Gene Conservation and Loss in the mutS-rpoS Genomic Region of Pathogenic Escherichia coli

The acquisition of new genes by horizontal transfer has played a major role in the adaptation and ecological specialization of bacterial lineages (17). It has been estimated, for example, that ∼18% of the current genome of Escherichia coli K-12 represents foreign DNA acquired by horizontal transfers since the divergence of E. coli and Salmonella enterica (18). Gene acquisitions have also contributed to the variation in virulence among strains and closely related bacterial species (11, 38). In E. coli and S. enterica, blocks of virulence genes, called pathogenicity islands, have been acquired at different times, thus generating a variety of pathogens with distinct virulence genes and mechanisms of pathogenesis (12, 31, 32). In some cases, loss of genes has been important in adaptive radiation and the evolution of bacterial virulence. For example, Maurelli and coworkers (25) present evidence that the universal deletion of the lysine decarboxylase gene (cadA) has enhanced the virulence of Shigella species because cadaverine, a product of the reaction catalyzed by lysine decarboxylase, inhibits the activity of Shigella enterotoxin. One active region of genomic evolution is located between 61 and 62 min in the E. coli genome (19). This region includes two essential genes (Fig. ​(Fig.1):1): mutS, which encodes one of the four proteins required for DNA mismatch repair (39); and rpoS, which encodes a sigma factor (ς38) that regulates many stationary-phase and environmental stress response genes (13). Both mutS and rpoS are highly conserved in sequence between E. coli and S. enterica; however, the nearby genomic regions have diverged in a variety of ways. In S. enterica, there is a 40-kb pathogenicity island (SPI-1 [Fig. 1]) that is inserted next to mutS and is required for epithelial cell invasion (11, 27). SPI-1 has been detected in all Salmonella groups but is absent in E. coli, suggesting that the island was acquired early in the evolutionary radiation of the salmonellae (31). Among different E. coli strains, the length of the genomic sequence between the mutS and rpoS genes is variable (Fig. ​(Fig.1).1). The region is 6.9 kb long in the E. coli K-12 genome (1) but varies in length among pathogenic strains of E. coli and Shigella (19, 20; P. E. Carter, L. Butler, I. R. Booth, and F. M. Thomson-Carter, Abstr. 99th Gen. Meet. Am. Soc. Microbiol., p. 32, 1999). Alterations in this region have been correlated with an enhanced mutation rate and are implicated in the emergence of new pathogenic clones (19). FIG. 1 The mutS-rpoS genomic region located at 61 min on E. coli K-12 chromosome. Primers designed from fhlA (FP1) and rpoS (RP1) of the K-12 genomic sequences (1) produce a long PCR amplicon of 10.9 kb. Previous studies have shown that Salmonella strains have ... The purpose of this study was to assess DNA polymorphism in the mutS-rpoS region and to infer the evolutionary history of divergence of this region among pathogenic strains of E. coli. The study focuses on four groups of pathogenic strains (45) representing enteropathogenic E. coli (EPEC), a prominent cause of infantile diarrhea in the developing world (29), and enterohemorrhagic E. coli (EHEC), a major cause of food-borne illness (29). We used a combination of restriction fragment length polymorphism (RFLP) analysis and nucleotide sequencing to characterize the genetic variation in the mutS-rpoS region among the EPEC and EHEC strains and compared the variation to that in nonpathogenic strains isolated from natural populations and strains closely related to laboratory strain K-12.