Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Journal article, 2021

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.

Author

Rosemary Yu

Egor Vorontsov

University of Gothenburg

C. Sihlbom

University of Gothenburg

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

BioInnovation Institute

Technical University of Denmark (DTU)

eLife

2050-084X (ISSN)

Vol. 10 e65722

Subject Categories

Cell Biology

Microbiology

Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)

DOI

10.7554/eLife.65722

PubMed

33720010

More information

Latest update

4/29/2021