Enzyme phylogenies as markers for the oxidation state of the environment: the case of respiratory arsenate reductase and related enzymes.
BACKGROUND
Phylogenies of certain bioenergetic enzymes have proved to be useful tools for deducing evolutionary ancestry of bioenergetic pathways and their relationship to geochemical parameters of the environment. Our previous phylogenetic analysis of arsenite oxidase, the molybdopterin enzyme responsible for the biological oxidation of arsenite to arsenate, indicated its probable emergence prior to the Archaea/Bacteria split more than 3 billion years ago, in line with the geochemical fact that arsenite was present in biological habitats on the early Earth. Respiratory arsenate reductase (Arr), another molybdopterin enzyme involved in microbial arsenic metabolism, serves as terminal oxidase, and is thus situated at the opposite end of bioenergetic electron transfer chains as compared to arsenite oxidase. The evolutionary history of the Arr-enzyme has not been studied in detail so far.


RESULTS
We performed a genomic search of genes related to arrA coding for the molybdopterin subunit. The multiple alignment of the retrieved sequences served to reconstruct a neighbor-joining phylogeny of Arr and closely related enzymes. Our analysis confirmed the previously proposed proximity of Arr to the cluster of polysulfide/thiosulfate reductases but also unravels a hitherto unrecognized clade even more closely related to Arr. The obtained phylogeny strongly suggests that Arr originated after the Bacteria/Archaea divergence in the domain Bacteria, and was subsequently laterally distributed within this domain. It further more indicates that, as a result of accumulation of arsenate in the environment, an enzyme related to polysulfide reductase and not to arsenite oxidase has evolved into Arr.


CONCLUSIONS
These findings are paleogeochemically rationalized by the fact that the accumulation of arsenate over arsenite required the increase in oxidation state of the environment brought about by oxygenic photosynthesis.
Duval
Simon
S
Laboratoire de Bioénergétique et Ingénierie des Protéines UPR 9036, Institut de Biologie Structurale et Microbiologie, CNRS, F-13402 Marseille Cedex 20, France. duval@ibsm.cnrs-mrs.fr
Ducluzeau
Anne-Lise
AL
Nitschke
Wolfgang
W
Schoepp-Cothenet
Barbara
B
D000595:Amino Acid Sequence; D053502:Arsenate Reductases / Q000235:genetics*; D003067:Coenzymes / Q000235:genetics*; D004777:Environment; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D007506:Iron-Sulfur Proteins / Q000235:genetics; D008667:Metalloproteins / Q000235:genetics*; D008969:Molecular Sequence Data; D000090006:Molybdenum Cofactors; D005810:Multigene Family; D016366:Open Reading Frames; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D011621:Pteridines; D012486:Salmonella typhimurium / Q000201:enzymology / Q000235:genetics; D020539:Sequence Analysis, Protein; D020592:Shewanella / Q000201:enzymology / Q000235:genetics; D016968:Wolinella / Q000201:enzymology / Q000235:genetics
D053502:Arsenate Reductases; D003067:Coenzymes; D007506:Iron-Sulfur Proteins; D008667:Metalloproteins; D000090006:Molybdenum Cofactors; D010088:Oxidoreductases; D011621:Pteridines; C022261:molybdopterin; C078179:arsenite oxidase; C045664:dimethyl sulfoxide reductase