU - Furner I FAU - Vaucheret, Herve AU - Vaucheret H FAU - Scheid, Ortrun Mittelsten AU - Scheid OM LA - eng GR - R01-GM60380/GM/NIGMS PT - Journal Article DEP - 20040322 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 PHST- 2004/Mar/22 [aheadofprint] AID - 10.1105/tpc.018754 [doi] AID - tpc.018754 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):1021-34. Epub 2004 Mar 22. PMID- 15037609 OWN - NLM STAT- publisher DA - 20040323 IS - 1083-351X DP - 2004 Mar 22 TI - Two exoribonucleases act sequentially to process mature 3' ends of atp9 mRNAs in arabidopsis mitochondria. AB - In plant mitochondria, transcription proceeds well beyond the region that will become mature 3' extremities of mRNAs and the mechanisms of 3' maturation are largely unknown. Here, we show the involvement of two exoribonucleases, AtmtPNPase and AtmtRNaseII, in the 3' processing of atp9 mRNAs in Arabidopsis thaliana mitochondria. Down-regulation of AtmtPNPase results in the accumulation of pre-transcripts of several times the sizes of mature atp9 mRNAs, indicating that 3' processing of these transcripts is performed mainly exonucleolytically by AtmtPNPase. This enzyme is however not sufficient to completely process atp9 mRNAs as upon down-regulation of another mitochondrial exoribonuclease, AtmtRNaseII, about half of atp9 transcripts exhibit short 3' nucleotidic extensions as compared with mature mRNAs. These short extensions can be efficiently removed by AtmtRNaseII in vitro. Taken together, these results show that 3' processing of atp9 mRNAs in Arabidopsis mitochondria is, at least, a two-step phenomenon. First, AtmtPNPase is involved in removing 3' extensions that may reach several kilobases. Second, AtmtRNaseII degrades short nucleotidic extensions to generate the mature 3' ends. AD - Institut de Biologie Molculaire des Plantes, Strasbourg 67084. AU - Perrin R AU - Meyer EH AU - Zaepfel M AU - Kim YJ AU - Mache R AU - Grienenberger JM AU - Gualberto JM AU - Gagliardi D LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 AID - 10.1074/jbc.M401182200 [doi] AID - M401182200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 22;. PMID- 15037505 OWN - NLM STAT- publisher DA - 20040323 IS - 1367-4803 DP - 2004 Mar 22 TI - Omic space: coordinate-based integration and analysis of genomic-phenomic interactions. AB - MOTIVATION: With the recent progress of genomics, various datasets of omic interactions describing network of omic elements, have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of datasets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic, metabolomic, phenomic, and other omic planes are defined by two orthogonal genomic-coordinate axes. RESULTS: We show that the omic space concept helps us to comprehensively assimilate biological findings into hypotheses or models combining higher order phenomena and lower order mechanisms, by demonstrating that a comprehensive ranking of correspondences among interactions in the space can be effectively used for estimating candidates of responsible gene pairs for epistatic interacting loci of tumor in mice. We also show that the omic space offers a convenient framework for database integration, by presenting a system named the "Genome <--> Phenome Superhighway" (GPS) which serves as a framework for integration and visualization of omic interactions based on omic spaces of some model species including Homo sapiens, Mus musculus, Caenorhabditis elegans, and Arabidopsis thaliana. AVAILABILITY: For the Genome<-->Phenome Superhighway web site, see http://omicspace.riken.jp/gps/. AD - Genomic Knowledge Base Research Team, Bioinformatics Group, Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. AU - Toyoda T AU - Wada A LA - ENG PT - JOURNAL ARTICLE TA - Bioinformatics JID - 9808944 EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 AID - 10.1093/bioinformatics/bth165 [doi] AID - bth165 [pii] PST - aheadofprint SO - Bioinformatics 2004 Mar 22;. PMID- 15037450 OWN - NLM STAT- publisher DA - 20040415 IS - 0305-7364 VI - 93 IP - 5 DP - 2004 May TI - Analysis of the Spatial Expression Pattern of Seven Kip Related Proteins (KRPs) in the Shoot Apex of Arabidopsis thaliana. PG - 575-580 AB - * Background and aims Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered in plants but their in planta function is as yet unclear. In this study the spatial expression of all seven KRP genes in shoot apices of Arabidopsis thaliana were compared.* Methods In situ hybridization analyses were performed on longitudinal sections of shoot apices from 2-month-old Arabidopsis plants. * Key Results The study provides evidence for different expression pattern groups. KRP1 and KRP2 expression is restricted to the endoreduplicating tissues. In contrast, KRP4 and KRP5 expression is mainly restricted to mitotically dividing cells. KRP3, KRP6 and KRP7 can be found in both mitotically dividing and endoreduplicating cells.* Conclusion The results suggest differential roles for the distinct KRPs. KRP1 and KRP2 might specifically be involved in the establishment of polyploidy. In contrast, KRP4 and KRP5 might be involved in regulating the progression through the mitotic cell cycle. KRP3, KRP6 and KRP7 might have a function in both types of cell cycle. AD - Laboratoire de Physiologie Vegetale, Universite de Liege, B22 Sart-Tilman, B-4000 Liege, Belgium. AU - Ormenese S AU - De Almeida Engler J AU - De Groodt R AU - De Veylder L AU - Inze D AU - Jacqmard A LA - ENG PT - JOURNAL ARTICLE DEP - 20040322 TA - Ann Bot (Lond) JID - 0372347 EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 PHST- 2004/Mar/22 [aheadofprint] AID - 10.1093/aob/mch077 [doi] AID - mch077 [pii] PST - ppublish SO - Ann Bot (Lond) 2004 May;93(5):575-580. Epub 2004 Mar 22. PMID- 15037448 OWN - NLM STAT- publisher DA - 20040415 IS - 0305-7364 VI - 93 IP - 5 DP - 2004 May TI - A Post-genomic Approach to Understanding Sphingolipid Metabolism in Arabidopsis thaliana. PG - 483-497 AB - * Aims To highlight the importance of sphingolipids and their metabolites in plant biology.* Scope The completion of the arabidopsis genome provides a platform for the identification and functional characterization of genes involved in sphingolipid biosynthesis. Using the yeast Saccharomyces cerevisiae as an experimental model, this review annotates arabidopsis open reading frames likely to be involved in sphingolipid metabolism. A number of these open reading frames have already been subject to functional characterization, though the majority still awaits investigation. Plant-specific aspects of sphingolipid biology (such as enhanced long chain base heterogeneity) are considered in the context of the emerging roles for these lipids in plant form and function.* Conclusions Arabidopsis provides an excellent genetic and post-genomic model for the characterization of the roles of sphingolipids in higher plants. AD - Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA. AU - Dunn TM AU - Lynch DV AU - Michaelson LV AU - Napier JA LA - ENG PT - JOURNAL ARTICLE DEP - 20040322 TA - Ann Bot (Lond) JID - 0372347 EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 PHST- 2004/Mar/22 [aheadofprint] AID - 10.1093/aob/mch071 [doi] AID - mch071 [pii] PST - ppublish SO - Ann Bot (Lond) 2004 May;93(5):483-497. Epub 2004 Mar 22. PMID- 15035986 OWN - NLM STAT- in-process DA - 20040323 IS - 0092-8674 VI - 116 IP - 6 DP - 2004 Mar 19 TI - Control of fruit patterning in Arabidopsis by INDEHISCENT. PG - 843-53 AB - The Arabidopsis seedpod opens through a spring-loaded mechanism known as pod shatter, which is essential for dispersal of the seeds. Here, we identify INDEHISCENT (IND), an atypical bHLH protein, that is necessary for fruit opening and is involved in patterning each of the three fruit cell types required for seed dispersal. Previous studies suggested that FRUITFULL (FUL), a member of the MADS-domain transcription factor family, is required for fruit growth since ful mutant fruit fail to undergo the dramatic enlargement that normally occurs after fertilization. Here we show, however, that FUL is not directly required for fruit elongation and instead is required to prevent ectopic activity of IND. Our molecular and genetic studies suggest a model for the regulatory interactions among the genes that control fruit development and the mechanism that results in the expression of IND in a narrow stripe of cells. AD - Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, Department 0116, La Jolla, CA 92093, USA. FAU - Liljegren, Sarah J AU - Liljegren SJ FAU - Roeder, Adrienne H K AU - Roeder AH FAU - Kempin, Sherry A AU - Kempin SA FAU - Gremski, Kristina AU - Gremski K FAU - Ostergaard, Lars AU - Ostergaard L FAU - Guimil, Sonia AU - Guimil S FAU - Reyes, Daengnoy K AU - Reyes DK FAU - Yanofsky, Martin F AU - Yanofsky MF LA - eng PT - Journal Article PL - United States TA - Cell JID - 0413066 SB - IM EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 PHST- 2003/Oct/10 [received] PHST- 2004/Feb/06 [revised] PHST- 2004/Feb/06 [accepted] AID - S009286740400217X [pii] PST - ppublish SO - Cell 2004 Mar 19;116(6):843-53. PMID- 15035984 OWN - NLM STAT- in-process DA - 20040323 IS - 0092-8674 VI - 116 IP - 6 DP - 2004 Mar 19 TI - The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification. PG - 817-29 AB - Polarization of the microtubule cytoskeleton during early oogenesis is required to specify the posterior of the Drosophila oocyte, which is essential for asymmetric mRNA localization during mid-oogenesis and for embryonic axis specification. The posterior determinant oskar mRNA is translationally silent until mid-oogenesis. We show that mutations in armitage and three components of the RNAi pathway disrupt oskar mRNA translational silencing, polarization of the microtubule cytoskeleton, and posterior localization of oskar mRNA. armitage encodes a homolog of SDE3, a presumptive RNA helicase involved in posttranscriptional gene silencing (RNAi) in Arabidopsis, and is required for RNAi in Drosophila ovaries. Armitage forms an asymmetric network associated with the polarized microtubule cytoskeleton and is concentrated with translationally silent oskar mRNA in the oocyte. We conclude that RNA silencing is essential for establishment of the cytoskeletal polarity that initiates embryonic axis specification and for translational control of oskar mRNA. AD - Program in Molecular Medicine and the Program in Cell Dynamics, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA. FAU - Cook, Heather A AU - Cook HA FAU - Koppetsch, Birgit S AU - Koppetsch BS FAU - Wu, Jing AU - Wu J FAU - Theurkauf, William E AU - Theurkauf WE LA - eng GR - T32 HD 07312/HD/NICHD PT - Journal Article PL - United States TA - Cell JID - 0413066 SB - IM EDAT- 2004/03/24 05:00 MHDA- 2004/03/24 05:00 PHST- 2003/Oct/03 [received] PHST- 2004/Feb/13 [revised] PHST- 2004/Feb/17 [accepted] AID - S0092867404002508 [pii] PST - ppublish SO - Cell 2004 Mar 19;116(6):817-29. PMID- 15034716 OWN - NLM STAT- publisher DA - 20040322 IS - 0032-0935 DP - 2004 Mar 19 TI - ERECTA is required for protection against heat-stress in the AS1/ AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. AB - In seed plants, formation of the adaxial-abaxial polarity is of primary importance in leaf patterning. Since Arabidopsis thaliana (L.) Heynh. genes ASYMMETRIC LEAVES1 ( AS1) and ASYMMETRIC LEAVES2 ( AS2) are key regulators in specifying adaxial leaf identity, and ERECTA is involved in the AS1/ AS2 pathway for regulating adaxial-abaxial polarity [L. Xu et al. (2003) Development 130:4097-4107], we studied the physiological functions of the ERECTA protein in plant development. We analyzed the effects of different environmental conditions on a special leaf structure in the as1 and as2 mutants. This structure, called the lotus-leaf, reflects a severe loss of adaxial-abaxial polarity in leaves. Higher concentrations of salt or other osmotic substance and lower temperature severely affected plant growth both in the wild type and the mutants, but did not affect lotus-leaf frequency in the as1 and as2 mutants. as1 and as2 mutants exhibited a very low lotus-leaf frequency at 22 degrees C, a temperature that favors Arabidopsis growth. The lotus-leaf frequency rose significantly with an increase in growth temperature, and only in plants that are in the erecta mutation background. These results suggest that ERECTA function is required for reducing plant sensitivity to heat stress during adaxial-abaxial polarity formation in leaves. AD - National Laboratory of Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China. AU - Qi Y AU - Sun Y AU - Xu L AU - Xu Y AU - Huang H LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1007/s00425-004-1248-z [doi] PST - aheadofprint SO - Planta 2004 Mar 19;. PMID- 15034145 OWN - NLM STAT- publisher DA - 20040322 IS - 1059-1524 DP - 2004 Mar 19 TI - Tissue-specific Expression and Dynamic Organization of SR Splicing Factors in Arabidopsis. AB - The organization of the premRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here we report on the expression, organization and dynamics of premRNA splicing factors (SR33, SR1/atSRp34 and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism. AD - Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724. AU - Fang Y AU - Hearn S AU - Spector DL LA - ENG PT - JOURNAL ARTICLE TA - Mol Biol Cell JID - 9201390 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1091/mbc.E04-02-0100 [doi] AID - E04-02-0100 [pii] PST - aheadofprint SO - Mol Biol Cell 2004 Mar 19;. PMID- 15033984 OWN - NLM STAT- publisher DA - 20040322 IS - 1083-351X DP - 2004 Mar 19 TI - OMTK1, a novel MAPKKK, channels oxidative stress signaling through direct MAPK interaction. AB - In common with other eukaryotes, plants utilize mitogen-activated protein kinase (MAPK) cascades to mediate responses to a wide variety of stimuli. In contrast to other eukaryotes, plants have an unusually large number of MAPK components, such as more than 20 MAPKs, 10 MAPK kinases (MAPKKs), and 60 MAPKK kinases (MAPKKKs) in Arabidopsis (1). Presently it is mostly unknown how MAPK signaling specificity is generated in plants. Here we have isolated OMTK1 (oxidative stress-activated MAP triple-kinase 1), a novel MAPKKK from alfalfa (Medicago sativa). In plant protoplasts, OMTK1 showed basal kinase activity and was found to induce cell death. Among a panel of hormones and stresses tested, only H2O2 was found to activate OMTK1. Out of four MAPKs, OMTK1 specifically activated MMK3 resulting in an increased cell death rate. Pull down analysis between recombinant proteins indicated that OMTK1 directly interacts with MMK3 and that OMTK1 and MMK3 are part of a protein complex in vivo. These results indicate that OMTK1 plays a MAPK scaffolding role and functions in activation of H2O2-induced cell death in plants. AD - University of Vienna, Institute of Microbiology and Genetics, Vienna A-1030. AU - Nakagami H AU - Kiegerl S AU - Hirt H LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1074/jbc.M312662200 [doi] AID - M312662200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 19;. PMID- 15033524 OWN - NLM STAT- in-data-review DA - 20040322 IS - 0378-1119 VI - 329 DP - 2004 Mar 31 TI - An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. PG - 11-6 AB - Proteins that form part of the chloroplast proteome can be identified by computational prediction of the N-terminal presequences (chloroplast transit peptides, cTPs) of their cytoplasmic precursor proteins. The accuracy of four different cTP predictors has been evaluated on a test set of 4500 proteins whose subcellular localization is known, and was found to be substantially lower than previously reported. A combination of cTP prediction programs was superior to any one of the predictors alone. This combination was employed to estimate the size and composition of the chloroplast proteomes of Arabidopsis and rice, and about 2,100 (Arabidopsis thaliana) and 4800 (Oryza sativa) different chloroplast proteins with a cTP are predicted to be encoded by their nuclear genomes. A subset of around 900 chloroplast proteins, predominantly derived from the cyanobacterial endosymbiont and with functions mostly related to metabolism, energy and transcription, is shared by the two species. This points to the existence of both conserved nucleus-encoded chloroplast proteins that are predominantly of prokaryotic origin, and a large fraction of taxon-specific chloroplast-targeted proteins, in flowering plants. AD - Abteilung fur Pflanzenzuchtung und Ertragsphysiologie, Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne Weg 10, D-50829 Cologne, Germany. FAU - Richly, Erik AU - Richly E FAU - Leister, Dario AU - Leister D LA - eng PT - Journal Article PL - Netherlands TA - Gene JID - 7706761 SB - IM EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 PHST- 2003/Dec/12 [received] PHST- 2004/Jan/08 [accepted] AID - 10.1016/j.gene.2004.01.008 [doi] AID - S0378111904000150 [pii] PST - ppublish SO - Gene 2004 Mar 31;329:11-6. PMID- 15032878 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 1 DP - 2004 Jan TI - The antioxidant status of photosynthesizing leaves under nutrient deficiency: redox regulation, gene expression and antioxidant activity in Arabidopsis thaliana. PG - 63-73 AB - Redox signals provide important information on plant metabolism during development and in dependence on environmental parameters and trigger compensatory responses and antioxidant defence. The aim of the study was to characterize the redox and antioxidant status of photosynthesizing leaves under N, P and S deficiency on a comparative basis. Therefore, redox signals, indicators of the cellular redox environment and parameters of antioxidant defence were determined and related to general growth parameters, namely (1) transcript levels of all chloroplast encoded genes; (2) ascorbate and glutathione; (3) activities of catalase (CAT) and ascorbate peroxidase (APX); and (4) transcript amounts of eight peroxiredoxins, three catalases and three ascorbate peroxidases. The results reveal distinct patterns of redox responses dependent on the type of nutrient deficiency. (1) Nitrogen deprivation caused up-regulation of psbA, psbC, petA, petG and clpP transcripts, down-regulation of psbG, psbK and ndhA, a five-fold increase in ascorbic acid, a severe drop in CAT and APX activities, although cat1 mRNA levels were increased in young and old leaves. (2) With the exception of psbA and psaJ transcripts, P-starvation induced a general trend to decreased mRNA abundance of plastome genes; ascorbate and glutathione levels were increased, as was the activity of APX and CAT. In accordance with that result, transcripts of all cat genes and stromal apx, as well as prxIIC, prxIID, were elevated under P deprivation. (3) Sulphur depletion increased transcripts of petA, petB, petD, petG, ndhJ and rpo-genes. mRNAs of psbG, psbK, atpA, atpB, atpE and atpF were decreased. Glutathione levels dropped to less than 25% of control, in parallel activities of APX were stimulated in young leaves. Transcripts of many antioxidant enzymes were unaltered or decreased, only cat2 mRNA was increased. It is concluded that N-, P- and S-nutrient deprivation trigger distinct redox changes and induce oxidative stress with a rather defined pattern in the context of nutrient-specific alterations in metabolism. AD - Biochemistry and Physiology of Plants, W5, University of Bielefeld, 33501 Bielefeld, Germany. AU - Kandlbinder A AU - Finkemeier I AU - Wormuth D AU - Hanitzsch M AU - Dietz KJ LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0272.x [doi] AID - PPL272 [pii] PST - ppublish SO - Physiol Plant 2004 Jan;120(1):63-73. PMID- 15032871 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 1 DP - 2004 Jan TI - Control of chloroplast redox by the IMMUTANS terminal oxidase. PG - 4-11 AB - Variegation mutants offer excellent opportunities to study interactions between the nucleus-cytoplasm, the chloroplast, and the mitochondrion. Variegation in the immutans (im) mutant of Arabidopsis is induced by a nuclear recessive gene and the extent of variegation can be modulated by light and temperature. Whereas the green sectors have morphologically normal chloroplasts, the white sectors are devoid of pigments and accumulate a colourless carotenoid, phytoene. The green sectors are hypothesized to arise from cells that have avoided irreversible photooxidative damage whereas the white sectors originate from cells that are photooxidized. Cloning of the IMMUTANS (IM) gene has revealed that IMMUTANS (IM) is a plastid homologue of the mitochondrial alternative oxidase. This finding suggested a model in which IM functions as a redox component of the phytoene desaturation pathway, which requires phytoene desaturase activity. Consistent with this idea, IM has quinol oxidase activity in vitro. Recent studies have revealed that IM plays a more global role in plastid metabolism. For example, it appears to be the elusive terminal oxidase of chlororespiration and also functions as a light stress protein. AD - Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, Iowa 50011, USA. AU - Aluru MR AU - Rodermel SR LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0217.x [doi] AID - PPL217 [pii] PST - ppublish SO - Physiol Plant 2004 Jan;120(1):4-11. PMID- 15032866 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 2 DP - 2004 Feb TI - Tissue-specific expression and developmental regulation of cytochrome b561 genes in Arabidopsis thaliana and Raphanus sativus. PG - 312-318 AB - Ascorbate (Asc) is an essential molecule in many aspects of development and stress responses in plants and animals. Cytochromes b561 (cyts b561) are tightly coupled to Asc homeostasis. These proteins are found in mammalian tissues, where they are involved in the regeneration of Asc, serving the synthesis of catecholamine neurotransmitters, and in intestinal iron reduction. Plant genomes encode homologous membrane-associated, Asc-reducible cyts b561. The expression of these proteins in plants, however, has so far not been studied. We have now examined the expression of two Arabidopsis thaliana cyt b561-encoding genes-Artb561-1 and Artb561-2-using relative-quantitative RT-PCR and in situ hybridization (ISH) techniques. The genes show overlapping and distinct tissue- and organ-specific expression patterns. Transcripts of both genes are found in leaf epidermal cells, and expression seems to correlate with leaf maturation and cessation of cell elongation. Both genes are also expressed in the epidermal cell layer of stems and roots in the L1 layer of the shoot apex, in the vascular system of leaves, stems and roots, and in the root pericycle. In addition, Artb561-1 is expressed in the root cap, whereas Artb561-2 mRNA is found in the epidermis of lateral roots, in the root meristem, and in unfertilized ovules. These observations provide important information for the elucidation of the physiological function of cyts b561 in plants. AD - Laboratory of Plant Physiology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. AU - Verelst W AU - Kapila J AU - De Almeida Engler J AU - Stone JM AU - Caubergs R AU - Asard H LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0235.x [doi] AID - PPL235 [pii] PST - ppublish SO - Physiol Plant 2004 Feb;120(2):312-318. PMID- 15032863 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 2 DP - 2004 Feb TI - Arsenic uptake, translocation and speciation in pho1 and pho2 mutants of Arabidopsis thaliana. PG - 280-286 AB - Arsenate [As (V)] is taken up by phosphate [P (V)] transporters in the plasma membrane of roots cells, but the translocation of As from roots to shoots is not well understood. Two mutants of Arabidopsis thaliana (L.) [(pho1, P deficient) and (pho2, P accumulator)], with defects in the regulation and translocation of P (V) from roots to shoots, were therefore used in this study to investigate uptake, translocation and speciation of As in roots and shoots of plants grown in soil or nutrient solution. The shoots of the pho2 mutant contained higher P concentrations, but similar or slightly higher As concentrations, in comparison with the wild type. In the pho1 mutant, the P concentration in the shoots was lower, and the As concentration was higher, in comparison with the wild type. Both pho2 and the wild type contained mainly As (III) in roots and shoot (67-90% of total As). Arsenic was likely to be translocated by a different pathway to P (V) in the pho2 and pho1 mutants. Therefore, it is suggested that As (III) is the main As species translocated from roots to shoots in Arabidopsis thaliana. AD - Soil Science and Plant Nutrition, School of Earth and Geographical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia. AU - Quaghebeur M AU - Rengel Z LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0240.x [doi] AID - PPL240 [pii] PST - ppublish SO - Physiol Plant 2004 Feb;120(2):280-286. PMID- 15032861 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 2 DP - 2004 Feb TI - Low-temperature-induced transmembrane potential changes in mesophyll cells of Arabidopsis thaliana, Helianthus annuus and Vicia faba. PG - 265-270 AB - Glass microelectrodes were inserted into mesophyll cells of intact leaves from higher plants: Arabidopsis thaliana, Helianthus annuus and Vicia faba var minor, and transient membrane potential changes were recorded in response to a sudden temperature drop. The cold-induced potential changes were unaffected by an anion channel inhibitor (anthracene-9-carboxylic acid) and potassium channel inhibitor (tetraethyl ammonium ion). Verapamil, a calcium channel inhibitor, caused significant suppression of the cold-induced potential changes. In the presence of calmoduline antagonists (trifluoperazine and N-6-aminohexyl-5-chloro-1-naphtalenesulphonamide), their amplitudes decreased and their durations were prolonged. Neomycin, which suppresses phospholipase C, also caused substantial inhibition of the amplitudes of the cold-induced potential changes. It is concluded that cold-evoked membrane potential changes are due to calcium influxes from both the apoplast and internal stores. AD - Department of Biophysics, Institute of Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland. AU - Krol E AU - Dziubinska H AU - Trebacz K LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0244.x [doi] AID - PPL244 [pii] PST - ppublish SO - Physiol Plant 2004 Feb;120(2):265-270. PMID- 15032858 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 2 DP - 2004 Feb TI - Growth and morphological responses to different UV wavebands in cucumber (Cucumis sativum) and other dicotyledonous seedlings. PG - 240-248 AB - We examined the influence of short-term exposure of different UV wavebands on the fine-scale kinetics of hypocotyl growth of dim red light-grown cucumbers (Cucumis sativus L.) and other selected dicotyledonous seedlings to evaluate: (1) whether responses induced by UV-B radiation (280-320 nm) are qualitatively different from those induced by UV-A (320-400 nm) radiation, and (2) whether different wavebands within the UV-B elicit different responses. Responses to brief (30 min) irradiations with 3 different UV wavebands all included transient inhibition of elongation during irradiation followed by wavelength specific responses. Irradiations with proportionally greater short wavelength UV-B (37% of UV-B between 280 and 300 nm) induced inhibition of hypocotyl elongation within 20 min of onset of irradiation, while UV-B including only wavelengths longer than 290 nm (and only 8% of UV-B between 290 and 300 nm) induced inhibition of hypocotyl elongation with a lag of 1-2 h. The response to short wavelength UV-B was persistent for at least 24 h, while the response to long wavelength UV-B lasted only 2-3 h. The UV-A treatment induced reductions in elongation rates of approximately 6-9 h following exposure followed by a continued decline in rates for the following 15-18 h. Short wavelength UV-B also induced positive phototropic curvature in both cucumber and Arabidopsis seedlings, and this response was present in nph-1 mutant Arabidopsis seedlings defective in normal blue light phototropism. Reciprocity was not found for the response to short wavelength UV-B. The short wavelength and long wavelength UV-B responses differed in dose-response relationships and both short wavelength responses (phototropic curvature and elongation inhibition) increased sharply at wavelengths below 300 nm. These results indicate that different photosensory processes are involved in mediating growth and morphological responses to short wavelength UV-B (280-300 nm), long wavelength UV-B (essentially 300-320 nm) and UV-A. The existence of two separate types of hypocotyl inhibition responses to UV-B, with one that depends on the intensity of the light source, provides alternate interpretations to findings in other studies of UV-B induced photomorphogenesis and may explain inconsistencies between action spectra for inhibition of stem growth. AD - Department of Biology, Trinity University, San Antonio TX 78212-7200, USA. AU - Shinkle JR AU - Atkins AK AU - Humphrey EE AU - Rodgers CW AU - Wheeler SL AU - Barnes PW LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0237.x [doi] AID - PPL237 [pii] PST - ppublish SO - Physiol Plant 2004 Feb;120(2):240-248. PMID- 15032850 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 2 DP - 2004 Feb TI - 14-3-3 proteins: regulation of signal-induced events. PG - 173-178 AB - The field of signal transduction has experienced a significant paradigm shift as a result of an increased understanding of the roles of 14-3-3 proteins. There are many cases where signal-induced phosphorylation itself may cause a change in protein function. This simple modification is, in fact, the primary basis of signal transduction events in many systems. There are a large and growing number of cases, however, where simple phosphorylation is not enough to effect a change in protein function. In these cases, the 14-3-3 proteins can be required to complete the change in function. Therefore signal transduction can be either the relatively simple process where phosphorylation alters target activity, or it can be a more complex, multistep process with the 14-3-3 proteins playing the major role of bringing the signal transduction event to completion. This makes 14-3-3-modulated signal transduction a more complicated process with additional avenues for regulation and variety. Adding further complexity to the process is the fact that 14-3-3 proteins are present as multigene families in most organisms (Aitken et al. Trends Biochem Sci 17: 498-501, 1992; Ferl Annu Rev Plant Physiol Plant Molecular Biology 47: 49-73, 1996), with each member of the family being differentially expressed in various tissues and with potentially differential affinity for various target proteins. This review focuses on the 14-3-3 family of Arabidopsis as a model for further developing understanding of the roles of the 14-3-3 proteins as modulators of signal transduction events in plants. The primary approaches to these questions are not unlike the approaches that would be used in the functional dissection of any multigene family, but the interpretation of these data will have wide implications since the 14-3-3 s physically interact with other protein families. AD - Program in Plant Molecular and Cellular Biology, Horticultural Sciences Department, University of Florida, Gainesville, FL 32601-0690, USA. AU - Ferl RJ LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0239.x [doi] AID - PPL239 [pii] PST - ppublish SO - Physiol Plant 2004 Feb;120(2):173-178. PMID- 15032847 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 3 DP - 2004 Mar TI - A new SBP-box gene BpSPL1 in silver birch (Betula pendula). PG - 491-500 AB - The SBP-box gene family represents a group of plant-specific genes encoding putative transcription factors. Thus far, SBP-domain protein binding sites have been found in the promoters of Arabidopsis APETALA1 and Antirrhinum SQUAMOSA. A putative SBP-domain binding element has been observed in the promoter of BpMADS5, a close homologue of Arabidopsis FRUITFULL in silver birch (Betula pendula). A novel SBP-box gene from birch named BpSPL1 has been cloned and characterized. The nucleotide sequence of BpSPL1 is similar to Antirrhinum SBP2 and Arabidopsis SPL3, apart from the unique finding that BpSPL1 does not contain an intron typical to all other known SBP-box genes studied thus far. According to Northern blot analysis, BpSPL1 is expressed in birch inflorescences as well as in shoots and leaves. Studies using electrophoretic mobility shift assay demonstrate that there are nuclear proteins in birch inflorescences which specifically bind to the SBP binding element of the promoter of BpMADS5. BpSPL1 expressed in Escherichia coli also specifically binds to this element. According to Southern blot analysis, there are at least two SBP-box genes in birch. The results suggest that SBP-box genes are involved in the regulation of flower development in birch. AD - Department of Biology, University of Joensuu. P.O.Box 111, FIN-80101 Joensuu, Finland. AU - Lannenpaa M AU - Janonen I AU - Holtta-Vuori M AU - Gardemeister M AU - Porali I AU - Sopanen T LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.00254.x [doi] AID - PPL254 [pii] PST - ppublish SO - Physiol Plant 2004 Mar;120(3):491-500. PMID- 15032825 OWN - NLM STAT- publisher DA - 20040322 IS - 0031-9317 VI - 120 IP - 4 DP - 2004 Apr TI - Cloning and characterization of cellulose synthase-like gene, PtrCSLD2 from developing xylem of aspen trees. PG - 631-641 AB - Genetic improvement of cell wall polymer synthesis in forest trees is one of the major goals of forest biotechnology that could possibly impact their end product utilization. Identification of genes involved in cell wall polymer biogenesis is essential for achieving this goal. Among various candidate cell wall-related genes, cellulose synthase-like D (CSLD) genes are intriguing due to their hitherto unknown functions in cell wall polymer synthesis but strong structural similarity with cellulose synthases (CesAs) involved in cellulose deposition. Little is known about CSLD genes from trees. In the present article PtrCSLD2, a first CSLD gene from an economically important tree, aspen (Populus tremuloides) is reported. PtrCSLD2 cDNA was isolated from an aspen xylem cDNA library and encodes a protein that shares 90% similarity with Arabidopsis AtCSLD3 protein involved in root hair tip growth. It is possible that xylem fibers that also grow by intrusive tip growth may need expression of PtrCSLD2 for controlling the length of xylem fibers, a wood quality trait of great economical importance. PtrCSLD2 protein has a N-terminal cysteine-rich putative zinc-binding domain; eight transmembrane domains; alternating conserved and hypervariable domains; and a processive glycosyltransferases signature, D, D, D, QXXRW; all similar to aspen CesA proteins. However, PtrCSLD2 shares only 43-48% overall identity with the known aspen CesAs suggesting its distinct functional role in cell wall polymer synthesis perhaps other than cellulose biosynthesis. Based on Southern analysis, the aspen CSLD gene family consists of at least three genes and this gene copy estimate is supported by phylogenetic analysis of available CSLDs from plants. Moreover, gene expression studies using RT-PCR and in situ mRNA hybridization showed that PtrCSLD2 is expressed at a low level in all aspen tissues examined with a slightly higher expression level in secondary cell wall-enriched aspen xylem as compared to primary cell wall enriched tissues. Together, these observations suggest that PtrCSLD2 gene may be involved in the synthesis of matrix polysaccharides that are dominant in secondary cell walls of poplar xylem. Future molecular genetic analyses will clarify the functional significance of CSLD genes in the development of woody trees. AD - Plant Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA. AU - Samuga A AU - Joshi CP LA - ENG PT - JOURNAL ARTICLE TA - Physiol Plant JID - 1256322 EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 AID - 10.1111/j.0031-9317.2004.0271.x [doi] AID - PPL271 [pii] PST - ppublish SO - Physiol Plant 2004 Apr;120(4):631-641. PMID- 15031951 OWN - NLM STAT- in-process DA - 20040322 IS - 1001-9332 VI - 14 IP - 12 DP - 2003 Dec TI - [Response of an Arabidopsis mutant to elevated CO2 concentration] PG - 2359-60 AB - The study on the response of a mutant and a wild-type of Arabidopsis to 660 microliters.L-1 CO2 and ambient CO2 showed that under elevated CO2, the stomatal numbers of the mutant increased, while those of the wild-type decreased. The chlorophyll content and NR (nitrate reductase) activity of the mutant increased, but those of the wild-type had no obvious response. The mutant was not reproductively mature after the continuous exposure to increased CO2 for five months. The results provided evidence of plant response to the changes of atmospheric CO2 concentration, and the clues to related studies on other plants. AD - Department of Environmental Science, Shenyang Normal University, Shenyang 110034, China. haolinwj2001@yahoo.com.cn FAU - Hao, Lin AU - Hao L FAU - Xu, Xin AU - Xu X FAU - Cao, Jun AU - Cao J LA - chi PT - Journal Article PL - China TA - Ying Yong Sheng Tai Xue Bao JID - 9425159 SB - IM EDAT- 2004/03/23 05:00 MHDA- 2004/03/23 05:00 PST - ppublish SO - Ying Yong Sheng Tai Xue Bao 2003 Dec;14(12):2359-60. PMID- 15031414 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - B1-type cyclin-dependent kinases are essential for the formation of stomatal complexes in Arabidopsis thaliana. PG - 945-55 AB - Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In yeasts, only one CDK is sufficient to drive cells through the cell cycle, whereas higher eukaryotes developed a family of related CDKs. Curiously, plants contain a unique class of CDKs (B-type CDKs), whose function is still unclear. We show that the CDKB1;1 gene of Arabidopsis (Arabidopsis thaliana) is highly expressed in guard cells and stomatal precursor cells of cotyledons, suggesting a prominent role for B-type CDKs in stomatal development. In accordance, transgenic Arabidopsis plants with reduced B-type CDK activity had a decreased stomatal index because of an early block of meristemoid division and inhibition of satellite meristemoid formation. Many aberrant stomatal cells were observed, all of them blocked in the G2 phase of the cell cycle. Although division of stomatal precursors was inhibited, cells still acquired stomatal identity, illustrating that stomatal cell differentiation is independent of cellular and nuclear division. AD - Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Gent, Belgium. FAU - Boudolf, Veronique AU - Boudolf V FAU - Barroco, Rosa AU - Barroco R FAU - Engler, Janice de Almeida AU - Engler Jde A FAU - Verkest, Aurine AU - Verkest A FAU - Beeckman, Tom AU - Beeckman T FAU - Naudts, Mirande AU - Naudts M FAU - Inze, Dirk AU - Inze D FAU - De Veylder, Lieven AU - De Veylder L LA - eng PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.021774 [doi] AID - tpc.021774 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):945-55. Epub 2004 Mar 18. PMID- 15031412 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - The Arabidopsis chloroplastic NifU-like protein CnfU, which can act as an iron-sulfur cluster scaffold protein, is required for biogenesis of ferredoxin and photosystem I. PG - 993-1007 AB - The biosynthesis of iron-sulfur clusters is a highly regulated process involving several proteins. Among them, so-called scaffold proteins play pivotal roles in both the assembly and delivery of iron-sulfur clusters. Here, we report the identification of two chloroplast-localized NifU-like proteins, AtCnfU-V and AtCnfU-IVb, from Arabidopsis (Arabidopsis thaliana) with high sequence similarity to a cyanobacterial NifU-like protein that was proposed to serve as a molecular scaffold. AtCnfU-V is constitutively expressed in several tissues of Arabidopsis, whereas the expression of AtCnfU-IVb is prominent in the aerial parts. Mutant Arabidopsis lacking AtCnfU-V exhibited a dwarf phenotype with faint pale-green leaves and had drastically impaired photosystem I accumulation. Chloroplasts in the mutants also showed a decrease in both the amount of ferredoxin, a major electron carrier of the stroma that contains a [2Fe-2S] cluster, and in the in vitro activity of iron-sulfur cluster insertion into apo-ferredoxin. When expressed in Escherichia coli cells, AtCnfU-V formed a homodimer carrying a [2Fe-2S]-like cluster, and this cluster could be transferred to apo-ferredoxin in vitro to form holo-ferredoxin. We propose that AtCnfU has an important function as a molecular scaffold for iron-sulfur cluster biosynthesis in chloroplasts and thereby is required for biogenesis of ferredoxin and photosystem I. AD - Institute for Protein Research, Osaka University, Suita, 565-0871, Japan. FAU - Yabe, Toshiki AU - Yabe T FAU - Morimoto, Kozo AU - Morimoto K FAU - Kikuchi, Shingo AU - Kikuchi S FAU - Nishio, Kazuaki AU - Nishio K FAU - Terashima, Ichiro AU - Terashima I FAU - Nakai, Masato AU - Nakai M LA - eng PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.020511 [doi] AID - tpc.020511 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):993-1007. Epub 2004 Mar 18. PMID- 15031411 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. PG - 1060-71 AB - Plant growth homeostasis and defense responses are regulated by BONZAI1 (BON1), an evolutionarily conserved gene. Here, we show that growth regulation by BON1 is mediated through defense responses. BON1 is a negative regulator of a haplotype-specific Resistance (R) gene SNC1. The bon1-1 loss-of-function mutation activates SNC1, leading to constitutive defense responses and, consequently, reduced cell growth. In addition, a feedback amplification of the SNC1 gene involving salicylic acid is subject to temperature control, accounting for the regulation of growth and defense by temperature in bon1-1 and many other mutants. Thus, plant growth homeostasis involves the regulation of an R gene by BON1 and the intricate interplay between defense responses and temperature responses. AD - Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA. FAU - Yang, Shuhua AU - Yang S FAU - Hua, Jian AU - Hua J LA - eng SI - GENBANK/AY510018 PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.020479 [doi] AID - tpc.020479 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):1060-71. Epub 2004 Mar 18. PMID- 15031410 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Circadian and diurnal calcium oscillations encode photoperiodic information in Arabidopsis. PG - 956-66 AB - We have tested the hypothesis that circadian oscillations in the concentration of cytosolic free calcium ([Ca2+]cyt) can encode information. We imaged oscillations of [Ca2+]cyt in the cotyledons and leaves of Arabidopsis (Arabidopsis thaliana) that have a 24-h period in light/dark cycles and also constant light. The amplitude, phase, and shape of the oscillations of [Ca2+]cyt and [Ca2+]cyt at critical daily time points were controlled by the light/dark regimes in which the plants were grown. These data provide evidence that 24-h oscillations in [Ca2+]cyt encode information concerning daylength and light intensity, which are two major regulators of plant growth and development. AD - Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK. FAU - Love, John AU - Love J FAU - Dodd, Antony N AU - Dodd AN FAU - Webb, Alex A R AU - Webb AA LA - eng PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.020214 [doi] AID - tpc.020214 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):956-66. Epub 2004 Mar 18. PMID- 15031408 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana. PG - 887-96 AB - Phototropin 1 (phot1) and phot2, which are blue light receptor kinases, function in blue light-induced hypocotyl phototropism, chloroplast relocation, and stomatal opening in Arabidopsis (Arabidopsis thaliana). Previous studies have shown that the proteins RPT2 (for ROOT PHOTOTROPISM2) and NPH3 (for NONPHOTOTROPIC HYPOCOTYL3) transduce signals downstream of phototropins to induce the phototropic response. However, the involvement of RPT2 and NPH3 in stomatal opening and in chloroplast relocation mediated by phot1 and phot2 was unknown. Genetic analysis of the rpt2 mutant and of a series of double mutants indicates that RPT2 is involved in the phot1-induced phototropic response and stomatal opening but not in chloroplast relocation or phot2-induced movements. Biochemical analyses indicate that RPT2 is purified in the crude microsomal fraction, as well as phot1 and NPH3, and that RPT2 makes a complex with phot1 in vivo. On the other hand, NPH3 is not necessary for stomatal opening or chloroplast relocation. Thus, these results suggest that phot1 and phot2 choose different signal transducers to induce three responses: phototropic response of hypocotyl, stomatal opening, and chloroplast relocation. AD - RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. FAU - Inada, Sayaka AU - Inada S FAU - Ohgishi, Maki AU - Ohgishi M FAU - Mayama, Tomoko AU - Mayama T FAU - Okada, Kiyotaka AU - Okada K FAU - Sakai, Tatsuya AU - Sakai T LA - eng SI - GENBANK/AF030864 SI - GENBANK/AF053941 SI - GENBANK/AF180390 SI - GENBANK/AF181683 PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.019901 [doi] AID - tpc.019901 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):887-96. Epub 2004 Mar 18. PMID- 15031406 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Arabidopsis peptide methionine sulfoxide reductase2 prevents cellular oxidative damage in long nights. PG - 908-19 AB - Peptide methionine sulfoxide reductase (PMSR) is a ubiquitous enzyme that repairs oxidatively damaged proteins. In Arabidopsis (Arabidopsis thaliana), a null mutation in PMSR2 (pmsr2-1), encoding a cytosolic isoform of the enzyme, exhibited reduced growth in short-day conditions. In wild-type plants, a diurnally regulated peak of total PMSR activity occurred at the end of the 16-h dark period that was absent in pmsr2-1 plants. This PMSR activity peak in the wild-type plant coincided with increased oxidative stress late in the dark period in the mutant. In pmsr2-1, the inability to repair proteins resulted in higher levels of their turnover, which in turn placed an increased burden on cellular metabolism. This caused increased respiration rates, leading to the observed higher levels of oxidative stress. In wild-type plants, the repair of damaged proteins by PMSR2 at the end of the night in a short-day diurnal cycle alleviates this potential burden on metabolism. Although PMSR2 is not absolutely required for viability of plants, the observation of increased damage to proteins in these long nights suggests the timing of expression of PMSR2 is an important adaptation for conservation of their resources. AD - Department of Disease and Stress Biology, John Ines Centre, Norwich NR4 7UH, UK. FAU - Bechtold, Ulrike AU - Bechtold U FAU - Murphy, Denis J AU - Murphy DJ FAU - Mullineaux, Philip M AU - Mullineaux PM LA - eng PT - Journal Article DEP - 20040318 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1105/tpc.015818 [doi] AID - tpc.015818 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):908-19. Epub 2004 Mar 18. PMID- 15031265 OWN - NLM STAT- in-process DA - 20040412 IS - 0890-9369 VI - 18 IP - 6 DP - 2004 Mar 15 TI - Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. PG - 700-14 AB - Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth. AD - Biology Department, McGill University, Montreal, Quebec H3A 1B1, Canada. FAU - Mouchel, Celine F AU - Mouchel CF FAU - Briggs, Georgette C AU - Briggs GC FAU - Hardtke, Christian S AU - Hardtke CS LA - eng PT - Journal Article DEP - 20040318 PL - United States TA - Genes Dev JID - 8711660 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PHST- 2004/Mar/18 [aheadofprint] AID - 10.1101/gad.1187704 [doi] AID - 1187704 [pii] PST - ppublish SO - Genes Dev 2004 Mar 15;18(6):700-14. Epub 2004 Mar 18. PMID- 15030755 OWN - NLM STAT- in-process DA - 20040319 IS - 1534-5807 VI - 6 IP - 3 DP - 2004 Mar TI - Cryptic bracts exposed: insights into the regulation of leaf expansion. PG - 318-9 AB - Arabidopsis is unusual in producing flowers that are not subtended by specialized leaves, called floral bracts. Writing in Development, Dinneny et al. and Ohno et al. show that gain-of-function mutations of the JAGGED transcription factor produce bracts, and provide evidence that this gene plays a key role in a developmental program that regulates the size and shape of all leaves and leaf-homologs. AD - Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA. FAU - Baum, David A AU - Baum DA FAU - Day, Christopher D AU - Day CD LA - eng PT - Journal Article PL - United States TA - Dev Cell JID - 101120028 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 AID - S1534580704000711 [pii] PST - ppublish SO - Dev Cell 2004 Mar;6(3):318-9. PMID- 15029956 OWN - NLM STAT- in-process DA - 20040319 IS - 1340-2838 VI - 10 IP - 6 DP - 2003 Dec 31 TI - Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. PG - 249-61 AB - We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA-or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively. AD - Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. FAU - Yazaki, Junshi AU - Yazaki J FAU - Kishimoto, Naoki AU - Kishimoto N FAU - Nagata, Yuko AU - Nagata Y FAU - Ishikawa, Masahiro AU - Ishikawa M FAU - Fujii, Fumiko AU - Fujii F FAU - Hashimoto, Akiko AU - Hashimoto A FAU - Shimbo, Kanako AU - Shimbo K FAU - Shimatani, Zenpei AU - Shimatani Z FAU - Kojima, Keiichi AU - Kojima K FAU - Suzuki, Kouji AU - Suzuki K FAU - Yamamoto, Makoto AU - Yamamoto M FAU - Honda, Sachiko AU - Honda S FAU - Endo, Ayano AU - Endo A FAU - Yoshida, Yumiko AU - Yoshida Y FAU - Sato, Yuki AU - Sato Y FAU - Takeuchi, Keiko AU - Takeuchi K FAU - Toyoshima, Kazuko AU - Toyoshima K FAU - Miyamoto, Chikako AU - Miyamoto C FAU - Wu, Jianzhong AU - Wu J FAU - Sasaki, Takuji AU - Sasaki T FAU - Sakata, Katsumi AU - Sakata K FAU - Yamamoto, Kimiko AU - Yamamoto K FAU - Iba, Koh AU - Iba K FAU - Oda, Takahiro AU - Oda T FAU - Otomo, Yasuhiro AU - Otomo Y FAU - Murakami, Kazuo AU - Murakami K FAU - Matsubara, Kenichi AU - Matsubara K FAU - Kawai, Jun AU - Kawai J FAU - Carninci, Piero AU - Carninci P FAU - Hayashizaki, Yoshihide AU - Hayashizaki Y FAU - Kikuchi, Shoshi AU - Kikuchi S LA - eng PT - Journal Article PL - Japan TA - DNA Res JID - 9423827 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PST - ppublish SO - DNA Res 2003 Dec 31;10(6):249-61. PMID- 15029955 OWN - NLM STAT- in-process DA - 20040319 IS - 1340-2838 VI - 10 IP - 6 DP - 2003 Dec 31 TI - Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. PG - 239-47 AB - The NAC domain was originally characterized from consensus sequences from petunia NAM and from Arabidopsis ATAF1, ATAF2, and CUC2. Genes containing the NAC domain (NAC family genes) are plant-specific transcriptional regulators and are expressed in various developmental stages and tissues. We performed a comprehensive analysis of NAC family genes in Oryza sativa (a monocot) and Arabidopsis thaliana (a dicot). We found 75 predicted NAC proteins in full-length cDNA data sets of O. sativa (28,469 clones) and 105 in putative genes (28,581 sequences) from the A. thaliana genome. NAC domains from both predicted and known NAC family proteins were classified into two groups and 18 subgroups by sequence similarity. There were a few differences in amino acid sequences in the NAC domains between O. sativa and A. thaliana. In addition, we found 13 common sequence motifs from transcriptional activation regions in the C-terminal regions of predicted NAC proteins. These motifs probably diverged having correlations with NAC domain structures. We discuss the relationship between the structure and function of the NAC family proteins in light of our results and the published data. Our results will aid further functional analysis of NAC family genes. AD - Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. FAU - Ooka, Hisako AU - Ooka H FAU - Satoh, Kouji AU - Satoh K FAU - Doi, Koji AU - Doi K FAU - Nagata, Toshifumi AU - Nagata T FAU - Otomo, Yasuhiro AU - Otomo Y FAU - Murakami, Kazuo AU - Murakami K FAU - Matsubara, Kenichi AU - Matsubara K FAU - Osato, Naoki AU - Osato N FAU - Kawai, Jun AU - Kawai J FAU - Carninci, Piero AU - Carninci P FAU - Hayashizaki, Yoshihide AU - Hayashizaki Y FAU - Suzuki, Koji AU - Suzuki K FAU - Kojima, Keiichi AU - Kojima K FAU - Takahara, Yoshinori AU - Takahara Y FAU - Yamamoto, Koji AU - Yamamoto K FAU - Kikuchi, Shoshi AU - Kikuchi S LA - eng PT - Journal Article PL - Japan TA - DNA Res JID - 9423827 SB - IM EDAT- 2004/03/20 05:00 MHDA- 2004/03/20 05:00 PST - ppublish SO - DNA Res 2003 Dec 31;10(6):239-47. PMID- 15028238 OWN - NLM STAT- in-process DA - 20040318 IS - 0960-9822 VI - 14 IP - 5 DP - 2004 Mar 9 TI - Epigenetics: imprinting in plants and mammals--the same but different? PG - R201-3 AB - Plants and animals both exhibit parental imprinting, but do they control it the same way? Recent studies show that in Arabidopsis, as in mammals, imprinted alleles are subject to DNA methylation--but, surprisingly, the default state is silence rather than activity. AD - Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. bssrjs@bath.ac.uk FAU - Scott, Rod J AU - Scott RJ FAU - Spielman, Melissa AU - Spielman M LA - eng PT - Journal Article PL - England TA - Curr Biol JID - 9107782 SB - IM EDAT- 2004/03/19 05:00 MHDA- 2004/03/19 05:00 AID - 10.1016/j.cub.2004.02.022 [doi] AID - S0960982204001228 [pii] PST - ppublish SO - Curr Biol 2004 Mar 9;14(5):R201-3. PMID- 15028217 OWN - NLM STAT- in-process DA - 20040318 IS - 0960-9822 VI - 14 IP - 5 DP - 2004 Mar 9 TI - The plant microtubule-associated protein AtMAP65-3/PLE is essential for cytokinetic phragmoplast function. PG - 412-7 AB - Directional cell expansion in interphase and nuclear and cell division in M-phase are mediated by four microtubule arrays, three of which are unique to plants: the interphase array, the preprophase band, and the phragmoplast. The plant microtubule-associated protein MAP65 has been identified as a key structural component in these arrays. The Arabidopsis genome has nine MAP65 genes, and here we show that one, AtMAP65-3/PLE, locates only to the mitotic arrays and is essential for cytokinesis. The Arabidopsis pleiade (ple) alleles are single recessive mutations, and we show that these mutations are in the AtMAP65-3 gene. Moreover, these mutations cause C-terminal truncations that abolish microtubule binding. In the ple mutants the anaphase spindle is normal, and the cytokinetic phragmoplast can form but is distorted; not only is it wider, but the midline, the region where oppositely oriented microtubules overlap, is unusually expanded. Here we present data that demonstrate an essential role for AtMAP65-3/PLE in cytokinesis in plant cells. AD - The Institute of Applied Genetics, BOKU-University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria. FAU - Muller, Sabine AU - Muller S FAU - Smertenko, Andrei AU - Smertenko A FAU - Wagner, Vera AU - Wagner V FAU - Heinrich, Maria AU - Heinrich M FAU - Hussey, Patrick J AU - Hussey PJ FAU - Hauser, Marie-Theres AU - Hauser MT LA - eng PT - Journal Article PL - England TA - Curr Biol JID - 9107782 SB - IM EDAT- 2004/03/19 05:00 MHDA- 2004/03/19 05:00 PHST- 2004/Jan/07 [received] PHST- 2004/Jan/21 [revised] PHST- 2004/Jan/21 [accepted] AID - 10.1016/j.cub.2004.02.032 [doi] AID - S0960982204001265 [pii] PST - ppublish SO - Curr Biol 2004 Mar 9;14(5):412-7. PMID- 15028209 OWN - NLM STAT- in-process DA - 20040318 IS - 0960-9822 VI - 14 IP - 5 DP - 2004 Mar 9 TI - The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. PG - 354-62 AB - BACKGROUND: Chloroplasts are plant cell organelles of cyanobacterial origin. They perform essential metabolic and biosynthetic functions of global significance, including photosynthesis and amino acid biosynthesis. Most of the proteins that constitute the functional chloroplast are encoded in the nuclear genome and imported into the chloroplast after translation in the cytosol. Since protein targeting is difficult to predict, many nuclear-encoded plastid proteins are still to be discovered. RESULTS: By tandem mass spectrometry, we identified 690 different proteins from purified Arabidopsis chloroplasts. Most proteins could be assigned to known protein complexes and metabolic pathways, but more than 30% of the proteins have unknown functions, and many are not predicted to localize to the chloroplast. Novel structure and function prediction methods provided more informative annotations for proteins of unknown functions. While near-complete protein coverage was accomplished for key chloroplast pathways such as carbon fixation and photosynthesis, fewer proteins were identified from pathways that are downregulated in the light. Parallel RNA profiling revealed a pathway-dependent correlation between transcript and relative protein abundance, suggesting gene regulation at different levels. CONCLUSIONS: The chloroplast proteome contains many proteins that are of unknown function and not predicted to localize to the chloroplast. Expression of nuclear-encoded chloroplast genes is regulated at multiple levels in a pathway-dependent context. The combined shotgun proteomics and RNA profiling approach is of high potential value to predict metabolic pathway prevalence and to define regulatory levels of gene expression on a pathway scale. AD - Institute of Plant Sciences and Functional Genomics Center Zurich, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51.1, Universitatstrasse 2, CH-8092 Zurich, Switzerland. FAU - Kleffmann, Torsten AU - Kleffmann T FAU - Russenberger, Doris AU - Russenberger D FAU - von Zychlinski, Anne AU - von Zychlinski A FAU - Christopher, Wayne AU - Christopher W FAU - Sjolander, Kimmen AU - Sjolander K FAU - Gruissem, Wilhelm AU - Gruissem W FAU - Baginsky, Sacha AU - Baginsky S LA - eng PT - Journal Article PL - England TA - Curr Biol JID - 9107782 SB - IM EDAT- 2004/03/19 05:00 MHDA- 2004/03/19 05:00 PHST- 2003/Nov/30 [received] PHST- 2004/Jan/19 [revised] PHST- 2004/Jan/19 [accepted] AID - 10.1016/j.cub.2004.02.039 [doi] AID - S0960982204000909 [pii] PST - ppublish SO - Curr Biol 2004 Mar 9;14(5):354-62. PMID- 15027212 OWN - NLM STAT- in-process DA - 20040318 IS - 0475-1450 VI - 35 IP - 1 DP - 2004 Jan-Feb TI - [In Process Citation] PG - 41-6 AB - In arabidopsis (Arabidopsis thaliana), the CLAVATA1 (CLV1) gene is involved in maintaining the balance between the stem cells in the central zone of the stem apical meristem and the determined cells at its periphery. However, CLV1 has not been previously characterized in other Brassicaceae. Using the direct amplification of genomic DNA, we obtained a full-length CLV1 ortholog from canola plants (Brassica napus), and also three CLV1 fragments from rape (B. rapa), canola (B. napus), and false flax (Camelina sativa), which corresponded to the transmembrane domain and a part of the kinase domain of the CLAVATA1 protein. The nucleotide and deduced amino acid sequences of the full-size CLV1 ortholog from B. napus were similar by 81 and 87% to the prototype gene from arabidopsis; in the case of shorter gene fragments, the similarity was as high as 91-93 and 98%, respectively. By their primary structure, the CLV1 genes in the Brassicaceae considerably differ from its putative structural homologs beyond this family. AD - Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya ul., 42, Moscow, 127550 Russia. LA - rus PT - Journal Article PL - Russia TA - Ontogenez JID - 0341527 SB - IM EDAT- 2004/03/19 05:00 MHDA- 2004/03/19 05:00 PST - ppublish SO - Ontogenez 2004 Jan-Feb;35(1):41-6. PMID- 15024409 OWN - NLM STAT- publisher DA - 20040316 IS - 1544-9173 VI - 2 IP - 5 DP - 2004 Feb 24 TI - Genetic and Functional Diversification of Small RNA Pathways in Plants. PG - E104 AB - Multicellular eukaryotes produce small RNA molecules (approximately 21-24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense. AD - Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America. AU - Xie Z AU - Johansen LK AU - Gustafson AM AU - Kasschau KD AU - Lellis AD AU - Zilberman D AU - Jacobsen SE AU - Carrington JC LA - ENG PT - JOURNAL ARTICLE TA - PLoS Biol JID - 101183755 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Dec/19 [received] PHST- 2004/Feb/05 [accepted] AID - 10.1371/journal.pbio.0020104 [doi] PST - aheadofprint SO - PLoS Biol 2004 Feb 24;2(5):E104. PMID- 15024005 OWN - NLM STAT- publisher DA - 20040316 IS - 1083-351X DP - 2004 Mar 15 TI - Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol. AB - The subcellular distribution of Met and S-adenosylmethionine (AdoMet) metabolism in plant cells discloses a complex partition between the cytosol and the organelles. In the present work we show that Arabidopsis contains three functional isoforms of vitamin B12-independent methionine synthase (MS), the enzyme that catalyzes the methylation of homocysteine to Met with 5-methyltetrahydrofolate as methyl-group donor. One MS isoform is present in chloroplasts and is most likely required to methylate homocysteine that is synthesized de novo in this compartment. Thus, chloroplasts are autonomous and are the unique site for de novo Met synthesis in plant cells. The additional MS isoforms are present in the cytosol and are most probably involved in the regeneration of Met from homocysteine produced in the course of the activated methyl cycle. Although Met synthesis can occur in chloroplasts, there is no evidence that AdoMet is synthesized anywhere but the cytosol. In accordance with this proposal, we show that AdoMet is transported into chloroplasts by a carrier-mediated facilitated diffusion process. This carrier is able to catalyze the uniport uptake of AdoMet into chloroplasts as well as the exchange between cytosolic AdoMet and chloroplastic AdoMet or S-adenosylhomocysteine. The obvious function for the carrier is to sustain methylation reactions and other AdoMet-dependent functions in chloroplasts and probably to remove S-adenosylhomocysteine generated in the stroma by methyltransferase activities. Therefore, the chloroplastic AdoMet carrier serves as a link between cytosolic and chloroplastic one-carbon metabolism. AD - DRDC / PCV, UMR5168, CEA-Grenoble, Grenoble 38054. AU - Ravanel S AU - Block MA AU - Rippert P AU - Jabrin S AU - Curien G AU - Rebeille F AU - Douce R LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1074/jbc.M313250200 [doi] AID - M313250200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 15;. PMID- 15022837 OWN - NLM STAT- in-process DA - 20040316 IS - 0176-1617 VI - 161 IP - 2 DP - 2004 Feb TI - Cloning and analysis of a cDNA encoding an endo-polygalacturonase expressed during the desiccation period of the silique-valves of turnip-tops (Brassica rapa L. cv. Rapa). PG - 219-27 AB - During zygotic embryogenesis of turnip-tops (Brassica rapa L. cv. Rapa), the polygalacturonase activity (PG; EC 3.2.1.15), measured as a decrease in viscosity of polygalacturonic acid, reached a high when the desiccation process in the seeded silique was triggered and the valves had lost more than 70-75% of their moisture (45-50 DPA). The PG activity was not detected in any phases of developing seeds. This work also characterizes a cDNA with an open reading frame of 1303 bp and that codes for a putative PG called BrPG1. This falls into the category of clade-B, which includes PG related to shattering and abscission processes. The deduced BrPG1 sequence predicted a 434-residue-long precursor protein (46.7kDa) with a transit peptide sequence 23 amino acids long. A molecular mass of 44.3 kDa was calculated for the mature form of BrPG1, which showed high sequence similarity to PGA1 (97%) of B. napus (X98373) and ADPG1 (87%) of Arabidopsis thaliana (AJ002532). All conserved amino acids at the catalytic site of PGs belonging to clade-B were preserved on BrPG1. This BrPG1 gene was specifically expressed in the silique valves of turnip-tops and was temporally expressed at the beginning of its desiccation. AD - Departamento de Fisiologia Vegetal, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Sur s/n. 15782-Santiago de Compostela, Spain. FAU - Rodriguez-Gacio, Maria del Carmen AU - Rodriguez-Gacio Mdel C FAU - Nicolas, Carlos AU - Nicolas C FAU - Matilla, Angel J AU - Matilla AJ LA - eng PT - Journal Article PL - Germany TA - J Plant Physiol JID - 9882059 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PST - ppublish SO - J Plant Physiol 2004 Feb;161(2):219-27. PMID- 15022831 OWN - NLM STAT- in-process DA - 20040316 IS - 0176-1617 VI - 161 IP - 2 DP - 2004 Feb TI - Analysis of an Arabidopsis thaliana protein family, structurally related to cytochromes b561 and potentially involved in catecholamine biochemistry in plants. PG - 175-81 AB - Cytochromes b561 (cyts b561) constitute a family of eukaryotic membrane proteins, catalysing ascorbate (Asc)-mediated trans-membrane electron transport, and hence likely involved in Asc regeneration. A class of proteins (DoH-CB) has been identified in plants and animals, containing the cyt b561 electron-transport domain (CB), combined with the catecholamine-binding regulatory domain of dopamine-beta-hydroxylase (DoH). A mammalian DoH-CB protein was previously reported to function as a cell-derived growth factor receptor (SDR2). We have performed an in silico analysis on DoH-CB proteins from Arabidopsis thaliana and demonstrate that structural features of both CB and DoH domains are well conserved. The combination of both domains may have evolved from a functional interaction between a cyt b561 and a DoH-containing protein, illustrating the so-called "Rosetta Stone" evolutionary principle, and this hypothesis is supported by sequence comparisons. DoH-CB proteins form a newly identified group of proteins, likely to play a key role in catecholamine action in plants. It is suggested that these proteins may function as trans-membrane electron shuttles, possibly regulated by catecholamines. The role and action of catecholamines in plants is poorly documented, but it is clear that they are involved in many aspects of growth and development. Whether the DoH-CB proteins functionally interact with Asc, as is the case for cyts b561, remains to be determined. AD - Department of Biology, University of Antwerp (RUCA), Groenenborgerlaan 171, B-2020 Antwerp, Belgium. wverelst@ruca.ua.ac.be FAU - Verelst, Wim AU - Verelst W FAU - Asard, Han AU - Asard H LA - eng PT - Journal Article PL - Germany TA - J Plant Physiol JID - 9882059 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PST - ppublish SO - J Plant Physiol 2004 Feb;161(2):175-81. PMID- 15020759 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Evaluation of monocot and eudicot divergence using the sugarcane transcriptome. PG - 951-9 AB - Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis. AD - Centro de Biologia Molecular e Engenharia Genetica, Universidade de Campinas, Caixa Postal 6010, 13083-970, Campinas SP, Brazil. FAU - Vincentz, Michel AU - Vincentz M FAU - Cara, Frank A A AU - Cara FA FAU - Okura, Vagner K AU - Okura VK FAU - da Silva, Felipe R AU - da Silva FR FAU - Pedrosa, Guilherme L AU - Pedrosa GL FAU - Hemerly, Adriana S AU - Hemerly AS FAU - Capella, Adriana N AU - Capella AN FAU - Marins, Mozart AU - Marins M FAU - Ferreira, Paulo C AU - Ferreira PC FAU - Franca, Suzelei C AU - Franca SC FAU - Grivet, Laurent AU - Grivet L FAU - Vettore, Andre L AU - Vettore AL FAU - Kemper, Edson L AU - Kemper EL FAU - Burnquist, Willian L AU - Burnquist WL FAU - Targon, Maria L P AU - Targon ML FAU - Siqueira, Walter J AU - Siqueira WJ FAU - Kuramae, Eiko E AU - Kuramae EE FAU - Marino, Celso L AU - Marino CL FAU - Camargo, Luis E A AU - Camargo LE FAU - Carrer, Helaine AU - Carrer H FAU - Coutinho, Luis L AU - Coutinho LL FAU - Furlan, Luiz R AU - Furlan LR FAU - Lemos, Manoel V F AU - Lemos MV FAU - Nunes, Luiz R AU - Nunes LR FAU - Gomes, Suely L AU - Gomes SL FAU - Santelli, Roberto V AU - Santelli RV FAU - Goldman, Maria H AU - Goldman MH FAU - Bacci, Mauricio Jr AU - Bacci M Jr FAU - Giglioti, Eder A AU - Giglioti EA FAU - Thiemann, Otavio H AU - Thiemann OH FAU - Silva, Flavio H AU - Silva FH FAU - Van Sluys, Marie-Anne AU - Van Sluys MA FAU - Nobrega, Francisco G AU - Nobrega FG FAU - Arruda, Paulo AU - Arruda P FAU - Menck, Carlos F M AU - Menck CF LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1104/pp.103.033878 [doi] AID - 134/3/951 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):951-9. PMID- 15020758 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Molecular analysis of 10 coding regions from Arabidopsis that are homologous to the MUR3 xyloglucan galactosyltransferase. PG - 940-50 AB - Plant cell walls are composed of a large number of complex polysaccharides, which contain at least 13 different monosaccharides in a multitude of linkages. This structural complexity of cell wall components is paralleled by a large number of predicted glycosyltransferases in plant genomes, which can be grouped into several distinct families based on conserved sequence motifs (B. Henrissat, G.J. Davies [2000] Plant Physiol 124: 1515-1519). Despite the wealth of genomic information in Arabidopsis and several crop plants, the biochemical functions of these coding regions have only been established in a few cases. To lay the foundation for the genetic and biochemical characterization of putative glycosyltransferase genes, we conducted a phylogenetic and expression analysis on 10 predicted coding regions (AtGT11-20) that are closely related to the MUR3 xyloglucan galactosyltransferase of Arabidopsis. All of these proteins contain the conserved sequence motif pfam 03016 that is the hallmark of the beta-d-glucuronosyltransferase domain of exostosins, a class of animal enzymes involved in the biosynthesis of the extracellular polysaccharide heparan sulfate. Reverse transcriptase-polymerase chain reaction and promoter:beta-glucuronidase studies indicate that all AtGT genes are transcribed. Although six of the 10 AtGT genes were expressed in all major plant organs, the remaining four genes showed more restricted expression patterns that were either confined to specific organs or to highly specialized cell types such as hydathodes or pollen grains. T-DNA insertion mutants in AtGT13 and AtGT18 displayed reductions in the Gal content of total cell wall material, suggesting that the disrupted genes encode galactosyltransferases in plant cell wall synthesis. AD - Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA. FAU - Li, Xuemei AU - Li X FAU - Cordero, Israel AU - Cordero I FAU - Caplan, Jeffrey AU - Caplan J FAU - Molhoj, Michael AU - Molhoj M FAU - Reiter, Wolf-Dieter AU - Reiter WD LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1104/pp.103.036285 [doi] AID - 134/3/940 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):940-50. PMID- 15020757 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database. PG - 927-39 AB - Increasing evidence demonstrates the importance of long coiled-coil proteins for the spatial organization of cellular processes. Although several protein classes with long coiled-coil domains have been studied in animals and yeast, our knowledge about plant long coiled-coil proteins is very limited. The repeat nature of the coiled-coil sequence motif often prevents the simple identification of homologs of animal coiled-coil proteins by generic sequence similarity searches. As a consequence, counterparts of many animal proteins with long coiled-coil domains, like lamins, golgins, or microtubule organization center components, have not been identified yet in plants. Here, all Arabidopsis proteins predicted to contain long stretches of coiled-coil domains were identified by applying the algorithm MultiCoil to a genome-wide screen. A searchable protein database, ARABI-COIL (http://www.coiled-coil.org/arabidopsis), was established that integrates information on number, size, and position of predicted coiled-coil domains with subcellular localization signals, transmembrane domains, and available functional annotations. ARABI-COIL serves as a tool to sort and browse Arabidopsis long coiled-coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas. Using the database, candidate proteins were identified for Arabidopsis membrane-bound, nuclear, and organellar long coiled-coil proteins. AD - Department of Plant Biology and Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, Ohio 43210, USA. FAU - Rose, Annkatrin AU - Rose A FAU - Manikantan, Sankaraganesh AU - Manikantan S FAU - Schraegle, Shannon J AU - Schraegle SJ FAU - Maloy, Michael A AU - Maloy MA FAU - Stahlberg, Eric A AU - Stahlberg EA FAU - Meier, Iris AU - Meier I LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1104/pp.103.035626 [doi] AID - 134/3/927 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):927-39. PMID- 15020756 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - The SOS3 family of calcium sensors and SOS2 family of protein kinases in Arabidopsis. PG - 919-26 AD - Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA. FAU - Gong, Deming AU - Gong D FAU - Guo, Yan AU - Guo Y FAU - Schumaker, Karen S AU - Schumaker KS FAU - Zhu, Jian-Kang AU - Zhu JK LA - eng GR - R01GM59138/GM/NIGMS PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1104/pp.103.037440 [doi] AID - 134/3/919 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):919-26. PMID- 15020753 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Self-reporting arabidopsis expressing pH and [Ca2+] indicators unveil ion dynamics in the cytoplasm and in the apoplast under abiotic stress. PG - 898-908 AB - For noninvasive in vivo measurements of intra- and extracellular ion concentrations, we produced transgenic Arabidopsis expressing pH and calcium indicators in the cytoplasm and in the apoplast. Ratiometric pH-sensitive derivatives of the green fluorescent protein (At-pHluorins) were used as pH indicators. For measurements of calcium ([Ca(2+)]), luminescent aequorin variants were expressed in fusion with pHluorins. An Arabidopsis chitinase signal sequence was used to deliver the indicator complex to the apoplast. Responses of pH and [Ca(2+)] in the apoplast and in the cytoplasm were studied under salt and "drought" (mannitol) stress. Results are discussed in the frame of ion flux, regulation, and signaling. They suggest that osmotic stress and salt stress are differently sensed, compiled, and processed in plant cells. AD - Institut fur Pflanzenernahrung und Bodenkunde, Christian-Albrechts-Universitat, D-24098 Kiel, Germany. FAU - Gao, Dongjie AU - Gao D FAU - Knight, Marc R AU - Knight MR FAU - Trewavas, Anthony J AU - Trewavas AJ FAU - Sattelmacher, Burkhard AU - Sattelmacher B FAU - Plieth, Christoph AU - Plieth C LA - eng PT - Journal Article PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1104/pp.103.032508 [doi] AID - 134/3/898 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):898-908. PMID- 15020749 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Electron tomographic analysis of somatic cell plate formation in meristematic cells of Arabidopsis preserved by high-pressure freezing. PG - 836-56 AB - We have investigated the process of somatic-type cytokinesis in Arabidopsis (Arabidopsis thaliana) meristem cells with a three-dimensional resolution of approximately 7 nm by electron tomography of high-pressure frozen/freeze-substituted samples. Our data demonstrate that this process can be divided into four phases: phragmoplast initials, solid phragmoplast, transitional phragmoplast, and ring-shaped phragmoplast. Phragmoplast initials arise from clusters of polar microtubules (MTs) during late anaphase. At their equatorial planes, cell plate assembly sites are formed, consisting of a filamentous ribosome-excluding cell plate assembly matrix (CPAM) and Golgi-derived vesicles. The CPAM, which is found only around growing cell plate regions, is suggested to be responsible for regulating cell plate growth. Virtually all phragmoplast MTs terminate inside the CPAM. This association directs vesicles to the CPAM and thereby to the growing cell plate. Cell plate formation within the CPAM appears to be initiated by the tethering of vesicles by exocyst-like complexes. After vesicle fusion, hourglass-shaped vesicle intermediates are stretched to dumbbells by a mechanism that appears to involve the expansion of dynamin-like springs. This stretching process reduces vesicle volume by approximately 50%. At the same time, the lateral expansion of the phragmoplast initials and their CPAMs gives rise to the solid phragmoplast. Later arriving vesicles begin to fuse to the bulbous ends of the dumbbells, giving rise to the tubulo-vesicular membrane network (TVN). During the transitional phragmoplast stage, the CPAM and MTs disassemble and then reform in a peripheral ring phragmoplast configuration. This creates the centrifugally expanding peripheral cell plate growth zone, which leads to cell plate fusion with the cell wall. Simultaneously, the central TVN begins to mature into a tubular network, and ultimately into a planar fenestrated sheet (PFS), through the removal of membrane via clathrin-coated vesicles and by callose synthesis. Small secondary CPAMs with attached MTs arise de novo over remaining large fenestrae to focus local growth to these regions. When all of the fenestrae are closed, the new cell wall is complete. Few endoplasmic reticulum (ER) membranes are seen associated with the phragmoplast initials and with the TVN cell plate that is formed within the solid phragmoplast. ER progressively accumulates thereafter, reaching a maximum during the late PFS stage, when most cell plate growth is completed. AD - Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA. FAU - Segui-Simarro, Jose M AU - Segui-Simarro JM FAU - Austin, Jotham R 2nd AU - Austin JR 2nd FAU - White, Erin A AU - White EA FAU - Staehelin, L Andrew AU - Staehelin LA LA - eng GR - EB002039/EB/NIBIB PT - Journal Article DEP - 20040312 