Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC)

Abstract

The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.

Keywords: Yersinia; outer membrane; pathogen adaptation; porins; recombination.

Figure 1

Maximum likelihood tree of Yersinia ompC. The scale displays the number of nucleotide substitutions per nucleotide site. Numbers at nodes of the tree – the bootstrap value in percentage (75% cutoff). Bootstrap values obtained for the neighbor-joining method are in parentheses. Note: *Difference in the tree topology when compared with the neighbor-joining one. S. marcescens CAV1492 – out-group.

Figure 2

Nucleotide divergence (Pi) of ompC. Regions encoding the periplasmic loops and transmembrane strands are indicated by gray shading, the regions encoding the external loops (L1–L8) are colored by black shading.

Figure 3

Multiple alignment of OmpC sequences from Yersinia species. Notes: β1–β16 – transmembrane β-strands; β16 – part of β16-strand; L1–L8 – external loops; P1–P8 – periplasmic loops. Amino acid residues that demonstrated negative selection are marked by light gray shading; amino acid residues that demonstrated positive selection are marked by dark gray shading.

Figure 4

Location of positively selected sites in simulated structure OmpC porin of Y. pseudotuberculosis. Note: Sites that show positive selection are marked by red spheres.

Figure 5

Location of antigenic determinant regions along OmpC of Yersinia species. Notes: External loops (L1–L8) are indicated by black shading; periplasmic loops and transmembrane β-strands are indicated by light gray shading; and antigenic determinants are indicated by dark gray shading.