title: Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.
abstract: We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.
authors.affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92039, USA.
authors.forename: C L
authors.initials: CL
authors.lastname: Dupont
authors.forename: K
authors.initials: K
authors.lastname: Neupane
authors.forename: J
authors.initials: J
authors.lastname: Shearer
authors.forename: B
authors.initials: B
authors.lastname: Palenik
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D008386:Marine Biology; D008969:Molecular Sequence Data; D009532:Nickel / Q000737:chemistry / Q000378:metabolism*; D013302:Streptomyces / Q000201:enzymology* / Q000235:genetics; D040681:Structural Homology, Protein; D013482:Superoxide Dismutase / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism
chemical_list: D009532:Nickel; D013482:Superoxide Dismutase