Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA323943 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3611490.fastq.gz | Fastqsanger.gz | |||
| SRR3611500.fastq.gz | Fastqsanger.gz | |||
| SRR3611510.fastq.gz | Fastqsanger.gz | |||
| SRR3611491.fastq.gz | Fastqsanger.gz | |||
| SRR3611501.fastq.gz | Fastqsanger.gz |
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Project description:Genome-wide transcriptome analysis of Arabidopsis thaliana was performed to understand the role of auxin in the response of leaf growth to osmotic stress. We studied transcriptional changes in proliferating leaves of the seedlings grown in vitro on control medium, medium supplemented with 25mM mannitol, 0.1μM NAA and 0.1μM NAA + 25mM mannitol.
2021-05-09 | GSE60870 | GEO
Project description:Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. Here we show that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated leaf cells in Arabidopsis. We demonstrate that intervention of histone acetyltransferases causes severe defects in callus formation from leaf mesophyll protoplasts. Our data suggest that histone acetylation affects transcription of auxin biosynthesis genes. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for the cell cycle reactivation in protoplasts. These findings provide novel mechanistic insights into how differentiated plant cells revert their fate and reinitiate the cell cycle to exert pluripotency.
2021-10-03 | GSE178645 | GEO
Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.
2022-08-25 | PXD031063 | Pride
Project description:Bag101 overexpression causes growth defects. The purpose of the experiment was to quantify gene expression differences caused by bag101 overexpression.
2017-08-22 | GSE86512 | GEO
Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved. Two color Experiment, Organism: Arabidopsis thaliana and Antirrhinum. Arrays Used: 1. Agilent Arabidopsis thaliana Gene expression Microarray 22k (AMADID: 013324) 2. Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226) 3. Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) designed by Genotypic Technology Private Limited.
2013-05-01 | E-GEOD-40621 | biostudies-arrayexpress
Project description:The veins of leaves are a highly evolved vascular network that allows plants to grow large and complex. The patterning process leading to their formation involves the integration of several internal and external signals, such as plant hormone auxin. Here, we show that an evolutionarily conserved transcription factor controlling leaf vein growth in flowering plants VDOF1 is dependent on autophagy for its activity in Arabidopsis thaliana leaf, suggesting that this pathway might be required for proper vascular system development in leaf. Taken together, our data forms that during leaf vein patterning there is presents a network in which a module that links VDOF1-ATG8-ANT1-SCR-SHR factors integrates Space-time dimension to provide more vein density, which establish a precondition for C4 photosynthesis transition.
2023-07-01 | GSE216739 | GEO
Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Moreover, previous studies highlighted an important impact of the fungus on auxin homeostasis during the infection of Arabidopsis thaliana plants. Auxin is a key determinant of plant growth, including the growth of the root system. Auxin overproducing mutants, like for instance YUC9oe (Hentrich et al., 2013 Plant J.), show a pronounced root phenotype that can be restored by the co-cultivation with S. indica. We here report the comparative analysis of the effect of a mock- and S. indica-infection on both wild-type Arabidopsis plants (Col-0) and YUC9 overexpressing mutants. Our data provide evidence for the induction of GRETCHEN HAGEN 3 (GH3) genes that are involved in conjugating active free indole-3-acetic acid with amino acids. The fungus triggered induction GH3s is suggested to be involved in affecting the cellular auxin homeostasis.
2023-08-30 | GSE240683 | GEO
Project description:Temperature passively affects many biological processes. It is therefore challenging to study dedicated temperature signalling pathways orchestrating plant thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf cooling capacity. We screened a chemical library for compounds that restored abolished hypocotyl elongation in the pif4-2 deficient mutant background in the model plant Arabidopsis thaliana to identify novel regulators of thermomorphogenesis. The small aromatic compound ‘Heatin’, with 1-aminomethyl-2-naphthol as minimal active moiety, was isolated as potent enhancer of elongation growth. Following a chemical proteomics approach, the NITRILASE1-subfamily auxin biosynthesis enzymes were identified as molecular targets of Heatin. We show that Heatin inhibits NIT1-subfamily enzymatic activity and that accumulation of its substrate indole-3-acetonitrile (IAN) is sufficient for elongation growth in a NIT1-subfamily-dependent manner. Our work assigns a role for NITRILASE1-subfamily in mediating elongation growth. Moreover, Heatin and its functional analogues present novel chemical entities for understanding auxin biology.
2021-09-08 | PXD015411 | Pride
Project description:The genome of Arabidopsis contains 122 ERF transcription factor genes, some of which play diverse roles in the development and stress responses. A previous transcriptome analysis of Arabidopsis revealed that gene expression under combinatory stress conditions is not predictable from the combination of individual stresses (GSE46760). Searching for commonly regulated genes verified that only 11 genes were regulated in all stress combinations . Among these 11 genes, Rap2.9 (AT4G06746) was down-regulated under all stress conditions. Transgenic Arabidopsis thaliana lines overexpressing Rap2.9 under CaMV 35S promotor were generated, and the microarray analysis revealed that overexpression of Rap2.9 in A. thaliana plants causes massive reprogramming of transcription resulting in the alteration of the hormonal homeostasis and imbalances in signalling cascades related to stress response. Further analysis also revealed that Rap2.9 played an crucial role in plant development and stress tolerance in Arabidopsis plants.
2018-07-31 | GSE102714 | GEO
Project description:Plants grown under a canopy recognize changes in light quality and modify their growth patterns; this modification is known as shade avoidance syndrome. In leaves, leaf blade expansion is suppressed, whereas petiole elongation is promoted under the shade. However, the mechanisms that control these responses are largely unclear. Here, we demonstrated that both auxin and brassinosteroid (BR) are required for the normal leaf responses to shade. The microarray analysis of leaf blades and petioles treated with end-of-day far-red light (EODFR) revealed that almost half of the genes induced by the treatment in both parts were previously identified as auxin-responsive genes. Likewise, BR-responsive genes were overrepresented in the EODFR-induced genes. Hence, the auxin and BR responses were elevated by EODFR treatment in both leaf blades and petioles, although opposing growth responses were observed in these two parts. The analysis of the auxin-deficient doc1/big mutant and BR-deficient rot3/cyp90c1 mutant further indicates that auxin and BR were equally required for the normal petiole elongation response to the shade stimulus. In addition, the spotlight irradiation experiment revealed that phytochrome in leaf blades but not that in petioles regulated petiole elongation, which was probably mediated through regulation of the auxin/BR responses in petioles. On the basis of these findings, we conclude that auxin and BR cooperatively promote petiole elongation in response to the shade stimulus under the control of phytochrome in the leaf blade.
2009-11-01 | GSE17845 | GEO