Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from shoots of rice seedlings after inoculation by Sinorhizobium meliloti 1021

ABSTRACT: Comparative transcriptome was profiled of rice seedling shoots in responding to live S. meliloti1021(LS) and dead S. meliloti1021 (DS) inoculation. The shoots with LS and DS were collected at 1, 2, 5 and 8 DAI respectively for microarry analysis. A total of 2413 differentially expressed genes (DEGs) were detected (q â¤ 0.05 and 1.5-fold change used as a cutoff), showing significantly differences between LS and DS. Enriched gene ontology terms and pathways analysis indicated that functions of these DEGs were observably involved in biotic stress, cellular regulation, plant hormone transduction, cell cycle and cell division. Among the classes of transcription factors, some key regulatory gene families such as WRKYs, NAC, bZIP, MYB and ZIM were involved in responding to defense. Others such as AUX, E2F/DP, BES1 and GASR were growth related. We used microarrays to profile the global view of gene expression underlying S. meliloti 1021 inoculation and identified regulated plant genes and pathway that likely key events in endophytic colonization and molecular promotion mechanism. Surface sterilized seeds were germinated in petri plates with distilled water in the dark for 3 days at 28Â°C. And then transferred aseptically into sterilized glass bottle, which containing 175 cm3 of sterile vermiculite and 100 mL of 1/4 Kimura B solution. After 2 days transferred to sterilized glass bottle, the seedling were inoculation with live S. meliloti1021 (LS) as treatment and dead S. meliloti1021 (DS) as control. Shoots from inoculated by live S. meliloti1021 (LS) and dead bacteria as control (DS) were collected at 1, 2, 5 and 8 DAI respectively. Every RNA sample was derived from 5 independent seedlings. In sum, four time points were selected and three biological replicates were performed, totally 24 rice genome arrays were used.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Shihua Shen

PROVIDER: E-GEOD-53535 | 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.

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Expression data from shoots of rice seedlings after inoculation by Sinorhizobium meliloti 1021

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