Expression data from Arabidopsis suspension cells overexpressing VND6 and SND1
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE20586 | GEO | 2010/10/28
SECONDARY ACCESSION(S): PRJNA125283
REPOSITORIES: GEO
Similar Datasets
Project description:The Arabidopsis thaliana NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), acts as a key regulator of xylem vessel differentiation. In order to identify direct target genes of VND7, we performed global transcriptome analysis using Arabidopsis transgenic lines in which VND7 activity could be induced post-translationally. This analysis identified 63 putative direct target genes of VND7, which encode a broad range of proteins, such as transcription factors, IRREGULAR XYLEM proteins and proteolytic enzymes, known to be closely associated with xylem vessel formation. Recombinant VND7 protein binds to several promoter sequences present in candidate direct target genes: specifically, in the promoter of XYLEM CYSTEINE PEPTIDASE1, two distinct regions were demonstrated to be responsible for VND7 binding. We also found that expression of VND7 restores secondary cell wall formation in the fiber cells of inflorescence stems of nst1 nst3 double mutants, as well as expression of NAC SECONDARY WALL THICKENING PROMOTING FACTOR3 (NST3, however, the vessel-type secondary wall deposition was observed only as a result of VND7 expression. These findings indicated that VND7 upregulates, directly and/or indirectly, many genes involved in a wide range of processes in xylem vessel differentiation, and that its target genes are partially different from those of NSTs.
2011-04-01 | GSE24169 | GEO
Project description:In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENINGS PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2, had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various above-ground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death was similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues. Experiment Overall Design: Total RNA was extracted from rosette leaves of two independent 2-week-old T1 plants over-expressing NST1 driven by 35S promoter and the whole transcriptome was compared with that of wild-type plant.
2008-06-12 | E-GEOD-3363 | biostudies-arrayexpress
Project description:In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENINGS PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2, had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various above-ground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death was similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues. Keywords: transgenic vs wt comparison
2005-09-29 | GSE3363 | GEO
Project description:Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plant. However, little is known about the epigenetic mechanism regulating secondary cell wall biosynthesis. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, positively regulates secondary wall deposition mainly through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1).
2020-11-29 | GSE153705 | GEO
Project description:Xylem vessels function in the long-distance conduction of water in land plants. The NAC transcription factor VASCULAR-RELATED NAC-DOMAIN7 (VND7) is a master regulator of xylem vessel cell differentiation in Arabidopsis (Arabidopsis thaliana). We previously isolated seiv (suppressor of ectopic xylem vessel cell differentiation induced by VND7) mutants, which are suppressor mutants of VND7-inducible xylem vessel cell differentiation. Here, we report that the responsible genes for seiv3, seiv4, seiv6, and seiv9 are protein ubiquitination-related genes encoding PLANT U-BOX46 (PUB46), uncharacterized F-BOX protein, PUB36, and UBIQUITIN-SPECIFIC PROTEASE1, respectively. We also found the decreased expression of genes downstream of VND7 and abnormal xylem transport activity in the seiv mutants. Upon VND7 induction, ubiquitinated levels from 492 and 180 protein groups were up- and down-regulated, respectively. Proteins for cell wall biosynthesis and protein transport were ubiquitinated by the VND7 induction, whereas such active protein ubiquitination was not observed in the seiv mutants. We detected the ubiquitination of three lysine residues in VND7: K94, K105, and K260. Substituting K94 with arginine significantly decreased the transactivation activity of VND7, suggesting that the ubiquitination of K94 is crucial for regulating VND7 activity. Our findings highlight the crucial roles of target protein ubiquitination in regulating xylem vessel activity.
2024-10-17 | PXD048830 | Pride
Project description:<p>Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.</p><p><br></p><p><strong>UPLC-MS assay of Wood fibre and ray cell tissue</strong> is reported in the current study <strong>MTBLS1831</strong>.</p><p><strong>UPLC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1797' rel='noopener noreferrer' target='_blank'><strong>MTBLS1797</strong></a>.</p><p><strong>GC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1796' rel='noopener noreferrer' target='_blank'><strong>MTBLS1796</strong></a>.</p>
2020-09-01 | MTBLS1831 | MetaboLights
Project description:<p>Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.</p><p><br></p><p><strong>UPLC-MS assay of Wood ring and extraxylary tissue</strong> is reported in the current study <strong>MTBLS1797</strong>.</p><p><strong>GC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1796' rel='noopener noreferrer' target='_blank'><strong>MTBLS1796</strong></a>.</p><p><strong>UPLC-MS assay of Wood fibre and ray cell tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1831' rel='noopener noreferrer' target='_blank'><strong>MTBLS1831</strong></a>.</p>
2020-09-01 | MTBLS1797 | MetaboLights
Project description:<p>Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.</p><p><br></p><p><strong>GC-MS assay of Wood ring and extraxylary tissue</strong> is reported in the current study <strong>MTBLS1796</strong>.</p><p><strong>UPLC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1797' rel='noopener noreferrer' target='_blank'><strong>MTBLS1797</strong></a>.</p><p><strong>UPLC-MS assay of Wood fibre and ray cell tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1831' rel='noopener noreferrer' target='_blank'><strong>MTBLS1831</strong></a>.</p>
2020-09-01 | MTBLS1796 | MetaboLights
Project description:During plant vascular development, xylem tracheary elements (TEs) form water conducting, empty pipes through genetically regulated cell death. Cell death is prevented from spreading to non-TEs by unidentified intercellular mechanisms, downstream of METACASPASE9 (MC9)-mediated regulation of autophagy in TEs. Here, we identified differentially abundant extracellular peptides in vascular11 differentiating wild type and MC9-downregulated Arabidopsis cell suspensions. The peptide Kratos rescued the abnormally high ectopic non-TE death resulting from either MC9 knockout or TE-specific overexpression of the ATG5 autophagy protein during experimentally induced vascular differentiation in Arabidopsis cotyledons. Kratos also reduced cell death following mechanical damage and extracellular ROS production in Arabidopsis leaves. Stress-induced but not vascular non-TE cell death was enhanced by another identified peptide, Bia. Bia is therefore reminiscent of several known plant cell death-inducing peptides acting as damage-associated molecular patterns. In contrast, Kratos plays a novel extracellular cell survival role in the context of development and during stress response.
2019-01-31 | PXD010886 | Pride
Project description:To gain novel insights into the molecular mechanisms of fiber secondary cell wall development, fiber transcriptomes of the immature fiber mutant (im) with defective secondary cell wall development and its near-isogenic line, TM-1 (wild-type) were compared using cDNA microarray technology. The expression profiling was performed at 5 developmental time points: 13, 16, 19, 22, and 25dpa. Secondary cell wall development related genes were identified by differentially expressed gene analysis. And these genes could be used as potential candidate genes for manipulation to improve fiber quality.
2014-06-30 | GSE49617 | GEO