title: Movement of DNA sequence recognition domains between non-orthologous proteins.
abstract: Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.
authors: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
authors: Yoshikazu
authors: Y
authors: Furuta
authors: Ichizo
authors: I
authors: Kobayashi
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D015254:DNA Modification Methylases / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D015280:DNA Restriction-Modification Enzymes / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D056426:Genetic Loci; D014644:Genetic Variation; D016680:Genome, Bacterial; D016998:Helicobacter / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics*; D059765:Homologous Recombination; D008969:Molecular Sequence Data; D010802:Phylogeny; D054730:Protein Interaction Domains and Motifs; D016415:Sequence Alignment; D048373:Treponema denticola / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004268:DNA-Binding Proteins; D015254:DNA Modification Methylases