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Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.

Jackson CR, Dugas SL - BMC Evol. Biol. (2003)

Bottom Line: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today.Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution.Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, SLU 10736, Southeastern Louisiana University, Hammond, LA 70402, USA. cjackson@selu.edu

ABSTRACT

Background: The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects.

Results: Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the gamma-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (gamma-Proteobacteria) possess similar plasmid-encoded arsC sequences.

Conclusion: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

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Phylogenetic tree based on 16S rRNA gene sequences.The tree was constructed by neighbor joining methods using 1326 informative positions. Numbers represent percentages of 1000 bootstraps and are only shown for bootstrap values <80%. The names of the major divisions of prokaryotes represented are shown to the right of corresponding clades.
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Figure 1: Phylogenetic tree based on 16S rRNA gene sequences.The tree was constructed by neighbor joining methods using 1326 informative positions. Numbers represent percentages of 1000 bootstraps and are only shown for bootstrap values <80%. The names of the major divisions of prokaryotes represented are shown to the right of corresponding clades.

Mentions: The 16S rRNA based phylogenetic tree (Figure 1) generally matched the accepted 16S rRNA model with clear separation of the two prokaryotic domains and the subsequent divergence of Eukarya (represented by Saccharomyces cerevisiae) from Archaea [31]. Minor inconsistencies such as Ralstonia solanacearum (β-Proteobacteria) forming a deep branch within the γ-Proteobacteria, or Fusobacterium nucleatum (Fusobacteria) and Leptospira interrogans (Spirochetes) grouping loosely with the Gram-positive Bacteria are likely the result of the limited data set used (they were the only representatives of their respective phyla that had listed arsC genes) and do not challenge established relationships. Otherwise the major divisions and subdivisions of the Bacteria (e.g. the various Proteobacteria, Low GC Gram-positives, Actinobacteria) formed expected patterns. An interesting finding was the grouping (albeit weak) of Nostoc muscorum and Synechosystis sp. with Deinococcus radiodurans to form a high level clade (Figure 1). This is similar to findings from genome trees that suggest a close relationship between the Cyanobacteria and Deinococcales [32], although our 16S rRNA tree does not suggest a relationship between these taxa and the Actinobacteria. However, the Actinobacteria (High GC Gram-positives) did clearly separate from the Low GC Gram-positive Bacteria (Figure 1).


Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.

Jackson CR, Dugas SL - BMC Evol. Biol. (2003)

Phylogenetic tree based on 16S rRNA gene sequences.The tree was constructed by neighbor joining methods using 1326 informative positions. Numbers represent percentages of 1000 bootstraps and are only shown for bootstrap values <80%. The names of the major divisions of prokaryotes represented are shown to the right of corresponding clades.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC183826&req=5

Figure 1: Phylogenetic tree based on 16S rRNA gene sequences.The tree was constructed by neighbor joining methods using 1326 informative positions. Numbers represent percentages of 1000 bootstraps and are only shown for bootstrap values <80%. The names of the major divisions of prokaryotes represented are shown to the right of corresponding clades.
Mentions: The 16S rRNA based phylogenetic tree (Figure 1) generally matched the accepted 16S rRNA model with clear separation of the two prokaryotic domains and the subsequent divergence of Eukarya (represented by Saccharomyces cerevisiae) from Archaea [31]. Minor inconsistencies such as Ralstonia solanacearum (β-Proteobacteria) forming a deep branch within the γ-Proteobacteria, or Fusobacterium nucleatum (Fusobacteria) and Leptospira interrogans (Spirochetes) grouping loosely with the Gram-positive Bacteria are likely the result of the limited data set used (they were the only representatives of their respective phyla that had listed arsC genes) and do not challenge established relationships. Otherwise the major divisions and subdivisions of the Bacteria (e.g. the various Proteobacteria, Low GC Gram-positives, Actinobacteria) formed expected patterns. An interesting finding was the grouping (albeit weak) of Nostoc muscorum and Synechosystis sp. with Deinococcus radiodurans to form a high level clade (Figure 1). This is similar to findings from genome trees that suggest a close relationship between the Cyanobacteria and Deinococcales [32], although our 16S rRNA tree does not suggest a relationship between these taxa and the Actinobacteria. However, the Actinobacteria (High GC Gram-positives) did clearly separate from the Low GC Gram-positive Bacteria (Figure 1).

Bottom Line: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today.Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution.Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, SLU 10736, Southeastern Louisiana University, Hammond, LA 70402, USA. cjackson@selu.edu

ABSTRACT

Background: The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects.

Results: Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the gamma-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (gamma-Proteobacteria) possess similar plasmid-encoded arsC sequences.

Conclusion: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

Show MeSH
Related in: MedlinePlus