Proteome Turnover in the Green Alga Ostreococcus tauri

November 2011, Dr Sarah Martin has recently published in the Journal of Proteome Research, which explores high protein turnover and its impact on biological processes.

Proteome Turnover in the Green Alga Ostreococcus tauri by Time Course 15N Metabolic Labeling Mass Spectrometry 

'Protein turnover is an important aspect of biological processes, which has recently been the subject of large scale analyses in human cells,(1, 2) animals(3) and plants.(4) Biosynthesis and degradation rates determine the rate of protein turnover.(5) In system-wide studies, experimental data for transcription are commonly used as substitutes for practical reasons, however it has been shown that RNA and protein measurements can poorly correlate in experiments of abundance and stability.(3, 6) The quantification of protein turnover has been a key research drive in mass spectrometry-based proteomics to generate proteome-scale results. In cell culture and animal models, pulsed(7) and dynamic(2) stable isotope labeling with amino acids in culture (SILAC) methods have been developed to this end, while in microbial(8, 9) and photoautotrophic organisms(10-13) stable isotope labeling with ¹³C and ²H atoms has been applied.' (as taken from the journal)

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 ¹⁵N. 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.