Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label-Free Quantitative Proteomics.

Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra-species variation at the proteome level is currently unknown. We investigated the proteomes of 16 pathogenic E. coli, two non-pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages. By applying label-free quantitative proteomics on trypsin-digested cell extracts from bacteria grown on blood agar, we detected 4,018 proteins, 3,285 of which were quantified, and 261 represented virulence factors. Of 753 proteins quantified in all strains, the levels of 153 varied substantially between strains and were functionally associated mostly with stress response and peripheral metabolism. The levels of proteins associated with the central metabolism varied considerably less than the levels of proteins from other metabolic pathways. Hierarchical clustering analysis based on the protein levels resulted in strains grouping that differed from that obtained by gene-based phylogenetic analysis. Finally, strains of some E. coli pathotypes had more similar protein profiles even when the strains were not genetically closely related. The results suggest that the degree of genetic relatedness may not necessarily be a good predictor of E. coli phenotypic characteristics. This article is protected by copyright. All rights reserved.