Next generation sequencing has led to an increase the number of sequenced bacterial genomes which offer insights into the coding capacity of the bacterial genome without unraveling the biological significance of the presence and function of predicted genes in the system. Proteomics, on the other hand, leads to the identification of expressed genes under specified conditions and thus provides a functional perspective of the genomic data. For most proteome studies bacteria are cultured using a standard in vitro medium that supports growth but bears little resemblance to the conditions the organism is likely to encounter in its natural environment. The aim of this project was to investigate the potential of a proteogenomic pipeline that will aid in identification of differential expression of pathogenic determinants in bacteria.
The emerging human pathogen Shewanella algae (S. algae) was used in this project. The S. algae proteome and its secretome were harvested after growth in diverse growth media including LB media, blood agar, brain heart infusion (BHI) broth and thiosulfate citrate bile-salts sucrose (TCBS) agar and processed for SDS-PAGE. A ‘slice n dice’ approach was taken to examine protein expression and tryptic peptides were identified by LC-MS/MS.
The results of this study show that the proteome and secretome of S. algae change significantly with growth on different media. Interestingly, many virulence factors are expressed under specific growth conditions, for example only when grown on media containing the components expressed by eukaryotic cells or on solid (agar) media. These results demonstrate that the approach gives a more complete picture of the bacterial proteome and secretome and an idea of what conditions are required for the expression of putative virulence factors.This study highlights the power of an improved proteogenomic approach that increases our understanding of the expression profile of proteins important in bacterial pathogenesis.