Comparison of gene expression profiles between erf5/6 and WT Arabidopsis in response to chitooctaose
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE28227 | GEO | 2011/12/31
SECONDARY ACCESSION(S): PRJNA139615
REPOSITORIES: GEO
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. Both the double mutant erf5/6 and WT plants were grown in liquid MS medium in a growth chamber with constant light. Two-week-old seedlings were treated with chitooctaose at a final concentration of 1 uM for 30 minutes. The controls were similarly treated with an equivalent amount of ddH2O. The treated seedlings were harvested for RNA isolation. Three biological replicates were conducted for the experiment.
2011-12-31 | E-GEOD-28227 | biostudies-arrayexpress
Project description:Reactive oxygen species (ROS) have been characterized as both important signaling molecules and universal stressors that mediate many developmental and physiological responses. So far, details of the transcriptional mechanism of ROS-responsive genes are still largely unknown. In the study reported herein, we identified eight potential ROS-responsive cis-acting elements (ROSEs) from the promoters of genes upregulated by ROS. We also found that the APETALA2 (AP2/EREBP)-type transcription factor ERF6 could bind specifically to the ROSE7/GCC box. Co-expression of ERF6 enhanced luciferase activity driven by ROSE7. ERF6 interacted physically with mitogen-activated protein kinase 6 (MPK6), and also served as a substrate of MPK6. MPK6-mediated ERF6 phosphorylation at both Ser 266 and Ser 269 affected the dynamic alternation of ERF6 protein, which resulted in changes in ROS-responsive gene transcription. These data might provide new insight into the mechanisms that regulate ROS-responsive gene transcription via a complex of MPK6, ERF6, and the ROSE7/GCC box.
2012-05-15 | GSE37818 | 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:Reactive oxygen species (ROS) have been characterized as both important signaling molecules and universal stressors that mediate many developmental and physiological responses. So far, details of the transcriptional mechanism of ROS-responsive genes are still largely unknown. In the study reported herein, we identified eight potential ROS-responsive cis-acting elements (ROSEs) from the promoters of genes upregulated by ROS. We also found that the APETALA2 (AP2/EREBP)-type transcription factor ERF6 could bind specifically to the ROSE7/GCC box. Co-expression of ERF6 enhanced luciferase activity driven by ROSE7. ERF6 interacted physically with mitogen-activated protein kinase 6 (MPK6), and also served as a substrate of MPK6. MPK6-mediated ERF6 phosphorylation at both Ser 266 and Ser 269 affected the dynamic alternation of ERF6 protein, which resulted in changes in ROS-responsive gene transcription. These data might provide new insight into the mechanisms that regulate ROS-responsive gene transcription via a complex of MPK6, ERF6, and the ROSE7/GCC box. To identifiy the ERF6 regualted genes under ROS and HL treatment. Three-week old Col-0 and erf6-1 mutant plants before and after exposed to 2000 umol m-2s-1 illumination for 2 h were used for RNA extracted hybridization on Affymetrix microarrays.
2012-05-14 | E-GEOD-37818 | biostudies-arrayexpress
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:To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2014-01-01 | GSE51480 | GEO
Project description:Chitin, a polymer of N-acetyl-glucosamne, is a component of the cell walls of many plant fungal pathogens. During the infection process, the released chitin fragments (such as chitooctaose) from fungal cell walls by plant enzymes can trigger plant defense response and gene activation. The current work studies the regulation of Arabidopsis genes by the purified chitin fragment chitooctaose. We used the Affymetric Arabidopsis whole gene arrays to study the gene expression caused by chitin (chitooctaose). Keywords: chitooctaose vs water treatments, with 3 biological replicates
2006-05-03 | GSE4746 | GEO
Project description:A LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis Jinrong Wan,1 Xuecheng Zhang,1 David Neece,2 Katrina M. Ramonell,3 Steve Clough,2,4 Sung-yong Kim,1 Minviluz Stacey,1 and Gary Stacey1* 1Division of Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA 2Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA 3Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA 4US Department of Agriculture, Soybean/Maize Germplasm, Pathology and Genetics Research, Urbana, IL 61801, USA *To whom correspondence should be addressed. E-mail: staceyg@missouri.edu Abstract: Chitin, a polymer of N-acetyl-D-glucosamine, is found in fungal cell walls, but not in plants. Plant cells are capable of perceiving chitin fragments (chitooligosaccharides) to trigger various defense responses. We identified a LysM receptor-like protein (AtLysM RLK1) that is required for the perception of chitooligosaccharides in Arabidopsis. Mutation of this gene blocked the induction of almost all chitooligosaccharide-responsive genes (CRGs) and led to more susceptibility to fungal pathogens, but not to a bacterial pathogen. In addition, exogenously applied chitooligosaccharides enhanced resistance against both fungal and bacterial pathogens in the wild-type plants, but not in the mutant. Together, our data strongly suggest AtLysM RLK1 is the chitin receptor or a key part of the receptor complex and chitin is a PAMP (pathogen-associated molecular pattern) in fungi recognized by the receptor leading to the induction of plant innate immunity against fungal pathogens. Since LysM RLKs were also recently shown to be critical for the perception of the rhizobial lipo-chitin Nod signals, our data suggest that LysM RLKs not just recognize friendly symbiotic rhizobia (via their lipo-chitin Nod signals), but also hostile fungal pathogens (via their cell wall chitin). These data suggest a possible evolutionary relationship between the perception mechanisms of Nod signals and chitin by plants. Keywords: chitooctaose, chitin receptor mutant
2008-03-27 | GSE8319 | GEO
Project description:Comparison of the Arabidopsis stn7-stn8 double mutant invlolved in state transition vs WT Keywords: other
2005-10-20 | GSE2622 | GEO
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