Journal
JOURNAL OF PROTEOME RESEARCH
Volume 9, Issue 7, Pages 3638-3646Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr100150w
Keywords
SILAC; Orbitrap; proteomics; bacteria; starvation; gluconeogenic growth
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Funding
- Max-Planck Society
- Institut National de la Recherche Agronomique (INRA)
- Lundbeckfonden
- Landesstiftung Baden-Wurttemberg
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We applied stable isotope labeling by amino acids in cell culture (SILAC) to large-scale quantitative proteomics analyses of the model bacterium Bacillus subtilis in two physiological conditions: growth on succinate and growth under phosphate starvation. Using a B. subtilis strain auxotrophic for lysine and high accuracy mass spectrometry for downstream analysis, we identified and quantified changes in the levels of more than 1500 proteins in each of the tested conditions with high biological and technical reproducibility. With a total of 1928 identified proteins, this study presents one of the most comprehensive quantitative proteomics studies in bacteria, covering more than 75% of the B. subtilis genes expressed in the log phase of growth. Furthermore, we detect and quantify dynamics of 35 Ser/Thr/Tyr phosphorylation sites under growth on succinate, and 10 phosphorylation sites under phosphate starvation, demonstrating the full compatibility of the method with site-specific detection and quantitation of phosphorylation events in bacteria.
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