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.

Molecular Characterization, Phylogenetic, Expression, and Protective Immunity Analysis of OmpF, a Promising Candidate Immunogen Against Yersinia ruckeri Infection in Channel Catfish

“…As the major components and one of the most abundant proteins in the outer membrane, bacterial porin proteins play a critical role in bacterial pathogenesis and interactions with the host immune system ( 68 , 69 ). OmpF, as one of the best-studied bacterial porins on structural and functional characteristics ( 70 – 74 ), has been reported to be a protective antigen against some bacterial infections ( 40 , 74 – 77 ) and been predicted to be a conserved porin located on the surface of Yersinia ( 42 ), which suggests it is possible to use as an immunogen candidate providing immunoprotection against Yersinia infection.…”

“…OmpF is one of the major porins of Enterobacteriaceae , and has been reported to be the protective antigen and to provide desirable immunoprotection against pathogenic Escherichia coli ( 40 ) and Salmonella enterica ( 41 ). Besides, based on the perspective of structure and evolution, OmpF porin gene in genus Yersinia was comparably conserved in structure and homology and had putative antigenic epitopes located on several loops ( 42 ), indicating that it could be used as candidate protective antigen against Y. ruckeri infection.…”

Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF

“…First, a multiple alignment of OmpF amino acid sequences of Y. enterocolitica (from a BLASTP search of sequence databases using the O:3 OmpF sequence as the query) suggests that the restricted host range of these phages among Y. enterocolitica serotypes could be due to OmpF. The alignment provided a distribution of conserved amino acid residues and the presence of regions with high and low homologies, which coincide with eight transmembrane domains and eight "external" loops, respectively, of the topology of the OmpF porin from E. coli (72,73). The search and alignment of the sequences (see Fig.…”

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

“…These sequences were obtained from the DNAs of the 39 previously described strains14 and from the genomes of 51 strains retrieved from the GenBank and SRA databases (http://www.ncbi.nlm.nih.gov/). All row data were assembled in the CLC Genomics Workbench (Qiagen), followed by annotation on the RAST server 16.…”