Comparison of gene expression profiles between erf5/6 and WT Arabidopsis in response to chitooctaose
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Gary Stacey
PROVIDER: E-GEOD-28227 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcription factors ERF5 and ERF6 may play a regulatory role in regulating the expression of chitin-responsive genes. We compared the gene expression profiles between the double mutant erf5/6 and WT plants in response to chitooctaose using the Affymetrix Arabidopsis Whole Genome Arrays.
2011-12-31 | GSE28227 | GEO
Project description:Leaf growth is a complex developmental process that is continuously fine-tuned by the environment. Various abiotic stresses, including mild drought stress, have been shown to inhibit leaf growth in Arabidopsis thaliana (Arabidopsis), but the underlying mechanisms remain largely unknown. Here we identify the redundant Arabidopsis transcription factors ETHYLENE RESPONSE FACTOR 5 (ERF5) and ERF6 as master regulators which adapt leaf growth to environmental changes. ERF5 and ERF6 gene expression is induced very rapidly and specifically in actively growing leaves after sudden exposure to osmotic stress that mimics mild drought. Subsequently, enhanced ERF6 expression inhibits cell proliferation and leaf growth by a process involving GA and DELLA signaling. Using an ERF6 inducible overexpression line, we demonstrate that the GA-degrading enzyme GA2-OX6 is transcriptionally induced by ERF6 and that consequently DELLA proteins are stabilized. As a result, ERF6 gain-of-function lines are dwarfed and hypersensitive to osmotic stress, while growth of erf5erf6 loss-of-function mutants is less affected by stress. Next to its role in plant growth under stress, ERF6 also activates the expression of a plethora of osmotic stress-responsive genes, including the well-known stress tolerance genes STZ, MYB51 and WRKY33. Interestingly, the activation of the stress tolerance genes by ERF6 occurs independently from the ERF6-mediated growth inhibition. Together, these data fit into a leaf growth regulatory model in which ERF5 and ERF6 form a missing link between the previously observed stress-induced 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation and DELLA-mediated cell cycle exit and execute a dual role by regulating both stress tolerance and growth-inhibition.
2013-04-06 | GSE45830 | GEO
Project description:Leaf growth is a complex developmental process that is continuously fine-tuned by the environment. Various abiotic stresses, including mild drought stress, have been shown to inhibit leaf growth in Arabidopsis thaliana (Arabidopsis), but the underlying mechanisms remain largely unknown. Here we identify the redundant Arabidopsis transcription factors ETHYLENE RESPONSE FACTOR 5 (ERF5) and ERF6 as master regulators which adapt leaf growth to environmental changes. ERF5 and ERF6 gene expression is induced very rapidly and specifically in actively growing leaves after sudden exposure to osmotic stress that mimics mild drought. Subsequently, enhanced ERF6 expression inhibits cell proliferation and leaf growth by a process involving GA and DELLA signaling. Using an ERF6 inducible overexpression line, we demonstrate that the GA-degrading enzyme GA2-OX6 is transcriptionally induced by ERF6 and that consequently DELLA proteins are stabilized. As a result, ERF6 gain-of-function lines are dwarfed and hypersensitive to osmotic stress, while growth of erf5erf6 loss-of-function mutants is less affected by stress. Next to its role in plant growth under stress, ERF6 also activates the expression of a plethora of osmotic stress-responsive genes, including the well-known stress tolerance genes STZ, MYB51 and WRKY33. Interestingly, the activation of the stress tolerance genes by ERF6 occurs independently from the ERF6-mediated growth inhibition. Together, these data fit into a leaf growth regulatory model in which ERF5 and ERF6 form a missing link between the previously observed stress-induced 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation and DELLA-mediated cell cycle exit and execute a dual role by regulating both stress tolerance and growth-inhibition. Samples were obtained from three independent experiments and from multiple plates within the experiment. Whole seedlings were harvested rapidly in an excess of RNAlater® solution (Ambion), and after overnight storage at 4°C, dissected under a binocular microscope on a cooling plate with precision microscissors. Dissected leaves were transferred to a new tube, frozen in liquid nitrogen, and ground with a Retsch machine and 3-mm metal balls. RNA was extracted with TriZol (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen). DNA digestion was done on columns with RNase-free DNase I (Roche). For the identification of genome-wide expression changes, samples of the strong ERF6-overexpressing line (ERF6IOE-S) and the control line (GFP:IOE) were harvested 4 h after transfer to DEX. Two µg of pure RNA samples were hybridized to AGRONOMICS1 Arabidopsis Tiling Arrays (Rehrauer et al., 2010) at the VIB Microarray Facility (Leuven, Belgium).
