Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mature fruits, root tips and leaves from wild type, vector control and trangenic tomato plants expressing InsP 5-ptase

ABSTRACT: To reduce the level of major second messenger inositol-1,4,5-triphosphate (InsP3), we generated transgenic tomato plants (cv. Micro-Tom) that are expressing InsP 5-ptase gene. To understand effects of transgene (InsP 5-ptase) on gene expression we carried out microarray analysis from different parts of transgenic and control (wild type, empty vector control) tomato plants; Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in transgenic tomato plants expressing InsP 5-ptase gene Experiment Overall Design: Ripe fruits of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene were selected for RNA extraction and hybridization on Affymetrix microarrays Experiment Overall Design: First two leaves of 10 day old light grown in vitro seedlings of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene were selected for RNA extraction and hybridization on Affymetrix microarrays Experiment Overall Design: 10 day old etiolated root tips of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene were selected for RNA extraction and hybridization on Affymetrix microarrays

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Mariya Khodakovskaya

PROVIDER: E-GEOD-9683 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Colletotrichum coccodes secretes ammonium during germination and colonization of host tissue as a mechanism for dual activation of fungal pathogenicity factors and plant cell death via activation of host NADPH oxidase. Ammonium accumulation during colonization of tomato fruits by C. coccodes induced host nucleus integrity changes and program cell death (PCD). Transcriptome analysis at the leading edge of colonized tissue and ammonium treated tomato fruits revealed 82 and 237 common up-regulated and common down-regulated genes, respectively. The common-up-regulated genes showed over representation of pathogen related (PR) proteins, salicylic acid (SA) dependent and systemic acquired resistance (SAR) related genes and genes related to biotic stress. The down regulated genes showed over representation of Jasmonic acid (JA) dependent genes. Consistent with this observation the direct application of SA enhanced C. coccodes colonization, whereas the application of JA delayed colonization. Candidate genes were selected for QRT-PCR analysis of transcripts in normal and transgenic RBOH antisense plants and showed dependence on RBOH regulation. In all, the results suggest that ammonia accumulation during C. coccodes colonization activates SA and suppress JA pathways through activation of RBOH. The effects of ammonium on the expression of the selected up-and down regulated genes were examined in fruit of different maturation stages. Red, susceptible and green resistant, tomato fruit displayed similar behavior, suggesting that resistance of green fruits to C. coccodes colonization is not modulated by the JA and SA pathways but depends on other factors Ten micrograms of total RNA was processed for the microarray hybridizations using the Affymetrix GeneChip one-cycle target-labeling kit (Affymetrix). The four treatments were: C. coccodes "mat inoculation" compared to a wound control (24 hours after the tomato fruit peel was removed). 5 mM Ammonium treatment in PBS compared to PBS treatments as a control for ammonium treatment, the treatments applied every four hours. Each treatment had a duplicate. The biotinylated complementary RNA was fragmented and hybridized to the GeneChip Tomato Genome Array (10,038 tomato probe sets for more than 9,200 tomato genes). The arrays were washed, stained, and scanned at the biological services (Weizmann institute of science, Rehovot, Israel). CEL files for the Affymetrix microarray data arising from the microarray experiments were analyzed utilizing the Partek genomics software (Downey, 2006).

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Transcription profiling of mature fruits, root tips and leaves from wild type, vector control and trangenic tomato plants expressing InsP 5-ptase

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