The metabolic background is a global player in Saccharomyces gene expression epistasis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-02-01

AUTHORS

Mohammad Tauqeer Alam, Aleksej Zelezniak, Michael Mülleder, Pavel Shliaha, Roland Schwarz, Floriana Capuano, Jakob Vowinckel, Elahe Radmaneshfar, Antje Krüger, Enrica Calvani, Steve Michel, Stefan Börno, Stefan Christen, Kiran Raosaheb Patil, Bernd Timmermann, Kathryn S. Lilley, Markus Ralser

ABSTRACT

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. More... »

PAGES

15030

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nmicrobiol.2015.30

    DOI

    http://dx.doi.org/10.1038/nmicrobiol.2015.30

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1020959530

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27572163


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