2013-04-06 | E-GEOD-45830 | biostudies-arrayexpress
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA. 15-day old Arabidopsis seedlings (Col 0) and gapcp1gapcp2 double mutants were used for RNA extraction and hybridization on Affymetrix microarrays.
2010-05-28 | E-GEOD-21765 | biostudies-arrayexpress
Project description:Chromatin remodeling factors of the Imitation Switch (ISWI) family play important roles in epigenetic regulations of gene expression in yeast and animals, whereas their function in plants remains elusive. Here we report characterization of the Arabidopsis ISWI genes CHR11 and CHR17. Double mutant chr11 chr17 displayed a dramatically reduced plant size with early flowering. In addition, epidermis of the double mutant leaves showed cell characteristics seen only in floral organs. These phenotypes resemble, at least partially, those of the Polycomb mutants curly leaf (clf) and like heterochromatin protein1 (lhp1). Microarray analysis revealed that a number of targets of the Polycomb pathway were derepressed in chr11 chr17 leaves. Furthermore, triple mutants combining chr11 chr17 with clf-29 or lhp1-6 both greatly enhanced clf-29 and lhp1-6 phenotypes, respectively. All these results strongly suggest that the ISWI family genes in Arabidopsis may function in gene silencing via the Polycomb pathway Leaves from 15-day-old seedlings of wild-type Col-0 and chr11-1 chr17-1 were used for RNA preparation.In the experiment data,A refers to Col-0, and B refers to chr11-1 chr17-1.
2010-06-23 | E-GEOD-22159 | biostudies-arrayexpress
Project description:Microarray analyses were performed on Arabidopsis thaliana plants overexpressing ERF5. In this way it was hoped that any changes in the Arabidopsis transcriptome caused by overexpression would provide clues as to the role this gene plays in vivo.<br>Arabidopsis thaliana plants were transformed with 35S::ERF5 or the empty vector pK2GW7 (used as a control). Total RNA was extracted from untreated 10-day old seedlings. Three separate arrays were performed (the RNA for each slide having been extracted from an independent biological replicate).
2010-12-31 | E-MTAB-436 | biostudies-arrayexpress
Project description:Microarray analyses were performed on Arabidopsis thaliana plants overexpressing ERF6. In this way it was hoped that any changes in the Arabidopsis transcriptome caused by overexpression would provide clues as to the role this gene plays in vivo.<br>Arabidopsis thaliana plants were transformed with 35S::ERF6 or the empty vector pK2GW7 (used as a control). Total RNA was extracted from untreated 10-day old seedlings. Three separate arrays were performed (the RNA for each slide having been extracted from an independent biological replicate).
