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The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination.

Norberg P, Bergström M, Jethava V, Dubhashi D, Hermansson M - Nat Commun (2011)

Bottom Line: We also found that homologous recombination is a prominent feature of the plasmid backbone evolution.Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species.Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Microbiology, University of Gothenburg, Box 462, SE 413 46, Gothenburg, Sweden. peter.norberg@gu.se

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SimPlot analysis.Similarity plots with plasmids R751, pBP136 and pB3 as reference plasmids. Each coloured plot corresponds to a specific plasmid depicted in the colour shemes to the right and demonstrates the genetic distances from each plasmid to the reference strain in different parts of the genome. The similarity plot of R751 (a) highlights one putative recombination event in plasmid pB3 and three putative recombination events in plasmid pBP136. The similarity plots of these two plasmids (b, c) demonstrate that none of the plasmids included in this study are donors of the recombinant regions in pBP136. Instead, other plasmids from clades that were not previously described were probably involved in these recombination events.
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f4: SimPlot analysis.Similarity plots with plasmids R751, pBP136 and pB3 as reference plasmids. Each coloured plot corresponds to a specific plasmid depicted in the colour shemes to the right and demonstrates the genetic distances from each plasmid to the reference strain in different parts of the genome. The similarity plot of R751 (a) highlights one putative recombination event in plasmid pB3 and three putative recombination events in plasmid pBP136. The similarity plots of these two plasmids (b, c) demonstrate that none of the plasmids included in this study are donors of the recombinant regions in pBP136. Instead, other plasmids from clades that were not previously described were probably involved in these recombination events.

Mentions: The Bootscan and similarity plots support recombination. One example is pAOVO02, which showed a pattern consistent with recombination between the putative parental plasmids R751, pA1 and pKJK5 (Fig. 3a). These were also supported as parental plasmids by the similarity plot, except for pKJK5, which showed a lesser similarity to pAOVO02 than the other two. Another example is pB3, which generally presented the closest evolutionary relationship to R751 (Fig. 3b) and a close sequence similarity (>95% on average). In a specific pB3 region, however, the Bootscan plot indicated a closer evolutionary relationship to pKJK5, even though the sequence similarity was only 68–88%. A similar alteration in bootstrap support was seen for pB10 (Fig. 3c), which mostly showed the closest relationship to R751 except in one region that was more related to plasmid pA1, supporting a previous suggestion about recombination in pB10 (ref. 24). The SimPlot also indicated a generally high similarity of >95% to R751 and a high similarity to pA1 in the specific region. Finally, additional SimPlot analyses were performed to investigate the ancestry of specific recombination fragments. For example, plasmids pB3 and pBP136 shared almost identical sequences with plasmid R751, except in a few regions in which the sequence similarity was significantly less (Fig. 4a). When pBP136 (Fig. 4b) and pB3 (Fig. 4c) were compared with all other plasmids studied here, none of them presented high similarities in these regions for plasmid pBP136 and only plasmid pAOVO02 showed a high similarity in the specific region of pB3. A BLAST search identified no sequence with close similarity to the three regions in pBP136. In summary, we find that the φ-test supports recombination between IncP-1 plasmids and Bootscan, and similarity plots further illustrate the recombination crossovers.


The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination.

Norberg P, Bergström M, Jethava V, Dubhashi D, Hermansson M - Nat Commun (2011)

SimPlot analysis.Similarity plots with plasmids R751, pBP136 and pB3 as reference plasmids. Each coloured plot corresponds to a specific plasmid depicted in the colour shemes to the right and demonstrates the genetic distances from each plasmid to the reference strain in different parts of the genome. The similarity plot of R751 (a) highlights one putative recombination event in plasmid pB3 and three putative recombination events in plasmid pBP136. The similarity plots of these two plasmids (b, c) demonstrate that none of the plasmids included in this study are donors of the recombinant regions in pBP136. Instead, other plasmids from clades that were not previously described were probably involved in these recombination events.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3104523&req=5

f4: SimPlot analysis.Similarity plots with plasmids R751, pBP136 and pB3 as reference plasmids. Each coloured plot corresponds to a specific plasmid depicted in the colour shemes to the right and demonstrates the genetic distances from each plasmid to the reference strain in different parts of the genome. The similarity plot of R751 (a) highlights one putative recombination event in plasmid pB3 and three putative recombination events in plasmid pBP136. The similarity plots of these two plasmids (b, c) demonstrate that none of the plasmids included in this study are donors of the recombinant regions in pBP136. Instead, other plasmids from clades that were not previously described were probably involved in these recombination events.
Mentions: The Bootscan and similarity plots support recombination. One example is pAOVO02, which showed a pattern consistent with recombination between the putative parental plasmids R751, pA1 and pKJK5 (Fig. 3a). These were also supported as parental plasmids by the similarity plot, except for pKJK5, which showed a lesser similarity to pAOVO02 than the other two. Another example is pB3, which generally presented the closest evolutionary relationship to R751 (Fig. 3b) and a close sequence similarity (>95% on average). In a specific pB3 region, however, the Bootscan plot indicated a closer evolutionary relationship to pKJK5, even though the sequence similarity was only 68–88%. A similar alteration in bootstrap support was seen for pB10 (Fig. 3c), which mostly showed the closest relationship to R751 except in one region that was more related to plasmid pA1, supporting a previous suggestion about recombination in pB10 (ref. 24). The SimPlot also indicated a generally high similarity of >95% to R751 and a high similarity to pA1 in the specific region. Finally, additional SimPlot analyses were performed to investigate the ancestry of specific recombination fragments. For example, plasmids pB3 and pBP136 shared almost identical sequences with plasmid R751, except in a few regions in which the sequence similarity was significantly less (Fig. 4a). When pBP136 (Fig. 4b) and pB3 (Fig. 4c) were compared with all other plasmids studied here, none of them presented high similarities in these regions for plasmid pBP136 and only plasmid pAOVO02 showed a high similarity in the specific region of pB3. A BLAST search identified no sequence with close similarity to the three regions in pBP136. In summary, we find that the φ-test supports recombination between IncP-1 plasmids and Bootscan, and similarity plots further illustrate the recombination crossovers.

Bottom Line: We also found that homologous recombination is a prominent feature of the plasmid backbone evolution.Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species.Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Microbiology, University of Gothenburg, Box 462, SE 413 46, Gothenburg, Sweden. peter.norberg@gu.se

Show MeSH
Related in: MedlinePlus