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PXD001491-4

PXD001491 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleThe metabolic background is a global player in Saccharomyces gene expression epistasis
DescriptionThe 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 E-MTAB-3991. Metabolome data has been deposited at Metabolights with accession number MTBLS168. 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.
HostingRepositoryPRIDE
AnnounceDate2016-08-02
AnnouncementXMLSubmission_2016-08-02_00:31:56.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterPavel Shliaha
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListiodoacetamide derivatized residue
InstrumentSynapt MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-11-13 23:28:16ID requested
12016-01-05 11:18:02announced
22016-03-09 02:34:42announcedUpdated publication reference for DOI(s): 10.1038/nmicrobiol.2015.30.
32016-03-10 00:30:41announcedUpdated project metadata.
42016-08-02 00:31:57announcedUpdated project metadata.
52023-11-14 08:48:51announced2023-11-14: Updated project metadata.
Publication List
10.1038/nmicrobiol.2015.30;
Keyword List
curator keyword: Biological
submitter keyword: S. cerevisiae
Contact List
Kathryn Lilley
contact affiliationCambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K.
contact emailksl23@cam.ac.uk
lab head
Pavel Shliaha
contact affiliationCambridge Center For Proteomics
contact emailpvs22@cam.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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