The Interaction of Protein Structure, Selection, and Recombination on the Evolution of the Type-1 Fimbrial Major Subunit (fimA) from Escherichia coli

Abstract

Abstract. Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including selection to constrain functional interactions or evolve novel epitopes to avoid recognition. We address these issues by studying genetic diversity in the Escherichia coli type-1 fimbrial major subunit, fimA. Overall, sequence diversity in fimA is high ( ‫ס‬ 0.07) relative to that in other E. coli genes. High diversity is a function of positive diversifying selection, as detected by d N /d S ratios higher than 1.0, and amino acid residuces subject to diversifying selection are nonrandomly clustered on the exterior surface of the peptide. In addition, McDonald and Kreitman tests suggest that there has been historical but not current directional selection at fimA between E. coli and Salmonella. Finally, some regions of the fimA peptide appear to be under strong structural constraint within E. coli, particularly the interior regions of the molecule that is involved in subunit to subunit interaction. Recombination also plays a major role contributing to E. coli fimA allelic variation and estimates of recombination (2N e c) and mutation (2N e ) are about the same.Recombination may act to separate the diverse evolutionary forces in different regions of the fimA peptide.

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

“…Nevertheless, in some of the MLST genes analyzed here, the observed values of ω and n M are so high that it is hard to believe that LRTs are completely misleading in their conclusions, especially for M7-M8 comparisons (e.g., N. gonorrhoeae and S. agalactiae). Moreover, it has been shown that LRTs are conservative (Anisimova et al, 2001(Anisimova et al, ,2003Yang et al, 2000a), so genes inferred by the test to undergo positive selection are most likely true cases of adaptation rather than an artifact of the method, as proven in most of the published studies (e.g., Bishop et al, 2000;Peek et al, 2001;Yang et al, 2000b;Yang and Swanson, 2002). Besides, we have adopted an even more conservative approach since we are not considering the loci under significant positive selection for which positively selected sites were not identified.…”

Sequence analysis demonstrates the conservation of fimH and variability of fimA throughout Avian Pathogenic Escherichia coli (APEC)

“…The grouping was consistent throughout the six domains, although the last two variable domains are identical for groups two and three. Our comparison also included the original sequenced fimA by Marc and Dho-Moulin [13] (GenBank accession number Z37500) and a fimA from E. coli of mammalian origin, from Peek et al [15] (GenBank accession number AF206642). We also included a fimA sequence, amplified from an E. coli strain isolated from infected ostrich eggs.…”

“…We noticed that the E. coli strains of mammalian origin fell into one of the established groups and did not take an exclusive position. Even additional fimA sequences of mammalian origin from the study of Peek et al [15] were incorporated into the multiple alignment: all of them fell within the proposed groups and the established variable domains (data not shown).…”

“…The APEC MT78 strain could be classified in group 1, while the AF206642 strain of mammalian origin belonged to group 3. When additional sequences of mammalian origin [15] were incorporated into the multiple alignment, all of them fell within the proposed groups and the established variable domains (data not shown).…”

“…For the fimA gene, the primers located in the constant intergenic regions flanking the fimA gene, as described by Peek et al [15], were used: 97FimAF (forward primer, starts at position -97, relative to the start codon):…”