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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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Genetic distances between pMCBF1 and other fully sequenced IncP-1 plasmids.Genetic distances between each gene in pMCBF1 and the corresponding genes in the other 23 analysed plasmids. The plasmid(s) with the longest distance to pMCBF1 is marked in red and the plasmid(s) with the shortest distance is marked in blue for respective gene. Genes not present in specific plasmids are marked with '–' and genes that are at least partially present but not expressed as proteins, or proteins not annotated in GenBank are marked with '*'. Three genomic regions, A (further divided into two subregions A1 and A2), B and C were identified as suitable targets for further phylogenetic and signature analysis as they were present in all plasmids.
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f1: Genetic distances between pMCBF1 and other fully sequenced IncP-1 plasmids.Genetic distances between each gene in pMCBF1 and the corresponding genes in the other 23 analysed plasmids. The plasmid(s) with the longest distance to pMCBF1 is marked in red and the plasmid(s) with the shortest distance is marked in blue for respective gene. Genes not present in specific plasmids are marked with '–' and genes that are at least partially present but not expressed as proteins, or proteins not annotated in GenBank are marked with '*'. Three genomic regions, A (further divided into two subregions A1 and A2), B and C were identified as suitable targets for further phylogenetic and signature analysis as they were present in all plasmids.

Mentions: The genetic distance between the amino-acid (AA) sequence of each backbone gene in pMCBF1 and their corresponding genes in the 23 previously described IncP-1 plasmids was estimated by a maximum likelihood approach. The backbone gene content in the 25 plasmids differs significantly and only 24 homologues of the 41 backbone genes in pMCBF1 were present in all analysed plasmids (Fig. 1). The AA similarity differed also widely with trbD being the most conserved gene. Among all 23 plasmids, plasmid pB4 presents the closest genetic distance to pMCBF1 in genes trbK, trbL, traG and traO, whereas pB4 genes traC2 and traK present the longest genetic distance. Similarly, the pKJK5 genes trbB, trbE, trbJ, traH, traJ, klcB and klcA presented the closest, and the two genes upf30.5 and kleB in the same plasmid presented the longest genetic distance to pMCBF1. Only plasmids pAKD4 and pQKH54 did not have any gene with the closest genetic distance to pMCBF1. Such alterations of relative genetic distances may be explained either by unequal nucleotide substitution rates or by an evolutionary history including homologous recombination (that is, the fact that the different genes in each plasmid backbone have different ancestries).


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)

Genetic distances between pMCBF1 and other fully sequenced IncP-1 plasmids.Genetic distances between each gene in pMCBF1 and the corresponding genes in the other 23 analysed plasmids. The plasmid(s) with the longest distance to pMCBF1 is marked in red and the plasmid(s) with the shortest distance is marked in blue for respective gene. Genes not present in specific plasmids are marked with '–' and genes that are at least partially present but not expressed as proteins, or proteins not annotated in GenBank are marked with '*'. Three genomic regions, A (further divided into two subregions A1 and A2), B and C were identified as suitable targets for further phylogenetic and signature analysis as they were present in all plasmids.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Genetic distances between pMCBF1 and other fully sequenced IncP-1 plasmids.Genetic distances between each gene in pMCBF1 and the corresponding genes in the other 23 analysed plasmids. The plasmid(s) with the longest distance to pMCBF1 is marked in red and the plasmid(s) with the shortest distance is marked in blue for respective gene. Genes not present in specific plasmids are marked with '–' and genes that are at least partially present but not expressed as proteins, or proteins not annotated in GenBank are marked with '*'. Three genomic regions, A (further divided into two subregions A1 and A2), B and C were identified as suitable targets for further phylogenetic and signature analysis as they were present in all plasmids.
Mentions: The genetic distance between the amino-acid (AA) sequence of each backbone gene in pMCBF1 and their corresponding genes in the 23 previously described IncP-1 plasmids was estimated by a maximum likelihood approach. The backbone gene content in the 25 plasmids differs significantly and only 24 homologues of the 41 backbone genes in pMCBF1 were present in all analysed plasmids (Fig. 1). The AA similarity differed also widely with trbD being the most conserved gene. Among all 23 plasmids, plasmid pB4 presents the closest genetic distance to pMCBF1 in genes trbK, trbL, traG and traO, whereas pB4 genes traC2 and traK present the longest genetic distance. Similarly, the pKJK5 genes trbB, trbE, trbJ, traH, traJ, klcB and klcA presented the closest, and the two genes upf30.5 and kleB in the same plasmid presented the longest genetic distance to pMCBF1. Only plasmids pAKD4 and pQKH54 did not have any gene with the closest genetic distance to pMCBF1. Such alterations of relative genetic distances may be explained either by unequal nucleotide substitution rates or by an evolutionary history including homologous recombination (that is, the fact that the different genes in each plasmid backbone have different ancestries).

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