Trends of the major porin gene (ompF) evolution: insight from the genus Yersinia

Abstract

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species.

Figure 1. Phylogenetic relationships among 16S rDNA-gyrB sequences of Yersinia.

The unrooted dendrogram was generated using neighbour-joining algorithm. The evolutionary distances were computed using the Kimura 2-parameter method and are expressed in number of base substitutions per site. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test are shown in nodes.

Figure 2. Phylogenetic relationships among ompF sequences of Yersinia.

The unrooted dendrogram was generated using neighbour-joining algorithm. The evolutionary distances were computed using the Kimura 2-parameter method and are expressed in number of base substitutions per site. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test are shown in nodes.

Figure 3. Schematic representation of recombination events with brake-points location in the ompF gene of Yersinia.

Figure 4. Nucleotide divergence (Pi) in 73 ompF sequences.

The regions predicted to correspond to the external loops (L1–L8) are colored green, regions putatively exposed to the periplasm and predicted transmembrane strands (1-16β) are indicated by black shading, the signal sequence (Sig.s.) is colored blue.

Figure 5. Location of positively selected sites in OmpF porins of Yersinia.

Group VII-Y. enterocolitica WA220; Group XIII-Y. intermedia 1948; Group IX-Y. frederiksenii 4648; Group I-Y. intermedia ATCC 29909; Group X-Y. kristensenii 5868; Group VIII-Y. pseudotuberculosis IP 31758. Sites that show positive selection (P<0.05) are depicted as yellow spheres and (P<0.01)-as red spheres.