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

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 <i>Ostreococcus tauri</i> 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 <i>k</i>_deg and <i>k</i>_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

Watson et al - Data

Data used in analyses presented in this paper. Please contact the corresponding author if you wish to use this data for anything other than exact replication of our our analyses. Note that individual sheep IDs have been scrambled and will not correspond to IDs in data associated with other publications using the same study system