Limits...
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.

Kanhere A, Vingron M - BMC Evol. Biol. (2009)

Bottom Line: One successful approach to the detection of HGT events is due to Novichkov et al. (J.Genes transferred between the archaea and bacteria are mostly metabolic genes.On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. a.kanhere@ucl.ac.uk

ABSTRACT

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.

Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.

Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

Show MeSH

Related in: MedlinePlus

Comparison of 16S rRNA distances with protein-protein distances in orthologous family of leucyl-tRNA synthetases (COG0495). The points indicated by red squares correspond to distances of VNG2223G (from Halobacterium sp. NRC-1) with other proteins from this family.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651853&req=5

Figure 4: Comparison of 16S rRNA distances with protein-protein distances in orthologous family of leucyl-tRNA synthetases (COG0495). The points indicated by red squares correspond to distances of VNG2223G (from Halobacterium sp. NRC-1) with other proteins from this family.

Mentions: The correlation plot of leucyl-tRNA synthetases is shown in Fig. 4. Recently, a detailed analysis of this family has shown that leucyl-tRNA synthetase has been horizontally transferred from bacteria to the archaeon, Halobacterium sp. NRC-1 [21]. It is clear from the Fig. 4 that the points corresponding to Halobacterium sp. NRC-1 (COG protein ID, VNG2223G) stand out in the plot, and they were picked up by our <CDISS> measure.


Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.

Kanhere A, Vingron M - BMC Evol. Biol. (2009)

Comparison of 16S rRNA distances with protein-protein distances in orthologous family of leucyl-tRNA synthetases (COG0495). The points indicated by red squares correspond to distances of VNG2223G (from Halobacterium sp. NRC-1) with other proteins from this family.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651853&req=5

Figure 4: Comparison of 16S rRNA distances with protein-protein distances in orthologous family of leucyl-tRNA synthetases (COG0495). The points indicated by red squares correspond to distances of VNG2223G (from Halobacterium sp. NRC-1) with other proteins from this family.
Mentions: The correlation plot of leucyl-tRNA synthetases is shown in Fig. 4. Recently, a detailed analysis of this family has shown that leucyl-tRNA synthetase has been horizontally transferred from bacteria to the archaeon, Halobacterium sp. NRC-1 [21]. It is clear from the Fig. 4 that the points corresponding to Halobacterium sp. NRC-1 (COG protein ID, VNG2223G) stand out in the plot, and they were picked up by our <CDISS> measure.

Bottom Line: One successful approach to the detection of HGT events is due to Novichkov et al. (J.Genes transferred between the archaea and bacteria are mostly metabolic genes.On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. a.kanhere@ucl.ac.uk

ABSTRACT

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.

Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.

Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

Show MeSH
Related in: MedlinePlus