Genomes and Genes
Experts and Doctors on arabidopsis in St Louis, Missouri, United States
Locale: St Louis, Missouri, United States
- Herrmann J, Ravilious G, McKinney S, Westfall C, Lee S, Baraniecka P, et al. Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation. J Biol Chem. 2014;289:10919-29 pubmed publisher..Mutations that alter sulfate assimilation in Arabidopsis were mapped to the structure, which provides a molecular basis for understanding their effects on the sulfur assimilation pathway. ..
- McDonnell M, Burkhart S, Stoddard J, Wright Z, Strader L, Bartel B. The Early-Acting Peroxin PEX19 Is Redundantly Encoded, Farnesylated, and Essential for Viability in Arabidopsis thaliana. PLoS ONE. 2016;11:e0148335 pubmed publisher..Together, our data indicate that Arabidopsis PEX19 promotes peroxisome function and is essential for viability. ..
- Markham J, Molino D, Gissot L, Bellec Y, Hematy K, Marion J, et al. Sphingolipids containing very-long-chain fatty acids define a secretory pathway for specific polar plasma membrane protein targeting in Arabidopsis. Plant Cell. 2011;23:2362-78 pubmed publisher..In conclusion, sphingolipids with very long acyl chains define a trafficking pathway with specific endomembrane compartments and polar auxin transport protein cargoes. ..
- Guo L, Mishra G, Taylor K, Wang X. Phosphatidic acid binds and stimulates Arabidopsis sphingosine kinases. J Biol Chem. 2011;286:13336-45 pubmed publisher..The PA-SPHK interaction depends on the PA molecular species. The data suggest that these two Arabidopsis SPHKs are molecular targets of PA, and the PA stimulation of SPHK is part of the signaling networks in Arabidopsis. ..
- Earley K, Lawrence R, Pontes O, Reuther R, Enciso A, Silva M, et al. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 2006;20:1283-93 pubmed..HDA6 localizes, in part, to the nucleolus, supporting a model whereby HDA6 erases histone acetylation as a key step in an epigenetic switch mechanism that silences rRNA genes through concerted histone and DNA modifications. ..
- Chen M, Han G, Dietrich C, Dunn T, Cahoon E. The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase. Plant Cell. 2006;18:3576-93 pubmed publisher..These results demonstrate that plant SPT is a heteromeric enzyme and that sphingolipids are essential components of plant cells and contribute to growth and development...
- Huang H, Alvarez S, Bindbeutel R, Shen Z, Naldrett M, Evans B, et al. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics. 2016;15:201-17 pubmed publisher..thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways. ..
- Wilson M, Jensen G, Haswell E. Two mechanosensitive channel homologs influence division ring placement in Arabidopsis chloroplasts. Plant Cell. 2011;23:2939-49 pubmed publisher..These results establish MS channels as components of the chloroplast division machinery and suggest that their role is evolutionarily conserved. ..
- Dai S, Wei X, Pei L, Thompson R, Liu Y, Heard J, et al. BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock. Plant Cell. 2011;23:961-72 pubmed publisher..Rhythmic expression of BOA was also affected in mutant lines of toc1-1, gi-3, and gi-4. Results from these studies indicate that BOA is a critical component of the regulatory circuit of the circadian clock. ..
- Guo L, Mishra G, Markham J, Li M, Tawfall A, Welti R, et al. Connections between sphingosine kinase and phospholipase D in the abscisic acid signaling pathway in Arabidopsis. J Biol Chem. 2012;287:8286-96 pubmed publisher..PA is involved in the activation of SPHK, and activation of PLD?1 requires SPHK activity. The data suggest that SPHK/phyto-S1P and PLD?1A are co-dependent in amplification of response to ABA, mediating stomatal closure in Arabidopsis. ..
- Chen H, Xiong L. The bifunctional abiotic stress signalling regulator and endogenous RNA silencing suppressor FIERY1 is required for lateral root formation. Plant Cell Environ. 2010;33:2180-90 pubmed publisher..Our results indicate that RNA silencing modulated by FRY1 and XRN4 plays an important role in shaping root architecture. ..
- PREUSS S, Meister R, Xu Q, Urwin C, Tripodi F, Screen S, et al. Expression of the Arabidopsis thaliana BBX32 gene in soybean increases grain yield. PLoS ONE. 2012;7:e30717 pubmed publisher..These findings demonstrate a specific role for AtBBX32 in modulating soybean development, and demonstrate the validity of expressing single genes in crops to deliver increased agricultural productivity. ..
- Barbazuk W, Fu Y, McGinnis K. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 2008;18:1381-92 pubmed publisher..This review summarizes recent analyses of AS in plants, discusses the importance of further analysis, and suggests directions for future efforts. ..
