Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis response to Erysiphe orontii infection - AtGenExpress

ABSTRACT: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana; The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Responses to E. orontii infection were assayed in wild-type Col-0 plants at 6, 12, 18, 24, 48, 72, 96, and 120 hours after inoculation of adult leaves. Inoculation was done via settling tower, using 10 day old E. orontii cultures. Leaves number 7 to 10 were selected for profiling. Experimenter name = Fred Ausubel , Julia Dewdney; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)

PROVIDER: E-GEOD-5686 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Infection by the pathogen grape powdery mildew (Erysiphe necator) causes changes in the transcriptome of its susceptible host Vitis vinifera. Infection triggers the host to synthesize the signaling molecule salicylic acid (SA) which regulates the expression of a broad range of defense-related plant genes. In addition, it is hypothesized that E. necator directly modulates gene expression in V. vinifera via the haustorial complex. This microarray experiment was designed to dissect host transcriptome changes triggered directly by E. necator infection and indirectly through the SA response. We accomplished this by conducting two separate global leaf transcriptome analyses using the Vitis Affymetrix GeneChip platform: in one, we compared the leaves with fully established PM colonies to healthy reference leaves, in another, we compared healthy leaves with artificially elevated SA levels to healthy reference leaves. Overlaying host transcriptome changes from these two experiments enabled us to glean out V. vinifera genes that modulate their expression in response E. necator in an SA-independent manner. We characterized gene expression profiles in (1) healthy reference leaves, (2) leaves with well-established by E. necator colonies, and (3) healthy leaves in which SA levels were artificially elevated by the presence of methyl salicylate (15 µM) in the atmosphere. Treatments (1) and (2) differed only in the presence E. necator infection, whereas treatments (1) and (3) differed only in SA levels. Consequently, statistical comparisons were made only between signal intensities from treatments (1) and (2) and from treatments (1) and (3). Each treatment was done in three biological repeats, that is, each experiment was repeated three times in 14-day intervals with dedicated biological material (plants were used in a single replicate and not reused in another repeat or treatment). Each biological replicate consisted of 10 potted vines. For RNA extraction, two young leaves were harvested from each of the 10 vines and pooled into a single sample.

Project description:Phytophthora blight is a highly destructive soil borne disease caused by Phytophthora capsici Leonian, which seriously threatens global pepper production. Grafting is one of the important means to improve plant disease resistance and prevent soil borne diseases in vegetable production. However, the molecular mechanism by which grafting enhances the resistance of pepper to Phytophthora blight is still unclear. This study used Phytophthora capsici resistant strain ‘ZCM334’ and susceptible strain ‘Early Calwonder’ as rootstocks, and ‘Early Calwonder’ as scions for grafting. Phenotypic observation and cytological analysis showed that compared with the ‘Early Calwonder’ self rooted plants, the ‘ZCM334’ grafted plants had a later onset of disease, stronger resistance, and less damage to leaf cells, indicating that grafting can significantly improve the resistance of pepper to Phytophthora capsici. This study identified differentially expressed proteins (DEPs) in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants through proteomic analysis based on iTRAQ technology, and 478 and 349 DEPs were identified between their leaves and roots, respectively. These DEPs were mainly involved in metabolic process, cellular process, response to stimulus and catalytic activity processes. We identified and screened 12 DEPs with consistent expression trends in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants, including seven DEPs related to Phytophthora capsici resistance (CA01g31060, CA02g15780, CA02g30850, CA01g11410, CA05g12260, CA03g35150, and CA03g36980) and five proteins with unknown functions (CA01g26190, CA11g10620, CA12g02730, CA01g20890 and CA02g11340). Through qRT-PCR analysis, a significant correlation was observed between the protein and transcript levels of these 12 DEPs, and their expression characteristics were analyzed in the roots and leaves of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants at different stages (0h, 12h, 24h, and 36h) after inoculation with Phytophthora capsici. This study provides valuable information for exploring the molecular mechanisms by which grafting enhances the resistance of pepper to Phytophthora blight and the excavation of these key genes provides research ideas for studying the regulatory network of pepper resistance to Phytophthora capsici.

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Transcription profiling of Arabidopsis response to Erysiphe orontii infection - AtGenExpress

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