title: Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics.
abstract: Decades of biochemical research have identified most of the enzymes that catalyze metabolic reactions in the yeast Saccharomyces cerevisiae. The adaptation of metabolism to changing nutritional conditions, in contrast, is much less well understood. As an important stepping stone toward such understanding, we exploit the power of proteomics assays based on selected reaction monitoring (SRM) mass spectrometry to quantify abundance changes of the 228 proteins that constitute the central carbon and amino-acid metabolic network in the yeast Saccharomyces cerevisiae, at five different metabolic steady states. Overall, 90% of the targeted proteins, including families of isoenzymes, were consistently detected and quantified in each sample, generating a proteomic data set that represents a nutritionally perturbed biological system at high reproducibility. The data set is near comprehensive because we detect 95-99% of all proteins that are required under a given condition. Interpreted through flux balance modeling, the data indicate that S. cerevisiae retains proteins not necessarily used in a particular environment. Further, the data suggest differential functionality for several metabolic isoenzymes.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Roeland
authors.initials: R
authors.lastname: Costenoble
authors.forename: Paola
authors.initials: P
authors.lastname: Picotti
authors.forename: Lukas
authors.initials: L
authors.lastname: Reiter
authors.forename: Robert
authors.initials: R
authors.lastname: Stallmach
authors.forename: Matthias
authors.initials: M
authors.lastname: Heinemann
authors.forename: Uwe
authors.initials: U
authors.lastname: Sauer
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism*; D016000:Cluster Analysis; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D040901:Proteomics / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D049490:Systems Biology / Q000379:methods
chemical_list: D000596:Amino Acids; D029701:Saccharomyces cerevisiae Proteins; D002244:Carbon