Characterization of paralogous and orthologous members of the superoxide dismutase gene family from genera of the halophilic archaebacteria

Abstract

Four species representing three genera of halophilic archaebacteria were examined for the presence of genomic sequences that encode proteins of the superoxide dismutase family. Three species, Halobaterium cutirubrum, Halobacterium sp. strain GRB, and Haloferax volcanii, contain duplicated (paralogous) genes of the sod family; a fourth species, Haloarcula marismortui, contains only a single gene. These seven genes were cloned and sequenced, and their transcripts were characterized by Northern (RNA) hybridization, S1 nuclease protection, and primer extension. The expression of one of the two genes in H. cutirubrum, Halobacterium sp. strain GRB, and Haloferax volcanii was shown to be elevated in the presence of paraquat, a generator of superoxide radicals. The other genes, including the single gene from Haloarcula marismortui, exhibited no elevated expression in the presence of paraquat. The 5' and 3' flanking regions of all the genes contain recognizable promoter and terminator elements that are appropriately positioned relative to the 5' and 3' transcript end sites. Between genera, the orthologous paraquat-responsive genes exhibit no sequence similarity in either their 5' or 3' flanking regions, whereas the orthologous nonresponsive genes exhibit limited sequence similarity but only in the 5' flanking region. Within the coding region, the two paralogous genes of Haloferax volcanii are virtually identical (99.5%) despite the absence of similarity in the flanking regions. In contrast, the paralogous genes of H. cutirubrum and Halobacterium sp. strain GRB are only about 87% identical. In the alignment of all seven sequences, there are nine codon positions where both the TCN and AGY serine codons are utilized; some or all of these may well be examples of convergent evolution.Evolution is driven by a plethora of molecular processes. For example, genome expansion occurs by duplication of genes or sequences; random mutational processes introduce variability into these sequences which ultimately lead either to fixation and diversification or to elimination. Two homologous genes are paralogous if they are derived from a duplication event and orthologous if they are derived from a speciation event. Homologous sequences (both orthologous and paralogous) can also participate in recombination and/or gene conversion events which have the effect of maintaining homogeneity and minimizing apparent divergence. From a mechanistic point of view, charting the evolutionary diversification of paralogous and orthologous members of a gene family within a closely related group of organisms should be an informative process to visualize. For this purpose, the superoxide dismutase (SOD) family of genes from four species representing three genera of halophilic archaebacteria have been characterized and compared.Halophilic archaebacteria are a group of aerobic or microaerobic organisms that evolved from a strictly anaerobic and nonhalophilic methanogen ancestor (39). The adaptation to high-salt environments was achieved by raising the intracel...

Structure, function, and evolution of the family of superoxide dismutase proteins from halophilic archaebacteria

“…The consensus derived from these phylogenetic analyses is illustrated in Fig. 4 (7,25). This finding suggests that the halophilic ancestor may also have had only a single sod gene in its genome.…”

“…SOD activity has been detected in at least two representatives of the ancestral methanogen group and in numerous halophilic species (7,10,25). The SOD enzyme from both Halobacterium cutirubrum and its immediate relative, H. halobium, has been purified and extensively characterized; the enzyme contains Mn as a metal ion cofactor and is related to the Mnor Fe-type enzymes of eubacteria (13,19).…”

“…Halophilic archaebacteria are a collection of related organisms that evolved from an anaerobic methanogen ancestor and that now grow in nature either aerobically or microaerobically in high-salt environments (7,27). SOD activity has been detected in at least two representatives of the ancestral methanogen group and in numerous halophilic species (7,10,25).…”

Comparative genomic analysis of the Haloferax volcanii DS2 and Halobacterium salinarium GRB contig maps reveals extensive rearrangement

“…Ten of these 22 probes gave multiple signals in both genomes. We do not know the nature of the repeated sequences; they may represent gene families as have been documented for the haloarchaea (1,17,21,23,41), insertion sequences (especially in the plasmids [7] though of uncharacterized types [14]), or other repeat sequence structures (34).…”

A change of the metal-specific activity of a cambialistic superoxide dismutase from Porphyromonas gingivalis by a double mutation of Gln-70 to Gly and Ala-142 to Gln

“…The third difference is that Tyr-77 in FeSODs is changed to phenylalanine in Mn-SODs [9][10][11][12][13]. Although a few exceptions have been reported [17,18], these three differences could be the primary candidates to account for the metal specificity of the Fe-and Mn-SOD activity [19], improving on the suggestions by Parker and Blake [20] and Yamakura et al [21]. Recently, Yamano and Maruyama [22] reported that the substitution of Tyr-77 by Phe in the metal-specific Fe-SOD from Sulfolobus solfataricus did not change the metal-specific activity of the enzyme.…”