- Pontes O, Lawrence R, Silva M, Preuss S, Costa Nunes P, Earley K, et al. Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance. PLoS ONE. 2007;2:e1157 pubmed..thaliana NORs is disrupted. Collectively, these data demonstrate that HDA6 and HDT1 function in the postembryonic establishment of nucleolar dominance, a process which recurs in each generation...
- Zolman B, MARTINEZ N, Millius A, Adham A, Bartel B. Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes. Genetics. 2008;180:237-51 pubmed publisher..Both enzymes contain C-terminal peroxisomal-targeting signals, consistent with IBA metabolism occurring in peroxisomes. We present a model in which IBR3, IBR10, and IBR1 may act sequentially in peroxisomal IBA beta-oxidation to IAA. ..
- Li M, Welti R, Wang X. Quantitative profiling of Arabidopsis polar glycerolipids in response to phosphorus starvation. Roles of phospholipases D zeta1 and D zeta2 in phosphatidylcholine hydrolysis and digalactosyldiacylglycerol accumulation in phosphorus-starved plants. Plant Physiol. 2006;142:750-61 pubmed..The results suggest that hydrolysis of phosphatidylcholine by PLD zetas during phosphorus starvation contributes to the supply of inorganic phosphorus for cell metabolism and diacylglycerol moieties for galactolipid synthesis. ..
- Zeng Q, Wang X, Running M. Dual lipid modification of Arabidopsis Ggamma-subunits is required for efficient plasma membrane targeting. Plant Physiol. 2007;143:1119-31 pubmed..Our data show the large degree to which PFT and PGGT-I can compensate for each other in plants and suggest that differential lipid modification plays an important regulatory role in plant protein localization. ..
- Ahn S, Shin R, Schachtman D. Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. Plant Physiol. 2004;134:1135-45 pubmed..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...
- Jez J, Cahoon R. Kinetic mechanism of glutathione synthetase from Arabidopsis thaliana. J Biol Chem. 2004;279:42726-31 pubmed..Overall, these observations are consistent with a random Ter-reactant mechanism for the eukaryotic GS in which the binding order of certain substrates is kinetically preferred for catalysis. ..
- Li M, Bahn S, Guo L, Musgrave W, Berg H, Welti R, et al. Patatin-related phospholipase pPLAIII?-induced changes in lipid metabolism alter cellulose content and cell elongation in Arabidopsis. Plant Cell. 2011;23:1107-23 pubmed publisher..These data suggest that alteration of pPLAIII? expression and the resulting lipid changes alter cellulose content and cell elongation in Arabidopsis. ..
- Becker A, Chao D, Zhang X, Salt D, Baxter I. Bulk segregant analysis using single nucleotide polymorphism microarrays. PLoS ONE. 2011;6:e15993 pubmed publisher..We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files. ..
- Baxter I, Brazelton J, Yu D, Huang Y, Lahner B, Yakubova E, et al. A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet. 2010;6:e1001193 pubmed publisher..The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments. ..
- Peters C, Li M, Narasimhan R, Roth M, Welti R, Wang X. Nonspecific phospholipase C NPC4 promotes responses to abscisic acid and tolerance to hyperosmotic stress in Arabidopsis. Plant Cell. 2010;22:2642-59 pubmed publisher..These data suggest that NPC4-produced DAG is converted to PA and that NPC4 and its derived lipids positively modulate ABA response and promote plant tolerance to drought and salt stresses. ..
- Li M, Bahn S, Fan C, Li J, Phan T, Ortiz M, et al. Patatin-related phospholipase pPLAIII? increases seed oil content with long-chain fatty acids in Arabidopsis. Plant Physiol. 2013;162:39-51 pubmed publisher..These results indicate that pPLAIII?-mediated phospholipid turnover plays a role in fatty acid remodeling and glycerolipid production. ..
- Kim M, Shin R, Schachtman D. A nuclear factor regulates abscisic acid responses in Arabidopsis. Plant Physiol. 2009;151:1433-45 pubmed publisher..The characterization of this factor enhances our understanding of guard cell function and the mechanisms that plants use to modulate water loss from leaves under drought conditions. ..
- Khandelwal A, Elvitigala T, Ghosh B, Quatrano R. Arabidopsis transcriptome reveals control circuits regulating redox homeostasis and the role of an AP2 transcription factor. Plant Physiol. 2008;148:2050-8 pubmed publisher..Furthermore, Deltarrtf1 showed greater sensitivity to photosynthetic stress compared to the wild type. ..
