pseudotuberculosis virulence after comparative proteomic analyses. b Proteins identified in this study by TPP/LC-MSE c Searches of similarity against publicly available protein databases using Blast-p. Strikingly, one variant protein of the C. pseudotuberculosis exoproteome, a conserved hypothetical exported protein with a cutinase domain [GenBank:ADL10384], has its coding sequence present in the genome of the C231 strain but absent from the genome of the 1002 strain (additional file 6). The genomic structure of the gene’s

surroundings is indicative of a region prone to recombination events, such as horizontal gene transfer [58]. In fact, it seems that gene gain and loss are frequent events leading to variations observed in the bacterial exoproteomes EPZ5676 manufacturer [39, 59]. Variation of the core exoproteome: differential expression analysis of the common proteins by LC-MSE In addition to identifying qualitative variations in the exoproteomes of the two C. pseudotuberculosis strains, we were also able to detect relative differences in expression of the proteins common

to the two proteomes through label-free protein quantification by the LC-MSE method. Relative protein quantification by this method can be obtained with basis on the accurate precursor ion mass and electrospray intensity data, acquired Rabusertib during the low energy scan step PIK3C2G of the alternating scan mode of MS acquisition [14]. Importantly, this quantitative attribute of the technique opens up new possibilities of utilization, Enzalutamide nmr as grows the interest on the so-called physiological proteomics [21]. Thirty-four out of 44 proteins commonly identified in the exoproteomes of the strains 1002 and C231 of C. pseudotuberculosis were considered by the PLGS quantification algorithm as having significantly variable expression (score > 250; 95% CI) (Figure 3, additional files 2 and 7). If we further filter

these results for the proteins presenting differential expression higher than 2-fold between the strains, we end up with only four proteins up-regulated in the 1002 strain and sixteen in the C231 strain (Figure 3). Figure 3 Differential expression of the proteins composing the core C. pseudotuberculosis exoproteome, evaluated by label-free relative quantification using LC-MS E . Results are shown as natural log scale of the relative quantifications (1002:C231) for each protein. Only proteins that were given a variation score higher than 250 by PLGS quantification algorithm are presented. Proteins regulated more than 2-fold in each strain are indicated. Protein identification numbers correspond to additional files 2 and 7 : Tables S1 and S4. Among the group of proteins not presenting considerable variations in expression between the two C.