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

Stenkova AM, Isaeva MP, Shubin FN, Rasskazov VA, Rakin AV - PLoS ONE (2011)

Bottom Line: 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.To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae.

View Article: PubMed Central - PubMed

Affiliation: Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russian Federation. stenkova@gmail.com

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.

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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.
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pone-0020546-g001: 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.

Mentions: In order to correctly identify each strain examined, a neighbour-joining tree was constructed from the 16S rDNA-gyrB concatenated sequences (Fig. 1). Ten Yersinia species (Y. aldovae, Y. bercovieri, Y. enterocolitica, Y. intermedia, Y. mollaretii, Y. pestis, Y. pseudotuberculosis, Y. similis, Y. rohdei and Y. ruckeri) were clearly grouped into relatively distinct clusters. The intraspecies genetic distance means of these species were up to 0.012. Y. pestis strains clustered tightly with the Y. pseudotuberculosis strains and the distance mean for this group was 0,001. Since, only one Y. similis strain was examined, the genetic distance of that species could not be estimated. Y. similis is a novel species in Yersinia, recently separated from its nearest phylogenetic neighbor Y. pseudotuberculosis [3]. As expected, Y. similis Y239 was clustered with Y. pseudotuberculosis and Y. pestis, forming a distinctive long branch. Strains of Y. enterocolitica were divided into three groups mainly caused by gyrB sequences, while 16S rDNA sequences separated strains into two subspecies (Y. enterocolitica subsp. enterocolitica and Y. enterocolitica subsp. palearctica), previously described by Neubauer et al., 2000 [28]. Strain Y. frederiksenii 2043 did not group with other five isolates of this species. It branched with Y. aleksiciae, Y. bercovieri and Y. mollaretii. Based on these results phylogenetic relations and BLAST (data not shown), Y. frederiksenii 2043 was more closely related to Y. massiliensis. Similar partition was observed for Y. kristensenii, three of which (991, Y332 and 6266) diverged from the other eight strains (6572, 8914, H17-36/83, 5868, 6032, 5862, 5306 and 5932) with a genetic distance about 0.055 and clustered with Y. aleksiciae Y159, sharing the genetic distance by 0,005. The data definitely indicated that these uncommon strains of Y. kristensenii and Y. frederiksenii might be members of Y. aleksiciae sp. nov. and Y. massiliensis sp. nov., since, Y. aleksiciae was recently separated from Y. kristensenii [1] and Y. massiliensis is more closely related to Y. frederiksenii [2]. Therefore, these strains were designated as Y. aleksiciae-like and Y. massiliensis-like, respectively. Based on the 16S rDNA-gyrB tree, most Y. intermedia clustered together into one of two branches; four Russian strains (6044, 5934, 6270 and 601) were located on the line leading to the rest Y. intermedia, shared the intraspecies distances up to 0.007.


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

Stenkova AM, Isaeva MP, Shubin FN, Rasskazov VA, Rakin AV - PLoS ONE (2011)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105102&req=5

pone-0020546-g001: 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.
Mentions: In order to correctly identify each strain examined, a neighbour-joining tree was constructed from the 16S rDNA-gyrB concatenated sequences (Fig. 1). Ten Yersinia species (Y. aldovae, Y. bercovieri, Y. enterocolitica, Y. intermedia, Y. mollaretii, Y. pestis, Y. pseudotuberculosis, Y. similis, Y. rohdei and Y. ruckeri) were clearly grouped into relatively distinct clusters. The intraspecies genetic distance means of these species were up to 0.012. Y. pestis strains clustered tightly with the Y. pseudotuberculosis strains and the distance mean for this group was 0,001. Since, only one Y. similis strain was examined, the genetic distance of that species could not be estimated. Y. similis is a novel species in Yersinia, recently separated from its nearest phylogenetic neighbor Y. pseudotuberculosis [3]. As expected, Y. similis Y239 was clustered with Y. pseudotuberculosis and Y. pestis, forming a distinctive long branch. Strains of Y. enterocolitica were divided into three groups mainly caused by gyrB sequences, while 16S rDNA sequences separated strains into two subspecies (Y. enterocolitica subsp. enterocolitica and Y. enterocolitica subsp. palearctica), previously described by Neubauer et al., 2000 [28]. Strain Y. frederiksenii 2043 did not group with other five isolates of this species. It branched with Y. aleksiciae, Y. bercovieri and Y. mollaretii. Based on these results phylogenetic relations and BLAST (data not shown), Y. frederiksenii 2043 was more closely related to Y. massiliensis. Similar partition was observed for Y. kristensenii, three of which (991, Y332 and 6266) diverged from the other eight strains (6572, 8914, H17-36/83, 5868, 6032, 5862, 5306 and 5932) with a genetic distance about 0.055 and clustered with Y. aleksiciae Y159, sharing the genetic distance by 0,005. The data definitely indicated that these uncommon strains of Y. kristensenii and Y. frederiksenii might be members of Y. aleksiciae sp. nov. and Y. massiliensis sp. nov., since, Y. aleksiciae was recently separated from Y. kristensenii [1] and Y. massiliensis is more closely related to Y. frederiksenii [2]. Therefore, these strains were designated as Y. aleksiciae-like and Y. massiliensis-like, respectively. Based on the 16S rDNA-gyrB tree, most Y. intermedia clustered together into one of two branches; four Russian strains (6044, 5934, 6270 and 601) were located on the line leading to the rest Y. intermedia, shared the intraspecies distances up to 0.007.

Bottom Line: 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.To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae.

View Article: PubMed Central - PubMed

Affiliation: Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russian Federation. stenkova@gmail.com

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.

Show MeSH
Related in: MedlinePlus