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1105/tpc.017749 [doi] AID - tpc.017749 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):836-56. Epub 2004 Mar 12. PMID- 15020747 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development. PG - 1035-46 AB - The eukaryotic origin recognition complex (ORC) is made up of six subunits and functions in nuclear DNA replication, chromatin structure, and gene silencing in both fungi and metazoans. We demonstrate that disruption of a plant ORC subunit homolog, AtORC2 of Arabidopsis (Arabidopsis thaliana), causes a zygotic lethal mutant phenotype (orc2). Seeds of orc2 abort early, typically producing embryos with up to eight cells. Nuclear division in the endosperm is arrested at an earlier developmental stage: only approximately four nuclei are detected in orc2 endosperm. The endosperm nuclei in orc2 are dramatically enlarged, a phenotype that is most similar to class B titan mutants, which include mutants in structural maintenance of chromosomes (SMC) cohesins. The highest levels of ORC2 gene expression were found in preglobular embryos, coinciding with the stage at which homozygous orc2 mutant seeds arrest. The homologs of the other five Arabidopsis ORC subunits are also expressed at this developmental stage. The orc2 mutant phenotype is partly suppressed by a mutation in the Polycomb group gene MEDEA. In double mutants between orc2 and medea (mea), orc2 homozygotes arrest later with a phenotype intermediate between those of mea and orc2 single mutants. Either alterations in chromatin structure or the release of cell cycle checkpoints by the mea mutation may allow more cell and nuclear divisions to occur in orc2 homozygous seeds. AD - Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland. collinge@botinist.unizh.ch FAU - Collinge, Margaret A AU - Collinge MA FAU - Spillane, Charles AU - Spillane C FAU - Kohler, Claudia AU - Kohler C FAU - Gheyselinck, Jacqueline AU - Gheyselinck J FAU - Grossniklaus, Ueli AU - Grossniklaus U LA - eng SI - GENBANK/AJ586913 PT - Journal Article DEP - 20040312 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1105/tpc.019059 [doi] AID - tpc.019059 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):1035-46. Epub 2004 Mar 12. PMID- 15020746 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - The petunia ortholog of Arabidopsis SUPERMAN plays a distinct role in floral organ morphogenesis. PG - 920-32 AB - Arabidopsis (Arabidopsis thaliana) SUPERMAN (SUP) plays a role in establishing a boundary between whorls 3 and 4 of flowers and in ovule development. We characterized a Petunia hybrida (petunia) homolog of SUP, designated PhSUP1, to compare with SUP. Genomic DNA of the PhSUP1 partially restored the stamen number and ovule development phenotypes of the Arabidopsis sup mutant. Two P. hybrida lines of transposon (dTph1) insertion mutants of PhSUP1 exhibited increased stamen number at the cost of normal carpel development, and ovule development was defective owing to aberrant growth of the integument. Unlike Arabidopsis sup mutants, phsup1 mutants also showed extra tissues connecting stamens, a petal tube and an ovary, and aberrancies in the development of anther and placenta. PhSUP1 transcripts occurred in the basal region of wild-type flowers around developing organ primordia in whorls 2 and 3 as well as in the funiculus of the ovule, concave regions of the placenta, and interthecal regions of developing anthers. Overexpression of PhSUP1 in P. hybrida resulted in size reduction of petals, leaves, and inflorescence stems. The shortening of inflorescence stems and petal tubes was primarily attributable to suppression of cell elongation, whereas a decrease in cell number was mainly responsible for the size reduction of petal limbs. AD - Developmental Biology Laboratory, Plant Physiology Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. FAU - Nakagawa, Hitoshi AU - Nakagawa H FAU - Ferrario, Silvia AU - Ferrario S FAU - Angenent, Gerco C AU - Angenent GC FAU - Kobayashi, Akira AU - Kobayashi A FAU - Takatsuji, Hiroshi AU - Takatsuji H LA - eng SI - GENBANK/AB117749 PT - Journal Article DEP - 20040312 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1105/tpc.018838 [doi] AID - tpc.018838 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):920-32. Epub 2004 Mar 12. PMID- 15020743 OWN - NLM STAT- in-process DA - 20040405 IS - 1040-4651 VI - 16 IP - 4 DP - 2004 Apr TI - Silencing of the mitogen-activated protein kinase MPK6 compromises disease resistance in Arabidopsis. PG - 897-907 AB - Here, we use a loss-of-function approach to demonstrate that the Arabidopsis (Arabidopsis thaliana) mitogen-activated protein kinase (MAPK) MPK6 plays a role in resistance to certain pathogens. MPK6-silenced Arabidopsis showed no apparent morphological phenotype or reduced fertility, indicating MPK6 is not required for development. However, resistances to an avirulent strain of Peronospora parasitica and avirulent and virulent strains of Pseudomonas syringae were compromised, suggesting that MPK6 plays a role in both resistance gene-mediated and basal resistance. Furthermore, this result demonstrates that MPK6's function cannot be fully complemented by other endogenous MAPKs. Although MPK6-silenced plants exhibited enhanced disease susceptibility, their ability to develop systemic acquired resistance or induced systemic resistance was unaffected. Expression of the pathogen-inducible gene VEGETATIVE STORAGE PROTEIN1 (VSP1) in MPK6-silenced plants was severalfold lower than in control plants, but the expression of other defense genes was comparable to the level observed in control plants. Taken together, these results provide direct evidence that a specific MAPK positively regulates VSP1 expression and resistance to a primary infection by certain pathogens, whereas systemic resistance and expression of several other defense genes appears to be mediated either by a functionally redundant MAPK(s) or independently from MPK6-dependent resistance. AD - Boyce Thompson Institute for Plant Research, Ithaca, NY 14850, USA. FAU - Menke, Frank L H AU - Menke FL FAU - van Pelt, Johan A AU - van Pelt JA FAU - Pieterse, Corne M J AU - Pieterse CM FAU - Klessig, Daniel F AU - Klessig DF LA - eng PT - Journal Article DEP - 20040312 PL - United States TA - Plant Cell JID - 9208688 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1105/tpc.015552 [doi] AID - tpc.015552 [pii] PST - ppublish SO - Plant Cell 2004 Apr;16(4):897-907. Epub 2004 Mar 12. PMID- 15020741 OWN - NLM STAT- in-data-review DA - 20040415 IS - 0032-0889 VI - 134 IP - 4 DP - 2004 Apr TI - A bifunctional 3,5-epimerase/4-keto reductase for nucleotide-rhamnose synthesis in Arabidopsis. PG - 1337-46 AB - l-Rhamnose is a component of plant cell wall pectic polysaccharides, diverse secondary metabolites, and some glycoproteins. The biosynthesis of the activated nucleotide-sugar form(s) of rhamnose utilized by the various rhamnosyltransferases is still elusive, and no plant enzymes involved in their synthesis have been purified. In contrast, two genes (rmlC and rmlD) have been identified in bacteria and shown to encode a 3,5-epimerase and a 4-keto reductase that together convert dTDP-4-keto-6-deoxy-Glc to dTDP-beta-l-rhamnose. We have identified an Arabidopsis cDNA that contains domains that share similarity to both reductase and epimerase. The Arabidopsis gene encodes a protein with a predicated molecular mass of approximately 33.5 kD that is transcribed in all tissue examined. The Arabidopsis protein expressed in, and purified from, Escherichia coli converts dTDP-4-keto-6-deoxy-Glc to dTDP-beta-l-rhamnose in the presence of NADPH. These results suggest that a single plant enzyme has both the 3,5-epimerase and 4-keto reductase activities. The enzyme has maximum activity between pH 5.5 and 7.5 at 30 degrees C. The apparent K(m) for NADPH is 90 microm and 16.9 microm for dTDP-4-keto-6-deoxy-Glc. The Arabidopsis enzyme can also form UDP-beta-l-rhamnose. To our knowledge, this is the first example of a bifunctional plant enzyme involved in sugar nucleotide synthesis where a single polypeptide exhibits the same activities as two separate prokaryotic enzymes. AD - Complex Carbohydrate Research Center and Department of Plant Biology, University of Georgia, Athens, Georgia 30602-4712. FAU - Watt, Gregory AU - Watt G FAU - Leoff, Christine AU - Leoff C FAU - Harper, April D AU - Harper AD FAU - Bar-Peled, Maor AU - Bar-Peled M LA - eng PT - Journal Article DEP - 20040312 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1104/pp.103.037192 [doi] AID - pp.103.037192 [pii] PST - ppublish SO - Plant Physiol 2004 Apr;134(4):1337-46. Epub 2004 Mar 12. PMID- 15020705 OWN - NLM STAT- in-process DA - 20040315 IS - 1362-4962 VI - 32 IP - 5 DP - 2004 TI - Identification of 20 microRNAs from Oryza sativa. PG - 1688-95 AB - MicroRNAs (miRNAs) are present in both plant and animal kingdoms and represents a growing family of non-coding RNAs. These tiny RNAs act as small guides and direct negative regulations usually in the process of development through sequence complementarity to target mRNAs. Although a large number of miRNAs have been identified from various animals, so far plant miRNA studies have focused mainly on Arabidopsis. Here we describe the identification of 20 miRNAs from a rice cDNA library. All the miRNAs were presumably processed from precursors with stem-loop structures and were positively detected in rice cells from at least one tissue, some of which showed tissue-specific expression. Twenty-three unique rice genes were identified to be feasible targets for seven rice miRNAs, including four members of Scarecrow-like transcription factor, the targets of miR-39 that had been characterized in Arabidopsis. Lacking long complementarity, the regulatory targets of 13 miRNAs remain to be further investigated. A possible mechanism of translational repressor for plant miRNAs that lack perfect complementarity to target mRNAs is discussed. AD - Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, People's Republic of China. FAU - Wang, Jia-Fu AU - Wang JF FAU - Zhou, Hui AU - Zhou H FAU - Chen, Yue-Qin AU - Chen YQ FAU - Luo, Qing-Jun AU - Luo QJ FAU - Qu, Liang-Hu AU - Qu LH LA - eng PT - Journal Article DEP - 20040312 PL - England TA - Nucleic Acids Res JID - 0411011 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004 [ppublish] AID - 10.1093/nar/gkh332 [doi] AID - 32/5/1688 [pii] PST - epublish SO - Nucleic Acids Res 2004 Mar 12;32(5):1688-95. Print 2004. PMID- 15020642 OWN - NLM STAT- in-process DA - 20040326 IS - 0022-0957 VI - 55 IP - 398 DP - 2004 Apr TI - Caspase-like activity in the seedlings of Pisum sativum eliminates weaker shoots during early vegetative development by induction of cell death. PG - 889-97 AB - Activation of aspartate-specific cysteine proteases (caspases) plays a crucial role in programmed cell death (PCD) in animals. Although to date caspases have not been identified in plants, caspase-like activity was described in tobacco during a hypersensitive response to pathogens and in Arabidopsis and tomato cell cultures during chemical-induced PCD. Caspase-like activity was also detected in the course of plant development during petal senescence and endosperm PCD. It is shown here that caspase-like proteases play a crucial role in the developmental cell death of secondary shoots of pea seedlings that emerge after removal of the epicotyl. Caspase-like activity was induced in senescing secondary shoots, but not in dominant growing shoots, in contrast to the papain-like cysteine protease activity that was stronger in the dominant shoot. Revitalization of the senescing shoot by cutting of the dominant shoot reduced the caspase-like activity. Injection of caspase or cysteine protease inhibitors into the remaining epicotyl tissue suppressed the death of the secondary shoots, producing seedlings with two equal shoots. These results suggest that shoot selection in pea seedlings is controlled by PCD, through the activation of caspase-like proteases. AD - Department of Plant Sciences, The Hebrew University of Jerusalem, Givat-Ram Campus, Jerusalem 91904, Israel. FAU - Belenghi, Beatrice AU - Belenghi B FAU - Salomon, Mazal AU - Salomon M FAU - Levine, Alex AU - Levine A LA - eng PT - Journal Article DEP - 20040312 PL - England TA - J Exp Bot JID - 9882906 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2004/Mar/12 [aheadofprint] AID - 10.1093/jxb/erh097 [doi] AID - erh097 [pii] PST - ppublish SO - J Exp Bot 2004 Apr;55(398):889-97. Epub 2004 Mar 12. PMID- 15020636 OWN - NLM STAT- publisher DA - 20040315 IS - 0022-0957 DP - 2004 Mar 12 TI - Chloroplast proteomics: potentials and challenges. AB - With the available Arabidopsis genome and near-completion of the rice genome sequencing project, large-scale analysis of plant proteins with mass spectrometry has now become possible. Determining the proteome of a cell is a challenging task, which is complicated by proteome dynamics and complexity. The biochemical heterogeneity of proteins constrains the use of standardized analytical procedures and requires demanding techniques for proteome analysis. Several proteome studies of plant cell organelles have been reported, including chloroplasts and mitochondria. Chloroplasts are of particular interest for plant biologists because of their complex biochemical pathways for essential metabolic functions. Information from the chloroplast proteome will therefore provide new insights into pathway compartmentalization and protein sorting. Some approaches for the analysis of the chloroplast proteome and future prospects of plastid proteome research are discussed here. AD - Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51.1, Universitatstrasse 2, CH-8092 Zurich, Switzerland. AU - Baginsky S AU - Gruissem W LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1093/jxb/erh104 [doi] AID - erh104 [pii] PST - aheadofprint SO - J Exp Bot 2004 Mar 12;. PMID- 15020634 OWN - NLM STAT- publisher DA - 20040315 IS - 0022-0957 DP - 2004 Mar 12 TI - Surface growth at the reproductive shoot apex of Arabidopsis thaliana pin-formed 1 and wild type. AB - With the aid of a non-destructive replica method and computational protocol, surface geometry and expansion at the reproductive shoot apex are analysed for pin-formed 1 (pin1) Arabidopsis thaliana and compared with the wild type. The observed complexity of geometry and expansion at the pin1 apex indicates that both components of shoot apex growth, i.e. the meristem self-perpetuation and initiation of lateral organs, are realized by the pin1 apex. The realization of the latter component, however, is only occasionally completed. The pin1 apex is generally dome-shaped, but its curvature is not uniform, especially later during apex ontogeny, when bulges and saddle-shaped regions appear on its periphery. The only saddle-shaped regions at the wild-type shoot apex are creases separating flower primordia from the meristem. Surface expansion at the pin1 apex is faster than at the wild type. In both pin1 and wild type the apex surface is differentiated into regions of various areal strain rates. In the pin1 apex, but not in the wild type, these regions correspond to the geometrically distinguished central and peripheral zones. Expansion of the central zone of the pin1 apex is nearly isotropic and slower than in the peripheral zone. The peripheral zone is differentiated into ring-shaped portions of different expansion anisotropy. The distal portion of this zone expands anisotropically, similar to regions of the wild-type apex periphery, which contact older flower primordia. The proximal portion expands nearly isotropically, like sites of flower initiation in the wild type. The peripheral zone in pin1 is surrounded by a 'basal zone', a sui generis zone, where areal strain rates are low and expansion is anisotropic. The possible relationships between the observed regions of different expansion and the various gene expression patterns in the pin1 apex known from the literature are discussed. AD - Institute of Plant Biology, Wrocaw University, Kanonia 6/8, 50-328 Wrocaw, Poland. AU - Kwiatkowska D LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1093/jxb/erh109 [doi] AID - erh109 [pii] PST - aheadofprint SO - J Exp Bot 2004 Mar 12;. PMID- 15020633 OWN - NLM STAT- publisher DA - 20040315 IS - 0022-0957 DP - 2004 Mar 12 TI - Cloning of a cDNA encoding an ETR2-like protein (Os-ERL1) from deep water rice (Oryza sativa L.) and increase in its mRNA level by submergence, ethylene, and gibberellin treatments. AB - A cDNA from deep water rice treated with ethylene, encoding an ethylene receptor homologous to Arabidopsis thaliana ETR2 and EIN4, was isolated using differential display and RACE techniques. The cDNA (2880 bp), corresponding to the Os-ERL1 gene (Oryza sativa ETHYLENE RESPONSE 2 like 1; GenBank accession number AB107219), contained an open reading frame of 2289 bp coding for 763 amino acids. The protein Os-ERL1 has 50% and 52% similarity to Arabidopsis ETR2 and EIN4, respectively. The Os-ERL1 gene was up-regulated by flooding, and by treatment with ethylene and gibberellin. These results suggest that deep water rice responds to flooding by increasing the number of its ethylene receptors. AD - Division of Biological Resource Science, Graduate School of Agricultural Science, Tohoku University, Kawatabi, Naruko Miyagi 989-6711, Japan. AU - Watanabe H AU - Saigusa M AU - Hase S AU - Hayakawa T AU - Satoh S LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1093/jxb/erh110 [doi] AID - erh110 [pii] PST - aheadofprint SO - J Exp Bot 2004 Mar 12;. PMID- 15020631 OWN - NLM STAT- publisher DA - 20040315 IS - 0022-0957 DP - 2004 Mar 12 TI - Molecular cloning of low-temperature-inducible ribosomal proteins from soybean. AB - Three ribosomal protein genes induced by low-temperature treatment were isolated from soybean. GmRPS13 (742 bp) encodes a 17.1 kDa protein which has 95% identity with the 40S ribosomal protein S13 of Panax ginseng (AB043974). GmRPS6 (925 bp) encodes a 28.1 kDa protein which has 94% identity with the 40S ribosomal protein S6 of Asparagus officinalis (AJ277533). GmRPL37 (494 bp) encodes a 10.7 kDa protein which has 85% identity with the 60S ribosomal protein L37 of Arabidopsis thaliana (AF370216). The expression of these ribosomal protein genes started to increase 3 d after low-temperature treatment, whereas the cold-stress protein src1 was highly induced from the first day. Such late response of these ribosomal protein genes may be due to secondary signals during cold adaptation. The induction of ribosomal protein genes might enhance the translation process or help proper ribosome functioning under low-temperature conditions. AD - Department of Plant Biotechnology, Dong-A University, Busan, 604-714, South Korea. AU - Kim KY AU - Park SW AU - Chung YS AU - Chung CH AU - Kim JI AU - Lee JH LA - ENG PT - JOURNAL ARTICLE TA - J Exp Bot JID - 9882906 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 10.1093/jxb/erh125 [doi] AID - erh125 [pii] PST - aheadofprint SO - J Exp Bot 2004 Mar 12;. PMID- 15020484 OWN - NLM STAT- in-process DA - 20040315 IS - 0016-6731 VI - 166 IP - 2 DP - 2004 Feb TI - Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. PG - 1011-23 AB - Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG-like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity. AD - Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. ekramer@oeb.harvard.edu FAU - Kramer, Elena M AU - Kramer EM FAU - Jaramillo, M Alejandra AU - Jaramillo MA FAU - Di Stilio, Veronica S AU - Di Stilio VS LA - eng SI - GENBANK/AY464093 SI - GENBANK/AY464094 SI - GENBANK/AY464095 SI - GENBANK/AY464096 SI - GENBANK/AY464097 SI - GENBANK/AY464098 SI - GENBANK/AY464099 SI - GENBANK/AY464100 SI - GENBANK/AY464101 SI - GENBANK/AY464102 SI - GENBANK/AY464103 SI - GENBANK/AY464104 SI - GENBANK/AY464105 SI - GENBANK/AY464106 SI - GENBANK/AY464107 SI - GENBANK/AY464108 SI - GENBANK/AY464109 SI - GENBANK/AY464110 SI - GENBANK/AY464111 SI - GENBANK/AY464112 SI - GENBANK/AY464113 SI - GENBANK/AY464114 SI - GENBANK/AY464115 SI - GENBANK/AY464116 SI - GENBANK/AY464117 SI - GENBANK/AY464118 SI - GENBANK/AY464119 SI - GENBANK/AY464120 PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 166/2/1011 [pii] PST - ppublish SO - Genetics 2004 Feb;166(2):1011-23. PMID- 15020479 OWN - NLM STAT- in-process DA - 20040315 IS - 0016-6731 VI - 166 IP - 2 DP - 2004 Feb TI - Meiotic recombination between paralogous RBCSB genes on sister chromatids of Arabidopsis thaliana. PG - 947-57 AB - Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 x 10(-6). A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster. AD - Plant Pathology, Physiology, and Weed Science Department, Fralin Biotechnology Center, Virginia Polytechnic Institute and State University, Blacksburg 24061-0346, USA. jelesko@vt.edu FAU - Jelesko, John G AU - Jelesko JG FAU - Carter, Kristy AU - Carter K FAU - Thompson, Whitney AU - Thompson W FAU - Kinoshita, Yuki AU - Kinoshita Y FAU - Gruissem, Wilhelm AU - Gruissem W LA - eng GR - R01GM62352/GM/NIGMS PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 166/2/947 [pii] PST - ppublish SO - Genetics 2004 Feb;166(2):947-57. PMID- 15020435 OWN - NLM STAT- in-process DA - 20040315 IS - 0016-6731 VI - 166 IP - 1 DP - 2004 Jan TI - The dominance of the herbicide resistance cost in several Arabidopsis thaliana mutant lines. PG - 449-60 AB - Resistance evolution depends upon the balance between advantage and disadvantage (cost) conferred in treated and untreated areas. By analyzing morphological characters and simple fitness components, the cost associated with each of eight herbicide resistance alleles (acetolactate synthase, cellulose synthase, and auxin-induced target genes) was studied in the model plant Arabidopsis thaliana. The use of allele-specific PCR to discriminate between heterozygous and homozygous plants was used to provide insights into the dominance of the resistance cost, a parameter rarely described. Morphological characters appear more sensitive than fitness (seed production) because 6 vs. 4 differences between resistant and sensitive homozygous plants were detected, respectively. Dominance levels for the fitness cost ranged from recessivity (csr1-1, ixr1-2, and axr1-3) to dominance (axr2-1) to underdominance (aux1-7). Furthermore, the dominance level of the herbicide resistance trait did not predict the dominance level of the cost of resistance. The relationship of our results to theoretical predictions of dominance and the consequences of fitness cost and its dominance in resistance management are discussed. AD - UMR Biologie et Gestion des Adventices, Institut National de la Recherche Agronomique, 21065 Dijon Cedex, France. roux@dijon.inra.fr FAU - Roux, Fabrice AU - Roux F FAU - Gasquez, Jacques AU - Gasquez J FAU - Reboud, Xavier AU - Reboud X LA - eng PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 166/1/449 [pii] PST - ppublish SO - Genetics 2004 Jan;166(1):449-60. PMID- 15020434 OWN - NLM STAT- in-process DA - 20040315 IS - 0016-6731 VI - 166 IP - 1 DP - 2004 Jan TI - An internal rearrangement in an Arabidopsis inverted repeat locus impairs DNA methylation triggered by the locus. PG - 437-48 AB - In plants, transcribed inverted repeats trigger RNA interference (RNAi) and DNA methylation of identical sequences. RNAi is caused by processing of the double-stranded RNA (dsRNA) transcript into small RNAs that promote degradation of complementary RNA sequences. However, the signals for DNA methylation remain to be fully elucidated. The Arabidopsis tryptophan biosynthetic PAI genes provide an endogenous inverted repeat that triggers DNA methylation of PAI-identical sequences. In the Wassilewskija strain, two PAI genes are arranged as a tail-to-tail inverted repeat and transcribed from an unmethylated upstream promoter. This locus directs its own methylation, as well as methylation of two unlinked singlet PAI genes. Previously, we showed that the locus is likely to make an RNA signal for methylation because suppressed transcription of the inverted repeat leads to reduced PAI methylation. Here we characterize a central rearrangement in the inverted repeat that also confers reduced PAI methylation. The rearrangement creates a premature polyadenylation signal and suppresses readthrough transcription into palindromic PAI sequences. Thus, a likely explanation for the methylation defect of the mutant locus is a failure to produce readthrough dsRNA methylation triggers. AD - Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA. FAU - Melquist, Stacey AU - Melquist S FAU - Bender, Judith AU - Bender J LA - eng SI - GENBANK/AY357734 GR - ES 07141/ES/NIEHS GR - GM-61148/GM/NIGMS PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 166/1/437 [pii] PST - ppublish SO - Genetics 2004 Jan;166(1):437-48. PMID- 15020431 OWN - NLM STAT- in-process DA - 20040315 IS - 0016-6731 VI - 166 IP - 1 DP - 2004 Jan TI - Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. PG - 373-88 AB - Nucleotide variation in eight effectively unlinked genes was surveyed in species-wide samples of the closely related outbreeding species Arabidopsis halleri and A. lyrata ssp. petraea and in three of these genes in A. lyrata ssp. lyrata and A. thaliana. Significant genetic differentiation was observed more frequently in A. l. petraea than in A. halleri. Average estimates of nucleotide variation were highest in A. l. petraea and lowest in A. l. lyrata, reflecting differences among species in effective population size. The low level of variation in A. l. lyrata is concordant with a bottleneck effect associated with its origin. The A. halleri/A. l. petraea speciation process was studied, considering the orthologous sequences of an outgroup species (A. thaliana). The high number of ancestral mutations relative to exclusive polymorphisms detected in A. halleri and A. l. petraea, the significant results of the multilocus Fay and Wu H tests, and haplotype sharing between the species indicate introgression subsequent to speciation. Average among-population variation in A. halleri and A. l. petraea was approximately 1.5- and 3-fold higher than that in the inbreeder A. thaliana. The detected reduction of variation in A. thaliana is less than that expected from differences in mating system alone, and therefore from selective processes related to differences in the effective recombination rate, but could be explained by differences in population structure. AD - Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain. FAU - Ramos-Onsins, Sebastian E AU - Ramos-Onsins SE FAU - Stranger, Barbara E AU - Stranger BE FAU - Mitchell-Olds, Thomas AU - Mitchell-Olds T FAU - Aguade, Montserrat AU - Aguade M LA - eng SI - GENBANK/AJ582819 SI - GENBANK/AJ582820 SI - GENBANK/AJ582821 SI - GENBANK/AJ582822 SI - GENBANK/AJ582823 SI - GENBANK/AJ582824 SI - GENBANK/AJ582825 SI - GENBANK/AJ582826 SI - GENBANK/AJ582827 SI - GENBANK/AJ582828 SI - GENBANK/AJ582829 SI - GENBANK/AJ582830 SI - GENBANK/AJ582831 SI - GENBANK/AJ582832 SI - GENBANK/AJ582833 SI - GENBANK/AJ582834 SI - GENBANK/AJ582835 SI - GENBANK/AJ582836 SI - GENBANK/AJ582837 SI - GENBANK/AJ582838 SI - GENBANK/AJ582839 SI - GENBANK/AJ582840 SI - GENBANK/AJ582841 SI - GENBANK/AJ582842 SI - GENBANK/AJ582843 SI - GENBANK/AJ582844 SI - GENBANK/AJ582845 SI - GENBANK/AJ582846 SI - GENBANK/AJ582847 SI - GENBANK/AJ582848 SI - GENBANK/AJ582849 SI - GENBANK/AJ582850 SI - GENBANK/AJ582851 SI - GENBANK/AJ582852 SI - GENBANK/AJ582853 SI - GENBANK/AJ582854 SI - GENBANK/AJ582855 SI - GENBANK/AJ582856 SI - GENBANK/AJ582857 SI - GENBANK/AJ582858 SI - GENBANK/AJ582859 SI - GENBANK/AJ582860 SI - GENBANK/AJ582861 SI - GENBANK/AJ582862 SI - GENBANK/AJ582863 SI - GENBANK/AJ582864 SI - GENBANK/AJ582865 SI - GENBANK/AJ582866 SI - GENBANK/AJ582867 SI - GENBANK/AJ582868 SI - GENBANK/AJ582869 SI - GENBANK/AJ582870 SI - GENBANK/AJ582871 SI - GENBANK/AJ582872 SI - GENBANK/AJ582873 SI - GENBANK/AJ582874 SI - GENBANK/AJ582875 SI - GENBANK/AJ582876 SI - GENBANK/AJ582877 SI - GENBANK/AJ582878 SI - GENBANK/AJ582879 SI - GENBANK/AJ582880 SI - GENBANK/AJ582881 SI - GENBANK/AJ582882 SI - GENBANK/AJ582883 SI - GENBANK/AJ582884 SI - GENBANK/AJ582885 SI - GENBANK/AJ582886 SI - GENBANK/AJ582887 SI - GENBANK/AJ582888 SI - GENBANK/AJ582889 SI - GENBANK/AJ582890 SI - GENBANK/AJ582891 SI - GENBANK/AJ582892 SI - GENBANK/AJ582893 SI - GENBANK/AJ582894 SI - GENBANK/AJ582895 SI - GENBANK/AJ582896 SI - GENBANK/AJ582897 SI - GENBANK/AJ582898 SI - GENBANK/AJ582899 SI - GENBANK/AJ582900 SI - GENBANK/AJ582901 SI - GENBANK/AJ582902 SI - GENBANK/AJ582903 SI - GENBANK/AJ582904 SI - GENBANK/AJ582905 SI - GENBANK/AJ582906 SI - GENBANK/AJ582907 SI - GENBANK/AJ582908 SI - GENBANK/AJ582909 SI - GENBANK/AJ582910 SI - GENBANK/AJ619855 SI - GENBANK/AJ619856 SI - GENBANK/AJ619857 SI - GENBANK/AJ619858 SI - GENBANK/AJ619859 SI - GENBANK/AJ619860 SI - GENBANK/AJ619861 SI - GENBANK/AJ619862 SI - GENBANK/AJ619863 SI - GENBANK/AJ619864 SI - GENBANK/AJ619865 SI - GENBANK/AJ619866 SI - GENBANK/AJ619867 SI - GENBANK/AJ619868 SI - GENBANK/AJ619869 SI - GENBANK/AJ619870 SI - GENBANK/AJ619871 SI - GENBANK/AJ619872 SI - GENBANK/AJ619873 SI - GENBANK/AJ619874 SI - GENBANK/AJ619875 SI - GENBANK/AJ619876 SI - GENBANK/AJ619877 SI - GENBANK/AJ619878 SI - GENBANK/AJ619879 SI - GENBANK/AJ619880 SI - GENBANK/AJ619881 SI - GENBANK/AJ619882 SI - GENBANK/AJ619883 SI - GENBANK/AJ619884 SI - GENBANK/AJ619885 SI - GENBANK/AJ619886 SI - GENBANK/AJ619887 SI - GENBANK/AJ619888 SI - GENBANK/AJ619889 SI - GENBANK/AJ619890 SI - GENBANK/AJ619891 SI - GENBANK/AJ619892 SI - GENBANK/AJ619893 SI - GENBANK/AJ619894 SI - GENBANK/AJ619895 SI - GENBANK/AJ619896 SI - GENBANK/AJ619897 SI - GENBANK/AJ619898 SI - GENBANK/AJ619899 SI - GENBANK/AJ619900 SI - GENBANK/AJ619901 SI - GENBANK/AJ619902 SI - GENBANK/AJ619903 SI - GENBANK/AJ619904 SI - GENBANK/AJ619905 SI - GENBANK/AJ619906 SI - GENBANK/AJ619907 SI - GENBANK/AJ619908 SI - GENBANK/AJ619909 SI - GENBANK/AJ619910 SI - GENBANK/AJ619911 SI - GENBANK/AJ619912 SI - GENBANK/AJ619913 SI - GENBANK/AJ619914 SI - GENBANK/AJ619915 SI - GENBANK/AJ619916 SI - GENBANK/AJ619917 SI - GENBANK/AJ619918 SI - GENBANK/AJ619919 SI - GENBANK/AJ619920 SI - GENBANK/AJ619921 SI - GENBANK/AJ619922 SI - GENBANK/AJ619923 SI - GENBANK/AJ619924 SI - GENBANK/AJ619925 SI - GENBANK/AJ619926 SI - GENBANK/AJ619927 SI - GENBANK/AJ619928 SI - GENBANK/AJ619929 SI - GENBANK/AJ619930 SI - GENBANK/AJ619931 SI - GENBANK/AJ619932 SI - GENBANK/AJ619933 SI - GENBANK/AJ619934 SI - GENBANK/AJ619935 SI - GENBANK/AJ619936 SI - GENBANK/AJ619937 SI - GENBANK/AJ619938 SI - GENBANK/AJ619939 PT - Journal Article PL - United States TA - Genetics JID - 0374636 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 AID - 166/1/373 [pii] PST - ppublish SO - Genetics 2004 Jan;166(1):373-88. PMID- 15020054 OWN - NLM STAT- in-process DA - 20040315 IS - 0006-3002 VI - 1677 IP - 1-3 DP - 2004 Mar 15 TI - Genetic analysis of RNA-mediated transcriptional gene silencing. PG - 129-41 AB - The 'nuclear side' of RNA interference (RNAi) is increasingly recognized as an integral part of RNA-mediated gene silencing networks. Current data are consistent with the idea that epigenetic changes, such as DNA (cytosine-5) methylation and histone modifications, can be targeted to identical DNA sequences by short RNAs derived via Dicer cleavage of double-stranded RNA (dsRNA). To determine the relationships among RNA signals, DNA methylation and chromatin structure, we are carrying out a genetic analysis of RNA-mediated transcriptional gene silencing (TGS) in Arabidopsis. Results obtained so far indicate that in response to RNA signals, different site-specific DNA methyltransferases (DMTases) cooperate with each other and eventually with histone-modifying enzymes to establish and maintain a transcriptionally inactive state at a homologous target promoter. Processing of dsRNA in Arabidopsis occurs in the nucleus and in the cytoplasm, where distinct Dicer-like (DCL) activities are thought to generate functionally distinct classes of short RNAs. RNA silencing pathways thus operate throughout the cell to defend against invasive nucleic acids and to regulate genome structure and function. AD - Institute of Molecular Biology, Austrian Academy of Sciences, Billrothstrasse 11, A-5020, Salzburg, Austria. mmatzke@imb.oeaw.ac.at FAU - Matzke, Marjori AU - Matzke M FAU - Aufsatz, Werner AU - Aufsatz W FAU - Kanno, Tatsuo AU - Kanno T FAU - Daxinger, Lucia AU - Daxinger L FAU - Papp, Istvan AU - Papp I FAU - Mette, M Florian AU - Mette MF FAU - Matzke, Antonius J M AU - Matzke AJ LA - eng PT - Journal Article PL - Netherlands TA - Biochim Biophys Acta JID - 0217513 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Jul/25 [received] PHST- 2003/Oct/21 [revised] PHST- 2003/Oct/21 [accepted] AID - 10.1016/j.bbaexp.2003.10.015 [doi] AID - S0167478103002859 [pii] PST - ppublish SO - Biochim Biophys Acta 2004 Mar 15;1677(1-3):129-41. PMID- 15019989 OWN - NLM STAT- in-process DA - 20040315 IS - 0378-1119 VI - 328 DP - 2004 Mar 17 TI - VAAMANA--a BEL1-like homeodomain protein, interacts with KNOX proteins BP and STM and regulates inflorescence stem growth in Arabidopsis. PG - 103-11 AB - Plant shoot growth depends on the activity of the shoot apical meristem (SAM), where organ primordia are initiated. In turn, the function of the SAM depends on the activities of homeodomain (HD) proteins of the knotted1-like homeobox (KNOX) class [Long et al., Nature 379 (1996) 66; Vollbrecht et al., Development 127 (2000) 3161]. In plants, KNOX proteins have been shown to interact specifically with the BEL1-like (BELL) class of homeodomain proteins [Bellaoui et al., Plant Cell 13 (2001) 2455; Muller et al., Plant 27 (2001) 13; Smith et al., Proc. Natl. Acad. Sci. USA 99 (2002) 9579], through a domain conserved between plants and animals. We have isolated a mutation in a BELL homeobox gene VAAMANA (VAN) that causes a dwarf phenotype. In addition, van inflorescence stems have clusters of cauline leaves; typically three are produced at each node. VAN interacts specifically with the class I KNOX proteins SHOOTMERISTEMLESS (STM), BREVIPEDICELLUS (BP), and KNAT6 (K6), and nuclear localisation of a VAN-GFP fusion depends on co-expression of STM or BP in tobacco leaves. This suggests that localisation of VAN, like that of the animal PBC homeodomain protein [Rieckhof et al., Cell 91 (1997) 171; Berthelsen et al., Genes Dev. 13 (1999) 946], is also regulated by interaction with a partner homeodomain protein. AD - Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. Anuj.Bhatt@plants.ox.ac.uk FAU - Bhatt, Anuj M AU - Bhatt AM FAU - Etchells, J Peter AU - Etchells JP FAU - Canales, Claudia AU - Canales C FAU - Lagodienko, Andrey AU - Lagodienko A FAU - Dickinson, Hugh AU - Dickinson H LA - eng PT - Journal Article PL - Netherlands TA - Gene JID - 7706761 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Aug/28 [received] PHST- 2003/Nov/14 [revised] PHST- 2003/Dec/02 [accepted] AID - 10.1016/j.gene.2003.12.033 [doi] AID - S0378111903011302 [pii] PST - ppublish SO - Gene 2004 Mar 17;328:103-11. PMID- 15019988 OWN - NLM STAT- in-process DA - 20040315 IS - 0378-1119 VI - 328 DP - 2004 Mar 17 TI - AtPARN is an essential poly(A) ribonuclease in Arabidopsis. PG - 95-102 AB - Deadenylation is the first and rate-limiting step in the degradation of many mRNAs in a wide-range of organisms from yeast to higher eukaryotes. It can also play a regulatory role in early development. In this study, we examined the Arabidopsis homolog of poly(A) ribonuclease (PARN), a deadenylase first identified in mammals and absent from yeast. Consistent with the conservation of domains and residues important for catalytic activity, Arabidopsis PARN (AtPARN) expressed in Escherichia coli has poly(A) degradation activity in vitro. Protein localization experiments in plant cells indicate that AtPARN resides in both the nucleus and cytoplasm. To address the importance of the enzyme in vivo, we identified three independent T-DNA insertion mutants of AtPARN which interrupt the gene at different positions between the ATG and the stop codon. All three alleles cause lethality prior to seed germination, indicating that AtPARN is an essential gene first required during early development. Although homologous genes have yet to be inactivated in any other organism, our observations argue for the critical importance of PARN and suggest that it may be essential in many other multicellular eukaryotes. AD - Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA. FAU - Chiba, Yukako AU - Chiba Y FAU - Johnson, Mark A AU - Johnson MA FAU - Lidder, Preetmoninder AU - Lidder P FAU - Vogel, Jonathan T AU - Vogel JT FAU - van Erp, Harrie AU - van Erp H FAU - Green, Pamela J AU - Green PJ LA - eng PT - Journal Article PL - Netherlands TA - Gene JID - 7706761 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Nov/05 [received] PHST- 2003/Nov/24 [accepted] AID - 10.1016/j.gene.2003.11.028 [doi] AID - S0378111903011004 [pii] PST - ppublish SO - Gene 2004 Mar 17;328:95-102. PMID- 15019616 OWN - NLM STAT- in-process DA - 20040315 IS - 1055-7903 VI - 31 IP - 1 DP - 2004 Apr TI - Comparative analysis of NBS domain sequences of NBS-LRR disease resistance genes from sunflower, lettuce, and chicory. PG - 153-63 AB - Plant resistance to many types of pathogens and pests can be achieved by the presence of disease resistance (R) genes. The nucleotide binding site-leucine rich repeat (NBS-LRR) class of R-genes is the most commonly isolated class of R-genes and makes up a super-family, which is often arranged in the genome as large multi-gene clusters. The NBS domain of these genes can be targeted by polymerase chain reaction (PCR) amplification using degenerate primers. Previous studies have used PCR derived NBS sequences to investigate both ancient R-gene evolution and recent evolution within specific plant families. However, comparative studies with the Asteraceae family have largely been ignored. In this study, we address recent evolution of NBS sequences within the Asteraceae and extend the comparison to the Arabidopsis thaliana genome. Using multiple sets of primers, NBS fragments were amplified from genomic DNA of three species from the family Asteraceae: Helianthus annuus (sunflower), Lactuca sativa (lettuce), and Cichorium intybus (chicory). Analysis suggests that Asteraceae species share distinct families of R-genes, composed of genes related to both coiled-coil (CC) and toll-interleukin-receptor homology (TIR) domain containing NBS-LRR R-genes. Between the most closely related species, (lettuce and chicory) a striking similarity of CC subfamily composition was identified, while sunflower showed less similarity in structure. These sequences were also compared to the A. thaliana genome. Asteraceae NBS gene subfamilies appear to be distinct from Arabidopsis gene clades. These data suggest that NBS families in the Asteraceae family are ancient, but also that gene duplication and gene loss events occur and change the composition of these gene subfamilies over time. AD - Department of Biology, University of Massachusetts, Boston, MA 02125-3393, USA. FAU - Plocik, Alex AU - Plocik A FAU - Layden, Jenn AU - Layden J FAU - Kesseli, Rick AU - Kesseli R LA - eng PT - Journal Article PL - United States TA - Mol Phylogenet Evol JID - 9304400 SB - IM EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Mar/25 [received] PHST- 2003/Jul/02 [revised] AID - 10.1016/S1055-7903(03)00274-4 [doi] AID - S1055790303002744 [pii] PST - ppublish SO - Mol Phylogenet Evol 2004 Apr;31(1):153-63. PMID- 15018639 OWN - NLM STAT- publisher DA - 20040318 IS - 1471-2229 VI - 4 IP - 1 DP - 2004 Feb 10 TI - In vivo analysis of interactions between GFP-labeled microfilaments and plastid stromules. PG - 2 AB - BACKGROUND: Plastid stromules are stroma-filled tubules that extend from the surface of plastids in higher plants and allow the exchange of protein molecules between plastids. These structures are highly dynamic; stromules change both their shape and position in the cytoplasm very rapidly. Previous studies with microfilament inhibitors indicated that stromule shape and movement are dependent on the actin cytoskeleton. To learn more about the nature of the interactions of stromules and the cytoskeleton, we imaged fluorescently-labeled microfilaments and plastids. RESULTS: We have used Arabidopsis thaliana plants expressing green fluorescent protein fused to the human actin-binding protein talin to observe microfilaments and their relationship to stromules in vivo. Microfilaments were observed in close contact with stromules and plastid bodies of hypocotyl epidermis. Time-lapse confocal microscopy revealed that microfilament rearrangements were associated with changes in plastid and stromule morphology and position. We also observed close interactions between mitochondria and stromules in double-labeled cells. CONCLUSION: Our results indicate a correlation between the rearrangement of microfilaments and changes in the shape and position of plastids and stromules. Stromules interact with microfilaments that may also be utilized by mitochondria and other organelles. The interaction of microfilaments and plastids is likely to be mediated by actin-binding proteins on the plastid envelope membrane. AD - Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA. mrh5@cornell.edu AU - Kwok EY AU - Hanson MR LA - ENG PT - JOURNAL ARTICLE DEP - 20040210 TA - BMC Plant Biol JID - 100967807 EDAT- 2004/03/17 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Dec/01 [received] PHST- 2004/Feb/10 [accepted] PHST- 2004/Feb/10 [aheadofprint] AID - 10.1186/1471-2229-4-2 [doi] AID - 1471-2229-4-2 [pii] PST - epublish SO - BMC Plant Biol 2004 Feb 10;4(1):2. PMID- 15016992 OWN - NLM STAT- completed DA - 20040312 DCOM- 20040324 IS - 1095-9203 VI - 303 IP - 5664 DP - 2004 Mar 12 TI - The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. PG - 1640-4 AB - Plants with a winter growth habit flower earlier when exposed for several weeks to cold temperatures, a process called vernalization. We report here the positional cloning of the wheat vernalization gene VRN2, a dominant repressor of flowering that is down-regulated by vernalization. Loss of function of VRN2, whether by natural mutations or deletions, resulted in spring lines, which do not require vernalization to flower. Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month. AD - Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA. FAU - Yan, Liuling AU - Yan L FAU - Loukoianov, Artem AU - Loukoianov A FAU - Blechl, Ann AU - Blechl A FAU - Tranquilli, Gabriela AU - Tranquilli G FAU - Ramakrishna, Wusirika AU - Ramakrishna W FAU - SanMiguel, Phillip AU - SanMiguel P FAU - Bennetzen, Jeffrey L AU - Bennetzen JL FAU - Echenique, Viviana AU - Echenique V FAU - Dubcovsky, Jorge AU - Dubcovsky J LA - eng SI - GENBANK/AY485644 PT - Journal Article PL - United States TA - Science JID - 0404511 RN - 0 (Plant Proteins) RN - 0 (RNA, Messenger) RN - 0 (RNA, Plant) SB - IM CIN - Science. 2004 Mar 12;303(5664):1607. PMID: 15016978 MH - Alleles MH - Amino Acid Sequence MH - Arabidopsis/genetics/growth & development MH - Base Sequence MH - Chromosome Mapping MH - Cloning, Molecular MH - *Cold MH - Down-Regulation MH - Epistasis, Genetic MH - Evolution, Molecular MH - Flowers/*growth & development MH - Gene Deletion MH - *Gene Expression Regulation, Plant MH - Genes, Plant MH - Hordeum/genetics MH - Molecular Sequence Data MH - Mutation MH - Plant Proteins/chemistry/genetics/physiology MH - Plants, Genetically Modified MH - Promoter Regions (Genetics) MH - Protein Structure, Tertiary MH - RNA Interference MH - RNA, Messenger/genetics/metabolism MH - RNA, Plant/genetics/metabolism MH - Seasons MH - Support, U.S. Gov't, Non-P.H.S. MH - Transcription, Genetic MH - Triticum/*genetics/*growth & development MH - Variation (Genetics) EDAT- 2004/03/16 05:00 MHDA- 2004/03/25 05:00 AID - 10.1126/science.1094305 [doi] AID - 303/5664/1640 [pii] PST - ppublish SO - Science 2004 Mar 12;303(5664):1640-4. PMID- 15016978 OWN - NLM STAT- completed DA - 20040312 DCOM- 20040324 LR - 20040419 IS - 1095-9203 VI - 303 IP - 5664 DP - 2004 Mar 12 TI - Plant biology. Remembrance of winter past. PG - 1607 FAU - Marx, Jean AU - Marx J LA - eng PT - Comment PT - News PL - United States TA - Science JID - 0404511 RN - 0 (Arabidopsis Proteins) RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (FLF protein, Arabidopsis) RN - 0 (FRI protein, Arabidopsis) RN - 0 (MADS Domain Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Plant Proteins) RN - 0 (Repressor Proteins) RN - 0 (VRN1 protein, Arabidopsis) RN - 0 (VRN2 gene product) SB - IM CON - Science. 2004 Mar 12;303(5664):1640-4. PMID: 15016992 MH - Arabidopsis/*genetics/growth & development MH - Arabidopsis Proteins/genetics/physiology MH - Carrier Proteins/genetics/physiology MH - Cloning, Molecular MH - *Cold MH - DNA-Binding Proteins/genetics/physiology MH - Flowers/*growth & development MH - *Gene Expression Regulation, Plant MH - Genes, Plant MH - Genome, Plant MH - MADS Domain Proteins/genetics/physiology MH - Nuclear Proteins/genetics/physiology MH - Plant Proteins/physiology MH - Repressor Proteins/genetics/physiology MH - Triticum/*genetics/*growth & development EDAT- 2004/03/16 05:00 MHDA- 2004/03/25 05:00 AID - 10.1126/science.303.5664.1607 [doi] AID - 303/5664/1607 [pii] PST - ppublish SO - Science 2004 Mar 12;303(5664):1607. PMID- 15016565 OWN - NLM STAT- in-process DA - 20040312 IS - 0031-9422 VI - 65 IP - 6 DP - 2004 Mar TI - Universally occurring phenylpropanoid and species-specific indolic metabolites in infected and uninfected Arabidopsis thaliana roots and leaves. PG - 691-9 AB - A total of eleven alkali-released, aromatic compounds were identified by HPLC, MS and NMR analyses in cell wall extracts from Arabidopsis thaliana roots. Nine of them together constituted the three complete series of 4-hydroxy-, 4-hydroxy-3-methoxy, and 4-hydroxy-3,5-dimethoxy-substituted benzaldehydes, benzoic acids and cinnamic acids. The other two were indolic metabolites: indole-3-carboxylic acid and indole-3-carbaldehyde. Qualitatively similar, but quantitatively distinct profiles were obtained using cell-wall extracts from A. thaliana leaves. Several of these compounds, particularly indole-3-carboxylic acid, 4-hydroxybenzoic acid and all four aldehydes, increased considerably in concentration upon infection of roots with Pythium sylvaticum, as did at least some of them upon infection of leaves with Pseudomonas syringae pv tomato. Comparison of these results with analogous data on a variety of different plant species suggests a remarkable structural uniformity among the majority of constitutive as well as infection-induced, aromatic cell wall-bound compounds throughout the entire plant kingdom-in sharp contrast to the highly species-specific, chemically highly divers bouquets of soluble aromatic metabolites. AD - Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Cologne, Germany. FAU - Tan, Jianwen AU - Tan J FAU - Bednarek, Pawel AU - Bednarek P FAU - Liu, Jikai AU - Liu J FAU - Schneider, Bernd AU - Schneider B FAU - Svatos, Ales AU - Svatos A FAU - Hahlbrock, Klaus AU - Hahlbrock K LA - eng PT - Journal Article PL - United States TA - Phytochemistry JID - 0151434 SB - IM EDAT- 2004/03/16 05:00 MHDA- 2004/03/16 05:00 PHST- 2003/Sep/24 [received] PHST- 2003/Nov/21 [revised] AID - 10.1016/j.phytochem.2003.12.009 [doi] AID - S0031942203007271 [pii] PST - ppublish SO - Phytochemistry 2004 Mar;65(6):691-9. PMID- 15016364 OWN - NLM STAT- in-process DA - 20040312 IS - 0969-2126 VI - 12 IP - 3 DP - 2004 Mar TI - Crystal structure of the type III effector AvrB from Pseudomonas syringae. PG - 487-94 AB - AvrB is a Pseudomonas syringae type III effector protein that is translocated into host plant cells during attempted pathogenesis. Arabidopsis harboring the corresponding resistance protein RPM1 can detect AvrB and mount a rapid host defense response, thus avoiding active infection. In the plant cell, AvrB induces phosphorylation of RIN4, a key component in AvrB/RPM1 recognition. Although the AvrB/RPM1 system is among the best characterized of the numerous bacterial effector/plant resistance protein systems involved in plant disease resistance and pathogenesis, the details of the molecular recognition mechanism are still unclear. To gain further insights, the crystal structure of AvrB was determined. The 2.2 A structure exhibits a novel mixed alpha/beta bilobal fold. Aided by the structural information, we demonstrate that one lobe is the determinant of AvrB/RPM1 recognition specificity. This structural information and preliminary structure-function studies provide a framework for the future understanding of AvrB function on the molecular level. AD - Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. FAU - Lee, Christian C AU - Lee CC FAU - Wood, Michelle D AU - Wood MD FAU - Ng, Kenneth AU - Ng K FAU - Andersen, Carsten B AU - Andersen CB FAU - Liu, Yi AU - Liu Y FAU - Luginbuhl, Peter AU - Luginbuhl P FAU - Spraggon, Glen AU - Spraggon G FAU - Katagiri, Fumiaki AU - Katagiri F LA - eng SI - PDB/1NH1 PT - Journal Article PL - United States TA - Structure (Camb) JID - 101087697 SB - IM EDAT- 2004/03/16 05:00 MHDA- 2004/03/16 05:00 PHST- 2003/Jun/20 [received] PHST- 2003/Nov/12 [revised] PHST- 2003/Nov/28 [accepted] AID - 10.1016/j.str.2004.02.013 [doi] AID - S0969212604000553 [pii] PST - ppublish SO - Structure (Camb) 2004 Mar;12(3):487-94. PMID- 15015772 OWN - NLM STAT- completed DA - 20040312 DCOM- 20040401 LR - 20040420 IS - 0167-594X VI - 66 IP - 1-2 DP - 2004 Jan TI - Induction of apoptosis in resistant glioma cells by synthetic caspase-activation. PG - 71-9 AB - The detailed mechanisms behind the resistance of malignant gliomas to therapy are not known. Inherent resistance to apoptosis is, however, one plausible explanation. In the present study we tried to delineate the molecular defects and to induce apoptosis by inducible caspases in three apparently apoptosis resistant glioma cell lines. U-105 MG, U-251 MG, and SF-767 were resistant to Fas-induced apoptosis as shown by the lack of Fas-induced cell death, morphological changes, annexin-V reactivity, Parp cleavage, caspase-3 cleavage, and caspase-3 activation. The glioma cells showed no consistent down-regulation of the pro-apoptotic proteins Fas, Fadd, caspase-3, caspase-8, caspase-9, Apaf-1, Bid, Bad, or Bax, and no consistent up-regulation of the anti-apoptotic proteins Bcl-x or Bcl-2. In U-105 MG, Fas was, however, not detected at the cell surface indicating intracellular retention. To assess if the apoptotic blocks could be by-passed, we introduced the so-called artificial death switches, i.e., inducible caspases and Fadd, into the glioma cells. Synthetic activation of inducible caspase-3, but not of caspase-8, resulted in apoptosis in the three glioma cell lines and inducible Fadd induced apoptosis in SF-767. The results were consistent with a block in the apoptotic signaling pathways of glioma cells between caspase-8 and caspase-3 activation, and that inducible Fadd could induce caspase-8 independent apoptosis in some cells. Apparently resistant glioma cells could thus be induced to undergo apoptosis by activation of appropriate death switches. This might have implications for the design of future therapeutic strategies. AD - Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden. FAU - Karlsson, Terese AU - Karlsson T FAU - Henriksson, Roger AU - Henriksson R FAU - Hedman, Hakan AU - Hedman H LA - eng PT - Journal Article PL - Netherlands TA - J Neurooncol JID - 8309335 RN - 0 (Antigens, CD95) RN - 0 (Arabidopsis Proteins) RN - 0 (Neoplasm Proteins) RN - EC 1.14.99.- (Fad7 protein, Arabidopsis) RN - EC 1.14.99.- (Fatty Acid Desaturases) RN - EC 3.4.22.- (Caspases) RN - EC 3.4.22.- (caspase 8) RN - EC 3.4.22.- (caspase-3) SB - IM MH - Antigens, CD95/pharmacology MH - *Apoptosis/drug effects MH - Arabidopsis Proteins/metabolism MH - Caspases/*metabolism MH - Drug Resistance, Neoplasm MH - Enzyme Activation MH - Fatty Acid Desaturases/metabolism MH - Glioma/enzymology/metabolism/pathology/*physiopathology MH - Human MH - Jurkat Cells MH - Neoplasm Proteins/metabolism MH - Support, Non-U.S. Gov't EDAT- 2004/03/16 05:00 MHDA- 2004/04/02 05:00 PST - ppublish SO - J Neurooncol 2004 Jan;66(1-2):71-9. PMID- 15014998 OWN - NLM STAT- publisher DA - 20040311 IS - 0032-0935 DP - 2004 Mar 10 TI - Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase. AB - In contrast to oil seeds, potato ( Solanum tuberosum L.) is characterized by a high amount of starch stored in the tubers. To assess the capacity for oil synthesis in potato tubers, the changes in lipid content and flux into lipid synthesis were explored in transgenic potatoes altered in carbohydrate or lipid metabolism. A strong decrease in the amount of starch observed in antisense lines for ADP-glucose pyrophosphorylase or plastidic phosphoglucomutase had no effect on storage-lipid content. Similarly, potato lines over-expressing the Arabidopsis thaliana (L.) Heynh. plastidic ATP/ADP transporter that contained an increased amount of starch were not altered in oil content, indicating that the plastidic ATP level is not limiting fatty acid synthesis in potato tubers. However, over-expression of the acetyl-CoA carboxylase from Arabidopsis in the amyloplasts of potato tubers led to an increase in fatty acid synthesis and a more than 5-fold increase in the amount of triacylglycerol. Taken together, these data demonstrate that potato tubers have the capacity for storage-lipid synthesis and that malonyl-CoA, the substrate for elongation during fatty acid synthesis, represents one of the limiting factors for oil accumulation. AD - Department of Lothar Willmitzer, Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476, Golm, Germany. AU - Klaus D AU - Ohlrogge JB AU - Neuhaus HE AU - Dormann P LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1007/s00425-004-1236-3 [doi] PST - aheadofprint SO - Planta 2004 Mar 10;. PMID- 15014983 OWN - NLM STAT- publisher DA - 20040311 IS - 1617-4615 DP - 2004 Mar 10 TI - Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. AB - A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativaL. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.) AD - State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093, Nanjing, China. AU - Zhou T AU - Wang Y AU - Chen JQ AU - Araki H AU - Jing Z AU - Jiang K AU - Shen J AU - Tian D LA - ENG PT - JOURNAL ARTICLE TA - Mol Genet Genomics JID - 101093320 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1007/s00438-004-0990-z [doi] PST - aheadofprint SO - Mol Genet Genomics 2004 Mar 10;. PMID- 15014946 OWN - NLM STAT- in-data-review DA - 20040326 IS - 0009-5915 VI - 112 IP - 6 DP - 2004 Mar TI - Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. PG - 308-15 AB - The Arabidopsis KRYPTONITE gene encodes a member of the Su(var)3-9 family of histone methyltransferases. Mutations of kryptonite cause a reduction of methylated histone H3 lysine 9, a loss of DNA methylation, and reduced gene silencing. Lysine residues of histones can be either monomethylated, dimethylated or trimethylated and recent evidence suggests that different methylation states are found in different chromatin domains. Here we show that bulk Arabidopsis histones contain high levels of monomethylated and dimethylated, but not trimethylated histone H3 lysine 9. Using both immunostaining of nuclei and chromatin immunoprecipitation assays, we show that monomethyl and dimethyl histone H3 lysine 9 are concentrated in heterochromatin. In kryptonite mutants, dimethyl histone H3 lysine 9 is nearly completely lost, but monomethyl histone H3 lysine 9 levels are only slightly reduced. Recombinant KRYPTONITE can add one or two, but not three, methyl groups to the lysine 9 position of histone H3. Further, we identify a KRYPTONITE-related protein, SUVH6, which displays histone H3 lysine 9 methylation activity with a spectrum similar to that of KRYPTONITE. Our results suggest that multiple Su(var)3-9 family members are active in Arabidopsis and that dimethylation of histone H3 lysine 9 is the critical mark for gene silencing and DNA methylation. AD - Department of Molecular, Cell and Developmental Biology, University of California, 90095, Los Angeles, CA. FAU - Jackson, James P AU - Jackson JP FAU - Johnson, Lianna AU - Johnson L FAU - Jasencakova, Zuzana AU - Jasencakova Z FAU - Zhang, Xing AU - Zhang X FAU - PerezBurgos, Laura AU - PerezBurgos L FAU - Singh, Prim B AU - Singh PB FAU - Cheng, Xiaodong AU - Cheng X FAU - Schubert, Ingo AU - Schubert I FAU - Jenuwein, Thomas AU - Jenuwein T FAU - Jacobsen, Steven E AU - Jacobsen SE LA - eng PT - Journal Article DEP - 20040310 PL - Germany TA - Chromosoma JID - 2985138R SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2004/Jan/02 [received] PHST- 2004/Feb/17 [accepted] PHST- 2004/Mar/10 [aheadofprint] AID - 10.1007/s00412-004-0275-7 [doi] PST - ppublish SO - Chromosoma 2004 Mar;112(6):308-15. Epub 2004 Mar 10. PMID- 15014450 OWN - NLM STAT- in-data-review DA - 20040324 IS - 0261-4189 VI - 23 IP - 6 DP - 2004 Mar 24 TI - Induction of flowering by seasonal changes in photoperiod. PG - 1217-22 AB - In many plants, major developmental transitions such as the initiation of flowering are synchronized to the changing seasons. Day length provides one of the environmental cues used to achieve this. We describe the molecular mechanisms that measure day length and control flowering in Arabidopsis. Also, we compare these mechanisms with those that control flowering time in rice. This comparison suggests that components of the Arabidopsis regulatory network are conserved in other species, but that their regulation can be altered to generate different phenotypic responses. AD - Max Planck Institute for Plant Breeding, Carl von Linne Weg, Cologne, Germany. FAU - Searle, Iain AU - Searle I FAU - Coupland, George AU - Coupland G LA - eng PT - Journal Article DEP - 20040304 PL - England TA - EMBO J JID - 8208664 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2003/Nov/03 [received] PHST- 2004/Jan/13 [accepted] PHST- 2004/Mar/04 [aheadofprint] AID - 10.1038/sj.emboj.7600117 [doi] AID - 7600117 [pii] PST - ppublish SO - EMBO J 2004 Mar 24;23(6):1217-22. Epub 2004 Mar 4. PMID- 15014444 OWN - NLM STAT- in-data-review DA - 20040324 IS - 0261-4189 VI - 23 IP - 6 DP - 2004 Mar 24 TI - Brca2 is involved in meiosis in Arabidopsis thaliana as suggested by its interaction with Dmc1. PG - 1392-401 AB - Two BRCA2-like sequences are present in the Arabidopsis genome. Both genes are expressed in flower buds and encode nearly identical proteins, which contain four BRC motifs. In a yeast two-hybrid assay, the Arabidopsis Brca2 proteins interact with Rad51 and Dmc1. RNAi constructs aimed at silencing the BRCA2 genes at meiosis triggered a reproducible sterility phenotype, which was associated with dramatic meiosis alterations. We obtained the same phenotype upon introduction of RNAi constructs aimed at silencing the RAD51 gene at meiosis in dmc1 mutant plants. The meiotic figures we observed strongly suggest that homologous recombination is highly disturbed in these meiotic cells, leaving aberrant recombination events to repair the meiotic double-strand breaks. The 'brca2' meiotic phenotype was eliminated in spo11 mutant plants. Our experiments point to an essential role of Brca2 at meiosis in Arabidopsis. We also propose a role for Rad51 in the dmc1 context. AD - Institut de Biotechnologie des Plantes, CNRS UMR8618, Universite Paris XI, Orsay, France. FAU - Siaud, Nicolas AU - Siaud N FAU - Dray, Eloise AU - Dray E FAU - Gy, Isabelle AU - Gy I FAU - Gerard, Emmanuelle AU - Gerard E FAU - Takvorian, Najat AU - Takvorian N FAU - Doutriaux, Marie-Pascale AU - Doutriaux MP LA - eng PT - Journal Article DEP - 20040304 PL - England TA - EMBO J JID - 8208664 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2003/Sep/01 [received] PHST- 2004/Feb/10 [accepted] PHST- 2004/Mar/04 [aheadofprint] AID - 10.1038/sj.emboj.7600146 [doi] AID - 7600146 [pii] PST - ppublish SO - EMBO J 2004 Mar 24;23(6):1392-401. Epub 2004 Mar 4. PMID- 15014235 OWN - NLM STAT- in-process DA - 20040311 IS - 0925-2738 VI - 29 IP - 2 DP - 2004 Jun TI - NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana. PG - 207-8 FAU - Pantoja-Uceda, David AU - Pantoja-Uceda D FAU - Lopez-Mendez, Blanca AU - Lopez-Mendez B FAU - Koshiba, Seizo AU - Koshiba S FAU - Kigawa, Takanori AU - Kigawa T FAU - Shirouzu, Mikako AU - Shirouzu M FAU - Terada, Takaho AU - Terada T FAU - Inoue, Makoto AU - Inoue M FAU - Yabuki, Takashi AU - Yabuki T FAU - Aoki, Masaaki AU - Aoki M FAU - Seki, Eiko AU - Seki E FAU - Matsuda, Takayoshi AU - Matsuda T FAU - Hirota, Hiroshi AU - Hirota H FAU - Yoshida, Mayumi AU - Yoshida M FAU - Tanaka, Akiko AU - Tanaka A FAU - Osanai, Takashi AU - Osanai T FAU - Seki, Motoaki AU - Seki M FAU - Shinozaki, Kazuo AU - Shinozaki K FAU - Yokoyama, Shigeyuki AU - Yokoyama S FAU - Guntert, Peter AU - Guntert P LA - eng PT - Letter PL - Netherlands TA - J Biomol NMR JID - 9110829 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1023/B:JNMR.0000019241.66789.c3 [doi] AID - 5264483 [pii] PST - ppublish SO - J Biomol NMR 2004 Jun;29(2):207-8. PMID- 15014234 OWN - NLM STAT- in-process DA - 20040311 IS - 0925-2738 VI - 29 IP - 2 DP - 2004 Jun TI - NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana. PG - 205-6 FAU - Lopez-Mendez, Blanca AU - Lopez-Mendez B FAU - Pantoja-Uceda, David AU - Pantoja-Uceda D FAU - Tomizawa, Tadashi AU - Tomizawa T FAU - Koshiba, Seizo AU - Koshiba S FAU - Kigawa, Takanori AU - Kigawa T FAU - Shirouzu, Mikako AU - Shirouzu M FAU - Terada, Takaho AU - Terada T FAU - Inoue, Makoto AU - Inoue M FAU - Yabuki, Takashi AU - Yabuki T FAU - Aoki, Masaaki AU - Aoki M FAU - Seki, Eiko AU - Seki E FAU - Matsuda, Takayoshi AU - Matsuda T FAU - Hirota, Hiroshi AU - Hirota H FAU - Yoshida, Mayumi AU - Yoshida M FAU - Tanaka, Akiko AU - Tanaka A FAU - Osanai, Takashi AU - Osanai T FAU - Seki, Motoaki AU - Seki M FAU - Shinozaki, Kazuo AU - Shinozaki K FAU - Yokoyama, Shigeyuki AU - Yokoyama S FAU - Guntert, Peter AU - Guntert P LA - eng PT - Letter PL - Netherlands TA - J Biomol NMR JID - 9110829 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1023/B:JNMR.0000019239.44783.66 [doi] AID - 5264361 [pii] PST - ppublish SO - J Biomol NMR 2004 Jun;29(2):205-6. PMID- 15014143 OWN - NLM STAT- publisher DA - 20040311 IS - 0737-4038 DP - 2004 Mar 10 TI - NUMTs in Sequenced Eukaryotic Genomes. AB - Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called NUMTs (nuclear mitochondrial DNA). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabitis, Plasmodium, Drosophila and Fugu to more than 500 in human, rice and Arabidopsis. The average size is between 62 (baker's yeast) and 647 bps (Neurospora). A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, like the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation. AD - Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne Weg 10, D-50829 Koln, Germany. AU - Richly E AU - Leister D LA - ENG PT - JOURNAL ARTICLE TA - Mol Biol Evol JID - 8501455 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1093/molbev/msh110 [doi] AID - msh110 [pii] PST - aheadofprint SO - Mol Biol Evol 2004 Mar 10;. PMID- 15013764 OWN - NLM STAT- in-process DA - 20040311 IS - 0014-5793 VI - 561 IP - 1-3 DP - 2004 Mar 12 TI - Generation of Arabidopsis thaliana plants with complex N-glycans lacking beta1,2-linked xylose and core alpha1,3-linked fucose. PG - 132-6 AB - The plant glycosyltransferases, beta1,2-xylosyltransferase (XylT) and core alpha1,3-fucosyltransferase (FucT), are responsible for the transfer of beta1,2-linked xylose and core alpha1,3-linked fucose residues to glycoprotein N-glycans. These glycan epitopes are not present in humans and thus may cause immunological responses, which represent a limitation for the therapeutic use of recombinant mammalian glycoproteins produced in transgenic plants. Here we report the genetic modification of the N-glycosylation pathway in Arabidopsis thaliana plants. Knockout plants were generated with complete deficiency of XylT and FucT. These plants lack antigenic protein-bound N-glycans and instead synthesise predominantly structures with two terminal betaN-acetylglucosamine residues (GlcNAc(2)Man(3)GlcNAc(2)). AD - Institut fur Angewandte Genetik und Zellbiologie, Universitat fur Bodenkultur Wien, Muthgasse 18, A-1190 Wien, Austria. richard.strasser@boku.ac.at FAU - Strasser, R AU - Strasser R FAU - Altmann, F AU - Altmann F FAU - Mach, L AU - Mach L FAU - Glossl, J AU - Glossl J FAU - Steinkellner, H AU - Steinkellner H LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2004/Jan/21 [received] PHST- 2004/Jan/26 [accepted] AID - 10.1016/S0014-5793(04)00150-4 [doi] AID - S0014579304001504 [pii] PST - ppublish SO - FEBS Lett 2004 Mar 12;561(1-3):132-6. PMID- 15013763 OWN - NLM STAT- in-process DA - 20040311 IS - 0014-5793 VI - 561 IP - 1-3 DP - 2004 Mar 12 TI - Analysis of an activated ABI5 allele using a new selection method for transgenic Arabidopsis seeds. PG - 127-31 AB - The Arabidopsis abscisic acid (ABA) insensitive (ABI)5 transcription factor participates in the ABA-dependent induction of late embryogenesis abundant (LEA) genes in the final stages of seed development. We tested whether the VP16 transcriptional activation domain is sufficient to provide ABI5 with the ability to activate the AtEm LEA genes in vegetative tissues. We took advantage of a new transgenic seed selection assay based on green fluorescent protein (GFP) fluorescence and found that VP16-ABI5 triggered growth retardation and ABA-independent induction of AtEm1 in seedlings. These results indicate that ABI5 activation potential is a limiting step and might be a target for ABA signaling. AD - Institut des Sciences du Vegetal, UPR 2355 CNRS, 1, Av. de la terrasse, 91198 Gif-sur-Yvette Cedex, France. FAU - Bensmihen, Sandra AU - Bensmihen S FAU - To, Alexandra AU - To A FAU - Lambert, Guillaume AU - Lambert G FAU - Kroj, Thomas AU - Kroj T FAU - Giraudat, Jerome AU - Giraudat J FAU - Parcy, Francois AU - Parcy F LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2003/Dec/10 [received] PHST- 2004/Jan/30 [revised] PHST- 2004/Jan/30 [accepted] AID - 10.1016/S0014-5793(04)00148-6 [doi] AID - S0014579304001486 [pii] PST - ppublish SO - FEBS Lett 2004 Mar 12;561(1-3):127-31. PMID- 15013746 OWN - NLM STAT- in-process DA - 20040311 IS - 0014-5793 VI - 561 IP - 1-3 DP - 2004 Mar 12 TI - AtHMA3, a plant P1B-ATPase, functions as a Cd/Pb transporter in yeast. PG - 22-8 AB - The Arabidopsis thaliana AtHMA3 protein belongs to the P(1B)-adenosine triphosphatase (ATPase) transporter family, involved in heavy metal transport. Functional expression of AtHMA3 phenotypically complements the Cd/Pb-hypersensitive yeast strain Deltaycf1, but not the Zn-hypersensitive mutant Deltazrc1. AtHMA3-complemented Deltaycf1 cells accumulate the same amount of cadmium as YCF1-complemented Deltaycf1 cells or wild-type cells, suggesting that AtHMA3 carries out an intracellular sequestration of Cd. A mutant of AtHMA3 altered in the P-ATPase phosphorylation domain did not complement Deltaycf1, suggesting that metal transport rather than chelation is involved. The fusion protein AtHMA3::green fluorescent protein (GFP) is localized at the vacuole, consistent with a role in the influx of cadmium into the vacuolar compartment. In A. thaliana, the mRNA of AtHMA3 was detected mainly in roots, old rosette leaves and cauline leaves. The expression levels were not affected by cadmium or zinc treatments. AD - CEA Cadarache, DSV/DEVM/Laboratoire des Echanges Membranaires et Signalisation, UMR 6191 CNRS-CEA-Aix-Marseille II, Bat. 156, 13108 St Paul lez Durance Cedex, France. FAU - Gravot, Antoine AU - Gravot A FAU - Lieutaud, Aurelie AU - Lieutaud A FAU - Verret, Frederic AU - Verret F FAU - Auroy, Pascaline AU - Auroy P FAU - Vavasseur, Alain AU - Vavasseur A FAU - Richaud, Pierre AU - Richaud P LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JID - 0155157 SB - IM EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 PHST- 2003/Dec/17 [received] PHST- 2004/Jan/15 [revised] PHST- 2004/Jan/15 [accepted] AID - 10.1016/S0014-5793(04)00072-9 [doi] AID - S0014579304000729 [pii] PST - ppublish SO - FEBS Lett 2004 Mar 12;561(1-3):22-8. PMID- 15013421 OWN - NLM STAT- completed DA - 20040311 DCOM- 20040409 IS - 0006-291X VI - 315 IP - 1 DP - 2004 Feb 27 TI - Dextran sulfate provides a quantitative and quick microarray hybridization reaction. PG - 30-7 AB - Microarray technology is a powerful tool to speed up genomics study, yet many technical aspects need to be improved. The hybridization reaction of microarray experiments is carried out for 16h or overnight in order to obtain reasonably strong signals for analysis in the presence of high salt buffer, like SSC. However, the quantitative aspect of microarray hybridization has seldom been investigated. In this study, we showed that higher overall signals from hybridization were achieved in a buffer system containing dextran sulfate, which can accelerate the kinetics of reaction by increasing the local concentration of the reactants. The dextran sulfate containing hybridization solution increases the reaction 4-fold (median) for cDNA microarray and 29-fold for oligonucleotide microarray. More importantly, the solution also provides a quantitative hybridization reaction, where the hybridization signals are proportional to the abundance of transcript added. The enhancement in the kinetics of hybridization is due to both dextran sulfate and formamide present in the solution, but the effect is not due to the higher temperature used during the reaction. With a slightly longer reaction time the hybridization reaction with the solution allows the detection of hybridization signals from rare transcripts that is not possible with regular hybridization buffers. With appropriate washing, the enhancement of kinetics by the solution does not increase the background signals at all, allowing higher signal-to-noise ratios to be achieved. AD - Department of Research and Development, U-Vision Biotech, Inc., Taipei, Taiwan, ROC. FAU - Ku, Wei-Chi AU - Ku WC FAU - Lau, Wai Kwan AU - Lau WK FAU - Tseng, Yu-Tien AU - Tseng YT FAU - Tzeng, Chi-Meng AU - Tzeng CM FAU - Chiu, Sung-Kay AU - Chiu SK LA - eng PT - Journal Article PL - United States TA - Biochem Biophys Res Commun JID - 0372516 RN - 0 (Buffers) RN - 0 (Carbocyanines) RN - 0 (DNA, Complementary) RN - 0 (Formamides) RN - 0 (RNA, Messenger) RN - 0 (cyanine dye 3) RN - 0 (cyanine dye 5) RN - 75-12-7 (formamide) RN - 9042-14-2 (Dextran Sulfate) SB - IM MH - Arabidopsis/genetics MH - Buffers MH - Carbocyanines/chemistry MH - Cell Line MH - DNA, Complementary/chemistry/genetics MH - Dextran Sulfate/*chemistry MH - Formamides/chemistry MH - Human MH - Kinetics MH - Nucleic Acid Hybridization/*methods MH - Oligonucleotide Array Sequence Analysis/methods MH - RNA, Messenger/analysis MH - Sensitivity and Specificity EDAT- 2004/03/12 05:00 MHDA- 2004/04/10 05:00 PHST- 2003/Nov/05 [received] AID - 10.1016/j.bbrc.2004.01.013 [doi] AID - S0006291X04000361 [pii] PST - ppublish SO - Biochem Biophys Res Commun 2004 Feb 27;315(1):30-7. PMID- 15012509 OWN - NLM STAT- in-data-review DA - 20040311 IS - 0066-4286 VI - 36 DP - 1998 TI - Systemic resistance induced by rhizosphere bacteria. PG - 453-83 AB - Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Rhizobacteria-mediated induced systemic resistance (ISR) has been demonstrated against fungi, bacteria, and viruses in Arabidopsis, bean, carnation, cucumber, radish, tobacco, and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated. Bacterial strains differ in their ability to induce resistance in different plant species, and plants show variation in the expression of ISR upon induction by specific bacterial strains. Bacterial determinants of ISR include lipopolysaccharides, siderophores, and salicylic acid (SA). Whereas some of the rhizobacteria induce resistance through the SA-dependent SAR pathway, others do not and require jasmonic acid and ethylene perception by the plant for ISR to develop. No consistent host plant alterations are associated with the induced state, but upon challenge inoculation, resistance responses are accelerated and enhanced. ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease. AD - Department of Plant Ecology and Evolutionary Biology, Utrecht University, P.O. Box 800.84, TB Utrecht, The Netherlands; 3508 e-mail: L.C.vanloon@bio.uu.nl FAU - Van Loon, L C AU - Van Loon LC FAU - Bakker, P A AU - Bakker PA FAU - Pieterse, C M AU - Pieterse CM LA - eng PT - Journal Article PL - United States TA - Annu Rev Phytopathol JID - 0372373 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.phyto.36.1.453 [doi] PST - ppublish SO - Annu Rev Phytopathol 1998;36:453-83. PMID- 15012363 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - PERCEPTION AND SIGNAL TRANSDUCTION OF CYTOKININS. PG - 605-627 AB - Cytokinins are plant hormones implicated in diverse and essential processes in plant growth and development, and key genes for the metabolism and actions of cytokinins have recently been identified. Cytokinins are perceived by three histidine kinases-CRE1/WOL/AHK4, AHK2, and AHK3-which initiate intracellular phosphotransfer. The final destination of the transferred phosphoryl groups is response regulators. The type-B Arabidopsis response regulators (ARRs) are DNA-binding transcriptional activators that are required for cytokinin responses. On the other hand, the type-A ARRs act as repressors of cytokinin-activated transcription. How phosphorelay regulate response regulators and how response regulators control downstream events are open questions and discussed in this review. AD - Department of Biology, Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan; email: kakimto@bio.sci.osaka-u.ac.jp AU - Kakimoto T LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.031902.134802 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:605-627. PMID- 15012358 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - CRYPTOCHROME STRUCTURE AND SIGNAL TRANSDUCTION. PG - 469-496 AB - Cryptochromes are photosensory receptors mediating light regulation of growth and development in plants. Since the isolation of the Arabidopsis CRY1 gene in 1993, cryptochromes have been found in every multicellular eukaryote examined. Most plant cryptochromes have a chromophore-binding domain that shares similar structure with DNA photolyase, and a carboxyl terminal extension that contains a DQXVP-acidic-STAES (DAS) domain conserved from moss, to fern, to angiosperm. In Arabidopsis, cryptochromes are nuclear proteins that mediate light control of stem elongation, leaf expansion, photoperiodic flowering, and the circadian clock. Cryptochromes may act by interacting with proteins such as phytochromes, COP1, and clock proteins, or/and chromatin and DNA. Recent studies suggest that cryptochromes undergo a blue light-dependent phosphorylation that affects the conformation, intermolecular interactions, physiological activities, and protein abundance of the photoreceptors. AD - Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095; email: clin@mcdb.ucla.edu AU - Lin C AU - Shalitin D LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.110901.160901 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:469-496. PMID- 15012357 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - CHLOROPLAST MOVEMENT. PG - 455-468 AB - The study of chloroplast movement made a quantum leap at the beginning of the twenty-first century. Research based on reverse-genetic approaches using targeted mutants has brought new concepts to this field. One of the most exciting findings has been the discovery of photoreceptors for both accumulation and avoidance responses in Arabidopsis and in the fern Adiantum. Evidence for the adaptive advantage of chloroplast avoidance movements in plant survival has also been found. Additional discoveries include mechano-stress-induced chloroplast movement in ferns and mosses, and microtubule-mediated chloroplast movement in the moss Physcomitrella. The possible ecological significance of chloroplast movement is discussed in the final part of this review. AD - 1Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan. email: wada-masamitsu@c.metro-u.ac.jp, 2Division of Biological Regulation and Photobiology, Okazaki, Japan; kagawa@nibb.ac.jp, 3Division of Speciation Mechanisms 2, National Institute for Basic Biology, Okazaki, Japan; yoshi@nibb.ac.jp, 4PRESTO, Japan Science and Technology, Okazaki, Japan. AU - Wada M AU - Kagawa T AU - Sato Y LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.031902.135023 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:455-468. PMID- 15012355 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - HOW DO CELLS KNOW WHAT THEY WANT TO BE WHEN THEY GROW UP? Lessons from Epidermal Patterning in Arabidopsis. PG - 403-430 AB - Because the plant epidermis is readily accessible and consists of few cell types on most organs, the epidermis has become a well-studied model for cell differentiation and cell patterning in plants. Recent advances in our understanding of the development of three epidermal cell types, trichomes, root hairs, and stomata, allow a comparison of the underlying patterning mechanisms. In Arabidopsis, trichome development and root epidermal patterning use a common mechanism involving closely related cell fate transcription factors and a similar lateral inhibition signaling pathway. Yet the resulting patterns differ substantially, primarily due to the influence of a prepattern derived from subepidermal cortical cells in root epidermal patterning. Stomatal patterning uses a contrasting mechanism based primarily on control of the orientation of cell divisions that also involves an inhibitory signaling pathway. This review focuses on comparing and contrasting these patterning pathways to identify and illustrate general themes that may be broadly applicable to other systems. Where these pathways occur in the same tissue, interaction and competition between these pathways is also discussed. AD - 1Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; email: jlarkin@lsu.edu mbrown7@lsu.edu, 2Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109; email: schiefel@umich.edu AU - Larkin JC AU - Brown ML AU - Schiefelbein J LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.031902.134823 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:403-430. PMID- 15012353 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - STRUCTURE OF LINKAGE DISEQUILIBRIUM IN PLANTS* PG - 357-374 AB - Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed. AD - Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695; email: saflintg@unity.ncsu.edu, USDA-ARS, Plant Science Research Unit, Raleigh, North Carolina 27695;, Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695; email: jthornsb@unity.ncsu.edu buckler@statgen.ncsu.edu AU - Flint-Garcia SA AU - Thornsberry JM AU - S E AU - Iv B LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.031902.134907 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:357-374. PMID- 15012342 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 54 DP - 2003 Jun TI - PROTEIN PHOSPHATASES IN PLANTS. PG - 63-92 AB - Phosphorylation and dephosphorylation of a protein often serve as an "on-and-off" switch in the regulation of cellular activities. Recent studies demonstrate the involvement of protein phosphorylation in almost all signaling pathways in plants. A significant portion of the sequenced Arabidopsis genome encodes protein kinases and protein phosphatases that catalyze reversible phosphorylation. For optimal regulation, kinases and phosphatases must strike a balance in any given cell. Only a very small fraction of the thousands of protein kinases and phosphatases in plants has been studied experimentally. Nevertheless, the available results have demonstrated critical functions for these enzymes in plant growth and development. While serine/threonine phosphorylation is widely accepted as a predominant modification of plant proteins, the function of tyrosine phosphorylation, despite its overwhelming importance in animal systems, had been largely neglected until recently when tyrosine phosphatases (PTPs) were characterized from plants. This review focuses on the structure, regulation, and function of protein phosphatases in higher plants. AD - Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720; email: sluan@nature.berkeley.edu AU - Luan S LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.54.031902.134743 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2003 Jun;54:63-92. PMID- 15012288 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 47 DP - 1996 Jun TI - LIGHT CONTROL OF SEEDLING DEVELOPMENT. PG - 215-243 AB - Light control of plant development is most dramatically illustrated by seedling development. Seedling development patterns under light (photomorphogenesis) are distinct from those in darkness (skotomorphogenesis or etiolation) with respect to gene expression, cellular and subcellular differentiation, and organ morphology. A complex network of molecular interactions couples the regulatory photoreceptors to developmental decisions. Rapid progress in defining the roles of individual photoreceptors and the downstream regulators mediating light control of seedling development has been achieved in recent years, predominantly because of molecular genetic studies in Arabidopsis thaliana and other species. This review summarizes those important recent advances and highlights the working models underlying the light control of cellular development. We focus mainly on seedling morphogenesis in Arabidopsis but include complementary findings from other species. AD - Department of Biology, Yale University, New Haven, Connecticut 06520-8104. AU - Von Arnim A AU - Deng XW LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.47.1.215 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1996 Jun;47:215-243. PMID- 15012260 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 48 DP - 1997 Jun TI - MOLECULAR GENETIC ANALYSIS OF TRICHOME DEVELOPMENT IN ARABIDOPSIS. PG - 137-163 AB - Two basic questions in developmental biology are: How does a cell know when it should or should not differentiate, and once a cell is committed to differentiate, how is that process controlled? The first process regulates the arrangement or pattern of the various cell types, whereas the second makes cells functionally distinct. Together, these two processes define plant morphogenesis. Trichome development in Arabidopsis provides an excellent model to analyze these questions. First, trichome development in Arabidopsis is a relatively simple process. A single epidermal cell differentiates into a unicellular trichome. Second, this differentiation occurs in a nonrandom pattern on the plant surface. Finally, the process is amenable to genetic analysis because many mutations that affect trichome differentiation do not alter other aspects of plant development. Thus far, more than 20 genes affecting trichome development have been identified. This review examines the current state of our understanding of these genes. AD - Department of Genetics and Cell Biology and Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108. AU - Marks MD LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.48.1.137 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1997 Jun;48:137-163. PMID- 15012243 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 49 DP - 1998 Jun TI - BORON IN PLANT STRUCTURE AND FUNCTION. PG - 481-500 AB - New and exciting developments in boron research in the past few years greatly contributed to better understanding of the role of boron in plants. Purification and identification of the first boron-polyol transport molecules resolved much of the controversy about boron phloem mobility. Isolation and characterization of the boron-polysaccharide complex from cell walls provided the first direct evidence for boron crosslinking of pectin polymers. Inhibition and recovery of proton release upon boron withdrawal and restitution in plant culture medium demonstrated boron involvement in membrane processes. Rapid boron-induced changes in membrane function could be attributed to boron-complexing membrane constituents. Boron may affect metabolic pathways by binding apoplastic proteins to cis-hydroxyl groups of cell walls and membranes, and by interfering with manganese-dependent enzymatic reactions. In addition, boron has been implicated in counteracting toxic effects of aluminum on root growth of dicotyledonous plants. Molecular investigations of boron nutrition have been initiated by the discovery of a novel mutant of Arabidopsis thaliana with an altered requirement for boron. AD - Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211; blevins@psu.missouri.edu AU - Blevins DG AU - Lukaszewski KM LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.49.1.481 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1998 Jun;49:481-500. PMID- 15012238 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 49 DP - 1998 Jun TI - GENETIC CONTROL OF FLOWERING TIME IN ARABIDOPSIS. PG - 345-370 AB - The timing of the transition from vegetative to reproductive development is of great fundamental and applied interest but is still poorly understood. Recently, molecular-genetic approaches have been used to dissect this process in Arabidopsis. The genetic variation present among a large number of mutants with an early- or late-flowering phenotype, affecting the control of both environmental and endogenous factors that influence the transition to flowering, is described. The genetic, molecular, and physiological analyses have led to identification of different components involved, such as elements of photoperception and the circadian rhythm. Furthermore, elements involved in the signal transduction pathways to flowering have been identified by the cloning of some floral induction genes and their target genes. AD - Department of Genetics, Wageningen Agricultural University, Dreijenlaan 2, Wageningen, NL-6703 HA The Netherlands. AU - Koornneef M AU - Alonso-Blanco C AU - Peeters AJ AU - Soppe W LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.49.1.345 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1998 Jun;49:345-370. PMID- 15012234 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 49 DP - 1998 Jun TI - DNA METHYLATION IN PLANTS. PG - 223-247 AB - Methylation of cytosine residues in DNA provides a mechanism of gene control. There are two classes of methyltransferase in Arabidopsis; one has a carboxy-terminal methyltransferase domain fused to an amino-terminal regulatory domain and is similar to mammalian methyltransferases. The second class apparently lacks an amino-terminal domain and is less well conserved. Methylcytosine can occur at any cytosine residue, but it is likely that clonal transmission of methylation patterns only occurs for cytosines in strand-symmetrical sequences CpG and CpNpG. In plants, as in mammals, DNA methylation has dual roles in defense against invading DNA and transposable elements and in gene regulation. Although originally reported as having no phenotypic consequence, reduced DNA methylation disrupts normal plant development. AD - 1Commonwealth Scientific and Industrial Research Organization, Plant Industry, P.O. Box 1600, Canberra, ACT 2601, Australia, Cooperative Research Centre for Plant Science, P.O. Box 475, Canberra, ACT 2601, Australia; e-mail: jean.finnegan@pican.pi.csiro.au, 2Division of Biochemistry and Molecular Biology, Australian National University, Canberra, ACT 0200, Australia AU - Finnegan EJ AU - Genger RK AU - Peacock WJ AU - Dennis ES LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.49.1.223 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1998 Jun;49:223-247. PMID- 15012226 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 49 DP - 1998 Jun TI - POSTTRANSLATIONAL ASSEMBLY OF PHOTOSYNTHETIC METALLOPROTEINS. PG - 25-51 AB - The assembly of chloroplast metalloproteins requires biochemical catalysis. Assembly factors involved in the biosynthesis of metalloproteins might be required to synthesize, chaperone, or transport the cofactor; modify or chaperone the apoprotein; or catalyze cofactor-protein association. Genetic and biochemical approaches have been applied to the study of the assembly of chloroplast iron-sulfur centers, cytochromes, plastocyanin, and the manganese center of photosystem II. These have led to the discovery of NifS-homologues and cysteine desulfhydrase for iron-sulfur center assembly, six loci (CCS1-CCS5, ccsA) for c-type cytochrome assembly, four loci for cytochrome b6 assembly (CCB1-CCB4), the CtpA protease, which is involved in pre-D1 processing, and the PCY2 locus, which is involved in holoplastocyanin accumulation. New assembly factors are likely to be discovered via the study of assembly-defective mutants of Arabidopsis, cyanobacteria, Chlamydomonas, maize, and via the functional analysis of candidate cofactor metabolizing components identified in the genome databases. AD - Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569; e-mail: merchant@chem.ucla.edu; bdreyfus@ucla.edu AU - Merchant S AU - Dreyfuss BW LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.49.1.25 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1998 Jun;49:25-51. PMID- 15012220 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 50 DP - 1999 Jun TI - PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. PG - 571-599 AB - Many plants increase in freezing tolerance upon exposure to low nonfreezing temperatures, a phenomenon known as cold acclimation. In this review, recent advances in determining the nature and function of genes with roles in freezing tolerance and the mechanisms involved in low temperature gene regulation and signal transduction are described. One of the important conclusions to emerge from these studies is that cold acclimation includes the expression of certain cold-induced genes that function to stabilize membranes against freeze-induced injury. In addition, a family of Arabidopsis transcription factors, the CBF/DREB1 proteins, have been identified that control the expression of a regulon of cold-induced genes that increase plant freezing tolerance. These results along with many of the others summarized here further our understanding of the basic mechanisms that plants have evolved to survive freezing temperatures. In addition, the findings have potential practical applications as freezing temperatures are a major factor limiting the geographical locations suitable for growing crop and horticultural plants and periodically account for significant losses in plant productivity. AD - Department of Crop and Soil Sciences, Department of Microbiology, Michigan State University, East Lansing, Michigan 48824; e-mail: thomash6@pilot.msu.edu AU - Thomashow MF LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.50.1.571 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1999 Jun;50:571-599. PMID- 15012209 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 50 DP - 1999 Jun TI - GENETIC ANALYSIS OF HORMONE SIGNALING. PG - 219-243 AB - Phytohormones influence many diverse developmental processes ranging from seed germination to root, shoot, and flower formation. Recently, mutational analysis using the model plant Arabidopsis thaliana has been instrumental in determining the individual components of specific hormone signal transduction pathways. Moreover, epistasis and suppressor studies are beginning to explain how these genes and their products relate to one another. While no hormone transduction pathway is completely understood, the genes identified to date suggest that simple molecular rules can be established to explain how plant hormone signals are transduced. This review describes some of the shared characteristics of plant hormone signal transduction pathways and the properties for informational transfer common to many of the genes that specify the transduction of the signal. AD - Department of Botany, University of Toronto, Toronto, Ontario, M5S 3B2, Canada; e-mail: mccourt@botany.utoronto.ca AU - McCourt P LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.50.1.219 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1999 Jun;50:219-243. PMID- 15012205 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 50 DP - 1999 Jun TI - PLANT PROTEIN SERINE/THREONINE KINASES: Classification and Functions. PG - 97-131 AB - The first plant protein kinase sequences were reported as recently as 1989, but by mid-1998 there were more than 500, including 175 in Arabidopsis thaliana alone. Despite this impressive pace of discovery, progress in understanding the detailed functions of protein kinases in plants has been slower. Protein serine/threonine kinases from A. thaliana can be divided into around a dozen major groups based on their sequence relationships. For each of these groups, studies on animal and fungal homologs are briefly reviewed, and direct studies of their physiological functions in plants are then discussed in more detail. The network of protein-serine/threonine kinases in plant cells appears to act as a "central processor unit" (cpu), accepting input information from receptors that sense environmental conditions, phytohormones, and other external factors, and converting it into appropriate outputs such as changes in metabolism, gene expression, and cell growth and division. AD - Biochemistry Department, Dundee University, Dundee, Scotland, DD1 5EH, United Kingdom; e-mail: d.g.hardie@dundee.ac.uk AU - Hardie DG LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.50.1.97 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 1999 Jun;50:97-131. PMID- 15012199 OWN - NLM STAT- publisher DA - 20040311 IS - 1040-2519 VI - 51 DP - 2000 Jun TI - PLANT CELLULAR AND MOLECULAR RESPONSES TO HIGH SALINITY. PG - 463-499 AB - Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to those that regulate osmotic stress responses of yeast. There is evidence also of signaling cascades that are not known to exist in the unicellular eukaryote, some that presumably function in intercellular coordination or regulation of effector genes in a cell-/tissue-specific context required for tolerance of plants. A complex set of stress-responsive transcription factors is emerging. The imminent availability of genomic DNA sequences and global and cell-specific transcript expression data, combined with determinant identification based on gain- and loss-of-function molecular genetics, will provide the infrastructure for functional physiological dissection of salt tolerance determinants in an organismal context. Furthermore, protein interaction analysis and evaluation of allelism, additivity, and epistasis allow determination of ordered relationships between stress signaling components. Finally, genetic activation and suppression screens will lead inevitably to an understanding of the interrelationships of the multiple signaling systems that control stress-adaptive responses in plants. AD - Center for Plant Environmental Stress Physiology, 1165 Horticulture Building, Purdue University, West Lafayette, Indiana 47907-1165; e-mail: paul.m.hasegawa.1@purdue.edu, Departments of 1 Plant Sciences and 2Biochemistry, University of Arizona, Tucson, Arizona 85721; e-mail: bonerth@u.arizona.edu AU - Hasegawa PM AU - Bressan RA AU - Zhu JK AU - Bohnert HJ LA - ENG PT - JOURNAL ARTICLE TA - Annu Rev Plant Physiol Plant Mol Biol JID - 9883513 EDAT- 2004/03/12 05:00 MHDA- 2004/03/12 05:00 AID - 10.1146/annurev.arplant.51.1.463 [doi] PST - ppublish SO - Annu Rev Plant Physiol Plant Mol Biol 2000 Jun;51:463-499. PMID- 15010620 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - The elongation defective1 mutant of Arabidopsis is impaired in the gene encoding a serine-rich secreted protein. PG - 581-95 AB - Coordinated cell growth and differentiation is crucial for the development of higher plants. Using the elongation defective 1-1 (eld1-1) mutant, we cloned the ELD1 gene, which encodes a serine-rich protein. Genes homologous to ELD1 can be found in plants, including Arabidopsis, rice, and tobacco, but not in other organisms. Using reverse genetics, we identified a new allele, eld1-2, which is phenotypically indistinguishable from eld1-1, but does not produce a detectable ELD1 transcript. The ELD1 gene sequence is the same as that of the KOBITO1 sequence. However, the kob1 mutants display weak phenotype relative to the two eld1 mutants, which are likely null alleles. KOB1 was reported to be a membrane protein involved in cellulose synthesis. However, based on ELD1-GFP localization in plasmolyzed cells, we found that ELD1 is localized to the cell wall/extracellular matrix, rather than the membrane. Thus, ELD1/KOB1 is a secreted protein involved in promoting cell growth. To investigate the relationship between ELD1 and Arabidopsis genes with high sequence similarity, we analyzed the possible subcellular location of their proteins as well as their amino acid sequence. The ELD1-related proteins in Arabidopsis were predicted to be localized to subcellular compartments different from that of ELD1. Thus, ELD1 is likely to be functionally distinct from related Arabidopsis genes. These results suggest that ELD1 is a single-copy gene which belongs to a small family of plant-specific genes with diverse function. AD - Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. FAU - Lertpiriyapong, Kvin AU - Lertpiriyapong K FAU - Sung, Zinmay Renee AU - Sung ZR LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019067.05185.d6 [doi] AID - 5255411 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):581-95. PMID- 15010618 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Isolation, sequence analysis, and expression studies of florally expressed cDNAs in Arabidopsis. PG - 545-63 AB - Molecular genetics has identified dozens of genes that regulate flower development in Arabidopsis. However, the complexity of flower development suggests that many other genes are yet to be uncovered. To identify floral genes that are expressed at low levels in the flower, we have sequenced 1587 cDNA fragments from a subtractive floral cDNA library. A total of 1222 unique genes represented by these ESTs are distributed on all five chromosomes with similar frequencies as all predicted genes in the genome. Among these, 17 genes were shown to be expressed anywhere for the first time because they were not found in previous EST and full-length cDNA datasets. Furthermore, 724 of the genes revealed by this library were not definitively shown to be expressed in the flower by previous floral EST datasets. In addition, 49 transcriptional regulators, 31 protein kinases, 12 zinc-finger proteins and other signaling proteins were found to be present in floral buds. Moreover, the EST sequences likely extended the transcribed regions of 26 previously annotated genes, and may have uncovered several previously unrecognized genes. To obtain additional clues about possible gene function, we hybridized cDNA microarray with probes derived from wild-type Arabidopsis rosette leaves and floral buds. We estimated that over 50% of genes were expressed at levels lower than 1/30 of the highest detectable signal intensity, indicating that many floral genes are expressed at low levels. Furthermore, 97 genes were found to be expressed at a higher level in the flower than the leaf by the Significance Analysis of Microarray (SAM) method with a 1.0% false discovery rate (FDR). Further RT-PCR analyses of selected genes support the microarray results. We suggest that the genes encoding putative regulatory proteins and at least some proteins with currently unknown functions might play important roles during flowering. AD - Department of Biology, and the Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA. FAU - Hu, Wei AU - Hu W FAU - Wang, Yixing AU - Wang Y FAU - Bowers, Christian AU - Bowers C FAU - Ma, Hong AU - Ma H LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019063.18097.62 [doi] AID - 5255326 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):545-63. PMID- 15010616 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Expression of an Arabidopsis phosphoglycerate mutase homologue is localized to apical meristems, regulated by hormones, and induced by sedentary plant-parasitic nematodes. PG - 513-30 AB - We previously isolated a partial soybean cDNA clone whose transcript abundance is increased upon infection by the sedentary, endoparasitic soybean cyst nematode Heterodera glycines. We now isolated the corresponding full-length cDNA and determined that the predicted gene product was similar to the group of cofactor-dependent phosphoglycerate mutase/bisphosphoglycerate mutase enzymes (PGM/bPGM; EC 5.4.2.1/5.4.2.4). We designated the corresponding soybean gene GmPGM. PGM and bPGM are key catalysts of glycolysis that have been well characterized in animals but not plants. Using the GmPGM cDNA sequence, we identified a homologous Arabidopsis thaliana gene, which we designated AtPGM. Histochemical GUS analyses of transgenic Arabidopsis plants containing the AtPGM promoter ::GUS construct revealed that the AtPGM promoter directs GUS expression in uninfected plants only to the shoot and root apical meristems. In infected plants, GUS staining also is evident in the nematode feeding structures induced by the cyst nematode Heterodera schachtii and by the root-knot nematode Meloidogyne incognita. Furthermore, we discovered that the AtPGM promoter was down-regulated by abscisic acid and hydroxyurea, whereas it was induced by sucrose, oryzalin, and auxin, thereby revealing expression characteristics typical of genes with roles in meristematic cells. Assessment of the auxin-inducible AUX1 gene promoter (a gene coding for a polar auxin transport protein) similarly revealed feeding cell and meristem expression, suggesting that auxin may be responsible for the observed tissue specificity of the AtPGM promoter. These results provide first insight into the possible roles of PGM/bPGM in plant physiology and in plant-pathogen interactions. AD - Department of Plant Pathology, Iowa State University, Bessey Hall, Ames, IA 50011, USA. FAU - Mazarei, Mitra AU - Mazarei M FAU - Lennon, Kristen A AU - Lennon KA FAU - Puthoff, David P AU - Puthoff DP FAU - Rodermel, Steven R AU - Rodermel SR FAU - Baum, Thomas J AU - Baum TJ LA - eng SI - GENBANK/AY004240 PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019062.80459.80 [doi] AID - 5254441 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):513-30. PMID- 15010613 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. PG - 467-78 AB - Although large-scale gene expression data have been studied from many perspectives, they have not been systematically integrated to infer the regulatory potentials of individual genes in specific pathways. Here we report the analysis of expression patterns of genes in the Calvin cycle from 95 Arabidopsis microarray experiments, which revealed a consistent gene regulation pattern in most experiments. This identified pattern, likely due to gene regulation by light rather than feedback regulations of the metabolite fluxes in the Calvin cycle, is remarkably consistent with the rate-limiting roles of the enzymes encoded by these genes reported from both experimental and modeling approaches. Therefore, the regulatory potential of the genes in a pathway may be inferred from their expression patterns. Furthermore, gene expression analysis in the context of a known pathway helps to categorize various biological perturbations that would not be recognized with the prevailing methods. AD - Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA. ning.sun@yale.edu FAU - Sun, Ning AU - Sun N FAU - Ma, Ligeng AU - Ma L FAU - Pan, Deyun AU - Pan D FAU - Zhao, Hongyu AU - Zhao H FAU - Deng, Xing Wang AU - Deng XW LA - eng GR - GM-47850/GM/NIGMS GR - GM59507/GM/NIGMS PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019071.12878.9e [doi] AID - 5255598 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):467-78. PMID- 15010612 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Arabidopsis transcript profiling on Affymetrix GeneChip arrays. PG - 457-65 AB - DNA microarrays are becoming a frequently used research tool. Whilst several studies have confirmed the reproducibility of analysing the same RNA samples on duplicate arrays, there is little analysis of the reproducibility of the results of transcript profiling between microarrays carrying different probes to a common set of genes. To address this question, we compared the performance and reproducibility of two microarrays commonly used in plant research, the Affymetrix Arabidopsis AG array containing more than 8000 probe sets and the Affymetrix Arabidopsis ATH1 array containing more than 22,000 redesigned probe sets. A total of 21 different RNA samples were labelled and hybridized in parallel to the two microarray types. Focusing on the overlap of more than 7300 targets detected with both arrays, we found a high degree of reproducibility. Despite the use of different probe sets, both signal and signal log ratio were very similar for most genes. However, genes that were called absent or not changed by Affymetrix' statistical algorithm implemented in MAS5.0 showed considerably less conservation of expression patterns. Moreover, we identified about 300 genes that yielded strongly different measurements with the two microarrays, emphasizing that RNA profiling data need careful interpretation. Overall, this study shows that results obtained with ATH1 and AG arrays are very comparable and hence that the analysis is largely independent of probe sets. However, the result emphasize the need for appropriate filtering schemes such as those based on the present and change calls provided by MAS5.0 rather than reliance solely on signal values. AD - Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, Universitatstrasse 2, 8092 Zurich, Switzerland. lars.hennig@ipw.biol.ethz.ch FAU - Hennig, Lars AU - Hennig L FAU - Menges, Margit AU - Menges M FAU - Murray, James A H AU - Murray JA FAU - Gruissem, Wilhelm AU - Gruissem W LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019069.23317.97 [doi] AID - 5255414 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):457-65. PMID- 15010611 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Transcriptome analysis of O3-exposed Arabidopsis reveals that multiple signal pathways act mutually antagonistically to induce gene expression. PG - 443-56 AB - To analyze cellular responses to ozone (O3), we performed a large-scale analysis of the Arabidopsis transcriptome after plants were exposed to O3 for 12 h. By using cDNA macroarray technology, we identified 205 non-redundant expressed sequence tags (ESTs) that were regulated by O3. Of these, 157 were induced and 48 were suppressed by O3. A substantial proportion of these ESTs had predicted functions in cell rescue/defense processes. Using these isolated ESTs, we also undertook a comprehensive investigation of how three hormones, ethylene (ET), jasmonic acid (JA), and salicylic acid (SA), interact to regulate O3-induced genes in various genetic backgrounds of Arabidopsis, such as the ET-insensitive ein2-1, JA-resistant jar1-1, and SA-insensitive npr1-1. The expression of half of the 157 induced genes, especially cell rescue/defense genes, was controlled by ET and JA signaling, indicating that O3-induced defense gene expression at this stage was mainly regulated by ET and JA. Clustering analysis of the 157 O3-induced gene expressions revealed that multiple signal pathways act mutually antagonistically to induce the expression of these genes, and many cell rescue/defense genes induced by ET and JA signal pathways were suppressed by SA signaling, suggesting that the SA pathway acts as a strong antagonist to gene expression induced by ET and JA signaling. AD - Biodiversity Conservation Research Project, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506 Japan. mtamaoki@nies.go.jp FAU - Tamaoki, Masanori AU - Tamaoki M FAU - Nakajima, Nobuyoshi AU - Nakajima N FAU - Kubo, Akihiro AU - Kubo A FAU - Aono, Mitsuko AU - Aono M FAU - Matsuyama, Takashi AU - Matsuyama T FAU - Saji, Hikaru AU - Saji H LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019064.55734.52 [doi] AID - 5255327 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):443-56. PMID- 15010610 OWN - NLM STAT- in-process DA - 20040310 IS - 0167-4412 VI - 53 IP - 4 DP - 2003 Nov TI - Genome-wide gene expression in an Arabidopsis cell suspension. PG - 423-42 AB - Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Analysis of gene expression profiles during normal culture growth, during synchronous cell cycle re-entry and during synchronous cell cycle progression provides a unique integrated view of gene expression responses in a higher-plant system. Particularly striking is that expression of over 14 000 genes belonging to all defined categories can be reliably detected, suggesting that integrated and comparative analysis of data sets derived from transcript profiling of cultures is a powerful approach to identify candidate components involved in a wide range of biological processes. Combinatorial analysis of independent cell cycle synchrony methods allows the identification of genes that are apparently cell-cycle-regulated but are most likely responding to the induction of synchrony. We thus present an integrated genome-wide view of the transcriptional profile of a plant suspension culture and identify a refined set of 1082 cell cycle regulated genes largely independent of synchrony method. AD - Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK. FAU - Menges, Margit AU - Menges M FAU - Hennig, Lars AU - Hennig L FAU - Gruissem, Wilhelm AU - Gruissem W FAU - Murray, James A H AU - Murray JA LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019059.56489.ca [doi] AID - 5253963 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(4):423-42. PMID- 15010609 OWN - NLM STAT- in-data-review DA - 20040310 IS - 0167-4412 VI - 53 IP - 5 DP - 2003 Nov TI - Arabidopsis MBD proteins show different binding specificities and nuclear localization. PG - 755-71 AB - Recent results in animals and plants have shown a strong link between DNA methylation, chromatin structure and epigenetic control. In plants DNA methylation affects both symmetric and asymmetric cytosines by means of different DNA-methyltransferases. In vertebrates these modifications are interpreted by a group of proteins (methylated DNA-binding domain proteins, MBDs) able to specifically bind methylated CpG. In plants several genes sharing structural homology to mammalian MBD have been identified in Arabidopsis and maize, but their characterization is still to be completed. Here we present the characterization of six different MBDs from Arabidopsis. As judged by semi-quantitative RT-PCR, their expression proved to be differentially modulated in different organs. All the corresponding polypeptides, expressed in Escherichia coli as His-tagged recombinant proteins, have been functionally tested on gel shift experiments but only two of them (namely MBD5, 6) were able to specifically bind methylated CpG oligonucleotides. A third protein, AtMBD11, showed a strong affinity for DNA independently from the level of methylation. Moreover we were able to differentiate MBD5 and 6, despite their high homology, for their ability to recognize methylated asymmetrical sites. The binding specificity of these three AtMBD proteins was tested not only on arbitrarily chosen probes but also on the Arabidopsis E2F recognition sequence containing a single CpG site. Protoplasts transient expression experiments of GFP-fusion proteins showed for AtMBD5 and AtMBD6 a heterochromatic localization which was affected by 5-azacytidine treatment. These data demonstrate that AtMBD5 and AtMBD6 bind methylated DNA in vitro and in vivo with different specificity and might therefore have different roles in methylation-mediated transcriptional silencing. AD - Laboratorio di Terapia Genica e Molecolare-Istituto di Fisiologia Clinica-Area della Ricerca CNR, via Moruzzi 1, 56100 Pisa, Italy these authors contributed equally to the work. FAU - Scebba, Francesca AU - Scebba F FAU - Bernacchia, Giovanni AU - Bernacchia G FAU - De Bastiani, Morena AU - De Bastiani M FAU - Evangelista, Monica AU - Evangelista M FAU - Cantoni, Rita Maria AU - Cantoni RM FAU - Cella, Rino AU - Cella R FAU - Locci, Maria Tereasa AU - Locci MT FAU - Pitto, Letizia AU - Pitto L LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019118.56822.a9 [doi] AID - 5264596 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(5):755-71. PMID- 15010605 OWN - NLM STAT- in-data-review DA - 20040310 IS - 0167-4412 VI - 53 IP - 5 DP - 2003 Nov TI - Cestrum yellow leaf curling virus (CmYLCV) promoter: a new strong constitutive promoter for heterologous gene expression in a wide variety of crops. PG - 703-13 AB - Appropriately regulated gene expression requires a suitable promoter. A number of promoters have been isolated and shown to be functional in plants, but only a few of them activate transcription of transgenes at high levels constitutively. We report here the cloning and characterization of a novel, constitutively expressed promoter isolated from Cestrum yellow leaf curling virus (CmYLCV), a double-stranded DNA plant pararetrovirus belonging to the Caulimoviridae family. The CmYLCV promoter is highly active in callus, meristems and vegetative and reproductive tissues in Arabidopsis thaliana, Nicotiana tabacum, Lycopersicon esculentum, Zea mays and Oryza sativa. Furthermore, the level of expression is comparable to, or higher than, that from the CaMV 35S, the 'super-promoter' or the maize ubiquitin 1 promoters, three frequently used promoters in agricultural biotechnology. The heritable, strong and constitutive activity in both monocotyledonous and dicotyledonous plants, combined with the extremely narrow CmYLCV host range, makes the CmYLCV promoter an attractive tool for regulating transgene expression in a wide variety of plant species. AD - Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland Istituto di Virologia Vegetale-CNR, via Amendola 165/A, Bari, Italy e-mail l.stavolone@area.ba.cnr.it FAU - Stavolone, Livia AU - Stavolone L FAU - Kononova, Maria AU - Kononova M FAU - Pauli, Sandra AU - Pauli S FAU - Ragozzino, Antonio AU - Ragozzino A FAU - De Haan, Peter AU - De Haan P FAU - Milligan, Steve AU - Milligan S FAU - Lawton, Kay AU - Lawton K FAU - Hohn, Thomas AU - Hohn T LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019110.95420.bb [doi] AID - 5256710 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(5):703-13. PMID- 15010604 OWN - NLM STAT- in-data-review DA - 20040310 IS - 0167-4412 VI - 53 IP - 5 DP - 2003 Nov TI - Mutation of a family 8 glycosyltransferase gene alters cell wall carbohydrate composition and causes a humidity-sensitive semi-sterile dwarf phenotype in Arabidopsis. PG - 687-701 AB - The genome of Arabidopsis thaliana contains about 400 genes coding for glycosyltransferases, many of which are predicted to be involved in the synthesis and remodelling of cell wall components. We describe the isolation of a transposon-tagged mutant, parvus, which under low humidity conditions exhibits a severely dwarfed growth phenotype and failure of anther dehiscence resulting in semi-sterility. All aspects of the mutant phenotype were partially rescued by growth under high-humidity conditions, but not by the application of growth hormones or jasmonic acid. The mutation is caused by insertion of a maize Dissociation ( Ds ) element in a gene coding for a putative Golgi-localized glycosyltransferase belonging to family 8. Members of this family, originally identified on the basis of similarity to bacterial lipooligosaccharide glycosyltransferases, include enzymes known to be involved in the synthesis of bacterial and plant cell walls. Cell-wall carbohydrate analyses of the parvus mutant indicated reduced levels of rhamnogalacturonan I branching and alterations in the abundance of some xyloglucan linkages that may, however, be indirect consequences of the mutation. AD - Department of Genetics, Trinity College, Dublin 2, Ireland. FAU - Lao, Nga T AU - Lao NT FAU - Long, Debbie AU - Long D FAU - Kiang, Sophie AU - Kiang S FAU - Coupland, George AU - Coupland G FAU - Shoue, Douglas A AU - Shoue DA FAU - Carpita, Nicholas C AU - Carpita NC FAU - Kavanagh, Tony A AU - Kavanagh TA LA - eng PT - Journal Article PL - Netherlands TA - Plant Mol Biol JID - 9106343 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1023/B:PLAN.0000019074.60542.6c [doi] AID - 5255726 [pii] PST - ppublish SO - Plant Mol Biol 2003 Nov;53(5):687-701. PMID- 15010513 OWN - NLM STAT- publisher DA - 20040310 IS - 1040-4651 DP - 2004 Mar 9 TI - Nuclear Endosperm Development in Cereals and Arabidopsis thaliana. AD - Pioneer Hi-Bred International, A DuPont Company, Johnston, Iowa 50131. AU - Olsen OA LA - ENG