title: Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism.
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.
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.|RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan.
authors.forename: Fumio
authors.identifier: http://orcid.org/0000-0003-1091-778X
authors.initials: F
authors.lastname: Matsuda
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
authors.forename: Syohei
authors.initials: S
authors.lastname: Kinoshita
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Nishino
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
authors.forename: Atsumi
authors.initials: A
authors.lastname: Tomita
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shimizu
mesh_terms: D002244:Carbon / Q000378:metabolism*; D002853:Chromatography, Liquid; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D006019:Glycolysis; D009154:Mutation; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D014157:Transcription Factors / Q000378:metabolism; D014199:Trehalose / Q000378:metabolism
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D002244:Carbon; D014199:Trehalose