- Kankel M, Ramsey D, Stokes T, Flowers S, Haag J, Jeddeloh J, et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003;163:1109-22 pubmed..ddm1 met1 double mutants were constructed to further our understanding of the mechanism of DDM1 action and the interaction between two major genetic loci affecting global cytosine methylation levels in Arabidopsis. ..
- Huang H, Yoo C, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, et al. PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. elife. 2016;5:e13292 pubmed publisher..Thus, PCH1 is a new factor that regulates photoperiod-responsive growth by integrating the clock with light perception pathways through modulating daily phyB-signaling. ..
- Brands A, Ho T. Function of a plant stress-induced gene, HVA22. Synthetic enhancement screen with its yeast homolog reveals its role in vesicular traffic. Plant Physiol. 2002;130:1121-31 pubmed..Based on these observations, we suggest that Yop1p/HVA22 regulates vesicular traffic in stressed cells either to facilitate membrane turnover, or to decrease unnecessary secretion. ..
- Baxter I, Hermans C, Lahner B, Yakubova E, Tikhonova M, Verbruggen N, et al. Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana. PLoS ONE. 2012;7:e35121 pubmed publisher..The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org...
- Jez J, Cahoon R, Chen S. Arabidopsis thaliana glutamate-cysteine ligase: functional properties, kinetic mechanism, and regulation of activity. J Biol Chem. 2004;279:33463-70 pubmed..These results explain the reported posttranslational change in AtGCL activity in response to oxidative stress. ..
- Ge X, Dietrich C, Matsuno M, Li G, Berg H, Xia Y. An Arabidopsis aspartic protease functions as an anti-cell-death component in reproduction and embryogenesis. EMBO Rep. 2005;6:282-8 pubmed
- Yang W, Devaiah S, Pan X, Isaac G, Welti R, Wang X. AtPLAI is an acyl hydrolase involved in basal jasmonic acid production and Arabidopsis resistance to Botrytis cinerea. J Biol Chem. 2007;282:18116-28 pubmed..The study shows that AtPLAI is an acyl hydrolase, rather than a specific phospholipase A. AtPLAI is involved in basal JA production and Arabidopsis resistance to the necrotrophic fungus B. cinerea. ..
- Tulin A, McClerklin S, Huang Y, Dixit R. Single-molecule analysis of the microtubule cross-linking protein MAP65-1 reveals a molecular mechanism for contact-angle-dependent microtubule bundling. Biophys J. 2012;102:802-9 pubmed publisher..Together, our data show that the rod domain of MAP65-1 acts both as a spacer and as a structural element that specifies the MT encounter angles that are conducive for bundling. ..
- Wierzbicki A, Ream T, Haag J, Pikaard C. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 2009;41:630-4 pubmed publisher..Collectively, our data suggest that AGO4 is guided to target loci through base-pairing of associated siRNAs with nascent Pol V transcripts. ..
- Hicks L, Cahoon R, Bonner E, Rivard R, Sheffield J, Jez J. Thiol-based regulation of redox-active glutamate-cysteine ligase from Arabidopsis thaliana. Plant Cell. 2007;19:2653-61 pubmed
- Herrera K, Cahoon R, Kumaran S, Jez J. Reaction mechanism of glutathione synthetase from Arabidopsis thaliana: site-directed mutagenesis of active site residues. J Biol Chem. 2007;282:17157-65 pubmed..thaliana GS and the Arg-132 and Arg-454 mutants also suggest distinct mechanistic roles for these residues. Based on these results, a catalytic mechanism for the eukaryotic GS is proposed. ..
- Braud C, Zheng W, Xiao W. LONO1 encoding a nucleoporin is required for embryogenesis and seed viability in Arabidopsis. Plant Physiol. 2012;160:823-36 pubmed publisher..Our results suggest that LNO1 is a component of the nuclear pore complex required for mature mRNA export from the nucleus to the cytoplasm, which makes LNO1 essential for embryogenesis and seed viability in Arabidopsis. ..
- Zhu H, Kranz R. A nitrogen-regulated glutamine amidotransferase (GAT1_2.1) represses shoot branching in Arabidopsis. Plant Physiol. 2012;160:1770-80 pubmed publisher..This suggests a plant-specific function such as branching control. We discuss the possibility that the GAT1_2.1 enzyme may activate SLs (e.g. GR24) by amidation, or more likely could embody a new pathway for repression of branching. ..
- Guo L, Devaiah S, Narasimhan R, Pan X, Zhang Y, Zhang W, et al. Cytosolic glyceraldehyde-3-phosphate dehydrogenases interact with phospholipase D? to transduce hydrogen peroxide signals in the Arabidopsis response to stress. Plant Cell. 2012;24:2200-12 pubmed publisher..The results indicate that the H(2)O(2)-promoted interaction of GAPC and PLD? may provide a direct connection between membrane lipid-based signaling, energy metabolism and growth control in the plant response to ROS and water stress. ..
