In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins. Issue 1 (December 2018)

• Record Type: Journal Article
• Authors: Ravikumar, Vaishnavi; Nalpas, Nicolas; Anselm, Viktoria; Krug, Karsten; Lenuzzi, Maša; Šestak, Martin; Domazet-Lošo, Tomislav; Mijakovic, Ivan; Macek, Boris
• Is Part Of: Scientific reports. Volume 8:Issue 1(2018)
• Page Start: 1
• Page End: 11
• Publication Date: 2018-12
• Subjects: Natural history -- Research -- Periodicals; Biology -- Research -- Periodicals; Physical sciences -- Research -- Periodicals; Earth sciences -- Research -- Periodicals; Environmental sciences -- Research -- Periodicals; 502.85
• DOI: 10.1038/s41598-018-35589-9
• Languages: English
• ISSNs: 2045-2322

Abstract

Abstract Bacillus subtilis is a sporulating Gram-positive bacterium widely used in basic research and biotechnology. Despite being one of the best-characterized bacterial model organism, recent proteomics studies identified only about 50% of its theoretical protein count. Here we combined several hundred MS measurements to obtain a comprehensive map of the proteome, phosphoproteome and acetylome ofB. subtilis grown at 37 °C in minimal medium. We covered 75% of the theoretical proteome (3, 159 proteins), detected 1, 085 phosphorylation and 4, 893 lysine acetylation sites and performed a systematic bioinformatic characterization of the obtained data. A subset of analyzed MS files allowed us to reconstruct a network of Hanks-type protein kinases, Ser/Thr/Tyr phosphatases and their substrates. We applied genomic phylostratigraphy to gauge the evolutionary age ofB. subtilis protein classes and revealed that protein modifications were present on the oldest bacterial proteins. Finally, we performed a proteogenomic analysis by mapping all MS spectra onto a six-frame translation ofB. subtilis genome and found evidence for 19 novel ORFs. We provide the most extensive overview of the proteome and post-translational modifications forB. subtilis to date, with insights into functional annotation and evolutionary aspects of theB. subtilis genome.