Characterization of protein species and weighted protein co-expression network regulation of Escherichia coli in response to serum killing using a 2-DE based proteomics approach.

Posttranslational modifications, providing covalent alterations to extend their functions, show protein species on 2-DE gels, but our knowledge on protein species is still limited. In the present study, characteristics of protein species are determined in Escherichia coli using 2-DE based proteomics. In the E. coli proteome, 691 unique proteins (representing 1096 protein spots) accounting for 15.37% of gene-coding proteins of the bacterium are identified. Out of them, 191 have 596 protein species. Proteins with higher abundance, a higher proportion of Glu, Gly, Lys, and higher pI are more likely to have protein species. Further investigation on bacterial serum resistance indicates that more proteins with protein species are found in the bacterium in response to serum stress. A weighted protein co-expression network shows that protein species are related to topological connection as a result of protein regulation. The node protein IleS is demonstrated to contribute to serum resistance using a gene-deleted mutant. These results have revealed general characteristic features of bacterial species, and also provided novel insights into the biological significance of bacterial protein species, particularly the role in serum resistance.