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

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.

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Figure 1: Gene expression response to 16 combinatorial differences in the metabolic–genetic background.
Figure 2: Transcriptional response to a metabolic gene deletion is sensitive to the metabolic–genetic background.
Figure 3: Metabolic perturbations interact epistatically and dominate quantitative expression profiles.
Figure 4: Metabolism-induced epistasis propagates to the proteome and increases at the metabolome.

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Acknowledgements

The authors thank U. Sauer (ETH Zurich) for support with metabolite measurements and scientific discussions and M. Werber and S. Klages (Max Planck Institute for Molecular Genetics) for support with RNA sequencing analysis. The authors acknowledge the Wellcome Trust (RG 093735/Z/10/Z), the ERC (starting grant 260809), the Isaac Newton Trust (RG 68998) and the Darwin Trust of Edinburgh for a studentship for P.V.S. A.Z. is an EMBO fellow. M.R. is a Wellcome Trust Research Career Development and Wellcome-Beit Prize fellow.

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M.T.A., A.Z., R.S., E.R. and S.B. performed data analysis. M.M., P.S. and S.C. carried out raw data processing. M.M., P.S., F.C., J.V., A.K., E.C., S.M. and S.C. conducted the experiments. K.R.P., B.T., K.S.L. and M.R. conceived the study. M.R. wrote the first draft. M.T.A., A.Z. and M.R. wrote the paper. All authors contributed to preparing the final version.

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Correspondence to Markus Ralser.

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Supplementary Notes 1,2 and Figures 1–11 (PDF 10202 kb)

Supplementary Data 1

List of knock-out transcriptomes. (XLSX 89 kb)

Supplementary Data 2

Processed transcriptome, proteome and metabolome data, and epistasis values. (XLSX 5787 kb)

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Alam, M., Zelezniak, A., Mülleder, M. et al. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat Microbiol 1, 15030 (2016). https://doi.org/10.1038/nmicrobiol.2015.30

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