PT - JOURNAL ARTICLE TA - Plant Cell JID - 9208688 EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 10.1105/tpc.017111 [doi] AID - tpc.017111 [pii] PST - aheadofprint SO - Plant Cell 2004 Mar 9;. PMID- 15009186 OWN - NLM STAT- in-process DA - 20040310 IS - 0014-2956 VI - 271 IP - 6 DP - 2004 Mar TI - Trypanosoma brucei oleate desaturase may use a cytochrome b5-like domain in another desaturase as an electron donor. PG - 1079-86 AB - An open reading frame with fatty acid desaturase similarity was identified in the genome of Trypanosoma brucei. The 1224 bp sequence specifies a protein of 408 amino acids with 59% and 58% similarity to Mortierella alpina and Arabidopsis thaliana Delta12 desaturase, respectively, and 51% with A. thaliana omega3 desaturases. The histidine tracks that compose the iron-binding active centers of the enzyme were more similar to those of the omega3 desaturases. Expression of the trypanosome gene in Saccharomyces cerevisiae resulted in the production of fatty acids that are normally not synthesized in yeast, namely linoleic acid (18:2Delta9,12) and hexadecadienoic acid (16:2Delta9,12), the levels of which were dependent on the culture temperature. At low temperature, the production of bi-unsaturated fatty acids and the 16:2/18:2 ratio were higher. Transformed yeast cultures supplemented with 19:1Delta10 fatty acid yielded 19:2Delta10,13, indicating that the enzyme is able to introduce a double bond at three carbon atoms from a pre-existent olefinic bond. The expression of the gene in a S. cerevisiae mutant defective in cytochrome b5 showed a significant reduction in bi-unsaturated fatty acid production, although it was not totally abolished. Based on the regioselectivity and substrate preferences, we characterized the trypanosome enzyme as a cytochrome b5-dependent oleate desaturase. Expression of the ORF in a double mutant (ole1Delta,cytb5Delta) abolished all oleate desaturase activity completely. OLE1 codes for the endogenous stearoyl-CoA desaturase. Thus, Ole1p has, like Cytb5p, an additional cytochrome b5 function (actually an electron donor function), which is responsible for the activity detected when using the cytb5Delta single mutant. AD - Instituto de Biologia Molecular y Celular de Rosario (IBR), CONICET, Departamento de Microbiologia, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Santa Fe, Argentina. FAU - Petrini, Guillermo A AU - Petrini GA FAU - Altabe, Silvia G AU - Altabe SG FAU - Uttaro, Antonio D AU - Uttaro AD LA - eng SI - GENBANK/AY372529 PT - Journal Article PL - Germany TA - Eur J Biochem JID - 0107600 SB - IM EDAT- 2004/03/11 05:00 MHDA- 2004/03/11 05:00 AID - 4005 [pii] PST - ppublish SO - Eur J Biochem 2004 Mar;271(6):1079-86. PMID- 15007655 OWN - NLM STAT- in-data-review DA - 20040326 IS - 0009-5915 VI - 112 IP - 6 DP - 2004 Mar TI - Chromosomes associate premeiotically and in xylem vessel cells via their telomeres and centromeres in diploid rice ( Oryza sativa). PG - 300-7 AB - Studies of the meiosis of diploid plants such as Arabidopsis, maize and diploid progenitors of wheat have revealed no premeiotic association of chromosomes. Premeiotic and somatic association of chromosomes has only been previously observed in the anther tissues and xylem vessel cells of developing roots in polyploid plants such as hexaploid and tetraploid wheat, polyploid relatives of wheat and artificial polyploids made from the progenitor diploids of wheat. This suggested that this association was confined specifically to polyploids or was induced by polyploidy. However, we developed procedures for in situ hybridization on structurally well-preserved tissue sections of rice, and analysed two diploid rice species ( Oryza sativa and O. punctata). Contrary to expectation, this has revealed that centromeres and telomeres also associate both in the xylem vessel cells of developing root and in undifferentiated anther cells in these diploids. However, in contrast to wheat and related polyploids, where the initial association in undifferentiated anthers is between either non-homologous or related chromosomes, and not homologous chromosomes, the initial association of rice chromosomes seems to be between homologues. Thus, in contrast to the diploid dicot model Arabidopsis, meiotic studies on the diploid model cereal, rice, will now need to take into account the effects of premeiotic chromosome association. AD - Departments of Cell and Development Biology and Crop Genetics, John Innes Centre, Colney, NR4 7UH, Norwich, UK. FAU - Prieto, Pilar AU - Prieto P FAU - Santos, Ana Paula AU - Santos AP FAU - Moore, Graham AU - Moore G FAU - Shaw, Peter AU - Shaw P LA - eng PT - Journal Article DEP - 20040309 PL - Germany TA - Chromosoma JID - 2985138R SB - IM EDAT- 2004/03/10 05:00 MHDA- 2004/03/10 05:00 PHST- 2003/Dec/05 [received] PHST- 2004/Feb/04 [revised] PHST- 2004/Feb/04 [accepted] PHST- 2004/Mar/09 [aheadofprint] AID - 10.1007/s00412-004-0274-8 [doi] PST - ppublish SO - Chromosoma 2004 Mar;112(6):300-7. Epub 2004 Mar 9. PMID- 15005814 OWN - NLM STAT- publisher DA - 20040311 IS - 1471-2229 VI - 4 IP - 1 DP - 2004 Jan 28 TI - Production of Se-methylselenocysteine in transgenic plants expressing selenocysteine methyltransferase. PG - 1 AB - BACKGROUND: It has become increasingly evident that dietary Se plays a significant role in reducing the incidence of lung, colorectal and prostate cancer in humans. Different forms of Se vary in their chemopreventative efficacy, with Se-methylselenocysteine being one of the most potent. Interestingly, the Se accumulating plant Astragalus bisulcatus (Two-grooved poison vetch) contains up to 0.6% of its shoot dry weight as Se-methylselenocysteine. The ability of this Se accumulator to biosynthesize Se-methylselenocysteine provides a critical metabolic shunt that prevents selenocysteine and selenomethionine from entering the protein biosynthetic machinery. Such a metabolic shunt has been proposed to be vital for Se tolerance in A. bisulcatus. Utilization of this mechanism in other plants may provide a possible avenue for the genetic engineering of Se tolerance in plants ideally suited for the phytoremediation of Se contaminated land. Here, we describe the overexpression of a selenocysteine methyltransferase from A. bisulcatus to engineer Se-methylselenocysteine metabolism in the Se non-accumulator Arabidopsis thaliana (Thale cress). RESULTS: By over producing the A. bisulcatus enzyme selenocysteine methyltransferase in A. thaliana, we have introduced a novel biosynthetic ability that allows the non-accumulator to accumulate Se-methylselenocysteine and gamma-glutamylmethylselenocysteine in shoots. The biosynthesis of Se-methylselenocysteine in A. thaliana also confers significantly increased selenite tolerance and foliar Se accumulation. CONCLUSION: These results demonstrate the feasibility of developing transgenic plant-based production of Se-methylselenocysteine, as well as bioengineering selenite resistance in plants. Selenite resistance is the first step in engineering plants that are resistant to selenate, the predominant form of Se in the environment. AD - Center for Plant Environmental Stress Physiology, 1165 Horticulture Building, Purdue University, West Lafayette, IN 47907, USA. dsalt@purdue.edu AU - Ellis DR AU - Sors TG AU - Brunk DG AU - Albrecht C AU - Orser C AU - Lahner B AU - Wood KV AU - Harris HH AU - Pickering IJ AU - Salt DE LA - ENG PT - JOURNAL ARTICLE DEP - 20040128 TA - BMC Plant Biol JID - 100967807 EDAT- 2004/03/10 05:00 MHDA- 2004/03/10 05:00 PHST- 2003/Nov/10 [received] PHST- 2004/Jan/28 [accepted] PHST- 2004/Jan/28 [aheadofprint] AID - 10.1186/1471-2229-4-1 [doi] AID - 1471-2229-4-1 [pii] PST - epublish SO - BMC Plant Biol 2004 Jan 28;4(1):1. PMID- 15004566 OWN - NLM STAT- in-process DA - 20040402 IS - 1087-0156 VI - 22 IP - 4 DP - 2004 Apr TI - The plasma membrane-bound phospholipase Ddelta enhances freezing tolerance in Arabidopsis thaliana. PG - 427-33 AB - Freezing injury is a major environmental limitation on the productivity and geographical distribution of plants. Here we show that freezing tolerance can be manipulated in Arabidopsis thaliana by genetic alteration of the gene encoding phospholipase Ddelta (PLDdelta), which is involved in membrane lipid hydrolysis and cell signaling. Genetic knockout of the plasma membrane-associated PLDdelta rendered A. thaliana plants more sensitive to freezing, whereas overexpression of PLDdelta increased freezing tolerance. Lipid profiling revealed that PLDdelta contributed approximately 20% of the phosphatidic acid produced in wild-type plants during freezing, and overexpression of PLDdelta increased the production of phosphatidic acid species. The PLDdelta alterations did not affect the expression of the cold-regulated genes COR47 or COR78 or alter cold-induced increases in proline or soluble sugars, suggesting that the PLD pathway is a unique determinant of the response to freezing and may present opportunities for improving plant freezing tolerance. AD - Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506-3702, USA. FAU - Li, Weiqi AU - Li W FAU - Li, Maoyin AU - Li M FAU - Zhang, Wenhua AU - Zhang W FAU - Welti, Ruth AU - Welti R FAU - Wang, Xuemin AU - Wang X LA - eng PT - Journal Article DEP - 20040307 PL - United States TA - Nat Biotechnol JID - 9604648 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2003/Dec/01 [received] PHST- 2004/Jan/20 [accepted] PHST- 2004/Mar/07 [aheadofprint] AID - 10.1038/nbt949 [doi] AID - nbt949 [pii] PST - ppublish SO - Nat Biotechnol 2004 Apr;22(4):427-33. Epub 2004 Mar 7. PMID- 15004278 OWN - NLM STAT- in-process DA - 20040317 IS - 0027-8424 VI - 101 IP - 11 DP - 2004 Mar 16 TI - CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. PG - 3985-90 AB - CBF/DREB1 (C-repeat-binding factor/dehydration responsive element-binding factor 1) genes encode a small family of transcriptional activators that have been described as playing an important role in freezing tolerance and cold acclimation in Arabidopsis. To specify this role, we used a reverse genetic approach and identified a mutant, cbf2, in which the CBF2/DREB1C gene was disrupted. Here, we show that cbf2 plants have higher capacity to tolerate freezing than WT ones before and after cold acclimation and are more tolerant to dehydration and salt stress. All these phenotypes correlate with a stronger and more sustained expression of CBF/DREB1-regulated genes, which results from an increased expression of CBF1/DREB1B and CBF3/DREB1A in the mutant. In addition, we show that the expression of CBF1/DREB1B and CBF3/DREB1A in response to low temperature precedes that of CBF2/DREB1C. These results indicate that CBF2/DREB1C negatively regulates CBF1/DREB1B and CBF3/DREB1A, ensuring that their expression is transient and tightly controlled, which, in turn, guarantees the proper induction of downstream genes and the accurate development of Arabidopsis tolerance to freezing and related stresses. AD - Departamento de Biotecnologia, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, Carretera de la Coruna, Kilometro 7, 28040 Madrid, Spain. FAU - Novillo, Fernando AU - Novillo F FAU - Alonso, Jose M AU - Alonso JM FAU - Ecker, Joseph R AU - Ecker JR FAU - Salinas, Julio AU - Salinas J LA - eng PT - Journal Article DEP - 20040302 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2004/Mar/02 [aheadofprint] AID - 10.1073/pnas.0303029101 [doi] AID - 0303029101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Mar 16;101(11):3985-90. Epub 2004 Mar 2. PMID- 15004220 OWN - NLM STAT- in-process DA - 20040308 IS - 1362-4962 VI - 32 IP - 4 DP - 2004 Feb TI - SNPWave: a flexible multiplexed SNP genotyping technology. PG - e47 AB - Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave is based on highly multiplexed ligation, followed by amplification of up to 20 ligated probes in a single PCR. Depending on the multiplexing level of the ligation reaction, the latter employs selective amplification using the amplified fragment length polymorphism (AFLP) technology. Detection of SNPWave reaction products is based on size separation on a sequencing instrument with multiple fluorescence labels and short run times. The SNPWave technique is illustrated by a 100-plex genotyping assay for Arabidopsis, a 40-plex assay for tomato and a 10-plex assay for Caenorhabditis elegans, detected on the MegaBACE 1000 capillary sequencer. AD - Keygene NV, Agro Business Park 90, PO Box 216, 6700 AE Wageningen, The Netherlands. michiel.van-eijk@keygene.com FAU - van Eijk, Michiel J T AU - van Eijk MJ FAU - Broekhof, Jose L N AU - Broekhof JL FAU - van der Poel, Hein J A AU - van der Poel HJ FAU - Hogers, Rene C J AU - Hogers RC FAU - Schneiders, Harrie AU - Schneiders H FAU - Kamerbeek, Judith AU - Kamerbeek J FAU - Verstege, Esther AU - Verstege E FAU - van Aart, Joris W AU - van Aart JW FAU - Geerlings, Henk AU - Geerlings H FAU - Buntjer, Jaap B AU - Buntjer JB FAU - van Oeveren, A Jan AU - van Oeveren AJ FAU - Vos, Pieter AU - Vos P LA - eng PT - Journal Article DEP - 20040305 PL - England TA - Nucleic Acids Res JID - 0411011 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 AID - 10.1093/nar/gnh045 [doi] AID - 32/4/e47 [pii] PST - epublish SO - Nucleic Acids Res 2004 Feb;32(4):e47. PMID- 15004167 OWN - NLM STAT- in-process DA - 20040308 IS - 0022-1767 VI - 172 IP - 6 DP - 2004 Mar 15 TI - A major allergen from pollen defines a novel family of plant proteins and shows intra- and interspecie cross-reactivity. PG - 3644-51 AB - Olive tree (Olea europaea) pollen is a main cause of allergy associated with extensive areas of Europe and North America. Ole e 10, a small (10.8 kDa) and acidic (pI 5.8) protein, has been identified as a major allergen from the olive pollen, isolated, and characterized. Circular dichroism analysis gave 17% alpha helix, 33% beta sheet, and 21% beta turn for its secondary structure. Based on amino acid sequences of tryptic peptides, the protein was cloned and sequenced. The allergen consists of a single polypeptide chain of 102 aa, with a signal peptide of 21 residues. Ole e 10 showed homology with the C-terminal domain of another olive allergen, Ole e 9 (1,3-beta-glucanase, 53% identity), with deduced sequences from Arabidopsis thaliana genes (42-46% identity) and with polypeptide segments (Cys boxes) of proteins involved in yeast development (Epd1/Gas-1p/Phr2 families; 42-43% similarity). Ole e 10 showed 55% prevalence for olive-allergic patients and exhibited an IgE response dependent on its conformation. Remarkable IgE cross-reactivity was detected with Ole e 9, but no correlation was observed between the individual IgE responses to both allergens. Ole e 10 shares IgE B cell epitopes with proteins from Oleaceae, Gramineae, Betulaceae, Chenopodiaceae, Cupressaceae, Ambrosia, and Parietaria pollens, latex, and vegetable foods, such as tomato, kiwi, potato, and peach. These data indicate that Ole e 10 is a new pan-allergenic plant protein that shows notable intra- and interspecie IgE cross-reactivity and is a powerful candidate to be involved in pollen-latex-fruit syndrome. AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, Madrid, Spain. FAU - Barral, Patricia AU - Barral P FAU - Batanero, Eva AU - Batanero E FAU - Palomares, Oscar AU - Palomares O FAU - Quiralte, Joaquin AU - Quiralte J FAU - Villalba, Mayte AU - Villalba M FAU - Rodriguez, Rosalia AU - Rodriguez R LA - eng PT - Journal Article PL - United States TA - J Immunol JID - 2985117R SB - AIM SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PST - ppublish SO - J Immunol 2004 Mar 15;172(6):3644-51. PMID- 15003699 OWN - NLM STAT- in-process DA - 20040308 IS - 0166-445X VI - 67 IP - 2 DP - 2004 Apr 14 TI - Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. PG - 143-54 AB - Rapid progress in the field of genomics (the study of how an individual's entire genetic make-up, the genome, translates into biological functions) is beginning to provide tools that may assist our understanding of how chemicals can impact on human and ecosystem health. In many ways, if scientific and regulatory efforts in the 20th century have sought to establish which chemicals cause damage to ecosystems, then the challenge in ecotoxicology for the 21st century is to understand the mechanisms of toxicity to different wildlife species. In the human context, 'toxicogenomics' is the study of expression of genes important in adaptive responses to toxic exposures and a reflection of the toxic processes per se. Given the parallel implications for ecological (environmental) risk assessment, we propose the term 'ecotoxicogenomics' to describe the integration of genomics (transcriptomics, proteomics and metabolomics) into ecotoxicology. Ecotoxicogenomics is defined as the study of gene and protein expression in non-target organisms that is important in responses to environmental toxicant exposures. The potential of ecotoxicogenomic tools in ecological risk assessment seems great. Many of the standardized methods used to assess potential impact of chemicals on aquatic organisms rely on measuring whole-organism responses (e.g. mortality, growth, reproduction) of generally sensitive indicator species at maintained concentrations, and deriving 'endpoints' based on these phenomena (e.g. median lethal concentrations, no observed effect concentrations, etc.). Whilst such phenomenological approaches are useful for identifying chemicals of potential concern they provide little understanding of the mechanism of chemical toxicity. Without this understanding, it will be difficult to address some of the key challenges that currently face aquatic ecotoxicology, e.g. predicting toxicant responses across the very broad diversity of the phylogenetic groups present in aquatic ecosystems; estimating how changes at one ecological level or organisation will affect other levels (e.g. predicting population-level effects); predicting the influence of time-varying exposure on toxicant responses. Ecotoxicogenomic tools may provide us with a better mechanistic understanding of aquatic ecotoxicology. For ecotoxicogenomics to fulfil its potential, collaborative efforts are necessary through the parallel use of model microorganisms (e.g. Saccharomyces cerevisiae) together with aquatic (e.g. Danio rerio, Daphnia magna, Lemna minor and Xenopus tropicalis) and terrestrial (e.g. Arabidopsis thailiana, Caenorhabdites elegans and Eisenia foetida) plants, animals and microorganisms. AD - AstraZeneca Global Safety Health and Environment, Brixham Environmental Laboratory, Freshwater Quarry, Brixham, Devon TQ5 8BA, UK. jason.snape@brixham.astrazeneca.com FAU - Snape, Jason R AU - Snape JR FAU - Maund, Steve J AU - Maund SJ FAU - Pickford, Daniel B AU - Pickford DB FAU - Hutchinson, Thomas H AU - Hutchinson TH LA - eng PT - Journal Article PL - Netherlands TA - Aquat Toxicol JID - 8500246 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2002/Oct/20 [received] PHST- 2003/Nov/30 [accepted] AID - 10.1016/j.aquatox.2003.11.011 [doi] AID - S0166445X03002510 [pii] PST - ppublish SO - Aquat Toxicol 2004 Apr 14;67(2):143-54. PMID- 15003414 OWN - NLM STAT- in-process DA - 20040308 IS - 0031-9422 VI - 65 IP - 5 DP - 2004 Mar TI - Serine carboxypeptidase-like acyltransferases. PG - 517-24 AB - In plant secondary metabolism, an alternative pathway of ester formation is facilitated by acyltransferases accepting 1-O-beta-acetal esters (1-O-beta-glucose esters) as acyl donors instead of coenzyme A thioesters. Molecular data indicate homology of these transferases with hydrolases of the serine carboxypeptidase type defining them as serine carboxypeptidase-like (SCPL) acyltransferases. During evolution, they apparently have been recruited from serine carboxypeptidases and adapted to take over acyl transfer function. SCPL acyltransferases belong to the highly divergent class of alpha/beta hydrolases. These enzymes make use of a catalytic triad formed by a nucleophile, an acid and histidine acting as a charge relay system for the nucleophilic attack on amide or ester bonds. In analogy to SCPL acyltransferases, bacterial thioesterase domains are known which favour transferase activity over hydrolysis. Structure elucidation reveals water exclusion and a distortion of the oxyanion hole responsible for the changed activity. In plants, SCPL proteins form a large family. By sequence comparison, a distinguished number of Arabidopsis SCPL proteins cluster with proven SCPL acyltransferases. This indicates the occurrence of a large number of SCPL proteins co-opted to catalyse acyltransfer reactions. SCPL acyltransferases are ideal systems to investigate principles of functional adaptation and molecular evolution of plant genes. AD - Leibniz-Institut fur Pflanzenbiochemie, Weinberg 3, 06120 Halle (Saale), Germany. cmilkows@ipb-halle.de FAU - Milkowski, Carsten AU - Milkowski C FAU - Strack, Dieter AU - Strack D LA - eng PT - Journal Article PL - United States TA - Phytochemistry JID - 0151434 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2003/Dec/19 [received] PHST- 2003/Dec/19 [revised] AID - 10.1016/j.phytochem.2003.12.018 [doi] AID - S0031942203007489 [pii] PST - ppublish SO - Phytochemistry 2004 Mar;65(5):517-24. PMID- 15003262 OWN - NLM STAT- in-process DA - 20040308 IS - 1046-5928 VI - 34 IP - 2 DP - 2004 Apr TI - Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination. PG - 280-3 AB - The gene coding for APG8a (At4g21980), a protein from Arabidopsis thaliana, is involved in the autophagy process. The protein is an interesting candidate for structure determination by NMR spectroscopy. Toward this end, APG8a fused to an N-terminal His-tag has been expressed in Escherichia coli under a T7 expression system, refolded in vitro, and kept soluble by slight destabilization. The expressed protein appeared in both the soluble and the insoluble fractions. The whole-cell lysate was denatured by the addition of guanidinium chloride. The protein was immobilized on nickel-agarose resin and refolded by stepwise decrement of the denaturant. The elution buffer was 20 mM sodium phosphate, pH 7.0, with 1% glycerol, 0.5 M urea, 300 mM NaCl, and 1 M imidazole. After the removal of imidazole by ultrafiltration, the His-tag was cleaved with biotinylated thrombin. The protein product was kept in 20 mM sodium phosphate, pH 7.0, with 1% glycerol, 0.5 M urea, and 300 mM NaCl. The protein was found to aggregate extensively over time if any one of the three ingredients (sodium chloride, urea, or glycerol) was omitted. The yield of the protein was around 20 mg/L Luria-Bertani culture medium. The (1)H-(15)N NMR correlation spectrum of (15)N-labeled APG8a showed the characteristic signature of a folded protein; thus, the solutes appear to have no deleterious effect on the sample. These solution conditions kept the protein soluble and unaggregated for at least 2 days (enough time for NMR data collection). This approach of balanced stabilization-destabilization may offer a general approach for structural investigations of proteins that tend to aggregate. AD - Department of Applied Chemistry and Molecular Biology, Sejong University, 98 Gunja-Dong, Gwangjin-Gu, Seoul 143-747, Republic of Korea. FAU - Chae, Young Kee AU - Chae YK FAU - Im, Hana AU - Im H FAU - Zhao, Qin AU - Zhao Q FAU - Doelling, Jed H AU - Doelling JH FAU - Vierstra, Richard D AU - Vierstra RD FAU - Markley, John L AU - Markley JL LA - eng GR - GM66326/GM/NIGMS GR - P50 GM64598/GM/NIGMS GR - RR02301/RR/NCRR GR - RR02781/RR/NCRR GR - RR08438/RR/NCRR PT - Journal Article PL - United States TA - Protein Expr Purif JID - 9101496 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2003/Oct/11 [received] PHST- 2003/Nov/12 [revised] AID - 10.1016/j.pep.2003.11.007 [doi] AID - S1046592803003723 [pii] PST - ppublish SO - Protein Expr Purif 2004 Apr;34(2):280-3. PMID- 15003237 OWN - NLM STAT- in-process DA - 20040308 IS - 1360-1385 VI - 9 IP - 3 DP - 2004 Mar TI - The growing family of mitochondrial carriers in Arabidopsis. PG - 138-46 AD - Institut de Biotechnologie des Plantes, CNRS UMR8618, Batiment 630, Universite de Paris Sud-XI, 91405 Orsay Cedex, France. FAU - Picault, Nathalie AU - Picault N FAU - Hodges, Michael AU - Hodges M FAU - Palmieri, Luigi AU - Palmieri L FAU - Palmieri, Ferdinando AU - Palmieri F LA - eng PT - Journal Article PL - England TA - Trends Plant Sci JID - 9890299 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 AID - 10.1016/j.tplants.2004.01.007 [doi] AID - S1360138504000251 [pii] PST - ppublish SO - Trends Plant Sci 2004 Mar;9(3):138-46. PMID- 15003234 OWN - NLM STAT- in-process DA - 20040308 IS - 1360-1385 VI - 9 IP - 3 DP - 2004 Mar TI - Can Arabidopsis make complex alkaloids? PG - 116-22 AD - Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4. pfacchin@ucalgary.ca FAU - Facchini, Peter J AU - Facchini PJ FAU - Bird, David A AU - Bird DA FAU - St-Pierre, Benoit AU - St-Pierre B LA - eng PT - Journal Article PL - England TA - Trends Plant Sci JID - 9890299 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 AID - 10.1016/j.tplants.2004.01.004 [doi] AID - S1360138504000226 [pii] PST - ppublish SO - Trends Plant Sci 2004 Mar;9(3):116-22. PMID- 15003225 OWN - NLM STAT- in-process DA - 20040308 IS - 1369-5266 VI - 7 IP - 2 DP - 2004 Apr TI - Genomics applications to biotech traits: a revolution in progress? PG - 226-30 AB - Twenty years since the inception of the agricultural biotechnology era, only two products have had a significant impact in the market place: herbicide-resistant and insect-resistant crops. Additional products have been pursued but little success has been achieved, principally because of limited understanding of key genetic intervention points. Genomics tools have fueled a new strategy for identifying candidate genes. Primarily thanks to the application of functional genomics in Arabidopsis and other plants, the industry is now overwhelmed with candidate genes for transgenic intervention points. This success necessitates the application of genomics to the rapid validation of gene function and mode of action. As one example, the development of C-box binding factors (CBFs) for enhanced freezing and drought tolerance has been rapidly advanced because of the improved understanding generated by genomics technologies. AD - Mendel Biotechnology, 21375 Cabot Boulevard, Hayward, California 94545, USA. ngutterson@medelbio.com FAU - Gutterson, Neal AU - Gutterson N FAU - Zhang, James Z AU - Zhang JZ LA - eng PT - Journal Article PL - United States TA - Curr Opin Plant Biol JID - 100883395 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 AID - 10.1016/j.pbi.2003.12.002 [doi] AID - S1369526603001559 [pii] PST - ppublish SO - Curr Opin Plant Biol 2004 Apr;7(2):226-30. PMID- 15003211 OWN - NLM STAT- in-process DA - 20040308 IS - 1369-5266 VI - 7 IP - 2 DP - 2004 Apr TI - Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. PG - 126-31 AB - In addition to the Arabidopsis and rice genomic sequences, numerous expressed sequence tags (ESTs) and sequenced tag sites are now available for many species. These tools have made it possible to re-evaluate the extent of synteny and collinearity not only between Arabidopsis and related crops or between rice and other cereals but also between Arabidopsis and rice, between Arabidopsis and other dicots, and between cereals other than rice. Major progress in describing synteny relies on statistical tests. Overall, the data point to the occurrence of ancestral genome fragments in which a framework of common markers can be recognised. Micro-synteny studies reveal numerous rearrangements, which are likely to complicate map-based cloning strategies that use information from a model genome. AD - Laboratoire Genome et Developpement des Plantes, UMR 5096, CNRS-IRD-UP, University of Perpignan, 66860 Perpignan, France. delsany@univ-perp.fr FAU - Delseny, Michel AU - Delseny M LA - eng PT - Journal Article PL - United States TA - Curr Opin Plant Biol JID - 100883395 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 AID - 10.1016/j.pbi.2004.01.005 [doi] AID - S1369526604000081 [pii] PST - ppublish SO - Curr Opin Plant Biol 2004 Apr;7(2):126-31. PMID- 15003111 OWN - NLM STAT- in-data-review DA - 20040308 IS - 1465-6914 VI - 5 IP - 3 DP - 2004 TI - Interactions between light and carbon signaling pathways in Arabidopsis. PG - 213 AB - Two major signals perceived by plants are light and the source of carbon. A new report has examined the interactions between the signaling pathways from these two stimuli on a genome-wide scale in the model plant Arabidopsis thaliana. AD - The Rockefeller University, 130 York Avenue, New York, NY 10021, USA. chua@rockefeller.edu FAU - Reyes, Jose L AU - Reyes JL FAU - Chua, Nam-Hai AU - Chua NH LA - eng PT - Journal Article DEP - 20040227 PL - England TA - Genome Biol JID - 100960660 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2004/Feb/27 [aheadofprint] AID - 10.1186/gb-2004-5-3-213 [doi] AID - gb-2004-5-3-213 [pii] PST - ppublish SO - Genome Biol 2004;5(3):213. Epub 2004 Feb 27. PMID- 15003110 OWN - NLM STAT- in-data-review DA - 20040308 IS - 1465-6914 VI - 5 IP - 3 DP - 2004 TI - Leaf senescence - not just a 'wear and tear' phenomenon. PG - 212 AB - A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex, reflecting the activation of more than 2,000 genes in Arabidopsis, with gene products involved in a broad spectrum of regulatory, biochemical and cellular events. AD - Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel. gepstein@tx.technion.ac.il FAU - Gepstein, Shimon AU - Gepstein S LA - eng PT - Journal Article DEP - 20040227 PL - England TA - Genome Biol JID - 100960660 SB - IM EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PHST- 2004/Feb/27 [aheadofprint] AID - 10.1186/gb-2004-5-3-212 [doi] AID - gb-2004-5-3-212 [pii] PST - ppublish SO - Genome Biol 2004;5(3):212. Epub 2004 Feb 27. PMID- 15002557 OWN - NASA STAT- in-process DA - 20040306 IS - 1077-9248 VI - 9 IP - 1 DP - 2002 Jul TI - Plant growth using EMCS hardware on the ISS. PG - P223-4 AB - Under separate contracts with ESA (FUMO and ERM Study) and as a link in the development of the European Modular Cultivation System's (EMCS) functionality and biocompatibility, plant studies have been performed at The Plant Biocentre in Trondheim, Norway. The main goal was to test whether the breadboards containing the major components planned for use in the EMCS would be optimal for space experiments with plant material. The test plans and the experimental set-up for the verification of biocompatibility and biological functionality included the use of a few model plant species including cress (Lepidium sativum L.) and Arabidopsis thaliana. The plants were tested at different developmental levels of morphological and physiological complexity (illumination, life support, humidity control, water supply, observation, short- and long-term plant growth experiments and contamination prevention). Results from the tests show that the EMCS concept is useful for long duration plant growth on the ISS. AD - The Plant Biocentre, Department of Botany, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. Tor-Henning.Iversen@chembio.ntnu.no FAU - Iversen, Tor-Henning AU - Iversen TH FAU - Fossum, Knut R AU - Fossum KR FAU - Svare, Hakon AU - Svare H FAU - Johnsson, Anders AU - Johnsson A FAU - Schiller, Peter AU - Schiller P LA - eng PT - Journal Article PL - United States TA - J Gravit Physiol JID - 9437868 SB - S OID - NASA: 00030217 EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PST - ppublish SO - J Gravit Physiol 2002 Jul;9(1):P223-4. PMID- 15002554 OWN - NASA STAT- in-process DA - 20040306 IS - 1077-9248 VI - 9 IP - 1 DP - 2002 Jul TI - Understanding the gravitropic response of plants through the study of new arabidopsis mutants and the random positioning machine. PG - P217-8 AD - Institute of Plant Biochemistry and Ecophysiology/Consiglio Nazionale delle Ricerche, Monterotondo, Roma. FAU - Migliaccio, F AU - Migliaccio F FAU - Piconese, S AU - Piconese S FAU - Faggiano, M AU - Faggiano M FAU - Rosi, C AU - Rosi C LA - eng PT - Journal Article PL - United States TA - J Gravit Physiol JID - 9437868 SB - S OID - NASA: 00030214 EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PST - ppublish SO - J Gravit Physiol 2002 Jul;9(1):P217-8. PMID- 15002552 OWN - NASA STAT- in-process DA - 20040306 IS - 1077-9248 VI - 9 IP - 1 DP - 2002 Jul TI - Calcium/calmodulin-mediated gravitropic response in plants. PG - P211-4 AB - Calcium and calmodulin (CaM) play an important role in gravity signal transduction. However, the molecular and biochemical mechanisms involved in gravity signal transduction are not clearly understood. It is becoming evident that hydrogen peroxide is involved in gravity-induced response. Recent results indicate that Ca 2+/CaM is involved in hydrogen peroxide homeostasis by regulating catalase activity in plants (Yang and Poovaiah, 2002). It is well established that auxin controls differential growth during gravitropic bending. Results indicated that an auxin-responsive gene family (SAURs) encodes for Ca 2+ /CaM-binding proteins (Yang and Poovaiah, 2000a). To investigate the effects of gravity on the expression of genes involved in Ca 2+/CaM-mediated signaling, Arabidopsis and corn seedlings were subjected to simulated microgravity using the Random Positioning Machine (RPM), and hypergravity using the MidiCAR centrifuge. The changes in mRNA levels were studied. Selective and significant differences in gene expression were observed in simulated microgravity- and hypergravity- treated plants. The relevance of these genes in gravity signal perception and transduction is discussed. AD - Laboratory of Plant Molecular Biology and Physiology, Department of Horticulture, Washington State University, Pullman, WA, USA. FAU - Poovaiah, B W AU - Poovaiah BW FAU - Yang, T AU - Yang T FAU - van Loon, J J W A AU - van Loon JJ LA - eng PT - Journal Article PL - United States TA - J Gravit Physiol JID - 9437868 SB - S OID - NASA: 00030212 IR - Pooviah BW FIR - Pooviah, B W IRAD- Wash St U, Pullman GN - NASA: Grant numbers: NAG5-4841, #MG-051. EDAT- 2004/03/09 05:00 MHDA- 2004/03/09 05:00 PST - ppublish SO - J Gravit Physiol 2002 Jul;9(1):P211-4. PMID- 15001763 OWN - NLM STAT- completed DA - 20040305 DCOM- 20040325 IS - 1095-9203 VI - 303 IP - 5663 DP - 2004 Mar 5 TI - Plant sciences. Self-rejection--a new kinase connection. PG - 1474-5 AD - Department of Botany, University of Toronto, Toronto, M5S 3B2, Canada. goring@botany.utoronto.ca FAU - Goring, Daphne R AU - Goring DR FAU - Walker, John C AU - Walker JC LA - eng PT - Comment PT - Journal Article PL - United States TA - Science JID - 0404511 RN - 0 (Arc1 protein, plant) RN - 0 (Carrier Proteins) RN - 0 (Plant Proteins) RN - EC 2.7.1.- (S-receptor kinase) RN - EC 2.7.1.37 (Protein Kinases) RN - EC 2.7.1.37 (Protein-Serine-Threonine Kinases) SB - IM CON - Science. 