Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Journal article, 2022

Saccharomyces cerevisiae is a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis of S. cerevisiae by culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis. Understanding how yeast organizes its functional proteome is a fundamental task in systems biology. Here, the authors conduct a multiomics analysis on yeast cells cultured with different growth rates, identifying a linear dependence of the functional proteome on the growth rate.

Author

Jianye Xia

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Benjamín José Sánchez

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Yu Chen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Kate Campbell

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

S. Kasvandik

University of Tartu

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Nature Communications

2041-1723 (ISSN) 20411723 (eISSN)

Vol. 13 1 2819

Subject Categories

Biochemistry and Molecular Biology

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

Bioinformatics and Systems Biology

DOI

10.1038/s41467-022-30513-2

PubMed

35595797

More information

Latest update

6/3/2022 9