Trends of the major porin gene (ompF) evolution

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

Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia

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

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences

<i>Yersinia</i> strains and the distribution of their 16S rDNA, <i>gyrB</i> and <i>ompF</i> gene alleles.

<p>A–NT-nucleotide sequence type, AT-amino acid sequence type.</p><p>B–Species identity corrected by 16S-<i>gyrB </i>genotype.</p

Phylogenetic relationships among 16S rDNA-<i>gyrB</i> sequences of <i>Yersinia</i>.

<p>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.</p

Location of positively selected sites in OmpF porins of <i>Yersinia</i>.

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

Phylogenetic relationships among <i>ompF</i> sequences of <i>Yersinia</i>.

<p>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.</p