2010-12-31 | E-MTAB-435 | biostudies-arrayexpress
Project description:Nitric oxide regulates plant development and responses to stress. However, the mechanisms underlying its regulatory role are still poorly known, and the impact of endogenous NO on the genome-wide transcriptome of plants has not been studied. For that purpose, we compared the transcriptomes of NO-deficient nia1nia2, noa1-2 and nia1nia2noa1-2 mutant versus wild type Arabidopsis thaliana plants. A core comprising 66 NO-responsive genes with similar expression in all NO-deficient genotypes was identified. Among them, 46 were down- and 20 up-regulated in NO-deficient plants, and thus positively and negatively regulated by endogenous NO, respectively. Accordingly with changes in its transcriptome, the NO-deficient nia1nia2noa1-2 mutant accumulated anthocyanins and indolic glucosinolates, displayed abnormal iron homeostasis in shoots and roots, and also showed altered root sensitivity to hormones such as ABA, ET, CYK and IAA. Together the presented data suggest NO functions essentially as a modulator of hormone action. Compared analysis of the transcriptomes of 15-day old seedlings from 3 different nitric oxide (NO)-deficient mutant genotypes versus wild type background Col-0 (3 independent biological replicates per genotype). NO-deficient mutant seedlings in Col-0 background were the double nia1nia2 mutant in nitrate reductases (NR/NIA) 1 and 2 (abbreviated as nia); the noa1-2 mutant allele in Nitric Oxide Associated 1 (AtNOA1) (abbreviated as noa); and, the triple nia1nia2noa1-2 (abreviated as nino).
2012-11-01 | E-GEOD-41958 | biostudies-arrayexpress
Project description:The Arabidopsis thaliana Imitation Switch (AtISWI) subfamily of ATP-dependent chromatin remodeling factors play essential roles in plant development. Here we show that the DDT domain transcription factor RINGLET (RLT) form a complex with AtISWI. RLT1 physically interacts with CHR11 in yeast cells. Single mutants rlt1-1 and rlt2-1 show no obvious developmental defects, while the rlt1-1 rlt2-1 double mutant phenocopies the AtISWI mutant chr11-1 chr17-1. In addtion, the RLT-ISWI complex selectively represses SEPALLATA, FRUITFULL and SUPPRESSOR OF OVEREXPRESSION OF CO 1, but not AGAMOUS and PISTILLATA in leaves. Leaves from 15-day-old seedlings of wild-type Col-0 and rlt1-1 rlt2-1 were used for RNA preparation.In the experiment data,3a3b refers to rlt1-1 rlt2-1.
2010-07-29 | E-GEOD-22584 | biostudies-arrayexpress
Project description:The proposal aims to characterise the pathways of DSB repair and recombination in Arabidopsis with the main focus of this research being the NHEJ pathway of illegitimate recombination. We will build on our expertise and resources in the field of DSB repair in plants, using the Arabidopsis NHEJ mutant atku80 which is an excellent model system for the study of DSB repair in higher eukaryotes (West et al., 2002 Plant J. 31, 517-28). Comparison of the transcriptome in NHEJ mutant and wild type plants under different experimental conditions will identify novel candidate genes involved in DNA DSB repair or damage signalling pathways.We will conduct 4 separate experiments on Arabidopsis seedlings grown on 0.5 MS media: the first will be a control consisting of Wassilewskija (WS-2) plants grown under standard conditions. In the second experiment WS plants will be exposed to the chemotherapeutic agent bleomycin (1 microgram per ml). This agent has been shown to cause both single and double strand breaks in the genome of Arabidopsis seedlings (Menke et al., 2001 Mut. Res. 493, 87-93). This agent is used in preference to gamma irradiation, which causes high levels of oxidative damage to cellular components. These experiments will characterise for the first time the transcriptional responses of Arabidopsis cells to the specific induction of DNA strand breaks. The transcript profile will also be determined in untreated atku80 mutants. This experiment will identify the components of novel and previously characterised DNA repair pathways up regulated in the mutant background. Finally, transcript analysis of bleomycin treated atku80 mutants and comparison with untreated mutant plants and both untreated and treated WS plants will identify novel putative DSB repair genes up regulated in response to genotoxic stress in the absence of a Ku80 mediated DSB repair pathway.The results of these studies will provide new and important information which will be instrumental in identifying novel genes and pathways involved in DNA repair and genome stability in plants and help elucidate the fundamental differences that exist between animal and plant DSB repair processes. Experiment Overall Design: Number of plants pooled:20
2008-06-14 | E-GEOD-6178 | biostudies-arrayexpress