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

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

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

Yersinia enterocolitica palearctica serobiotype O:3/4 - a successful group of emerging zoonotic pathogens

<p>Abstract</p> <p>Background</p> <p>High-pathogenic <it>Y. enterocolitica </it>ssp. <it>enterocolitica </it>caused several human outbreaks in Northern America. In contrast, low pathogenic <it>Y. enterocolitica </it>ssp. <it>palearctica </it>serobiotype O:3/4 is responsible for sporadic cases worldwide with asymptomatic pigs being the main source of infection. Genomes of three <it>Y. enterocolitica </it>ssp. <it>palearctica </it>serobiotype O:3/4 human isolates (including the completely sequenced Y11 German DSMZ type strain) were compared to the high-pathogenic <it>Y. enterocolitica </it>ssp. <it>enterocolitica </it>8081 O:8/1B to address the peculiarities of the O:3/4 group.</p> <p>Results</p> <p>Most high-pathogenicity-associated determinants of <it>Y. enterocolitica </it>ssp. <it>enterocolitica </it>(like the High-Pathogenicity Island, <it>yts1 </it>type 2 and <it>ysa </it>type 3 secretion systems) are absent in <it>Y. enterocolitica </it>ssp. <it>palearctica </it>serobiotype O:3/4 genomes. On the other hand they possess alternative putative virulence and fitness factors, such as a different <it>ysp </it>type 3 secretion system, an RtxA-like and insecticidal toxins, and a N-acetyl-galactosamine (GalNAc) PTS system (<it>aga</it>-operon). Horizontal acquisition of two prophages and a tRNA-Asn-associated GIYep-01 genomic island might also influence the <it>Y. enterocolitica </it>ssp. <it>palearctica </it>serobiotype O:3/4 pathoadaptation. We demonstrated recombination activity of the PhiYep-3 prophage and the GIYep-01 island and the ability of the <it>aga</it>-operon to support the growth of the <it>Y. enterocolitica </it>ssp. <it>enterocolitica </it>O:8/1B on GalNAc.</p> <p>Conclusions</p> <p><it>Y. enterocolitica </it>ssp. <it>palearctica </it>serobiotype O:3/4 experienced a shift to an alternative patchwork of virulence and fitness determinants that might play a significant role in its host pathoadaptation and successful worldwide dissemination.</p

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

On the Influence of Initial Stresses on the Velocity of Elastic Waves in Composites

The paper is devoted to the problem of propagation of elastic waves in composites with initial stresses. We suppose initial stresses are well within the elastic regime. We deal with the long-wave case and use the asymptotic homogenization technique based on the two-scale asymptotic approach. The main problem lies in solving the local (cell) problem, i.e., boundary value problem on a periodically repeating fragment of a composite. In general, the local problem cannot be solved explicitly. In our work, it is obtained for any initial stresses formulas, which is convenient for solving by standard codes. An analytical solution is obtained for small initial stresses. Asymptotic expansions used a small parameter characterizing the smallness of the initial stresses. In the zero approximation, composites without initial stresses are considered; the first approximation takes into account their influence on waves propagation. Two particular cases are considered in detail: laminated media and frame (honeycomb cell) composites. The analyzed frame composite can be used for the modeling of porous media. We select these two cases for the following reasons. First, the laminated and porous material are widely used in practice. Second, for these materials, the homogenized coefficients may be computed in the explicit form for an arbitrary value of the initial stresses. The dependence of the velocity of elastic waves on the initial stresses in laminated and homogeneous bodies differs. The initial tension increases the velocity of elastic waves in both cases, but the quantitative effect of the increase can vary greatly. For frame composites modeling porous bodies, the initial tension can increase or decrease the velocity of elastic waves (the initial tension decreases the velocity of elastic waves in the porous body with an inverted honeycomb periodicity cell). The decrease of the velocity of elastic waves is impossible in homogeneous media. The problem under consideration is related, in particular, to the core sample analysis in the geophysics. This question is discussed in the paper. We also analyzed some features of applications of asymptotic homogenization procedure for the dynamical problem of stressed composite materials, i.e., the nonadditivity of homogenization of sum of operators

On the Influence of Initial Stresses on the Velocity of Elastic Waves in Composites

The paper is devoted to the problem of propagation of elastic waves in composites with initial stresses. We suppose initial stresses are well within the elastic regime. We deal with the long-wave case and use the asymptotic homogenization technique based on the two-scale asymptotic approach. The main problem lies in solving the local (cell) problem, i.e., boundary value problem on a periodically repeating fragment of a composite. In general, the local problem cannot be solved explicitly. In our work, it is obtained for any initial stresses formulas, which is convenient for solving by standard codes. An analytical solution is obtained for small initial stresses. Asymptotic expansions used a small parameter characterizing the smallness of the initial stresses. In the zero approximation, composites without initial stresses are considered; the first approximation takes into account their influence on waves propagation. Two particular cases are considered in detail: laminated media and frame (honeycomb cell) composites. The analyzed frame composite can be used for the modeling of porous media. We select these two cases for the following reasons. First, the laminated and porous material are widely used in practice. Second, for these materials, the homogenized coefficients may be computed in the explicit form for an arbitrary value of the initial stresses. The dependence of the velocity of elastic waves on the initial stresses in laminated and homogeneous bodies differs. The initial tension increases the velocity of elastic waves in both cases, but the quantitative effect of the increase can vary greatly. For frame composites modeling porous bodies, the initial tension can increase or decrease the velocity of elastic waves (the initial tension decreases the velocity of elastic waves in the porous body with an inverted honeycomb periodicity cell). The decrease of the velocity of elastic waves is impossible in homogeneous media. The problem under consideration is related, in particular, to the core sample analysis in the geophysics. This question is discussed in the paper. We also analyzed some features of applications of asymptotic homogenization procedure for the dynamical problem of stressed composite materials, i.e., the nonadditivity of homogenization of sum of operators

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

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

Schematic representation of recombination events with brake-points location in the <i>ompF</i> gene of <i>Yersinia</i>.

<p>Schematic representation of recombination events with brake-points location in the <i>ompF</i> gene of <i>Yersinia</i>.</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