Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Open accessPublished version of a preprint
Abstract
In addition to controlled expression of genes by specific regulatory circuits, the abundance of proteins and transcripts can also be influenced by physiological states of the cell such as growth rate and metabolism. Here we examine the control of gene expression by growth rate and metabolism, by analyzing a multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and amino acids in 22 steady-state yeast cultures. We find that transcription and translation are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but they are independently controlled by nitrogen metabolism via amino acid and nucleotide availabilities. Genes in central carbon metabolism, however, are distinctly regulated and do not respond to the cell growth rate or nitrogen metabolism as all other genes. Understanding these effects allows the confounding factors of growth rate and metabolism to be accounted for in gene expression profiling studies.
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Data integration across conditions improves turnover number estimates and metabolic predictions
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- Authors
- Yu, R., Vorontsov, E., Sihlbom, C., & Nielsen, J.
- Affiliations
- Chalmers University of Technology (SE)
- University of Gothenburg (SE)
- Novo Nordisk Foundation (DK)
- Corresponding author
- Nielsen, Jens
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2021-03-15
- Volume
- 10
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC8016476
- OpenAlex
- W3136840376
- Cited by
- 35
- References
- 5
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 7 · 2023: 10 · 2022: 4 · 2021: 5
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- Funders
- Novo Nordisk Fonden (NNF10CC1016517)
- Knut och Alice Wallenbergs Stiftelse
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- gene expression regulation, central carbon metabolism, Saccharomyces cerevisiae, growth rate, nitrogen metabolism, amino acid availability, RNA polymerase II, ribosome abundance, transcription, translation (biology), transcriptome, proteome, multi-omics
- MeSH terms
- Carbon, Genes, Fungal, Nitrogen, Saccharomyces cerevisiae, Transcriptome
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