Dataset Information

MetaboLights MTBLS36 - GNPS Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants

ABSTRACT: This data set is downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS36 Abstract:Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights via the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.

INSTRUMENT(S): LTQ Orbitrap Velos (Thermo Scientific)

ORGANISM(S): Solanum Lycopersicum

SUBMITTER: Beisken

PROVIDER: MSV000080958 | GNPS | Sun Apr 16 17:48:00 BST 2017

REPOSITORIES: GNPS

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Project description:The transcriptome, proteome and metabolome of 16 S.cerevisiae backgrounds, combinatorially perturbed in HIS3, LEU2, URA3 and MET15strains are compared. The project was jointly supervised by Kathryn Lilley and Markus Ralser. Transcriptome data has been deposited at ArrayExpress under accession <a href="http://www.ebi.ac.uk/microarray-as/aer/result?queryFor=Experiment&eAccession=E-MTAB-3991">E-MTAB-3991</a>. Metabolome data has been deposited at Metabolights with accession number <a href="http://www.ebi.ac.uk/metabolights/MTBLS168">MTBLS168</a>. The regulation of gene expression in response to nutrient availability is fundamental to the genotype–phenotype relationship. The metabolic–genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic–genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale.

Dataset Information

MetaboLights MTBLS36 - GNPS Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants

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