title: Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry.
abstract: Protein synthesis and degradation determine the cellular levels of proteins, and their control hence enables organisms to respond to environmental change. Experimentally, these are little known proteome parameters; however, recently, SILAC-based mass spectrometry studies have begun to quantify turnover in the proteomes of cell lines, yeast, and animals. Here, we present a proteome-scale method to quantify turnover and calculate synthesis and degradation rate constants of individual proteins in autotrophic organisms such as algae and plants. The workflow is based on the automated analysis of partial stable isotope incorporation with (15)N. We applied it in a study of the unicellular pico-alga Ostreococcus tauri and observed high relative turnover in chloroplast-encoded ATPases (0.42-0.58% h(-1)), core photosystem II proteins (0.34-0.51% h(-1)), and RbcL (0.47% h(-1)), while nuclear-encoded RbcS2 is more stable (0.23% h(-1)). Mitochondrial targeted ATPases (0.14-0.16% h(-1)), photosystem antennae (0.09-0.14% h(-1)), and histones (0.07-0.1% h(-1)) were comparatively stable. The calculation of degradation and synthesis rate constants k(deg) and k(syn) confirms RbcL as the bulk contributor to overall protein turnover. This study performed over 144 h of incorporation reveals dynamics of protein complex subunits as well as isoforms targeted to different organelles.
authors.affiliation: Centre for Systems Biology at Edinburgh, University of Edinburgh, CH Waddington Building, The Kings Buildings, Mayfield Road, EH9 3JD, United Kingdom.
authors.forename: Sarah F
authors.initials: SF
authors.lastname: Martin
authors.forename: Vijaya S
authors.initials: VS
authors.lastname: Munagapati
authors.forename: Eliane
authors.initials: E
authors.lastname: Salvo-Chirnside
authors.forename: Lorraine E
authors.initials: LE
authors.lastname: Kerr
authors.forename: Thierry
authors.initials: T
authors.lastname: Le Bihan
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000460:Chlorophyta / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009587:Nitrogen Isotopes; D010446:Peptide Fragments / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D014176:Protein Biosynthesis; D055550:Protein Stability; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D013194:Staining and Labeling; D053719:Tandem Mass Spectrometry
chemical_list: D009587:Nitrogen Isotopes; D010446:Peptide Fragments; D010940:Plant Proteins; D020543:Proteome