Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Affy_med_2011_14-Transcriptomic analysis of roots of WT (A17) Medicago truncatula plants and of a hypermycorrhizal mutant (B9) grown on limiting (P/10) or non-limiting phosphate (P2).

ABSTRACT: affy_med_2011_14 - affy_med_2011_14 - -In natural ecosystems most terrestrial plants form arbuscular mycorrhiza (AM), mutualistic symbioses with soil fungi belonging to the order Glomeromycota. This symbiosis takes place when phosphate is limiting and enables the plant to acquire nutrients (in particular phosphate) in exchange of carbon provided to the fungus A hypermycorrhizal mutant B9 was identified (Morandi et al. Mycorrhiza (2009) 19: 435) which displayed higher root colonization by Glomus intraradices. This phenotype could be linked to a defect in phosphate sensing or transport. We have undertaken the analysis of the root transcriptome of both WT and mutant plants grown on limiting or non-limiting phosphate to determine which processes are affected in the hypermycorrhizal mutant.-- Roots were harvested from 4 week-old WT and B9 mutant plants grown in a culture chamber with limiting (P/10, 130 ÂµM phosphate) or non limiting (P2, 2.6 mM phosphate) phosphate under long days (16 hrs day at 22Â°C with 380 ÂµE.m-2.s-1 light and 8hrs night at 19Â°C). RNAs were then extracted for transcriptomic analysis. We will compare WT (or mutant) root transcriptome on P/10 versus WT (or mutant) root transcriptome on P2 as well as mutant versus WT transcriptome on either P/10 or P2. 12 arrays - Medicago; dose response,gene knock out

ORGANISM(S): Medicago truncatula

SUBMITTER: stephanie huguet

PROVIDER: E-GEOD-44102 | 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

Affy_med_2011_14-Transcriptomic analysis of roots of WT (A17) Medicago truncatula plants and of a hypermycorrhizal mutant (B9) grown on limiting (P/10) or non-limiting phosphate (P2).

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