Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Lycopersicon esculentum roots in wild-type and ABA-deficient, control and Glomus intraradices inoculated plants to characterise variations in mycorrhization.

ABSTRACT: Abscisic acid (ABA) determines mycorrhiza functionality and arbuscule development. Transcriptome analysis in response to different mycorrhization status according to the ABA concentration in the root was performed to identify genes that may play a role in arbuscule functionality. Tomato Affymetrix GeneChip (around 10,000 probes) allowed us to detect and compare the transcriptional root profiling of tomato (Solanum lycopersicum) wild-type and ABA-deficient sitiens plants colonized by the arbuscular mycorrhizal fungus Glomus intraradices.

ORGANISM(S): Lycopersicon esculentum

SUBMITTER: Jose Garcia

PROVIDER: E-MEXP-2356 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.

Dataset Information

Transcription profiling of Lycopersicon esculentum roots in wild-type and ABA-deficient, control and Glomus intraradices inoculated plants to characterise variations in mycorrhization.

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