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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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Nucleotide divergence (Pi) in 73 ompF sequences.The regions predicted to correspond to the external loops (L1–L8) are colored green, regions putatively exposed to the periplasm and predicted transmembrane strands (1-16β) are indicated by black shading, the signal sequence (Sig.s.) is colored blue.
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pone-0020546-g004: Nucleotide divergence (Pi) in 73 ompF sequences.The regions predicted to correspond to the external loops (L1–L8) are colored green, regions putatively exposed to the periplasm and predicted transmembrane strands (1-16β) are indicated by black shading, the signal sequence (Sig.s.) is colored blue.

Mentions: As it was shown above, the ompF gene of Yersinia is more divergent than the 16S rDNA and gyrB genes. The nucleotide diversity for all ompF genes (0,131±0,005) is twofold higher than for housekeeping genes (0,051±0,004). The common alignment of 73 ompF sequences contain 40% (479/1200 bp) of polymorphic nucleotide sites, which distributed strikingly nonrandom and formed hypervariable and conserved regions (Fig. 4). We have divided yersinia's ompF gene into 18 regions, according to domain organization of Escherichia coli OmpF protein [9]. Loops L2, L4–L7 were characterized by nucleotide deletions and/or insertions. Comparative analysis of surface-exposed loops exhibited significant heterogeneity of L4 and L5 (46±4.5%). The highest homology was conserved in L3 (8.2±1.6%). The same nonrandom heterogeneity with characteristic conserved regions forming the β-barrel structure of the proteins, and variable regions, making up the putative surface-exposed loops, has been shown in some other porins [39], [40].


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)

Nucleotide divergence (Pi) in 73 ompF sequences.The regions predicted to correspond to the external loops (L1–L8) are colored green, regions putatively exposed to the periplasm and predicted transmembrane strands (1-16β) are indicated by black shading, the signal sequence (Sig.s.) is colored blue.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020546-g004: Nucleotide divergence (Pi) in 73 ompF sequences.The regions predicted to correspond to the external loops (L1–L8) are colored green, regions putatively exposed to the periplasm and predicted transmembrane strands (1-16β) are indicated by black shading, the signal sequence (Sig.s.) is colored blue.
Mentions: As it was shown above, the ompF gene of Yersinia is more divergent than the 16S rDNA and gyrB genes. The nucleotide diversity for all ompF genes (0,131±0,005) is twofold higher than for housekeeping genes (0,051±0,004). The common alignment of 73 ompF sequences contain 40% (479/1200 bp) of polymorphic nucleotide sites, which distributed strikingly nonrandom and formed hypervariable and conserved regions (Fig. 4). We have divided yersinia's ompF gene into 18 regions, according to domain organization of Escherichia coli OmpF protein [9]. Loops L2, L4–L7 were characterized by nucleotide deletions and/or insertions. Comparative analysis of surface-exposed loops exhibited significant heterogeneity of L4 and L5 (46±4.5%). The highest homology was conserved in L3 (8.2±1.6%). The same nonrandom heterogeneity with characteristic conserved regions forming the β-barrel structure of the proteins, and variable regions, making up the putative surface-exposed loops, has been shown in some other porins [39], [40].

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