2004 Mar 5;303(5663):1516-9. PMID: 15001779 MH - Arabidopsis/enzymology/genetics/physiology MH - Brassica rapa/enzymology/genetics/*physiology MH - Carrier Proteins/metabolism MH - Cell Membrane/*enzymology MH - Flowers/enzymology/*physiology MH - Genes, Plant MH - Phosphorylation MH - Plant Proteins/metabolism MH - Pollen/physiology MH - Protein Kinases/*metabolism MH - Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism MH - *Signal Transduction EDAT- 2004/03/06 05:00 MHDA- 2004/03/26 05:00 AID - 10.1126/science.1095764 [doi] AID - 303/5663/1474 [pii] PST - ppublish SO - Science 2004 Mar 5;303(5663):1474-5. PMID- 15001572 OWN - NLM STAT- publisher DA - 20040309 IS - 1083-351X DP - 2004 Mar 4 TI - Dynamic changes in the localization of MAP kinase cascade components controlling pathogenesis-related (PR) gene expression during innate immunity in parsley. AB - The activation of mitogen-activated protein kinase cascades is an important mechanism for stress adaptation through the control of gene expression in mammals, yeast and plants. MAPK activation has emerged as a common mechanism by which plants trigger pathogen defense responses following innate immune recognition of potential microbial pathogens. We are studying the non-host plant defense response of parsley to attempted infection by Phytophthora species using an experimental system of cultured parsley cells and the Phytophthora-derived Pep-13 peptide elicitor. Following receptor-mediated recognition of this peptide, parsley cells trigger a multifaceted innate immune response, involving the activation of three MAPKs that have been shown to function in the oxidative burst-independent activation of defense gene expression. Using this same experimental model we now report the identification of a MAPK-kinase (MAPKK) that functions upstream in this pathway. This kinase, referred to as PcMKK5 based on sequence homology to Arabidopsis thaliana AtMKK5, is activated in parsley cells following Pep-13 treatment and functions as an in vivo activator of all 3 MAPKs previously shown to be involved in this response. Gain and loss of function mutant versions of PcMKK5, when used in protoplast co-transfection assays, demonstrated that kinase activity of PcMKK5 is required for PR-gene promoter activation following Pep-13 treatment. Furthermore, using specific antibodies and immunofluorescent labeling, we demonstrate that activation of MAPKs in parsley cells correlates with an increase in their nuclear localization, which is not detectable for activated PcMKK5. These results suggest that activation of gene expression through MAPK cascades during innate immune responses in plants involves dynamic changes in the localization of the proteins involved, which may reflect the distribution of key protein substrates for the activated MAPKs. AD - Stress and Developmental Biology, Institute of Plant Biochemistry, Halle (Saale) D-06120. AU - Lee J AU - Rudd JJ AU - Macioszek VK AU - Scheel D LA - ENG PT - JOURNAL ARTICLE TA - J Biol Chem JID - 2985121R EDAT- 2004/03/06 05:00 MHDA- 2004/03/06 05:00 AID - 10.1074/jbc.M401099200 [doi] AID - M401099200 [pii] PST - aheadofprint SO - J Biol Chem 2004 Mar 4;. PMID- 15001351 OWN - NLM STAT- completed DA - 20040305 DCOM- 20040408 IS - 0022-2836 VI - 337 IP - 1 DP - 2004 Mar 12 TI - A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. PG - 49-63 AB - SQUAMOSA promoter binding proteins (SBPs) form a major family of plant-specific transcription factors related to flower development. Although SBPs are heterogeneous in primary structure, they share a highly conserved DNA-binding domain (DBD) that has been suggested to be zinc binding. Here we report the NMR solution structures of DBDs of two SBPs of Arabidopsis thaliana, SPL4 and SPL7. The two share essentially the same structural features. Each structure contains two zinc-binding sites consisting of eight Cys or His residues in a Cys3HisCys2HisCys or Cys6HisCys sequence motif in which the first four residues coordinate to one zinc and the last four coordinate to the other. These structures are dissimilar to other known zinc-binding structures, and thus represent a novel type of zinc-binding motif. The electrostatic profile on the surface suggested that a continuous region, including all the conserved basic residues, is involved in the DNA binding, the mode of which is likely to be novel as well. AD - Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan. k-yamasaki@aist.go.jp FAU - Yamasaki, Kazuhiko AU - Yamasaki K FAU - Kigawa, Takanori AU - Kigawa T FAU - Inoue, Makoto AU - Inoue M FAU - Tateno, Masaru AU - Tateno M FAU - Yamasaki, Tomoko AU - Yamasaki T FAU - Yabuki, Takashi AU - Yabuki T FAU - Aoki, Masaaki AU - Aoki M FAU - Seki, Eiko AU - Seki E FAU - Matsuda, Takayoshi AU - Matsuda T FAU - Nunokawa, Emi AU - Nunokawa E FAU - Ishizuka, Yoshiko AU - Ishizuka Y FAU - Terada, Takaho AU - Terada T FAU - Shirouzu, Mikako AU - Shirouzu M FAU - Osanai, Takashi AU - Osanai T FAU - Tanaka, Akiko AU - Tanaka A FAU - Seki, Motoaki AU - Seki M FAU - Shinozaki, Kazuo AU - Shinozaki K FAU - Yokoyama, Shigeyuki AU - Yokoyama S LA - eng SI - PDB/1UL4 SI - PDB/1UL5 PT - Journal Article PL - England TA - J Mol Biol JID - 2985088R RN - 0 (Arabidopsis Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Systems) RN - 0 (SPL4 protein, Arabidopsis) RN - 0 (SPL7 protein, Arabidopsis) RN - 0 (Transcription Factors) RN - 7440-66-6 (Zinc) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/chemistry/genetics MH - Arabidopsis Proteins/*chemistry/metabolism MH - Binding Sites MH - Circular Dichroism MH - DNA/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Macromolecular Systems MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Sequence Alignment MH - Support, Non-U.S. Gov't MH - Surface Plasmon Resonance MH - Transcription Factors/*chemistry/metabolism MH - Zinc/*metabolism EDAT- 2004/03/06 05:00 MHDA- 2004/04/09 05:00 PHST- 2003/Oct/07 [received] PHST- 2004/Jan/09 [revised] PHST- 2004/Jan/14 [accepted] AID - 10.1016/j.jmb.2004.01.015 [doi] AID - S0022283604000610 [pii] PST - ppublish SO - J Mol Biol 2004 Mar 12;337(1):49-63. PMID- 15000662 OWN - NLM STAT- completed DA - 20040305 DCOM- 20040317 IS - 1010-061X VI - 17 IP - 1 DP - 2004 Jan TI - Flowering time plasticity in Arabidopsis thaliana: a reanalysis of Westerman & Lawrence (1970). PG - 197-207 AB - Environmental variation in temperature can have dramatic effects on plant morphology, phenology, and fitness, and for this reason it is important to understand the evolutionary dynamics of phenotypic plasticity in response to temperature. We investigated constraints on the evolution of phenotypic plasticity in response to a temperature gradient in the model plant Arabidopsis thaliana by applying modern analytical tools to the classic data of Westerman & Lawrence (1970). We found significant evidence for two types of constraints. First, we detected numerous significant genetic correlations between plastic responses to temperature and the mean value of a trait across all environments, which differed qualitatively in pattern between the set of ecotypes and the set of mutant lines in the original sample. Secondly, we detected significant costs of flowering time plasticity in two of the three experimental environments, and a net pattern of selection against flowering time plasticity in the experiment overall. Thus, when explored with contemporary methods, the prescient work of Westerman & Lawrence (1970) provides new insights about evolutionary constraints on the evolution of plasticity. AD - Ecology and Evolutionary Biology Department, Brown University, Box G-W, Providence, RI 02912, USA. john_stinchcombe@brown.edu FAU - Stinchcombe, J R AU - Stinchcombe JR FAU - Dorn, L A AU - Dorn LA FAU - Schmitt, J AU - Schmitt J LA - eng PT - Journal Article PL - Switzerland TA - J Evol Biol JID - 8809954 SB - IM MH - Arabidopsis/genetics/*physiology MH - Comparative Study MH - *Evolution MH - Flowers/*physiology MH - *Phenotype MH - Selection (Genetics) MH - Statistics MH - Support, U.S. Gov't, Non-P.H.S. MH - *Temperature MH - Time Factors EDAT- 2004/03/06 05:00 MHDA- 2004/03/18 05:00 PST - ppublish SO - J Evol Biol 2004 Jan;17(1):197-207. PMID- 15000398 OWN - NLM STAT- in-process DA - 20040305 IS - 0894-0282 VI - 17 IP - 3 DP - 2004 Mar TI - Mutations in the Pseudomonas syringae avrRpt2 gene that dissociate its virulence and avirulence activities lead to decreased efficiency in AvrRpt2-induced disappearance of RIN4. PG - 313-21 AB - The avrRpt2 gene from Pseudomonas syringae pv. tomato exhibits avirulence activity on Arabidopsis expressing the resistance gene RPS2 but promotes bacterial virulence on susceptible rps2 Arabidopsis. To understand the functional relationship between the avirulence and virulence activities of avrRpt2, we analyzed a series of six avrRpt2 mutants deficient in eliciting the RPS2-dependent hypersensitive response. We show that the mutants are also severely impaired in triggering RSP2-dependent resistance. Four of these mutants are severely impaired in their virulence activity, whereas two alleles, encoding C-terminal deletions of AvrRpt2, retain significant but slightly reduced virulence activity. Thus, the avirulence and virulence activities of avrRpt2 can be genetically uncoupled. We tested the ability of the two C-terminal deletion mutants to trigger AvrRpt2-induced elimination of the Arabidopsis RIN4 protein and show that they retain this activity but are less efficient than wild-type AvrRpt2. Thus, reduced AvrRpt2 virulence activity is correlated with reduced efficiency in the induction of RIN4 disappearance. This suggests that an alteration in kinetics of RIN4 disappearance triggered by the C-terminal deletion mutants may provide the mechanistic basis for the uncoupling of the avirulence and virulence activities of avrRpt2. AD - Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA. FAU - Lim, Melisa T S AU - Lim MT FAU - Kunkel, Barbara N AU - Kunkel BN LA - eng PT - Journal Article PL - United States TA - Mol Plant Microbe Interact JID - 9107902 SB - IM EDAT- 2004/03/06 05:00 MHDA- 2004/03/06 05:00 PST - ppublish SO - Mol Plant Microbe Interact 2004 Mar;17(3):313-21. PMID- 15000394 OWN - NLM STAT- in-process DA - 20040305 IS - 0894-0282 VI - 17 IP - 3 DP - 2004 Mar TI - A novel Arabidopsis-Colletotrichum pathosystem for the molecular dissection of plant-fungal interactions. PG - 272-82 AB - The ability of a Colletotrichum sp., originally isolated from Brassica campestris, to infect Arabidopsis thaliana was examined. Sequence analysis of the internal transcribed spacer (ITS)1, 5.8S RNA gene and ITS2 regions of ribosomal (r)DNA showed the pathogen to be Colletotrichum destructivum. The host range was broad, including many cruciferous plants and some legumes. At 25 degrees C, all A. thaliana accessions tested were susceptible to the Brassica isolates of C. destructivum; however, at 15 degrees C, the accession Ws-2 showed a temperature-dependant resistance, in which single epidermal cells underwent a rapid hypersensitive response. Legume isolates of C. destructivum were unable to infect A. thaliana and induced deposition of callose papillae at sites of attempted penetration. In compatible interactions, C. destructivum showed a two-stage, hemibiotrophic infection process. The initial biotrophic phase was associated with large, intracellular primary hyphae and was confined to one epidermal cell; whereas, in the subsequent necrotrophic phase, narrow secondary hyphae extensively colonized the tissue and conidia were produced in acervuli. An efficient transformation system was established for C. destructivum, using Agrobacterium-mediated transfer of DNA. The ability to genetically manipulate both partners in the interaction is an important advantage, and the Arabidopsis-Colletotrichum pathosystem should provide a valuable new model for dissecting plant-fungal interactions. AD - UMR 5546, CNRS-Universite Paul Sabatier, Pole de Biotechnologie Vegetale, 24 Chemin de Borde Rouge, BP17 Auzeville, 31326 Castanet-Tolosan, France. oconnel@smcv.ups-tlse.fr FAU - O'Connell, Richard AU - O'Connell R FAU - Herbert, Corentin AU - Herbert C FAU - Sreenivasaprasad, Surapareddy AU - Sreenivasaprasad S FAU - Khatib, Moustafa AU - Khatib M FAU - Esquerre-Tugaye, Marie-Therese AU - Esquerre-Tugaye MT FAU - Dumas, Bernard AU - Dumas B LA - eng SI - GENBANK/AJ558106 SI - GENBANK/AJ558107 SI - GENBANK/AJ558108 SI - GENBANK/AJ558109 SI - GENBANK/AJ558110 SI - GENBANK/AJ558111 PT - Journal Article PL - United States TA - Mol Plant Microbe Interact JID - 9107902 SB - IM EDAT- 2004/03/06 05:00 MHDA- 2004/03/06 05:00 PST - ppublish SO - Mol Plant Microbe Interact 2004 Mar;17(3):272-82. PMID- 15000392 OWN - NLM STAT- in-process DA - 20040305 IS - 0894-0282 VI - 17 IP - 3 DP - 2004 Mar TI - Identification of a novel Pseudomonas syringae Psy61 effector with virulence and avirulence functions by a HrpL-dependent promoter-trap assay. PG - 254-62 AB - The hrp pathogenicity island of Pseudomonas syringae encodes a type III secretion system (TTSS) that translocates effectors into plant cells. Most genes encoding effectors are dispersed in the P. syringae genome. Regardless of location, all are regulated coordinately by the alternative sigma factor HrpL. An HrpL-dependent promoter-trap assay was developed to screen genomic libraries of P. syringae strains for promoters whose activity in Escherichia coli is dependent on an inducible hrpL construct. Twenty-two HrpL-dependent promoter fragments were isolated from P. syringae Psy61 that included promoters for known HrpL-dependent genes. One fragment also was isolated that shared no similarity with known genes but retained a near consensus HrpL-dependent promoter. The sequence of the region revealed a 375-amino acid open reading frame encoding a 40.5-kDa product that was designated HopPsyL. HopPsyL was structurally similar to other secreted effectors and carried a putative chloroplast-targeting signal and two predicted transmembrane domains. HopPsyL':'AvrRpt2 fusions were translocated into host cells via the P. syringae pv. tomato DC3000 hrp TTSS. A hopPsyL::kan mutant of Psy61 exhibited strongly reduced virulence in Phaseolus vulgaris cv. Kentucky Wonder, but did not appear to act as a defense response suppressor. The ectopically expressed gene reduced the virulence of Pseudomonas syringae DC3000 transformants in Arabidopsis thaliana Col-0. The gene was shown to be conserved in 6 of 10 P. syringae pv. syringae strains but was not detected in 35 strains of other pathovars. HopPsyL appears to be a novel TTSS-dependent effector that functions as a host-species-specific virulence factor in Psy61. AD - Department of Cell Biology and Molecular Genetics, Microbiology Bldg, University of Maryland, College Park 20742, USA. FAU - Losada, L AU - Losada L FAU - Sussan, T AU - Sussan T FAU - Pak, K AU - Pak K FAU - Zeyad, S AU - Zeyad S FAU - Rozenbaum, I AU - Rozenbaum I FAU - Hutcheson, S W AU - Hutcheson SW LA - eng SI - GENBANK/AY349161 PT - Journal Article PL - United States TA - Mol Plant Microbe Interact JID - 9107902 SB - IM EDAT- 2004/03/06 05:00 MHDA- 2004/03/06 05:00 PST - ppublish SO - Mol Plant Microbe Interact 2004 Mar;17(3):254-62. PMID- 14999285 OWN - NLM STAT- completed DA - 20040304 DCOM- 20040316 IS - 1476-4687 VI - 428 IP - 6978 DP - 2004 Mar 4 TI - microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. PG - 84-8 AB - In both animals and plants, many developmentally important regulatory genes have complementary microRNAs (miRNAs), which suggests that these miRNAs constitute a class of developmental signalling molecules. Leaves of higher plants exhibit a varying degree of asymmetry along the adaxial/abaxial (upper/lower) axis. This asymmetry is specified through the polarized expression of class III homeodomain/leucine zipper (HD-ZIPIII) genes. In Arabidopsis, three such genes, PHABULOSA (PHB), PHAVOLUTA (PHV) and REVOLUTA (REV), are expressed throughout the incipient leaf, but become adaxially localized after primordium emergence. Downregulation of the HD-ZIPIII genes allows expression of the KANADI and YABBY genes, which specify abaxial fate. PHB, PHV and REV transcripts contain a complementary site for miRNA165 and miRNA166, which can direct their cleavage in vitro. Here we show that miRNA166 constitutes a highly conserved polarizing signal whose expression pattern spatially defines the expression domain of the maize hd-zipIII family member rolled leaf1 (rld1). Moreover, the progressively expanding expression pattern of miRNA166 during leaf development and its accumulation in phloem suggests that miRNA166 may form a movable signal that emanates from a signalling centre below the incipient leaf. AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. FAU - Juarez, Michelle T AU - Juarez MT FAU - Kui, Jonathan S AU - Kui JS FAU - Thomas, Julie AU - Thomas J FAU - Heller, Bradley A AU - Heller BA FAU - Timmermans, Marja C P AU - Timmermans MC LA - eng SI - GENBANK/AY501430 SI - GENBANK/AY501431 SI - GENBANK/AY501432 SI - GENBANK/AY501433 SI - GENBANK/AY501434 PT - Journal Article PL - England TA - Nature JID - 0410462 RN - 0 (MicroRNAs) RN - 0 (Plant Proteins) RN - 0 (RNA, Plant) SB - IM MH - Alleles MH - Amino Acid Sequence MH - Base Sequence MH - *Body Patterning MH - Down-Regulation MH - Gene Expression Regulation, Plant MH - Genes, Plant/*genetics MH - MicroRNAs/genetics/*metabolism MH - Molecular Sequence Data MH - Phenotype MH - Plant Leaves/*embryology/genetics MH - Plant Proteins/chemistry/genetics/metabolism MH - *RNA Interference MH - RNA, Plant/genetics/metabolism MH - Support, Non-U.S. Gov't MH - Support, U.S. Gov't, Non-P.H.S. MH - Support, U.S. Gov't, P.H.S. MH - Zea mays/*embryology/*genetics EDAT- 2004/03/06 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Dec/04 [received] PHST- 2004/Jan/23 [accepted] AID - 10.1038/nature02363 [doi] AID - nature02363 [pii] PST - ppublish SO - Nature 2004 Mar 4;428(6978):84-8. PMID- 14999284 OWN - NLM STAT- completed DA - 20040304 DCOM- 20040316 IS - 1476-4687 VI - 428 IP - 6978 DP - 2004 Mar 4 TI - Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. PG - 81-4 AB - Gene regulation by RNA interference requires the functions of the PAZ domain protein Argonaute. In plants, mutations in ARGONAUTE1 (AGO1) are associated with distinctive developmental defects that suggest a role for microRNA (miRNA) in organ polarity. Potential targets of miRNA regulation are the homeodomain/leucine zipper genes PHABULOSA (PHB) and PHAVOLUTA (PHV). These genes are expressed in a polar fashion in leaf primordia and are required for adaxial cell fate. Here we show that a 21-nucleotide miRNA that directs cleavage of PHB/PHV messenger RNA accumulates first in the embryonic meristem, and then in the abaxial domain of the developing leaf. miRNA distribution is disrupted by mutations in AGO1, indicating that AGO1 affects the regulation of miRNA. In addition, interactions between homeodomain/leucine zipper genes and an allelic series of ago1 indicate that miRNA acts as a signal to specify leaf polarity. AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. FAU - Kidner, Catherine A AU - Kidner CA FAU - Martienssen, Robert A AU - Martienssen RA LA - eng PT - Journal Article PL - England TA - Nature JID - 0410462 RN - 0 (AGO1 protein, Arabidopsis) RN - 0 (Arabidopsis Proteins) RN - 0 (MicroRNAs) RN - 0 (RNA, Messenger) RN - 0 (RNA, Plant) SB - IM MH - Alleles MH - Arabidopsis/*embryology/genetics/metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - *Body Patterning MH - Gene Expression Regulation, Plant MH - Genes, Plant/genetics MH - Genes, Reporter MH - Meristem/embryology/genetics/metabolism MH - MicroRNAs/*genetics/*metabolism MH - Mutation/genetics MH - Plant Leaves/*embryology/genetics/metabolism MH - RNA, Messenger/genetics/metabolism MH - RNA, Plant/genetics/metabolism MH - Support, Non-U.S. Gov't MH - Support, U.S. Gov't, Non-P.H.S. MH - Support, U.S. Gov't, P.H.S. EDAT- 2004/03/06 05:00 MHDA- 2004/03/17 05:00 PHST- 2003/Aug/06 [received] PHST- 2004/Jan/23 [accepted] AID - 10.1038/nature02366 [doi] AID - nature02366 [pii] PST - ppublish SO - Nature 2004 Mar 4;428(6978):81-4. PMID- 14999409 OWN - NLM STAT- completed DA - 20040304 DCOM- 20040330 IS - 1420-682X VI - 61 IP - 4 DP - 2004 Feb TI - High affinity recognition of a Phytophthora protein by Arabidopsis via an RGD motif. PG - 502-9 AB - The RGD tripeptide sequence, a cell adhesion motif present in several extracellular matrix proteins of mammalians, is involved in numerous plant processes. In plant-pathogen interactions, the RGD motif is believed to reduce plant defence responses by disrupting adhesions between the cell wall and plasma membrane. Photoaffinity cross-linking of [125I]-azido-RGD heptapeptide in the presence of purified plasma membrane vesicles of Arabidopsis thaliana led to label incorporation into a single protein with an apparent molecular mass of 80 kDa. Incorporation could be prevented by excess RGD peptides, but also by the IPI-O protein, an RGD-containing protein secreted by the oomycete plant pathogen Phytophthora infestans. Hydrophobic cluster analysis revealed that the RGD motif of IPI-O (positions 53-56) is readily accessible for interactions. Single amino acid mutations in the RGD motif in IPI-O (of Asp56 into Glu or Ala) resulted in the loss of protection of the 80-kDa protein from labelling. Thus, the interaction between the two proteins is mediated through RGD recognition and the 80-kDa RGD-binding protein has the characteristics of a receptor for IPI-O. The IPI-O protein also disrupted cell wall-plasma membrane adhesions in plasmolysed A. thaliana cells, whereas IPI-O proteins mutated in the RGD motif (D56A and D56E) did not. AD - Surfaces Cellulaires et Signalisation chez les Vegetaux, UMR 5546 CNRS-Universite Paul Sabatier, 31326 Castanet Tolosan cedex, France. FAU - Senchou, V AU - Senchou V FAU - Weide, R AU - Weide R FAU - Carrasco, A AU - Carrasco A FAU - Bouyssou, H AU - Bouyssou H FAU - Pont-Lezica, R AU - Pont-Lezica R FAU - Govers, F AU - Govers F FAU - Canut, H AU - Canut H LA - eng PT - Journal Article PL - Switzerland TA - Cell Mol Life Sci JID - 9705402 RN - 0 (Arabidopsis Proteins) RN - 0 (Fungal Proteins) RN - 0 (IpiO1 protein, Phytophthora infestans) RN - 0 (Membrane Proteins) RN - 0 (Oligopeptides) RN - 99896-85-2 (arginyl-glycyl-aspartic acid) SB - IM MH - Amino Acid Motifs MH - Arabidopsis/*metabolism MH - Arabidopsis Proteins/*metabolism MH - Cell Membrane/metabolism MH - Cell Wall/metabolism MH - Fungal Proteins/*metabolism MH - Membrane Proteins/metabolism MH - Oligopeptides/metabolism MH - Phytophthora/*metabolism MH - Support, Non-U.S. Gov't EDAT- 2004/03/05 05:00 MHDA- 2004/03/31 05:00 AID - 10.1007/s00018-003-3394-z [doi] PST - ppublish SO - Cell Mol Life Sci 2004 Feb;61(4):502-9. PMID- 14999098 OWN - NLM STAT- in-process DA - 20040317 IS - 0027-8424 VI - 101 IP - 11 DP - 2004 Mar 16 TI - Universality and flexibility in gene expression from bacteria to human. PG - 3765-9 AB - Highly parallel experimental biology is offering opportunities to not just accomplish work more easily, but to explore for underlying governing principles. Recent analysis of the large-scale organization of gene expression has revealed its complex and dynamic nature. However, the underlying dynamics that generate complex gene expression and cellular organization are not yet understood. To comprehensively and quantitatively elucidate these underlying gene expression dynamics, we have analyzed genome-wide gene expression in many experimental conditions in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Mus musculus, and Homo sapiens. Here we demonstrate that the gene expression dynamics follows the same and surprisingly simple principle from E. coli to human, where gene expression changes are proportional to their expression levels, and show that this "proportional" dynamics or "rich-travel-more" mechanism can regenerate the observed complex and dynamic organization of the transcriptome. These findings provide a universal principle in the regulation of gene expression, show how complex and dynamic organization can emerge from simple underlying dynamics, and demonstrate the flexibility of transcription across a wide range of expression levels. AD - Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. uedah-tky@umin.ac.jp FAU - Ueda, Hiroki R AU - Ueda HR FAU - Hayashi, Satoko AU - Hayashi S FAU - Matsuyama, Shinichi AU - Matsuyama S FAU - Yomo, Tetsuya AU - Yomo T FAU - Hashimoto, Seiichi AU - Hashimoto S FAU - Kay, Steve A AU - Kay SA FAU - Hogenesch, John B AU - Hogenesch JB FAU - Iino, Masamitsu AU - Iino M LA - eng PT - Journal Article DEP - 20040303 PL - United States TA - Proc Natl Acad Sci U S A JID - 7505876 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 PHST- 2004/Mar/03 [aheadofprint] AID - 10.1073/pnas.0306244101 [doi] AID - 0306244101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A 2004 Mar 16;101(11):3765-9. Epub 2004 Mar 3. PMID- 14996658 OWN - NLM STAT- in-data-review DA - 20040303 IS - 0829-318X VI - 24 IP - 5 DP - 2004 May TI - Molecular cloning of ten distinct hypervariable regions from the cellulose synthase gene superfamily in aspen trees. PG - 543-50 AB - Recent molecular genetic data suggest that cellulose synthase (CesA) genes coding for the enzymes that catalyze cellulose biosynthesis (CESAs) in Arabidopsis and other herbaceous plants belong to a large gene family. Much less is known about CesA genes from forest trees. To isolate new CesA genes from tree species, discriminative but easily obtainable homologous DNA probes are required. Hypervariable regions (HVRII) of CesA genes represent highly divergent DNA sequences that can be used to examine structural, expressional and functional relationships among CesA genes. We used a reverse transcriptase-polymerase chain reaction (RT-PCR)-based technique to identify HVRII regions from eight types of CesA genes and two types of CesA-like D (CslD) genes in quaking aspen (Populus tremuloides Michx.). Comparison of these aspen CESA/CSLD HVRII regions with the predicted proteins from eight full-length CesA/CslD cDNAs available in our laboratory and with searches for aspen CesA/CslD homologs in the recently released Populus trichocarpa Torr. & A. Gray. genome confirmed the utility of this approach in identifying several CesA/CslD gene members from the Populus genome. Phylogenetic analysis of 56 HVRII domains from a variety of plant species suggested that at least six distinct classes of CESAs exist in plants, supporting a previous proposal for renaming HVRII regions as class-specific regions (CSR). This method of CSR cloning could be applied to other crop plants and tree species, especially softwoods, for which the whole genome sequence is unlikely to become available in the near future because of the large size of these genomes. AD - Plant Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA. FAU - Liang, Xiaoe AU - Liang X FAU - Joshi, Chandrashekhar P AU - Joshi CP LA - eng PT - Journal Article PL - Canada TA - Tree Physiol JID - 100955338 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 PST - ppublish SO - Tree Physiol 2004 May;24(5):543-50. PMID- 14996223 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. PG - 914-39 AB - MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion. AD - Max Planck Institute for Molecular Plant Physiology, Golm, Germany. FAU - Thimm, Oliver AU - Thimm O FAU - Blasing, Oliver AU - Blasing O FAU - Gibon, Yves AU - Gibon Y FAU - Nagel, Axel AU - Nagel A FAU - Meyer, Svenja AU - Meyer S FAU - Kruger, Peter AU - Kruger P FAU - Selbig, Joachim AU - Selbig J FAU - Muller, Lukas A AU - Muller LA FAU - Rhee, Seung Y AU - Rhee SY FAU - Stitt, Mark AU - Stitt M LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2016 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):914-39. PMID- 14996221 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. PG - 897-905 AB - More than 10 000 transposon-tagged lines were constructed by using the Activator (Ac)/Dissociation (Ds) system in order to collect insertional mutants as a useful resource for functional genomics of Arabidopsis. The flanking sequences of the Ds element in the 11 800 independent lines were determined by high-throughput analysis using a semi-automated method. The sequence data allowed us to map the unique insertion site on the Arabidopsis genome in each line. The Ds element of 7566 lines is inserted in or close to coding regions, potentially affecting the function of 5031 of 25 000 Arabidopsis genes. Half of the lines have Ds insertions on chromosome 1 (Chr. 1), in which donor lines have a donor site. In the other half, the Ds insertions are distributed throughout the other four chromosomes. The intrachromosomal distribution of Ds insertions varies with the donor lines. We found that there are hot spots for Ds transposition near the ends of every chromosome, and we found some statistical preference for Ds insertion targets at the nucleotide level. On the basis of systematic analysis of the Ds insertion sites in the 11 800 lines, we propose the use of Ds-tagged lines with a single insertion in annotated genes for systematic analysis of phenotypes (phenome analysis) in functional genomics. We have opened a searchable database of the insertion-site sequences and mutated genes (http://rarge.gsc.riken.go.jp/) and are depositing these lines in the RIKEN BioResource Center as available resources (http://www.brc.riken.go.jp/Eng/). AD - Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. FAU - Kuromori, Takashi AU - Kuromori T FAU - Hirayama, Takashi AU - Hirayama T FAU - Kiyosue, Yuki AU - Kiyosue Y FAU - Takabe, Hiroko AU - Takabe H FAU - Mizukado, Saho AU - Mizukado S FAU - Sakurai, Tetsuya AU - Sakurai T FAU - Akiyama, Kenji AU - Akiyama K FAU - Kamiya, Asako AU - Kamiya A FAU - Ito, Takuya AU - Ito T FAU - Shinozaki, Kazuo AU - Shinozaki K LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2009 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):897-905. PMID- 14996219 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde. PG - 877-88 AB - The provenance, half-life and biological activity of malondialdehyde (MDA) were investigated in Arabidopsis thaliana. We provide genetic confirmation of the hypothesis that MDA originates from fatty acids containing more than two methylene-linked double bonds, showing that tri-unsaturated fatty acids are the in vivo source of up to 75% of MDA. The abundance of the combined pool of free and reversibly bound MDA did not change dramatically in stress, although a significant increase in the free MDA pool under oxidative conditions was observed. The half-life of infiltrated MDA indicated rapid metabolic turnover/sequestration. Exposure of plants to low levels of MDA using a recently developed protocol powerfully upregulated many genes on a cDNA microarray with a bias towards those implicated in abiotic/environmental stress (e.g. ROF1 and XERO2). Remarkably, and in contrast to the activities of other reactive electrophile species (i.e. small vinyl ketones), none of the pathogenesis-related (PR) genes tested responded to MDA. The use of structural mimics of MDA isomers suggested that the propensity of the molecule to act as a cross-linking/modifying reagent might contribute to the activation of gene expression. Changes in the concentration/localisation of unbound MDA in vivo could strongly affect stress-related transcription. AD - Gene Expression Laboratory, Plant Molecular Biology, University of Lausanne, Biology Building, 1015 Lausanne, Switzerland. FAU - Weber, Hans AU - Weber H FAU - Chetelat, Aurore AU - Chetelat A FAU - Reymond, Philippe AU - Reymond P FAU - Farmer, Edward E AU - Farmer EE LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2013 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):877-88. PMID- 14996218 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes. PG - 864-76 AB - The Arabidopsis At filamentation temperature sensitive (FtsH) metalloprotease gene family comprises 12 members (AtFtsH1-AtFtsH12), including three pairs of closely related genes that are targeted to chloroplasts (AtFtsH2 and AtFtsH8; AtFtsH1 and AtFtsH5; and AtFtsH7 and AtFtsH9). Mutations in AtFtsH5 (var1) and AtFtsH2 (var2) give rise to variegated plants with green- and white-sectored leaves. Cells in the green sectors contain morphologically normal chloroplasts, whereas cells in the white sectors are blocked in chloroplast biogenesis. A major question is how chloroplasts arise in cells that have a mutant genotype. We have found by two-dimensional (2-D) green gel and gel filtration analyses that AtFtsH2/VAR2 forms oligomeric complexes. Two bands in the 2-D green gels that correspond to AtFtsH5/VAR1 + AtFtsH1 and AtFtsH2/VAR2 + AtFtsH8 have been identified, and these bands are coordinately reduced in amount in var1 and var2 thylakoids that lack AtFtsH5/VAR1 and AtFtsH2/VAR2, respectively. These reductions are not because of alterations in transcript abundance. Overexpression of AtFtsH8 in var2-4 (a putative null allele) normalizes the variegation phenotype of the mutant and restores the two bands to their wild-type levels. These results suggest that AtFtsH8 is interchangeable with AtFtsH2/VAR2 in AtFtsH-containing oligomers, and that the two proteins have redundant functions. Consistent with this hypothesis, AtFtsH2 and AtFtsH8 have similar expression patterns, as monitored by promoter-beta-glucuronidase (GUS) fusion and RT-PCR experiments. Based on our findings, we propose that AtFtsH1, AtFtsH2/VAR2, AtFtsH5/VAR1, and AtFtsH8 interact to form oligomeric structures, and that subunit stoichiometry is controlled post-transcriptionally in var1 and var2, perhaps by turnover. A threshold model is presented to explain the pattern of variegation in var2 in which AtFtsH8 provides a compensating activity in the green sectors of the mutant. AD - Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA. FAU - Yu, Fei AU - Yu F FAU - Park, Sungsoon AU - Park S FAU - Rodermel, Steven R AU - Rodermel SR LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2014 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):864-76. PMID- 14996217 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - Mutants for photosystem I subunit D of Arabidopsis thaliana: effects on photosynthesis, photosystem I stability and expression of nuclear genes for chloroplast functions. PG - 839-52 AB - In Arabidopsis thaliana, the D-subunit of photosystem I (PSI-D) is encoded by two functional genes, PsaD1 and PsaD2, which are highly homologous. Knock-out alleles for each of the loci have been identified by a combination of forward and reverse genetics. The double mutant psad1-1 psad2-1 is seedling-lethal, high-chlorophyll-fluorescent and deficient for all tested PSI subunits, indicating that PSI-D is essential for photosynthesis. In addition, psad1-1 psad2-1 plants show a defect in the accumulation of thylakoid multiprotein complexes other than PSI. Of the single-gene mutations, psad2 plants behave like wild-type (WT) plants, whereas psad1-1 markedly affects the accumulation of PsaD mRNA and protein, and photosynthetic electron flow. Additional effects of the psad1-1 mutation include a decrease in growth rate under greenhouse conditions and downregulation of the mRNA expression of most genes involved in the light phase of photosynthesis. In the same mutant, a marked decrease in the levels of PSI and PSII polypeptides is evident, as well as a light-green leaf coloration and increased photosensitivity. Increased dosage of PsaD2 in the psad1-1 background restores the WT phenotype, indicating that PSI-D1 and PSI-D2 have redundant functions. AD - Abteilung fur Pflanzenzuchtung und Ertragsphysiologie, Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne Weg 10, D-50829 Koln, Germany. FAU - Ihnatowicz, Anna AU - Ihnatowicz A FAU - Pesaresi, Paolo AU - Pesaresi P FAU - Varotto, Claudio AU - Varotto C FAU - Richly, Erik AU - Richly E FAU - Schneider, Anja AU - Schneider A FAU - Jahns, Peter AU - Jahns P FAU - Salamini, Francesco AU - Salamini F FAU - Leister, Dario AU - Leister D LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2011 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):839-52. PMID- 14996216 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - Auxin activates KAT1 and KAT2, two K+-channel genes expressed in seedlings of Arabidopsis thaliana. PG - 815-27 AB - The transcript abundance of the K+-channel gene ZMK1 (Zea mays K+ channel 1) in maize coleoptiles is controlled by the phytohormone auxin. Thus, ZMK1 is thought to function in auxin-regulated coleoptile elongation, as well as during gravitropism and phototropism. To investigate related growth phenomena in the dicotyledonous plant Arabidopsis thaliana, we screened etiolated seedlings for auxin-induced K+-channel genes. Among the members of the Shaker-like K+ channels, we thereby identified transcripts of the inward rectifiers, KAT1 (K+ transporter of Arabidopsis thaliana) and KAT2, to be upregulated by auxin. The phloem-associated KAT2 was localised in cotyledons and the apical part of etiolated seedlings. In contrast, the K+-channel gene KAT1 was expressed in the cortex and epidermis of etiolated hypocotyls, as well as in flower stalks. Furthermore, KAT1 was induced by active auxins in auxin-sensitive tissues characterised by rapid cell elongation. Applying the patch-clamp technique to protoplasts of etiolated hypocotyls, we correlated the electrical properties of K+ currents with the expression profile of K+-channel genes. In KAT1-knockout mutants, K+ currents after auxin stimulation were characterised by reduced amplitudes. Thus, this change in the electrical properties of the K+-uptake channel in hypocotyl protoplasts resulted from an auxin-induced increase of active KAT1 proteins. The loss of KAT1-channel subunits, however, did not affect the auxin-induced growth rate of hypocotyls, pointing to compensation by residual, constitutive K+ transporters. From gene expression and electrophysiological data, we suggest that auxin regulation of KAT1 is involved in elongation growth of Arabidopsis. Furthermore, a role for KAT2 in the auxin-controlled vascular patterning of leaves is discussed. AD - Julius-von-Sachs-Institut, Lehrstuhl Molekulare Pflanzenphysiologie und Biophysik, Universitat Wurzburg, Julius-von-Sachs-Platz 2, D-97082 Wurzburg, Germany. FAU - Philippar, Katrin AU - Philippar K FAU - Ivashikina, Natalya AU - Ivashikina N FAU - Ache, Peter AU - Ache P FAU - Christian, May AU - Christian M FAU - Luthen, Hartwig AU - Luthen H FAU - Palme, Klaus AU - Palme K FAU - Hedrich, Rainer AU - Hedrich R LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2006 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):815-27. PMID- 14996215 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - Arabidopsis pdr2 reveals a phosphate-sensitive checkpoint in root development. PG - 801-14 AB - Plants have evolved complex strategies to maintain phosphate (Pi) homeostasis and to maximize Pi acquisition when the macronutrient is limiting. Adjustment of root system architecture via changes in meristem initiation and activity is integral to the acclimation process. However, the mechanisms that monitor external Pi status and interpret the nutritional signal remain to be elucidated. Here, we present evidence that the Pi deficiency response, pdr2, mutation disrupts local Pi sensing. The sensitivity and amplitude of metabolic Pi-starvation responses, such as Pi-responsive gene expression or accumulation of anthocyanins and starch, are enhanced in pdr2 seedlings. However, the most conspicuous alteration of pdr2 is a conditional short-root phenotype that is specific for Pi deficiency and caused by selective inhibition of root cell division followed by cell death below a threshold concentration of about 0.1 mm external Pi. Measurements of general Pi uptake and of total phosphorus (P) in root tips exclude a defect in high-affinity Pi acquisition. Rescue of root meristem activity in Pi-starved pdr2 by phosphite (Phi), a non-metabolizable Pi analog, and divided-root experiments suggest that pdr2 disrupts sensing of low external Pi availability. Thus, PDR2 is proposed to function at a Pi-sensitive checkpoint in root development, which monitors environmental Pi status, maintains and fine-tunes meristematic activity, and finally adjusts root system architecture to maximize Pi acquisition. AD - Department of Vegetable Crops, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA. FAU - Ticconi, Carla A AU - Ticconi CA FAU - Delatorre, Carla A AU - Delatorre CA FAU - Lahner, Brett AU - Lahner B FAU - Salt, David E AU - Salt DE FAU - Abel, Steffen AU - Abel S LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2005 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):801-14. PMID- 14996213 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. PG - 853-63 AB - Maltose is exported from the Arabidopsis chloroplast as the main product of starch degradation at night. To investigate its fate in the cytosol, we characterised plants with mutations in a gene encoding a putative glucanotransferase (disproportionating enzyme; DPE2), a protein similar to the maltase Q (MalQ) gene product involved in maltose metabolism in bacteria. Use of a DPE2 antiserum revealed that the DPE2 protein is cytosolic. Four independent mutant lines lacked this protein and displayed a decreased capacity for both starch synthesis and starch degradation in leaves. They contained exceptionally high levels of maltose, and elevated levels of glucose, fructose and other malto-oligosaccharides. Sucrose levels were lower than those in wild-type plants, especially at the start of the dark period. A glucosyltransferase activity, capable of transferring one of the glucosyl units of maltose to glycogen or amylopectin and releasing the other, was identified in leaves of wild-type plants. Its activity was sufficient to account for the rate of starch degradation. This activity was absent from dpe2 mutant plants. Based on these results, we suggest that DPE2 is an essential component of the pathway from starch to sucrose and cellular metabolism in leaves at night. Its role is probably to metabolise maltose exported from the chloroplast. We propose a pathway for the conversion of starch to sucrose in an Arabidopsis leaf. AD - Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK. FAU - Chia, Tansy AU - Chia T FAU - Thorneycroft, David AU - Thorneycroft D FAU - Chapple, Andrew AU - Chapple A FAU - Messerli, Gaelle AU - Messerli G FAU - Chen, Jychian AU - Chen J FAU - Zeeman, Samuel C AU - Zeeman SC FAU - Smith, Steven M AU - Smith SM FAU - Smith, Alison M AU - Smith AM LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2012 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):853-63. PMID- 14996212 OWN - NLM STAT- in-process DA - 20040303 IS - 0960-7412 VI - 37 IP - 6 DP - 2004 Mar TI - The poplar K+ channel KPT1 is associated with K+ uptake during stomatal opening and bud development. PG - 828-38 AB - To gain insights into the performance of poplar guard cells, we have measured stomatal conductance and aperture, guard cell K+ content and K+-channel activity of the guard cell plasma membrane in