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Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry

Research output: Contribution to journalArticle

Original languageEnglish
Pages (from-to)476-486
Number of pages11
JournalJournal Of Proteome Research
Volume11
Issue number1
DOIs
Publication statusPublished - 2012

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 kdeg and ksyn 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.

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