Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation

Jianye Xia, Benjamin J. Sánchez, Yu Chen, Kate Campbell, Sergo Kasvandik and Jens Nielsen ()
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Jianye Xia: East China University of Science and Technology
Benjamin J. Sánchez: Chalmers University of Technology
Yu Chen: East China University of Science and Technology
Kate Campbell: Chalmers University of Technology
Sergo Kasvandik: University of Tartu
Jens Nielsen: Chalmers University of Technology

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-30513-2

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