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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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Analysis of genomic signatures to identify putative hosts.A signature profile was created according to the word frequency for each of the available 1,047 complete genomic bacterial DNA sequences. Further, segments A1, A2, B and C of each plasmid were tested independently against these profiles. A P-value indicating the statistical significance was also calculated and indicated for each best match together with the taxonomic level for which the significance was achieved. The background colours in the table demonstrate the order that the putative hosts belong to, and the specific host species are denoted as colour-coded abbreviations.
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f5: Analysis of genomic signatures to identify putative hosts.A signature profile was created according to the word frequency for each of the available 1,047 complete genomic bacterial DNA sequences. Further, segments A1, A2, B and C of each plasmid were tested independently against these profiles. A P-value indicating the statistical significance was also calculated and indicated for each best match together with the taxonomic level for which the significance was achieved. The background colours in the table demonstrate the order that the putative hosts belong to, and the specific host species are denoted as colour-coded abbreviations.

Mentions: By applying recently developed algorithms3031, we analysed the genomic signatures in the plasmid backbones to identify putative bacterial hosts. We first created a genomic profile for each of all 1,047 bacterial complete genomic DNA sequences currently available from GenBank. The genomic signatures in the four segments A1, A2, B and C for each of the 25 plasmids were then matched against these profiles. To test for statistical significance, we started by investigating whether any of the bacterial species within the genus, which contained the best match, had a high probability of being the host. If no significance was found on the genus level, we stepped up one taxonomic level, testing all members in that specific family. If statistical significance was still not detected, this procedure was repeated until we reached the class level. Thus, the P-value indicates whether the signature in a plasmid segment is significantly similar to the signatures of the species in that specific genus, family, order or class (Fig. 5).


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)

Analysis of genomic signatures to identify putative hosts.A signature profile was created according to the word frequency for each of the available 1,047 complete genomic bacterial DNA sequences. Further, segments A1, A2, B and C of each plasmid were tested independently against these profiles. A P-value indicating the statistical significance was also calculated and indicated for each best match together with the taxonomic level for which the significance was achieved. The background colours in the table demonstrate the order that the putative hosts belong to, and the specific host species are denoted as colour-coded abbreviations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Analysis of genomic signatures to identify putative hosts.A signature profile was created according to the word frequency for each of the available 1,047 complete genomic bacterial DNA sequences. Further, segments A1, A2, B and C of each plasmid were tested independently against these profiles. A P-value indicating the statistical significance was also calculated and indicated for each best match together with the taxonomic level for which the significance was achieved. The background colours in the table demonstrate the order that the putative hosts belong to, and the specific host species are denoted as colour-coded abbreviations.
Mentions: By applying recently developed algorithms3031, we analysed the genomic signatures in the plasmid backbones to identify putative bacterial hosts. We first created a genomic profile for each of all 1,047 bacterial complete genomic DNA sequences currently available from GenBank. The genomic signatures in the four segments A1, A2, B and C for each of the 25 plasmids were then matched against these profiles. To test for statistical significance, we started by investigating whether any of the bacterial species within the genus, which contained the best match, had a high probability of being the host. If no significance was found on the genus level, we stepped up one taxonomic level, testing all members in that specific family. If statistical significance was still not detected, this procedure was repeated until we reached the class level. Thus, the P-value indicates whether the signature in a plasmid segment is significantly similar to the signatures of the species in that specific genus, family, order or class (Fig. 5).

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