title: The diversity of protein turnover and abundance under nitrogen-limited steady-state conditions in Saccharomyces cerevisiae.
abstract: To establish more advanced models of molecular dynamics within cells, protein characteristics such as turnover rate and absolute instead of relative abundance have to be analyzed. We applied a proteomics strategy to analyze protein degradation and abundance in Saccharomyces cerevisiae. We used steady-state chemostat cultures to ascertain well-defined growth conditions and nitrogen limited media, which allowed us to rapidly switch from (14)N to (15)N-isotope containing media and to monitor the decay of the (14)N mono-isotope signals in time. We acquired both protein abundance information and degradation rates of 641 proteins. Half-lives of individual proteins were very diverse under nitrogen-limited steady-state conditions, ranging from less than 30 min to over 20 h. Proteins that act as single physical complexes do not always show alike half-lives. For example the chaperonin-containing TCP-1 complex showed similar intermediate half-lives ranging from 7 to 20 h. In contrast, the ribosome exhibited a wide diversity of half-lives ranging from 2.5 to over 20 h, although their cellular abundances were rather similar. The stabilities of proteins involved in the central sugar metabolism were found to be intermediary, except for the glycolytic enzymes Hxk1p and Fba1p and the TCA-cycle proteins Lsc2p and Kgd1p, which showed half-lives of over 20 h. These data stress the need for inclusion of quantitative data of protein turn-over rates in yeast systems biology.
authors: Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors: Andreas O
authors: AO
authors: Helbig
authors: Pascale
authors: P
authors: Daran-Lapujade
authors: Antonius J A
authors: AJ
authors: van Maris
authors: Erik A F
authors: EA
authors: de Hulster
authors: Dick
authors: D
authors: de Ridder
authors: Jack T
authors: JT
authors: Pronk
authors: Albert J R
authors: AJ
authors: Heck
authors: Monique
authors: M
authors: Slijper
mesh_terms: D004734:Energy Metabolism; D013058:Mass Spectrometry; D055432:Metabolomics; D009584:Nitrogen / Q000378:metabolism; D014176:Protein Biosynthesis; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000254:growth & development / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000096:biosynthesis / Q000378:metabolism*
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D009584:Nitrogen