Genome-Wide ORFeome Cloning and Analysis of Arabidopsis Transcription Factor Genes

Gong, Wei; Shen, Yulong; Ma, Ligeng; Pan, Yi; Du, Yunlong; Wang, Donghui; Yang, Jianyu; Hu, Li-De; Liu, Xinfang; Dong, Chunxia; Ma, Li; Chen, Yanhui; Yang, Xiaoyuan; Gao, Ying; Zhu, Danmeng; Tan, Xiaoxiao; Mu, Jinye; Zhang, Dabing; Liu, Yule; Dinesh-Kumar, S. P.; Li, Yi; Wang, Xiping; Gu, Hongya; Liu, Qu; Bai, Shu-Nong; Lu, Ying‐Tang; Li, Jiayang; Zhao, Jindong; Zuo, Jianru; Huang, Hai; Deng, Xing Wang; Zhu, Yu-Xian

doi:10.1104/pp.104.042176

Cited by 208 publications

(151 citation statements)

References 36 publications

(27 reference statements)

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“…After the completion of sequencing of the Arabidopsis genome, there have been several large-scale analyses of the Arabidopsis TFs (Czechowski et al 2004;Gong et al 2004;Tian et al 2004;Guo et al 2005;Iida et al 2005;Okushima et al 2005;Overvoorde et al 2005). Previously, functional genomic analyses on two well-known transcription regulator gene families, AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA), provided insights into the unique and overlapping functions of the members of these two families Overvoorde et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…However, our knowledge of the biological roles and the biochemical properties of the majority of Arabidopsis TFs are fragmented. In recent years, there have been various attempts to analyzing the Arabidopsis TFs at a large scale (Czechowski et al 2004;Gong et al 2004;Tian et al 2004;Guo et al 2005;Iida et al 2005;Okushima et al 2005;Overvoorde et al 2005).…”

Section: Introductionmentioning

confidence: 99%

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Large-scale analysis of the GRAS gene family in Arabidopsis thaliana

et al. 2008

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GRAS proteins belong to a plant-specific transcription factor family. Currently, 33 GRAS members including a putative expressed pseudogene have been identified in the Arabidopsis genome. With a reverse genetic approach, we have constructed a ''phenome-ready unimutant collection'' of the GRAS genes in Arabidopsis thaliana. Of this collection, we focused on loss-of-function mutations in 23 novel GRAS members. Under standard conditions, homozygous mutants have no obvious morphological phenotypes compared with those of wild-type plants. Expression analysis of GRAS genes using quantitative realtime RT-PCR (qRT-PCR), microarray data mining, and promoter::GUS reporter fusions revealed their tissuespecific expression patterns. Our analysis of protein-protein interaction and subcellular localization of individual GRAS members indicated their roles as transcription regulators. In our yeast two-hybrid (Y2H) assay, we confirmed the protein-protein interaction between SHORT-ROOT (SHR) and SCARECROW (SCR). Furthermore, we identified a new SHR-interacting protein, SCARECROW-LIKE23 (SCL23), which is the most closely related to SCR. Our large-scale analysis provides a comprehensive evaluation on the Arabidopsis GRAS members, and also our phenome-ready unimutant collection will be a useful resource to better understand individual GRAS proteins that play diverse roles in plant growth and development.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Large-scale analysis of the GRAS gene family in Arabidopsis thaliana

et al. 2008

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“…The constructed vectors, pENTR TOPO::GhKCR1 and pENTR TOPO::GhKCR2 were verified by sequence analysis. The genes were transferred from pENTR TOPO to yeast expression vector pYTV [23] via LR reaction, using homologous sequences present on both vectors, resulting in pYTV::GhKCR1 and pYTV::GhKCR2. Gal1 promoter was fused at the N-terminus and 3× FLAG, 6× His and 2× IgG were present to facilitate detection of the fusion protein [23].…”

Section: Functional Complementation Of Yeast Ybr159w∆ Mutant Strain Bmentioning

confidence: 99%

Cloning and functional characterization of two cDNAs encoding NADPH-dependent 3-ketoacyl-CoA reductased from developing cotton fibers

et al. 2005

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Genes encoding enzymes involved in biosynthesis of very long chain fatty acids were significantly up-regulated during early cotton fiber development. Two cDNAs, GhKCR1 and GhKCR2 encoding putative cotton 3-ketoacyl-CoA reductases that catalyze the second step in fatty acid elongation, were isolated from developing cotton fibers. GhKCR1 and 2 contain open reading frames of 963 bp and 924 bp encoding proteins of 320 and 307 amino acid residues, respectively. Quantatitive RT-PCR analysis showed that both these genes were highly preferentially expressed during the cotton fiber elongation period with much lower levels recovered from roots, stems and leaves. GhKCR1 and 2 showed 30%-32% identity to Saccharomyces cerevisiae Ybr159p at the deduced amino acid level. These cotton cDNAs were cloned and expressed in yeast haploid ybr159w∆ mutant that was deficient in 3-ketoacyl-CoA reductase activity. Wild-type growth rate was restored in ybr159w∆ cells that expressed either GhKCR1 or 2. Further analysis showed that GhKCR1 and 2 were co-sedimented within the membranous pellet fraction after high-speed centrifugation, similar to the yeast endoplasmic reticulum marker ScKar2p. Both GhKCR(s) showed NADPH-dependent 3-ketoacyl-CoA reductase activity in an in vitro assay system using palmitoyl-CoA and malonyl-CoA as substrates. Our results suggest that GhKCR1 and 2 are functional orthologues of ScYbr159p.

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“…1,7 NAC (NAM, ATAF and CUC2) is one of the largest families of transcription factors in the plant genome, with 106 and 149 members predicted in Arabidopsis and rice, respectively. 8,9 A small number of the Arabidopsis NAC members have been studied, 10 but the function and regulation of most NAC genes are still largely unknown.…”

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confidence: 99%