1. Cell Biology
  2. Computational and Systems Biology
Download icon

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

  1. Rosemary Yu
  2. Egor Vorontsov
  3. Carina Sihlbom
  4. Jens Nielsen  Is a corresponding author
  1. Chalmers University of Technology, Sweden
  2. University of Gothenburg, Sweden
Tools and Resources
  • Cited 3
  • Views 1,240
  • Annotations
Cite this article as: eLife 2021;10:e65722 doi: 10.7554/eLife.65722


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.

Data availability

Processed quantitative transcriptomics and proteomics data are in Supplementary Table 2 and 3. Processed intracellular amino acid concentrations are in Supplementary Table 4. Raw RNAseq data are available at ArrayExpress, accession E-MTAB-9117. The mass spectrometry proteomics data are deposited to the Proteome Xchange Consortium via the PRIDE partner repository with dataset identifier PXD021218.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Rosemary Yu

    Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Competing interests
    No competing interests declared.
  2. Egor Vorontsov

    Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
    Competing interests
    No competing interests declared.
  3. Carina Sihlbom

    Proteomics core facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
    Competing interests
    No competing interests declared.
  4. Jens Nielsen

    Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    For correspondence
    Competing interests
    Jens Nielsen, J.N. is the CEO of the BioInnovation Institute, Denmark..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9955-6003


Novo Nordisk Fonden (NNF10CC1016517)

  • Rosemary Yu
  • Jens Nielsen

Knut och Alice Wallenbergs Stiftelse

  • Rosemary Yu
  • Jens Nielsen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kevin J Verstrepen, VIB-KU Leuven Center for Microbiology, Belgium

Publication history

  1. Received: December 13, 2020
  2. Accepted: March 13, 2021
  3. Accepted Manuscript published: March 15, 2021 (version 1)
  4. Version of Record published: April 1, 2021 (version 2)


© 2021, Yu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


  • 1,240
    Page views
  • 175
  • 3

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics
    Matthias Pöge et al.
    Research Article Updated

    The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations have been reported to compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkably precise arrangement of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data confirm the existence of two previously observed molecular connectors/spacers which likely contribute to the nanometer-scale precise stacking of the ROS disks. We further provide evidence that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers. We suggest that together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Our Cryo-ET data provide novel quantitative and structural information on the molecular architecture in ROS and substantiate previous results on proposed mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.

    1. Cell Biology
    2. Immunology and Inflammation
    Dasmanthie De Silva et al.
    Research Article Updated

    Activation of T cells requires a rapid surge in cellular protein synthesis. However, the role of translation initiation in the early induction of specific genes remains unclear. Here, we show human translation initiation factor eIF3 interacts with select immune system related mRNAs including those encoding the T cell receptor (TCR) subunits TCRA and TCRB. Binding of eIF3 to the TCRA and TCRB mRNA 3’-untranslated regions (3’-UTRs) depends on CD28 coreceptor signaling and regulates a burst in TCR translation required for robust T cell activation. Use of the TCRA or TCRB 3’-UTRs to control expression of an anti-CD19 chimeric antigen receptor (CAR) improves the ability of CAR-T cells to kill tumor cells in vitro. These results identify a new mechanism of eIF3-mediated translation control that can aid T cell engineering for immunotherapy applications.