Open AccessComprehensive quantitative analysis of central carbon and amino‐acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
Author(s) -
Costenoble Roeland,
Picotti Paola,
Reiter Lukas,
Stallmach Robert,
Heinemann Matthias,
Sauer Uwe,
Aebersold Ruedi
Publication year - 2011
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2010.122
Subject(s) - saccharomyces cerevisiae , biology , proteomics , yeast , biochemistry , computational biology , amino acid , flux (metallurgy) , systems biology , metabolic network , metabolic pathway , metabolic flux analysis , adaptation (eye) , metabolism , quantitative proteomics , gene , chemistry , organic chemistry , neuroscience
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.