Shedding & shaving: Disclosure of proteomic expressions on a bacterial face

Bacterial surface proteins are critically important in determining the success of bacterial strains in their competition for survival, which makes comprehensive knowledge of the microbial 'face' of high relevance to understand bacterial physiology. Therefore, the aim of this study was to inventorize the proteomic composition of a bacterial surface by gel-free approaches using Bacillus subtilis as a model organism. To this purpose, intact bacteria were incubated with trypsin to cleave surface proteins, after which these 'shaved' proteins were identified by LC-MS/MS analysis of tryptic peptides that were released into the incubation buffer. In parallel, proteins that were released from bacterial cells without trypsin treatment were inventorized and defined as 'shed' proteins. The results showed that peptides of 41 proteins, comprising transmembrane proteins, secretory and lipoproteins, known 'anchorless' surface proteins and ribosomal proteins, were specifically released by shaving. Some of these proteins were also cleaved by trypsin-beads, which are unable to penetrate the bacterial cell wall, indicating a genuine surface-exposed localization. Together this shows that these combined gel-free approaches can reveal novel proteomic decorations on a bacterial face and may provide leads for future studies on protein sorting in B. subtilis and other Gram-positive bacteria.