Studies On DNA Repair Related Genes And The Genome Of Deinococcus Radiodurans By Evolutionary Bioinformatics

Studies in a variety of species have identified many DNA repair pathways. The evolutionary perspective is useful in comparative study because of allowing a focus on how differences arose rather than the simple identification of differences. In this paper, we present a comparative analysis of DNA repair proteins and processes based upon the analysis of available database sequences. Detailed evolutionary studies for the genes such as recX and mutT/nudix involved in DNA repair has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of DNA repair. For studies of DNA repair, we believe that an evolutionary perspective is the important way to understanding differences in repair between species, as well as the mechanisms of repair processes. Deinococcus radiodurans is one of the most radiation-resistant organisms described to date. Researches on DNA damage and repair pathways of D. radiodurans show its extreme resistance to ionizing radiation, ultraviolet and reactive oxygen species. Complete genome sequences can provide potential sources of new information about DNA repair in different species. Comparison of different chromosomes in D. radiodurans and recent finished Deinococcus geothermalis is of use in understanding the origin and evolution of multi-chromosome in Deinococcus bacteria.RecX is a regulator of RecA activity by interacting with RecA protein or RecA filaments. In D. radiodurans, RecX not only down regulates recA transcription, but also directly inhibits RecA activities at protein level. DinI and RecX proteins constitute a regulatory network and work competitively as positive (DinI) and negative (RecX) modulators of RecA respectively. Genes encoding RecX were found in genomes of a wide diversity of bacteria and some plants (e.g.,Arabidopsis thaliana and Oryza sativa). The putative orthologues of RecX show only limited conservation among species. The distribution of RecX by searching microbial genomes database showed that the RecX presents in most bacterial species. And Rocha's recent work exhibited that orthologues of RecX were not found in several phyla of bacteria including Aquificae, Cyanobacteria, Chlamydiae, and some subdivisions of Proteobacteria and Firmicutes. Our comparative genome analysis showed that although members of the RecX family are found in many bacterial species, they are not found in archaea and the only gene found in eukaryotes is likely derived from bacteria genomes. It is therefore proposed that RecX is of bacterial origin, and the gene had presented in the common ancestor of bacteria. Moreover, bacterial RecX and plant RecX domain are homologues, and RecX domain in plants may have derived from bacteria via unknown pathways. Plant RecX-like protein was formed by a gene fusion event between a unique N-terminal domain of unknown origin and RecX domain within plant cells. The plant RecX domain was from a bacterial genome to plant. The recX and recA genes have been separated in sequences or even located in different chromosomes of plant nuclear genomes during RecX evolution. The interaction of RecA and RecX proteins appears to have not been conserved over long history of bacteria evolution. Three possible evolutionary pathways from bacteria to plant as well as functional evolution of the gene were also discussed in this paper. Evolutionary history of RecX might be a process involving gene loss, gene transfer, endosymbiosis, and gene fusion events.The superfamily of MutT proteins and Nudix hydrolases consists of widely distributed families of enzymes characterized by a shared motif: GX(5)EX(7) REUXEE. The MutT/Nudix enzymes repair DNA damage and play a role in human health and disease. Bacterial MutT protein is responsible for removing an oxidative damaged form of guanine from DNA and the nucleotide pool. In this paper, we examined three different double MutT/Nudix domain-containing proteins cases from eukaryotes and prokaryotes. First, these double domain proteins were discovered in both the melanogaster and the obscura groups of Drosophila, but only single Nudix domain proteins were found in other animals. The phylogenetic tree was constructed based on the protein sequence of Nudix1, Nudix2, and Nudix in other animals. The Nudix1 protein of Drosophila melanogaster and Drosophila pseudoobscura clearly separate them from the branch in which Nudix of other insects (e.g., mosquito and honeybee) and Nudix2 from D. melanogaster and D. pseudoobscura are grouped. The phylogenetic analysis suggested that the double Nudix domain proteins might have undergone an A-type gene duplication-fusion event. Second, two genes of the MutT family, DR0004 and DR0329, are fused by two mutT gene segments and form double MutT domain protein gene in Deinococcus radiodurans. Evolutionary tree of bacterial MutT proteins having significant bootstrap values revealed that the N-terminal MutT domains (DR0004a and DR0329a) and C-terminal ones (DR0004b and DR0329b) are grouped with 99% bootstrap value respectively, and then the two subtrees grouped with high bootstrap value indicating that the subtrees are highly related. This suggested that the double MutT domain proteins in D. radiodurans probably resulted from a B-type gene duplication-fusion event. Finally, the crystal structure 1VK6 (NADH pyrophosphatase from E. coli K12) and its sequence were examined. 1VK6 arose by fusion of two similar Nudix structures, although the N-terminal domain sequence shares little sequence similarity to the C-terminal one. We propose an ancient gene duplication-fusion model to explain this observation. Gene duplication-fusion is a basic and important gene innovation mechanism for the evolution of double MutT/Nudix domain proteins. Independent gene duplication-fusion events resulted in similar domain architectures of different double MutT/Nudix domain proteins. These findings have implications for our understanding of the nature of evolution after gene duplication followed by gene fusion events and may help to shed light on the evolution of novel functions by this process.Many bacterial species have a single circular chromosome. But the genome of D. radiodurans possesses a complex genome consisting of two circular chromosomes (DRCI and DRCII). Recent finished Deinococcus geothermalis genome holds two chromosomes (DGCI and DGCII) too. The comparative genomics study of D. radiodurans is important not just because of evolutionary perspective of DNA repair, but also because the evolution of multi-chromosome of bacteria provides useful information for understanding origin of chromosomes. Species of genus Deinococcus are resistant to agents that damage DNA, including ionizing radiation, ultraviolet and so on. Comparison of different chromosomes in D. radiodurans and recent finished D. geothermalis is of use in understanding the evolution of multi-chromosome process, and provides information about repair in Deinococcus bacteria. Our preliminary comparative study reveals that DRCI and DGCI share a common ancestor in genus Deinococcus. The result supports the former viewpoint that only chromosome I (DRCI) shares a common ancestry with the Thermus lineage (TTCI) and the smaller genetic elements may have been acquired separately. DRCI and DGCII share only 6% genes while DRCII and DGCI share only 6% genes too. However, our finding suggested DRCII and DGCII might have different origin because these two chromosomes share only 16% genes. We propose a putative evolutionary process of bacterial chromosomes in phylum Deinococcus-Thermus.