In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins
Journal article, 2018

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 of B. 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 of B. 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 of B. subtilis genome and found evidence for 19 novel ORFs. We provide the most extensive overview of the proteome and post-translational modifications for B. subtilis to date, with insights into functional annotation and evolutionary aspects of the B. subtilis genome.


V. Ravikumar

Technical University of Denmark (DTU)

Nicolas C. Nalpas

University of Tübingen

Viktoria Anselm

University of Tübingen

Karsten Krug

Broad Institute

University of Tübingen

Maša Lenuzzi

Ruder Boskovic Institute

Martin Sebastijan Šestak

Ruder Boskovic Institute

Tomislav Domazet-Lošo

Ruder Boskovic Institute

Catholic University of Croatia

Ivan Mijakovic

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Technical University of Denmark (DTU)

B. Macek

University of Tübingen

Scientific Reports

2045-2322 (ISSN) 20452322 (eISSN)

Vol. 8 1 17246

Subject Categories

Biochemistry and Molecular Biology


Bioinformatics and Systems Biology





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