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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.

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Distribution of recent transfer events in COG functional categories. Red bars indicate transfer between bacteria and archaea. Blue bars indicate transfer between different bacteria. The one letter code corresponds to following functional categories. J Translation, ribosomal structure and biogenesis; A RNA processing and modification; K Transcription; L Replication, recombination and repair; B Chromatin structure and dynamics; D Cell cycle control, cell division, chromosome partitioning; Y Nuclear structure; V Defense mechanisms; T Signal transduction mechanisms; M Cell wall/membrane/envelope biogenesis; N Cell motility; Z Cytoskeleton; W Extracellular structures; U Intracellular trafficking, secretion, and vesicular transport; O Posttranslational modification, protein turnover, chaperones; C Energy production and conversion; G Carbohydrate transport and metabolism; E Amino acid transport and metabolism; F Nucleotide transport and metabolism; H Coenzyme transport and metabolism; I Lipid transport and metabolism; P Inorganic ion transport and metabolism; Q Secondary metabolites biosynthesis, transport and catabolism; R General function prediction only; S Unknown function
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Figure 5: Distribution of recent transfer events in COG functional categories. Red bars indicate transfer between bacteria and archaea. Blue bars indicate transfer between different bacteria. The one letter code corresponds to following functional categories. J Translation, ribosomal structure and biogenesis; A RNA processing and modification; K Transcription; L Replication, recombination and repair; B Chromatin structure and dynamics; D Cell cycle control, cell division, chromosome partitioning; Y Nuclear structure; V Defense mechanisms; T Signal transduction mechanisms; M Cell wall/membrane/envelope biogenesis; N Cell motility; Z Cytoskeleton; W Extracellular structures; U Intracellular trafficking, secretion, and vesicular transport; O Posttranslational modification, protein turnover, chaperones; C Energy production and conversion; G Carbohydrate transport and metabolism; E Amino acid transport and metabolism; F Nucleotide transport and metabolism; H Coenzyme transport and metabolism; I Lipid transport and metabolism; P Inorganic ion transport and metabolism; Q Secondary metabolites biosynthesis, transport and catabolism; R General function prediction only; S Unknown function

Mentions: Therefore, we analyzed the functional categories of the 171 gene candidates, which most probably have been horizontally acquired – 118 transferred between archaea and bacteria along with 53 transferred between bacterial phyla. The analysis of their functional categories, as described in COG, clearly showed distinct functional preferences among different groups of transferred genes. The genes transferred from bacteria to archaea were very strongly enriched in metabolism related genes (Fig. 5). On the other hand, the genes, which were transferred within the bacterial domain, were more populated with translation related genes (COG category: J) than with metabolic genes (Fig. 5).


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

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

Distribution of recent transfer events in COG functional categories. Red bars indicate transfer between bacteria and archaea. Blue bars indicate transfer between different bacteria. The one letter code corresponds to following functional categories. J Translation, ribosomal structure and biogenesis; A RNA processing and modification; K Transcription; L Replication, recombination and repair; B Chromatin structure and dynamics; D Cell cycle control, cell division, chromosome partitioning; Y Nuclear structure; V Defense mechanisms; T Signal transduction mechanisms; M Cell wall/membrane/envelope biogenesis; N Cell motility; Z Cytoskeleton; W Extracellular structures; U Intracellular trafficking, secretion, and vesicular transport; O Posttranslational modification, protein turnover, chaperones; C Energy production and conversion; G Carbohydrate transport and metabolism; E Amino acid transport and metabolism; F Nucleotide transport and metabolism; H Coenzyme transport and metabolism; I Lipid transport and metabolism; P Inorganic ion transport and metabolism; Q Secondary metabolites biosynthesis, transport and catabolism; R General function prediction only; S Unknown function
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Distribution of recent transfer events in COG functional categories. Red bars indicate transfer between bacteria and archaea. Blue bars indicate transfer between different bacteria. The one letter code corresponds to following functional categories. J Translation, ribosomal structure and biogenesis; A RNA processing and modification; K Transcription; L Replication, recombination and repair; B Chromatin structure and dynamics; D Cell cycle control, cell division, chromosome partitioning; Y Nuclear structure; V Defense mechanisms; T Signal transduction mechanisms; M Cell wall/membrane/envelope biogenesis; N Cell motility; Z Cytoskeleton; W Extracellular structures; U Intracellular trafficking, secretion, and vesicular transport; O Posttranslational modification, protein turnover, chaperones; C Energy production and conversion; G Carbohydrate transport and metabolism; E Amino acid transport and metabolism; F Nucleotide transport and metabolism; H Coenzyme transport and metabolism; I Lipid transport and metabolism; P Inorganic ion transport and metabolism; Q Secondary metabolites biosynthesis, transport and catabolism; R General function prediction only; S Unknown function
Mentions: Therefore, we analyzed the functional categories of the 171 gene candidates, which most probably have been horizontally acquired – 118 transferred between archaea and bacteria along with 53 transferred between bacterial phyla. The analysis of their functional categories, as described in COG, clearly showed distinct functional preferences among different groups of transferred genes. The genes transferred from bacteria to archaea were very strongly enriched in metabolism related genes (Fig. 5). On the other hand, the genes, which were transferred within the bacterial domain, were more populated with translation related genes (COG category: J) than with metabolic genes (Fig. 5).

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