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.

Author

V. Ravikumar

Nicolas C. Nalpas

Viktoria Anselm

Karsten Krug

Maša Lenuzzi

Martin Sebastijan Šestak

Tomislav Domazet-Lošo

Ivan Mijakovic

B. Macek

Scientific Reports

2045-2322 (ISSN)

Vol. 8 1 17246

Subject Categories

Biochemistry and Molecular Biology

Biophysics

Bioinformatics and Systems Biology

DOI

10.1038/s41598-018-35589-9

PubMed

30467398

More information

Latest update

12/7/2018