Characterisation of the insoluble proteome of Lactococcus lactis by SDS-PAGE-LC-MS-MS leads to the identification of new markers of adaptation of the bacteria to the mouse digestive tract

Proteins located in the cell envelope are essential in interfacing bacteria with their environment but are still poorly characterised by proteomic approaches due to their low accessibility and solubility. Our goal was to characterise the envelope proteome also called insoluble proteome of L. lactis, used as a model. To do that, we coupled 1D gel electrophoresis and LC-MS/MS analysis. Using spectra and peptide counting, we compared protein abundances in two different environments: during the growth in rich medium (RM) and after transit of the mouse digestive tract (DT). We identified 145 proteins, membrane or cell wall located in L. lactis after the growth in M17 medium. Among them, we identified 46 membrane proteins containing up to 12 transmembrane helixes, lipoproteins and cell wall associated proteins including some with LysM domain. The insoluble fraction also contained many proteins predicted to be cytoplasmic. Most of them belonged to large protein complexes which probably co-purified with the bacterial envelopes. Some others are suspected to be associated to the inner part of the membrane. On the basis of spectral and peptide counting followed by an adapted statistical analysis, we compared the insoluble proteomes from L. lactis after growth in RM or after DT. As expected, we found proteins associated with translation, transcription, DNA replication, transport of nutrients, cell wall biosynthesis, and metabolism more abundant in M17 medium. After transit in digestive tract, L. lactis produced more proteins involved in carbon source diversification, response to osmotic downshift and stress and production of energy. The method used coupling 1D gel electrophoresis, LC-MS/MS and spectra and peptide counting appeared very promising for comparative proteomics of whole bacteria proteomes.