intact poplar leaves. In contrast to Arabidopsis, broad bean and tobacco grown under same conditions, poplar stomata operated just in the dynamic range - any change in conductance altered the rate of photosynthesis. In response to light, CO2 and abscisic acid (ABA), the stomatal opening velocity was two to five times faster than that measured for Arabidopsis thaliana, Nicotiana tabacum and Vicia faba. When stomata opened, the K+ content of guard cells increased almost twofold, indicating that the very fast stomatal opening in this species is mediated via potassium uptake. Following impalement of single guard cells embedded in their natural environment of intact leaves with triple-barrelled microelectrodes, time-dependent inward and outward-rectifying K+-channel-mediated currents of large amplitude were recorded. To analyse the molecular nature of genes encoding guard cell K+-uptake channels, we cloned K+-transporter Populustremula (KPT)1 and functionally expressed this potassium channel in a K+-uptake-deficient Escherichia coli mutant. In addition to guard cells, this K+-transporter gene was expressed in buds, where the KPT1 gene activity strongly correlated with bud break. Thus, KPT1 represents one of only few poplar genes associated with bud flush. AD - Julius-von-Sachs-Institut for Bioscience, Molecular Plant Physiology and Biophysics, University of Wurzburg, Julius-von-Sachs-Platz 2, 97082 Wurzburg, Germany. FAU - Langer, Katharina AU - Langer K FAU - Levchenko, Victor AU - Levchenko V FAU - Fromm, Jorg AU - Fromm J FAU - Geiger, Dietmar AU - Geiger D FAU - Steinmeyer, Ralf AU - Steinmeyer R FAU - Lautner, Silke AU - Lautner S FAU - Ache, Peter AU - Ache P FAU - Hedrich, Rainer AU - Hedrich R LA - eng PT - Journal Article PL - England TA - Plant J JID - 9207397 SB - IM EDAT- 2004/03/05 05:00 MHDA- 2004/03/05 05:00 AID - 2008 [pii] PST - ppublish SO - Plant J 2004 Mar;37(6):828-38. PMID- 14993207 OWN - NLM STAT- completed DA - 20040302 DCOM- 20040317 IS - 1088-9051 VI - 14 IP - 3 DP - 2004 Mar TI - Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. PG - 406-13 AB - To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel "full-length" enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new "full-length" cDNA sequences, raising the number of annotated genes with a corresponding "full-length" cDNA sequence to about 14,000. Detailed comparisons between these "full-length" cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by "full-length" cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation. AD - Genoscope-Centre National de Sequencage and Centre National de la Recherche Scientifique Unite Mixte de Recherche-3080, 91000 Evry, France. FAU - Castelli, Vanina AU - Castelli V FAU - Aury, Jean-Marc AU - Aury JM FAU - Jaillon, Olivier AU - Jaillon O FAU - Wincker, Patrick AU - Wincker P FAU - Clepet, Christian AU - Clepet C FAU - Menard, Manuella AU - Menard M FAU - Cruaud, Corinne AU - Cruaud C FAU - Quetier, Francis AU - Quetier F FAU - Scarpelli, Claude AU - Scarpelli C FAU - Schachter, Vincent AU - Schachter V FAU - Temple, Gary AU - Temple G FAU - Caboche, Michel AU - Caboche M FAU - Weissenbach, Jean AU - Weissenbach J FAU - Salanoubat, Marcel AU - Salanoubat M LA - eng PT - Evaluation Studies PT - Journal Article PL - United States TA - Genome Res JID - 9518021 RN - 0 (DNA, Complementary) RN - 0 (DNA, Plant) SB - IM MH - Arabidopsis/*genetics MH - Comparative Study MH - Conserved Sequence/genetics MH - DNA, Complementary/*genetics MH - DNA, Plant/genetics MH - Databases, Genetic MH - Evolution, Molecular MH - Genes, Structural, Plant/genetics MH - *Genome, Plant MH - Genomics/methods MH - Models, Genetic MH - Oryza sativa/genetics EDAT- 2004/03/03 05:00 MHDA- 2004/03/18 05:00 AID - 10.1101/gr.1515604 [doi] AID - 14/3/406 [pii] PST - ppublish SO - Genome Res 2004 Mar;14(3):406-13. PMID- 14993202 OWN - NLM STAT- completed DA - 20040302 DCOM- 20040317 IS - 1088-9051 VI - 14 IP - 3 DP - 2004 Mar TI - Comparative analysis of protein domain organization. PG - 343-53 AB - We have developed a set of graph theory-based tools, which we call Comparative Analysis of Protein Domain Organization (CADO), to survey and compare protein domain organizations of different organisms. In the language of CADO, the organization of protein domains in a given organism is shown as a domain graph in which protein domains are represented as vertices, and domain combinations, defined as instances of two domains found in one protein, are represented as edges. CADO provides a new way to analyze and compare whole proteomes, including identifying the consensus and difference of domain organization between organisms. CADO was used to analyze and compare >50 bacterial, archaeal, and eukaryotic genomes. Examples and overviews presented here include the analysis of the modularity of domain graphs and the functional study of domains based on the graph topology. We also report on the results of comparing domain graphs of two organisms, Pyrococcus horikoshii (an extremophile) and Haemophilus influenzae (a parasite with reduced genome) with other organisms. Our comparison provides new insights into the genome organization of these organisms. Finally, we report on the specific domain combinations characterizing the three kingdoms of life, and the kingdom "signature" domain organizations derived from those specific domain combinations. AD - Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, California 92037, USA. yy3@burnham.org FAU - Ye, Yuzhen AU - Ye Y FAU - Godzik, Adam AU - Godzik A LA - eng GR - GM60049/GM/NIGMS PT - Journal Article PL - United States TA - Genome Res JID - 9518021 RN - 0 (Arabidopsis Proteins) RN - 0 (Archaeal Proteins) RN - 0 (Caenorhabditis elegans Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Proteins) RN - 0 (Proteome) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Animals MH - Arabidopsis Proteins/chemistry/genetics/physiology MH - Archaeal Proteins/chemistry/genetics/physiology MH - Caenorhabditis elegans Proteins/chemistry/genetics/physiology MH - Cluster Analysis MH - Comparative Study MH - Computational Biology/methods/statistics & numerical data MH - Drosophila Proteins/chemistry/genetics MH - Genetic Heterogeneity MH - Genome MH - Genome, Archaeal MH - Genome, Bacterial MH - Genome, Fungal MH - Genome, Human MH - Genome, Plant MH - Human MH - Protein Structure, Tertiary/genetics/physiology MH - Proteins/*chemistry/genetics/physiology MH - Proteome/chemistry/genetics/physiology MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/physiology MH - Support, U.S. Gov't, P.H.S. EDAT- 2004/03/03 05:00 MHDA- 2004/03/18 05:00 AID - 10.1101/gr.1610504 [doi] AID - 14/3/343 [pii] PST - ppublish SO - Genome Res 2004 Mar;14(3):343-53. PMID- 14992728 OWN - NLM STAT- completed DA - 20040302 DCOM- 20040401 IS - 1097-2765 VI - 13 IP - 4 DP - 2004 Feb 27 TI - A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. PG - 599-609 AB - Eukaryotes regulate the effective dosage of their ribosomal RNA (rRNA) genes, expressing fewer than half of the genes at any one time. Likewise, genetic hybrids displaying nucleolar dominance transcribe rRNA genes inherited from one parent but silence the other parental set. We show that rRNA gene dosage control and nucleolar dominance utilize a common mechanism. Central to the mechanism is an epigenetic switch in which concerted changes in promoter cytosine methylation density and specific histone modifications dictate the on and off states of the rRNA genes. A key component of the off switch is HDT1, a plant-specific histone deacetylase that localizes to the nucleolus and is required for H3 lysine 9 deacetylation and subsequent H3 lysine 9 methylation. Collectively, the data support a model in which cytosine methylation and histone deacetylation are each upstream of one another in a self-reinforcing repression cycle. AD - Department of Biology, Washington University, St Louis, MO 63130, USA. FAU - Lawrence, Richard J AU - Lawrence RJ FAU - Earley, Keith AU - Earley K FAU - Pontes, Olga AU - Pontes O FAU - Silva, Manuela AU - Silva M FAU - Chen, Z Jeffrey AU - Chen ZJ FAU - Neves, Nuno AU - Neves N FAU - Viegas, Wanda AU - Viegas W FAU - Pikaard, Craig S AU - Pikaard CS LA - eng SI - GENBANK/AF195545 GR - R01-GM60380/GM/NIGMS PT - Journal Article PL - United States TA - Mol Cell JID - 9802571 RN - 0 (Histones) RN - 0 (RNA, Ribosomal) RN - 0 (RNA, Small Interfering) RN - EC 3.5.1.- (Histone Deacetylases) SB - IM MH - Arabidopsis/classification/genetics MH - Cell Nucleolus/*genetics/metabolism MH - Clone Cells MH - *DNA Methylation MH - *Gene Dosage MH - Gene Expression Regulation, Plant MH - Gene Silencing MH - Genes, Dominant MH - Histone Deacetylases/genetics/metabolism MH - Histones/genetics/*metabolism MH - Models, Genetic MH - Molecular Sequence Data MH - Promoter Regions (Genetics) MH - RNA, Ribosomal/*genetics MH - RNA, Small Interfering/genetics MH - Support, Non-U.S. Gov't MH - Support, U.S. Gov't, Non-P.H.S. MH - Support, U.S. Gov't, P.H.S. MH - Transgenes EDAT- 2004/03/03 05:00 MHDA- 2004/04/02 05:00 PHST- 2003/Sep/20 [received] PHST- 2004/Jan/14 [revised] PHST- 2004/Jan/15 [accepted] AID - S1097276504000644 [pii] PST - ppublish SO - Mol Cell 2004 Feb 27;13(4):599-609. PMID- 14991405 OWN - NLM STAT- publisher DA - 20040301 IS - 0032-0935 DP - 2004 Feb 26 TI - l-Galactose replaces l-fucose in the pectic polysaccharide rhamnogalacturonan II synthesized by the l-fucose-deficient mur1 Arabidopsis mutant. AB - Arabidopsis thaliana mur1 is a dwarf mutant with altered cell-wall properties, in which l-fucose is partially replaced by l-galactose in the xyloglucan and glycoproteins. We found that the mur1 mutation also affects the primary structure of the pectic polysaccharide rhamnogalacturonan II (RG-II). In mur1 RG-II a non-reducing terminal 2- O-methyl l-galactosyl residue and a 3,4-linked l-galactosyl residue replace the non-reducing terminal 2- O-methyl l-fucosyl residue and the 3,4-linked l-fucosyl residue, respectively, that are present in wild-type RG-II. Furthermore, we found that a terminal non-reducing l-galactosyl residue, rather than the previously reported d-galactosyl residue, is present on the 2- O-methyl xylose-containing side chain of RG-II in both wild type and mur1 plants. Approximately 95% of the RG-II from wild type and mur1 plants is solubilized as a high-molecular-weight (>100 kDa) complex, by treating walls with aqueous potassium phosphate. The molecular mass of RG-II in this complex was reduced to 5-10 kDa by treatment with endopolygalacturonase, providing additional evidence that RG-II is covalently linked to homogalacturonan. The results of this study provide additional information on the structure of RG-II and the role of this pectic polysaccharide in the plant cell wall. AD - Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, GA 30602-4712, Athens, USA. AU - Reuhs BL AU - Glenn J AU - Stephens SB AU - Kim JS AU - Christie DB AU - Glushka JG AU - Zablackis E AU - Albersheim P AU - Darvill AG AU - O'Neill MA LA - ENG PT - JOURNAL ARTICLE TA - Planta JID - 1250576 EDAT- 2004/03/03 05:00 MHDA- 2004/03/03 05:00 AID - 10.1007/s00425-004-1205-x [doi] PST - aheadofprint SO - Planta 2004 Feb 26;. PMID- 14991000 OWN - NLM STAT- completed DA - 20040301 DCOM- 20040413 IS - 1471-0072 VI - 5 IP - 3 DP - 2004 Mar TI - Protein import into chloroplasts. PG - 198-208 AD - Department fur Biologie I, Botanik, Ludwig-Maximilians-Universitat Munchen, Menzingerstrasse 67, D-80638 Munich, Germany. soll@uni-muenchen.de FAU - Soll, Jurgen AU - Soll J FAU - Schleiff, Enrico AU - Schleiff E LA - eng PT - Journal Article PT - Review PT - Review, Tutorial PL - England TA - Nat Rev Mol Cell Biol JID - 100962782 SB - IM MH - Arabidopsis/metabolism MH - Cell Nucleus/metabolism MH - Chloroplasts/*chemistry/ultrastructure MH - Cytosol/metabolism MH - Models, Biological MH - Peas/metabolism MH - Plant Physiology MH - Protein Transport MH - Support, Non-U.S. Gov't RF - 97 EDAT- 2004/03/03 05:00 MHDA- 2004/04/14 05:00 AID - 10.1038/nrm1333 [doi] AID - nrm1333 [pii] PST - ppublish SO - Nat Rev Mol Cell Biol 2004 Mar;5(3):198-208. PMID- 14990439 OWN - NLM STAT- in-process DA - 20040301 IS - 1367-4803 VI - 20 IP - 4 DP - 2004 Mar 1 TI - Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. PG - 445-7 AB - MOTIVATION: According to scanning model, 40S ribosomal subunits can either initiate translation at start AUG codon in suboptimal context or miss it and initiate translation at downstream AUG(s), thereby producing several proteins. Functional significance of such a protein translational polymorphism is still unknown. RESULTS: We compared predicted subcellular localizations of annotated Arabidopsis thaliana proteins and their potential N-terminally truncated forms started from the nearest downstream in-frame AUG codons. It was found that localizations of full and N-truncated proteins differ in many cases: 12.2% of N-truncated proteins acquired sorting signals de novo and 5.7% changed their predicted subcellular locations (mitochodria, chloroplast or secretory pathway). It is likely that the in-frame downstream AUGs may be frequently utilized to synthesize proteins possessing new functional properties and such a translational polymorphism may serve as an important source of cellular and organelle proteomes. AD - Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk 630090, Russia. Alex.Kochetov@bionet.nsc.ru FAU - Kochetov, Alex V AU - Kochetov AV FAU - Sarai, Akinori AU - Sarai A LA - eng PT - Journal Article DEP - 20040122 PL - England TA - Bioinformatics JID - 9808944 SB - IM EDAT- 2004/03/03 05:00 MHDA- 2004/03/03 05:00 PHST- 2004/Jan/22 [aheadofprint] AID - 10.1093/bioinformatics/btg443 [doi] AID - btg443 [pii] PST - ppublish SO - Bioinformatics 2004 Mar 1;20(4):445-7. Epub 2004 Jan 22. PMID- 14990384 OWN - NLM STAT- in-process DA - 20040301 IS - 0022-5193 VI - 227 IP - 2 DP - 2004 Mar 21 TI - Dynamics in a discrete two-species competition model: coexistence and over-compensation. PG - 197-203 AB - The dynamic features of an over-compensating discrete two-species competition system with stable coexistence are recaptured, and it is shown how the probabilities of the different possible ecological scenarios, e.g. coexistence, may be calculated when the assumption of no over-compensation is loosened. A Bayesian methodology for calculating the probability that stable oscillations or chaos may occur in plant populations or communities is outlined. The methodology is exemplified using an experimental population of Arabidopsis thaliana. It is concluded that, when making ecological predictions it is preferable and possibly important to test for the possibility of chaotic population dynamics due to over-compensation rather than assuming a priori that over-compensation does not occur. AD - Department of Terrestrial Ecology, DMU, Vejlsovej 25, 8600 Silkeborg, Denmark. cfd@dmu.dk FAU - Damgaard, Christian AU - Damgaard C LA - eng PT - Journal Article PL - England TA - J Theor Biol JID - 0376342 SB - IM EDAT- 2004/03/03 05:00 MHDA- 2004/03/03 05:00 PHST- 2003/May/01 [received] PHST- 2003/Oct/29 [revised] PHST- 2003/Nov/05 [accepted] AID - 10.1016/j.jtbi.2003.11.001 [doi] AID - S002251930300417X [pii] PST - ppublish SO - J Theor Biol 2004 Mar 21;227(2):197-203. PMID- 14988555 OWN - NLM STAT- completed DA - 20040227 DCOM- 20040318 IS - 1095-9203 VI - 303 IP - 5662 DP - 2004 Feb 27 TI - RNA silencing genes control de novo DNA methylation. PG - 1336 AD - Department of MCD Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA. FAU - Chan, Simon W-L AU - Chan SW FAU - Zilberman, Daniel AU - Zilberman D FAU - Xie, Zhixin AU - Xie Z FAU - Johansen, Lisa K AU - Johansen LK FAU - Carrington, James C AU - Carrington JC FAU - Jacobsen, Steven E AU - Jacobsen SE LA - eng GR - GM60398/GM/NIGMS PT - Journal Article PL - United States TA - Science JID - 0404511 RN - 0 (AGO4 protein, Arabidopsis) RN - 0 (Arabidopsis Proteins) RN - 0 (DNA, Plant) RN - 0 (FWA protein, Arabidopsis) RN - 0 (Homeodomain Proteins) RN - 0 (RNA, Small Interfering) RN - 0 (Transcription Factors) RN - 71-30-7 (Cytosine) SB - IM MH - Arabidopsis/*genetics/growth & development MH - Arabidopsis Proteins/*genetics/physiology MH - Cytosine/metabolism MH - *DNA Methylation MH - DNA, Plant/metabolism MH - Flowers/growth & development MH - *Genes, Plant MH - Homeodomain Proteins/*genetics MH - Mutation MH - *RNA Interference MH - RNA, Small Interfering/metabolism MH - Repetitive Sequences, Nucleic Acid MH - Support, Non-U.S. Gov't MH - Support, U.S. Gov't, Non-P.H.S. MH - Support, U.S. Gov't, P.H.S. MH - Transcription Factors/*genetics MH - Transformation, Genetic MH - Transgenes EDAT- 2004/02/28 05:00 MHDA- 2004/03/19 05:00 AID - 10.1126/science.1095989 [doi] AID - 303/5662/1336 [pii] PST - ppublish SO - Science 2004 Feb 27;303(5662):1336. PMID- 14988495 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - Arabidopsis dynamin-like protein 2a (ADL2a), like ADL2b, is involved in plant mitochondrial division. PG - 236-42 AB - The Arabidopsis genome has two similar dynamin-like proteins, ADL2a and ADL2b (76.7% identity). ADL2a is reported to be localized in chloroplasts [Kang et al. (1998) Plant Mol. Biol. 38: 437], while ADL2b functions in mitochondrial division [Arimura and Tsutsumi (2002) PROC: Natl. Acad. Sci. USA 99: 5727]. Using GFP fusion proteins, we observed both ADL2a and ADL2b in portions of mitochondria but not in chloroplasts. Furthermore, cells transformed with ADL2a and ADL2b with a defective GTPase domain had normal chloroplasts but elongated mitochondria. These results imply that both ADL2b and ADL2a are involved in the division of plant mitochondria. AD - Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan. arimura@mail.ecc.u-tokyo.ac.jp FAU - Arimura, Shin-ichi AU - Arimura S FAU - Aida, Gen Paul AU - Aida GP FAU - Fujimoto, Masaru AU - Fujimoto M FAU - Nakazono, Mikio AU - Nakazono M FAU - Tsutsumi, Nobuhiro AU - Tsutsumi N LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):236-42. PMID- 14988494 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - Characterization of transcriptional oscillation of an Arabidopsis homolog of PnC401 related to photoperiodic induction of flowering in Pharbitis nil. PG - 232-5 AB - AtC401 is an Arabidopsis homolog of PnC401 that is related to photoperiodic induction of flowering in Pharbitis nil. These genes show free-running rhythms. To study the free-running rhythm of AtC401, we fused a firefly luciferase reporter to the AtC401 promoter and transformed it into Arabidopsis plants. The observed bioluminescence oscillated under continuous light and continuous dark only with sucrose supplementation. The free-running period of bioluminescence was temperature-compensated between 22 degrees C and 30 degrees C. Light-pulse experiments under continuous darkness produced a phase-response curve typical of circadian rhythms. We conclude that rhythmic expression of AtC401 is controlled by a circadian oscillator. AD - Gene Research Center, Institute of Biological Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan. oguchit@sakura.cc.tsukuba.ac.jp FAU - Oguchi, Taichi AU - Oguchi T FAU - Sage-Ono, Kimiyo AU - Sage-Ono K FAU - Kamada, Hiroshi AU - Kamada H FAU - Ono, Michiyuki AU - Ono M LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):232-5. PMID- 14988493 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - Three Arabidopsis MBF1 homologs with distinct expression profiles play roles as transcriptional co-activators. PG - 225-31 AB - Multiprotein bridging factor 1 (MBF1) is known to be a transcriptional co-activator that mediates transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP). We demonstrated that expression of every three MBF1 from Arabidopsis partially rescues the yeast mbf1 mutant phenotype, indicating that all of them function as co-activators for GCN4-dependent transcriptional activation. We also report that each of their subtypes shows distinct tissue-specific expression patterns and responses to phytohormones. These observations suggest that even though they share a similar biochemical function, each MBF1 has distinct roles in various tissues and conditions. AD - Laboratory of Environmental Molecular Biology, Graduate School of Environmental Earth Science, Hokkaido University, Kita 10, Nishi 5, Kita-ku, Sapporo, 060-0810 Japan. FAU - Tsuda, Kenichi AU - Tsuda K FAU - Tsuji, Toshihiro AU - Tsuji T FAU - Hirose, Susumu AU - Hirose S FAU - Yamazaki, Ken-ichi AU - Yamazaki K LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):225-31. PMID- 14988492 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - A simple and efficient method for isolating trichomes for downstream analyses. PG - 221-4 AB - Arabidopsis trichomes are an excellent cell type to address many questions in plant biology including the control of cell shape, endoreplication, and cell expansion. Because trichomes comprise such a small percentage of the cells of a leaf, biochemical analyses of trichomes are limited. To overcome this limitation, we developed a method for removing trichomes from the leaf surface. Our method allows the isolation of intact trichomes for use in downstream applications such as cell wall analysis, immunolocalization of trichome proteins, analysis of DNA content, and proteomics. Also, this method will facilitate the isolation of trichomes from practically any plant species. AD - Department of Botany and the University of Florida Genetics Institute, University of Florida, PO Box 118526, Gainesville, FL 32611-8526, USA. FAU - Zhang, Xiaoguo AU - Zhang X FAU - Oppenheimer, David G AU - Oppenheimer DG LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):221-4. PMID- 14988491 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - Microtubule defects and cell morphogenesis in the lefty1lefty2 tubulin mutant of Arabidopsis thaliana. PG - 211-20 AB - lefty1 and lefty2 are semi-dominant left-handed helical growth mutants of Arabidopsis thaliana, which result from identical dominant-negative amino acid substitutions in alpha-tubulin 6 and alpha-tubulin 4, respectively. Here we characterized the expression patterns of the affected tubulin genes and the phenotypes of the lefty double mutant to address increasing effects of microtubule defects on cell morphogenesis. Both tubulin genes were expressed ubiquitously in examined tissue and cell types, and the alpha-tubulin 2/4/6 subfamily transcripts predominated over other alpha-tubulin transcripts in Arabidopsis seedlings. The lefty double mutant seedlings showed helical growth in hypocotyls and radial cell expansion in the root elongation zone where mutant cortical microtubule arrays were more fragmented and less well aligned than wild-type arrays. Branching of leaf trichomes was highly reduced. In adult mutant plants, anisotropic growth of anther filament cells was severely impaired. These results suggest that left-handed twisted elongation is an intermediate state that leads to full isotropic expansion as the cortical microtubules are increasingly destabilized. AD - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan. FAU - Abe, Tatsuya AU - Abe T FAU - Thitamadee, Siripong AU - Thitamadee S FAU - Hashimoto, Takashi AU - Hashimoto T LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):211-20. PMID- 14988484 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - The light-harvesting complex of photosystem I in Chlamydomonas reinhardtii: protein composition, gene structures and phylogenic implications. PG - 138-45 AB - Light-harvesting chlorophyll a/b-binding proteins (LHCI) associated with photosystem I (PSI) and the genes encoding these proteins have been characterized in the unicellular green alga Chlamydomonas reinhardtii, extending previous studies of the PSII-LHCII [Teramoto et al. (2001) Plant Cell Physiol. 42: 849]. In order to assign LHCI proteins in the thylakoid membranes, the PSI-LHCI supercomplex that retains all of the major LHCI proteins was purified. Seven distinct LHCI proteins were resolved from the purified supercomplex by a high-resolution SDS polyacrylamide gel electrophoresis, and their N-terminal amino acid sequences were determined. One LHCI protein (band e) was newly found, although the other six LHCI proteins corresponded to those previously reported. Genomic clones encoding these seven LHCI proteins were newly isolated and the nucleotide sequences were determined. A comprehensive characterization of all members of Lhc gene family in this alga revealed that LHCI proteins are more highly diverged than LHCII, suggesting functional differentiation of the protein components in LHCI. Neighbor joining trees were constructed for LHC proteins from C. reinhardtii and those of Arabidopsis thaliana or Galdieria sulphuraria to assess evolutionary relationships. Phylogenetic analysis revealed that (1). green algal LHCI and LHCII proteins are more closely related to one another than to LHCI proteins in red algae, (2). green algae and higher plants possess seven common lineages of LHC proteins, and (3). Type I and III LHCI proteins are conserved between green algae and higher plants, while Type II and IV are not. These findings are discussed in the context of evolution of multiple diverse antenna complexes. AD - Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819 Japan. FAU - Tokutsu, Ryutaro AU - Tokutsu R FAU - Teramoto, Haruhiko AU - Teramoto H FAU - Takahashi, Yuichiro AU - Takahashi Y FAU - Ono, Taka-aki AU - Ono TA FAU - Minagawa, Jun AU - Minagawa J LA - eng SI - GENBANK/AB122114 SI - GENBANK/AB122115 SI - GENBANK/AB122116 SI - GENBANK/AB122117 SI - GENBANK/AB122118 SI - GENBANK/AB122119 SI - GENBANK/AB122120 PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):138-45. PMID- 14988483 OWN - NLM STAT- in-process DA - 20040227 IS - 0032-0781 VI - 45 IP - 2 DP - 2004 Feb TI - Reduced glutathione is a novel regulator of vernalization-induced bolting in the rosette plant Eustoma grandiflorum. PG - 129-37 AB - The transition from the vegetative rosette stage to the reproductive growth stage (bolting) in the rosette plant Eustoma grandiflorum has a strict requirement for vernalization, a treatment that causes oxidative stress. Since we have shown that reduced glutathione (GSH) and its biosynthesis are associated with bolting in another rosette plant Arabidopsis thaliana, we here investigated whether a similar mechanism governs the vernalization-induced bolting of E. grandiflorum. Addition of GSH or its precursor cysteine, instead of vernalization, induced bolting but other thiols, dithiothreitol and 2-mercaptoethanol, did not. The inductive effect of vernalization on bolting was nullified by addition of buthionine sulfoximine (BSO), an inhibitor of GSH synthesis, without decreasing the plant growth rate. BSO-mediated inhibition of bolting was reversed by addition of GSH but not by cysteine. These indicate that vernalization-induced bolting involves GSH biosynthesis and is specifically regulated by GSH. Plant GSH increased during the early vernalization period along with the activity of gamma-glutamylcysteine synthetase that catalyzes the first step of GSH biosynthesis, although there was little change in amounts of GSH precursor thiols, cysteine and gamma-glutamylcysteine. These findings strongly suggest that vernalization stimulates GSH synthesis and synthesized GSH specifically determines the bolting time of E. grandiflorum. AD - RIBS Okayama (Research Institute for Biological Sciences, Okayama), 7549-1 Yoshikawa, Kayou-cho, Okayama, 716-1241 Japan. FAU - Yanagida, Mototsugu AU - Yanagida M FAU - Mino, Masanobu AU - Mino M FAU - Iwabuchi, Masaki AU - Iwabuchi M FAU - Ogawa, Ken'ichi AU - Ogawa K LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JID - 9430925 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PST - ppublish SO - Plant Cell Physiol 2004 Feb;45(2):129-37. PMID- 14988481 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Geminating pollen has tubular vacuoles, displays highly dynamic vacuole biogenesis, and requires VACUOLESS1 for proper function. PG - 1227-39 AB - Vacuoles perform multiple functions in plants, and VCL1 (VACUOLESS1) is essential for biogenesis with loss of expression in the vcl1 mutant leading to lethality. Vacuole biogenesis plays a prominent role in gametophytes, yet is poorly understood. Given the importance of VCL1, we asked if it contributes to vacuole biogenesis during pollen germination. To address this question, it was essential to first understand the dynamics of vacuoles. A tonoplast marker, delta-TIP::GFP, under a pollen-specific promoter permitted the examination of vacuole morphology in germinating pollen of Arabidopsis. Our results demonstrate that germination involves a complex, yet definable, progression of vacuole biogenesis. Pollen vacuoles are extremely dynamic with remarkable features such as elongated (tubular) vacuoles and highly mobile cytoplasmic invaginations. Surprisingly, vcl1 did not adversely impact vacuole morphology in pollen germinated in vitro. To focus further on VCL1 in pollen, reciprocal backcrosses demonstrated reduced transmission of vcl1 through male gametophytes, indicating that vcl1 was expressive after germination. Interestingly, vcl1 affected the fertility of female gametophytes that undergo similarly complex vacuole biogenesis. Our results indicate that vcl1 is lethal in the sporophyte but is not fully expressive in the gametophytes. They also point to the complexity of pollen vacuoles and suggest that the mechanism of vacuole biogenesis in pollen may differ from that in other plant tissues. AD - Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92521, USA. FAU - Hicks, Glenn R AU - Hicks GR FAU - Rojo, Enrique AU - Rojo E FAU - Hong, Seho AU - Hong S FAU - Carter, David G AU - Carter DG FAU - Raikhel, Natasha V AU - Raikhel NV LA - eng PT - Journal Article DEP - 20040226 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PHST- 2004/Feb/26 [aheadofprint] AID - 10.1104/pp.103.037382 [doi] AID - pp.103.037382 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):1227-39. Epub 2004 Feb 26. PMID- 14988479 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - A surprising diversity and abundance of xyloglucan endotransglucosylase/hydrolases in rice. Classification and expression analysis. PG - 1088-99 AB - A search of the recently completed genomic database of rice (Oryza sativa) identified a 29-member xyloglucan endotransglucosylase/hydrolase (OsXTH) gene family. This first report of a complete XTH family from a monocotyledonous species reveals that the OsXTH family is comparable in size with that of the dicotyledon Arabidopsis thaliana, which consists of 33 AtXTH genes. This is surprising because xyloglucan, the specific substrate of XTHs, is considerably less abundant in cell walls of monocotyledons than dicotyledons and is not typically ascribed an important structural role in monocotyledons. As a first step toward determining the roles of rice XTHs, the expression patterns of all 29 OsXTH genes were examined using a quantitative DNA microarray procedure with gene-specific oligonucleotide probes. The analysis showed that most members of the rice XTH family exhibited organ- and growth stage-specific expression. This was confirmed by quantitative real-time reverse transcriptase-polymerase chain reaction analysis of representative OsXTH members. This revealed in more detail the temporally and spatially controlled expression profiles of individual OsXTH genes at particular sites in rice. Previous reports indicated that grasses have relatively greater xyloglucan endotransglucosylase activities, one of the two enzyme activities catalyzed by XTHs, than in equivalent tissues in dicotyledons. This observation, together with the tissue-specific and growth stage-dependent expression of a large rice XTH gene family, suggests that xyloglucan metabolism plays a more central role in monocotyledon cell wall restructuring than has been reported previously. AD - Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan. FAU - Yokoyama, Ryusuke AU - Yokoyama R FAU - Rose, Jocelyn K C AU - Rose JK FAU - Nishitani, Kazuhiko AU - Nishitani K LA - eng PT - Journal Article DEP - 20040226 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PHST- 2004/Feb/26 [aheadofprint] AID - 10.1104/pp.103.035261 [doi] AID - pp.103.035261 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):1088-99. Epub 2004 Feb 26. PMID- 14988478 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. PG - 1135-45 AB - Potassium (K(+)) is the most abundant cation in plants and is required for plant growth. To ensure an adequate supply of K(+), plants have multiple mechanisms for uptake and translocation. However, relatively little is known about the physiological role of proteins encoded by a family of 13 genes, named AtKT/KUP, that are involved in K(+) transport and translocation. To begin to understand where and under what conditions these transporters function, we used reverse transcription-PCR to determine the spatial and temporal expression patterns of each AtKT/KUP gene across a range of organs and tested whether selected AtKT/KUP cDNAs function as K(+) transporters in Escherichia coli. Many AtKT/KUPs were expressed in roots, leaves, siliques, and flowers of plants grown under K(+)-sufficient conditions (1.75 mm KCl) in hydroponic culture. AtHAK5 was the only gene in this family that was up-regulated upon K(+) deprivation and rapidly down-regulated with resupply of K(+). Ten AtKT/KUPs were expressed in root hairs, but only five were expressed in root tip cells. This suggests an important role for root hairs in K(+) uptake. The growth and rubidium (Rb(+)) uptake of two root hair mutants, trh1-1 (tiny root hairs) and rhd6 (root hair defective), were studied to determine the contribution of root hairs to whole-plant K(+) status. Whole-plant biomass decreased in the root hair mutants only when K(+) concentrations were low; Rb(+) (used as a tracer for K(+)) uptake rates were lower in the mutants at all Rb(+) concentrations. Seven genes encoding AtKUP transporters were expressed in E. coli (AtKT3/KUP4, AtKT/KUP5, AtKT/KUP6, AtKT/KUP7, AtKT/KUP10, AtKT/KUP11, and AtHAK5), and their K(+) transport function was demonstrated. AD - Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132, USA. FAU - Ahn, Sung Ju AU - Ahn SJ FAU - Shin, Ryoung AU - Shin R FAU - Schachtman, Daniel P AU - Schachtman DP LA - eng PT - Journal Article DEP - 20040226 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PHST- 2004/Feb/26 [aheadofprint] AID - 10.1104/pp.103.034660 [doi] AID - pp.103.034660 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):1135-45. Epub 2004 Feb 26. PMID- 14988477 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - Alkamides isolated from plants promote growth and alter root development in Arabidopsis. PG - 1058-68 AB - To date, several classes of hormones have been described that influence plant development, including auxins, cytokinins, ethylene, and, more recently, brassinosteroids. However, it is known that many fungal and bacterial species produce substances that alter plant growth that, if naturally present in plants, might represent novel classes of plant growth regulators. Alkamides are metabolites widely distributed in plants with a broad range of biological activities. In this work, we investigated the effects of affinin, an alkamide naturally occurring in plants, and its derivates, N-isobutyl-2E-decenamide and N-isobutyl-decanamide, on plant growth and early root development in Arabidopsis. We found that treatments with affinin in the range of 10(-6) to 10(-4) m alter shoot and root biomass production. This effect correlated with alteration on primary root growth, lateral root formation, and root hair elongation. Low concentrations of affinin (7 x 10(-6)-2.8 x 10(-5) m) enhanced primary root growth and root hair elongation, whereas higher concentrations inhibited primary root growth that related with a reduction in cell proliferating activity and cell elongation. N-isobutyl-2E-decenamide and N-isobutyl-decanamide were found to stimulate root hair elongation at concentrations between 10(-8) to 10(-7) m. Although the effects of alkamides were similar to those produced by auxins on root growth and cell parameters, the ability of the root system to respond to affinin was found to be independent of auxin signaling. Our results suggest that alkamides may represent a new group of plant growth promoting substances with significant impact on root development and opens the possibility of using these compounds for improved plant production. AD - Departamento de Biotecnologia y Bioquimica, Unidad Irapuato del Centro de Investigacion y Estudios Avanzados del Instituto Politecnico Nacional, Apartado Postal 629, 36500 Irapuato, Guanajuato, Mexico. FAU - Ramirez-Chavez, Enrique AU - Ramirez-Chavez E FAU - Lopez-Bucio, Jose AU - Lopez-Bucio J FAU - Herrera-Estrella, Luis AU - Herrera-Estrella L FAU - Molina-Torres, Jorge AU - Molina-Torres J LA - eng PT - Journal Article DEP - 20040226 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PHST- 2004/Feb/26 [aheadofprint] AID - 10.1104/pp.103.034553 [doi] AID - pp.103.034553 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):1058-68. Epub 2004 Feb 26. PMID- 14988475 OWN - NLM STAT- in-process DA - 20040315 IS - 0032-0889 VI - 134 IP - 3 DP - 2004 Mar TI - The pea gene LH encodes ent-kaurene oxidase. PG - 1123-34 AB - The pea (Pisum sativum) homolog, PsKO1, of the Arabidopsis GA3 gene was isolated. It codes for a cytochrome P450 from the CYP701A subfamily and has ent-kaurene oxidase (KO) activity, catalyzing the three step oxidation of ent-kaurene to ent-kaurenoic acid in the gibberellin (GA) biosynthetic pathway when expressed in yeast (Saccharomyces cerevisiae). PsKO1 is encoded by the LH gene because in three independent mutant alleles, lh-1, lh-2, and lh-3, PsKO1 has altered sequence, and the lh-1 allele, when expressed in yeast, failed to metabolize ent-kaurene. The lh mutants of pea are GA deficient and have reduced internode elongation and root growth. One mutant (lh-2) also causes a large increase in seed abortion. PsKO1 (LH) is expressed in all tissues examined, including stems, roots, and seeds, and appears to be a single-copy gene. Differences in sensitivity to the GA synthesis inhibitor, paclobutrazol, between the mutants appear to result from the distinct nature of the genetic lesions. These differences may also explain the tissue-specific differences between the mutants. AD - School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia. FAU - Davidson, Sandra E AU - Davidson SE FAU - Smith, Jennifer J AU - Smith JJ FAU - Helliwell, Chris A AU - Helliwell CA FAU - Poole, Andrew T AU - Poole AT FAU - Reid, James B AU - Reid JB LA - eng PT - Journal Article DEP - 20040226 PL - United States TA - Plant Physiol JID - 0401224 SB - IM EDAT- 2004/02/28 05:00 MHDA- 2004/02/28 05:00 PHST- 2004/Feb/26 [aheadofprint] AID - 10.1104/pp.103.032706 [doi] AID - pp.103.032706 [pii] PST - ppublish SO - Plant Physiol 2004 Mar;134(3):1123-34. Epub 2004 Feb 26.