- Preuss M, Serna J, Falbel T, Bednarek S, Nielsen E. The Arabidopsis Rab GTPase RabA4b localizes to the tips of growing root hair cells. Plant Cell. 2004;16:1589-603 pubmed..We propose that RabA4b regulates membrane trafficking through a compartment involved in the polarized secretion of cell wall components in plant cells. ..
- Bonner E, Cahoon R, Knapke S, Jez J. Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana. J Biol Chem. 2005;280:38803-13 pubmed..Initial protein-protein interaction experiments using AtOASS mutants targeted to this loop support this hypothesis. ..
- Lewis M, Cheverud J, Pikaard C. Evidence for nucleolus organizer regions as the units of regulation in nucleolar dominance in Arabidopsis thaliana interecotype hybrids. Genetics. 2004;167:931-9 pubmed..NOR2. Collectively, the data indicate that nucleolar dominance is a complex trait in which NORs, rather than individual rRNA genes, are the likely units of regulation...
- Chen H, Zhang B, Hicks L, Xiong L. A nucleotide metabolite controls stress-responsive gene expression and plant development. PLoS ONE. 2011;6:e26661 pubmed publisher..Taken together, our results demonstrate that PAP is critical for stress gene regulation and plant development, yet the FRY1 nucleotidase that catabolizes PAP may not be an in vivo salt toxicity target in Arabidopsis. ..
- Francois J, Kumaran S, Jez J. Structural basis for interaction of O-acetylserine sulfhydrylase and serine acetyltransferase in the Arabidopsis cysteine synthase complex. Plant Cell. 2006;18:3647-55 pubmed..These results provide new insights into the molecular mechanism underlying formation of the Cys synthase complex and provide a structural basis for the biochemical regulation of Cys biosynthesis in plants. ..
- Wilson M, Majerus P. Characterization of a cDNA encoding Arabidopsis thaliana inositol 1,3,4-trisphosphate 5/6-kinase. Biochem Biophys Res Commun. 1997;232:678-81 pubmed..The Arabidopsis enzyme produced both inositol 1,3,4,6-tetrakisphosphate and inositol 1,3,4,5-tetrakisphosphate as products in a ratio of 1:3, in contrast with the human enzyme which gives a product ratio of 3:1. ..
- Woo H, Pontes O, Pikaard C, Richards E. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev. 2007;21:267-77 pubmed..VIM1 associates with methylated genomic loci in vivo and is enriched in chromocenters. Our findings suggest that VIM1 acts at the DNA methylation-histone interface to maintain centromeric heterochromatin. ..
- Ward J, Cufr C, Denzel M, Neff M. The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in Arabidopsis. Plant Cell. 2005;17:475-85 pubmed..An alternate, though not mutually exclusive, model places OBP3 as a general inhibitor of tissue expansion with phyB and cry1, differentially modulating OBP3's role in this response. ..
- Ward J, Smith A, Shah P, Galanti S, Yi H, Demianski A, et al. A new role for the Arabidopsis AP2 transcription factor, LEAFY PETIOLE, in gibberellin-induced germination is revealed by the misexpression of a homologous gene, SOB2/DRN-LIKE. Plant Cell. 2006;18:29-39 pubmed..These results suggest LEP is a positive regulator of GA-induced germination acting independently of RGL2. An alternative model places LEP downstream of RGL2 in the GA-signaling cascade. ..
- Chen C, Chen H, Yeh S, Vittore G, Ho T. Autophagy is enhanced and floral development is impaired in AtHVA22d RNA interference Arabidopsis. Plant Physiol. 2009;149:1679-89 pubmed publisher..Potential mechanisms of this suppression and the roles of abscisic acid-induced HVA22 expression in vegetative and reproductive tissues are discussed. ..
- Woo H, Dittmer T, Richards E. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet. 2008;4:e1000156 pubmed publisher..Our findings demonstrate that VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing. ..
- Jeddeloh J, Bender J, Richards E. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 1998;12:1714-25 pubmed..The results also support our earlier hypothesis that ddm1 homozygotes act as "epigenetic mutators" by accumulating heritable changes in DNA methylation that can lead to changes in gene expression. ..
- Kumaran S, Jez J. Thermodynamics of the interaction between O-acetylserine sulfhydrylase and the C-terminus of serine acetyltransferase. Biochemistry. 2007;46:5586-94 pubmed..C10 peptide complex. The potential regulatory effect of temperature on the plant cysteine synthase complex is discussed. ..