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.
Bibliographical noteFunding Information:
We thank the National Bioinformatics Infrastructure Sweden (NBIS) for discussions. We thank Pannipa Pornpitakpong and Alexandra Hoffmeyer (Technical University of Denmark) for conducting RNA sequencing. The Proteomics Core Facility of the University of Gothenburg is grateful to the Inga-Britt and Arne Lundbergs Forskningsstiftlese for the donation of the Orbitrap Fusion Tribrid MS instrument. This research was supported by funding from the Novo Nordisk Foundation (grant number NNF10CC1016517) and the Knut and Alice Wallenberg Foundation.
© 2021, eLife Sciences Publications Ltd. All rights reserved.