Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from 2-week-old Arabidopsis untreated seedlings grown under a short day condition

ABSTRACT: The Arabidopsis thaliana defense regulator EDM2 was previously shown to be specifically required for disease resistance to the pathogenic oomycete Hyaloperonospora parasitica aradidopsis mediated by the R protein RPP7. We found EDM2 to have a promoting effect on several distinct developmental processes, such as leaf pavement cell development, vegetative phase change or the floral transition. We further identified the atypical protein kinase WNK8 to physically interact with EDM2 in nuclei. Microarray data support regulatory interactions between WNK8 and EDM2 as well as their functional association with the autonomous floral promotion pathway. To assess interactions between EDM2 and WNK8 at the transcriptome level, we profiled transcript patterns of Col-0, edm2-2, wnk8-1, wnk8-2, wnk8-3 and an edm2-2 complementation line pXVE:HA-EDM2-a seedlings using Affymetrix ATH1 whole genome arrays. Plant materials were grown under short day conditions for 2 weeks. Total RNA was isolated from untreated seedlings and hybridized to the GeneChip following the manufacturer's instructions. Each genotype has three independent biological replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Tokuji Tsuchiya

PROVIDER: E-GEOD-17499 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development.

Tsuchiya Tokuji T Eulgem Thomas T

BMC plant biology 20100914

<h4>Background</h4>Strong immunity of plants to pathogenic microorganisms is often mediated by highly specific mechanisms of non-self recognition that are dependent on disease resistance (R) genes. The Arabidopsis thaliana protein EDM2 is required for immunity mediated by the R gene RPP7. EDM2 is nuclear localized and contains typical features of transcriptional and epigenetic regulators. In addition, to its role in immunity, EDM2 plays also a role in promoting floral transition. This developmen ...[more]

PMID: 20840782

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Project description:Changes in gene expression form a crucial part of the plant response to pathogen infection. Whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, for highly localised infections, such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response. Highly localised expression changes may be diluted by the comparative abundance of non-responding leaf cells or the Hpa oomycete evading detection by cells. Furthermore, local and systemic Hpa responses of a differing nature may become convoluted. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. Using the promoter of Downy Mildew Resistant 6 (DMR6) linked to GFP as a fluorescent marker of pathogen-contacting cells, we isolated Hpa-proximal and Hpa-distal cells from infected leaf samples using FACS, and measured global gene expression. The whole experiment was carried out in triplicate, with two time points (5 and 7 days post-inoculation) and three cell types (pathogen-proximal, pathogen-distal and uninfected control), totalling 18 microarrays. Transgenic Arabidopsis thaliana Col-0 with the transgene pDMR6:GFP was used for all experiments. Seedling populations were inoculated with 30,000-60,000 spores/ml of Hyaloperonospora arabidopsis strain Noks1 at 7 days old, and overground tissue sampled at 5 and 7 days post-inoculation. Protoplasts were generated from these samples according to Grønlund et al. 2012 JOVE, and sorted by fluorescence activated cell sorting into a GFP-positive (pathogen-proximal) and GFP-negative (pathogen-distal) population. As a control, uninfected seedlings were also sampled at 12 and 14 days old (equivalent age of 5 and 7 days post-inoculation), protoplasts generated and sorted to yield a GFP-negative population of uninfected control cells. Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Data was normalised using the Robust Multichip Averaging algorithm.

Dataset Information

Expression data from 2-week-old Arabidopsis untreated seedlings grown under a short day condition

Publications

Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development.

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