A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli : The search for the unit of selection

Abstract

Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in Escherichia coli and in Citrobacter rodentium. The locus of enterocyte and effacement in E. coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (i) the complete pathogenic island, (ii) the five operons in which the island is organized, and (iii) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E. coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.natural selection ͉ pathogenicity island ͉ positive Darwinian selection ͉ mutation ͉ GC content

Molecular Evolution of Pathogenicity-Island Genes in Pseudomonas viridiflava

“…Rather, there appears to be considerable independence in the genealogical histories of individual loci and ample opportunity for simultaneous adaptive evolution of constituent PAI genes. That the components of the enteroocyte effacement island in Escherichia coli are, at best, weakly coupled in their evolution, has similarly been reported (Castillo et al 2005).…”

Use of the espZ Gene Encoded in the Locus of Enterocyte Effacement for Molecular Typing of Shiga Toxin-Producing Escherichia coli

“…Furthermore, there was no evidence of recombination between espZ alleles (Fig. 4), whereas recombination was observed using split decomposition analysis for entire or partial coding sequences of eae subtypes (3,40) or the 945-bp 3Ј terminus of ␤1, ␥1, ␥2, and ε alleles (data not shown). The lack of observable recombination between espZ alleles is favorable for molecular typing, because the sites deemed characteristic for each allele are independently inherited in that lineage and are not recombined between unrelated lineages.…”

“…The intimin-encoding gene eae was identified to exhibit a high degree of genetic diversity between A/E pathotypes of E. coli (3), and eae alleles are generally conserved between strains of the same STEC serotypes; therefore, this is also an appropriate target gene for molecular subtyping of E. coli. The diversity between eae alleles was calculated as ϭ 0.14 for six A/E pathogens (3) and ϭ 0.14 for the ␤1, ␥1, ␥2, and ε alleles of eae (data not shown).…”

“…It was our goal to select a LEE-encoded gene that would support the detection and subtyping of STEC, relying upon the ubiquity of the LEE among the most significant STEC serotypes and the large degree of genetic diversity observed at individual LEE genes. The loci that demonstrated the highest rates of diversity (measured as ) include those involved in interaction with the host cell (i.e., effectors and receptors), whereas the type III secretion apparatus had a lesser amount of diversity (3). Furthermore, the ratio of nonsynonymous mutation (dN) to synonymous mutation (dS) was markedly higher at those same loci involved in host interactions, and therefore these coding sequences may be undergoing positive selection (3), a process reflective of functional adaptation in different host environments and E. coli genetic backgrounds.…”

“…Among the individual LEE-encoded genes present in different A/E pathotypes, including enteropathogenic E. coli (EPEC) and EHEC, a heterogeneous rate of genetic diversity has been observed (3,27). It was our goal to select a LEE-encoded gene that would support the detection and subtyping of STEC, relying upon the ubiquity of the LEE among the most significant STEC serotypes and the large degree of genetic diversity observed at individual LEE genes.…”