The superoxide dismutase gene family in the halobacteria : structure, expression and evolution
Creators: name: Joshi, Phalgun B.
Publisher: name: University of British Columbia
Year: 2008

description: The halophilic archaebacteria belong to a group of closely related organisms that evolved from the methanogens. Since the methanogens are strict anaerobes, the divergence of the aerobichalophiles from this lineage may have required the acquisition of protection against oxygen toxicity; a number of reactions involving oxygen produce highly reactive free-radical by-products. An example of such by-products is the superoxide radical, 02-. Most aerobic organisms possess the enzyme superoxide dismutase (SOD) to protect against this free radical. It has previously been shown that the halophile, Halobacterium cutirubrum possesses a type of SOD that contains manganese. The genome of this organism contains two closely related genes; one that encodes the SOD enzyme, designated sod, and another sod-like gene designated slg. The two genes are 87% identical and their putative proteins are 83% identical. For most genes that are homologous, the DNA sequence identity initially decreases more rapidly than the corresponding amino acid sequence identity of the proteins they encode. The disparity in the identities between the sod and slg genes and between their corresponding proteins can be attributed to the almost even distribution of substitutions between the three codon positions. This pattern of substitutions results in a high incidence of non-synonymous nucleotide substitutions. The two genes also differ in their response to exposure to paraquat, a generator of superoxide free radicals; mRNA levels from the sod gene were seen to be elevated whereas those from slg were unaffected. To investigate whether other halophiles contain similar paralogous genes (i.e., products of gene duplication in an organism) and whether they exhibit similar patterns of evolutionary divergence and gene expression, sod genes from three different halophiles were isolated and characterized. The number of copies of genes homologous to sod from Hb.cutirubrum varies from one in Haloarcula marismortui to two in Halobacterium sp. GRB and Haloferax volcanii. The pattern of substitutions between the paralogous genes in Hb. sp. GRB (sod and slg) is almost identical to that observed between the sod and slggenes in Hb. cutirubrum. In contrast, the sod1 and sod2 genes in Hf.volcanii are 99% identical. Comparison of the nucleotide sequences reveals that all the genes are related (identities vary from 76% to 99%) and form a coherent family. Within the entire family, substitutions in the first and second positions are much more frequent than expected; this results in a large number of amino acid substitutions in the encoded protein. Both Hb. sp. GRB and Hf volcanii contain one gene each that is induced by paraquat and one that is unaffected. The single sod gene in Ha. Maris mortui is unaffected by paraquat treatment. Comparison of the protein sequences encoded by the superoxide dismutase gene family in the halobacteria with sequences from other organisms has enabled the identification of halobacterial-specific residues. Phylogenetic analyses were performed to determine the evolutionary relationship between the members of the sod gene family in the halobacteria. Results from these analyses together with the comparison of upstream flanking sequences and response to paraquat have enabled the postulation of possible evolutionary histories of the genes.