Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

PLoS One. 2017 Feb 27;12(2):e0172742. doi: 10.1371/journal.pone.0172742. eCollection 2017.

Abstract

Central carbon metabolism is controlled by modulating the protein abundance profiles of enzymes that maintain the essential systems in living organisms. In this study, metabolic adaptation mechanisms in the model organism Saccharomyces cerevisiae were investigated by direct determination of enzyme abundance levels in 30 wild type and mutant strains. We performed a targeted proteome analysis using S. cerevisiae strains that lack genes encoding the enzymes responsible for central carbon metabolism. Our analysis revealed that at least 30% of the observed variations in enzyme abundance levels could be explained by global regulatory mechanisms. A enzyme-enzyme co-abundance analysis revealed that the abundances of enzyme proteins involved in the trehalose metabolism and glycolysis changed in a coordinated manner under the control of the transcription factors for global regulation. The remaining variations were derived from local mechanisms such as a mutant-specific increase in the abundances of remote enzymes. The proteome data also suggested that, although the functional compensation of the deficient enzyme was attained by using more resources for protein biosynthesis, available resources for the biosynthesis of the enzymes responsible for central metabolism were not abundant in S. cerevisiae cells. These results showed that global and local regulation of enzyme abundance levels shape central carbon metabolism in S. cerevisiae by using a limited resource for protein biosynthesis.

MeSH terms

  • Carbon / metabolism*
  • Chromatography, Liquid
  • Gene Deletion*
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal*
  • Glycolysis
  • Mutation
  • Proteome
  • Proteomics / methods*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Tandem Mass Spectrometry
  • Transcription Factors / metabolism
  • Trehalose / metabolism

Substances

  • Proteome
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Carbon
  • Trehalose

Grants and funding

This work was supported by the Industrial Technology Research Grant Program for 2011 of the New Energy and Industrial Technology Development Organization (NEDO, http://www.nedo.go.jp/) of Japan No 11B05004c and by JSPS (https://www.jsps.go.jp/) Grants in Aid for Scientific Research (C) No 15K06579.