title: In silico analysis of nickel containing superoxide dismutase evolution and regulation.
abstract: Superoxide dismutases are essential enzymes involved in detoxification of reactive oxygen by dismutation of the superoxide radical anion. A class of nickel containing superoxide dismutases has been described for streptomycetes and cyanobacteria. In silico analysis was used to study the distribution of genes coding for NiSOD in other taxa and to elucidate signals linked to nickel incorporation and maturation of NiSOD. Data mining revealed homologous proteins from actinobacteria, proteobacteria, chlamydiae, and eukarya (green algae) thus allowing a comparison of protein structural elements. Nickel ligands and maturation signals for N-terminal proteolysis were highly conserved. Genomic sequences surrounding genes encoding NiSOD homologs were compared in order to detect putative accessory enzymes involved in maturation. An endopeptidase gene linked to sodN coding for NiSOD was found in actinobacteria and cyanobacteria, but not in other taxa. The distribution of NiSOD encoding sequences showed four clusters which are not consistent with the phylogeny of the species. In addition, the different genomic context argues for heterologous gene transfer, most likely from actinobacteria to other taxa. In order to address regulation by nickel availability and incorporation into the mature protein, we present first evidence for putative regulatory nucleotide sequences which will be useful in future studies on nickel uptake and incorporation.
authors.affiliation: Microbial Phytopathology, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich-Schiller-University, Jena, Germany.
authors.forename: Astrid
authors.initials: A
authors.lastname: Schmidt
authors.forename: Matthias
authors.initials: M
authors.lastname: Gube
authors.forename: André
authors.initials: A
authors.lastname: Schmidt
authors.forename: Erika
authors.initials: E
authors.lastname: Kothe
mesh_terms: D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D000460:Chlorophyta / Q000201:enzymology / Q000235:genetics; D017124:Conserved Sequence; D019143:Evolution, Molecular; D009532:Nickel / Q000378:metabolism*; D010802:Phylogeny; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013482:Superoxide Dismutase / Q000235:genetics / Q000378:metabolism*
chemical_list: D009532:Nickel; D013482:Superoxide Dismutase