Roles of restriction-modification gene complexes in generation of genome diversity in bacteria

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A. Experimental analyses of genome dynamics.(A-1) Multiplication of a restriction-modification gene complex.Here we found amplification of a restriction-modification gene complex. BamHI gene complex inserted into Bacillus chromosome showed resistance to replacement by a homologous stretch of DNA. The multiplication takes place in a bacterium with natural capacity for DNA release, uptake and transformation and might contribute to spreading of RM gene complexes in a virus like life cycle.(A-2) Intragenomic movement of a restriction-modification gene complex.We detected movement of a restriction-modification gene complex within a cell when attempts were made to eliminate it from the cell. From sequence determination of these products, we discussed mechanisms of the underlying cooperation between restriction-modification gene complexes, IS and host homologous recombination functions.(A-3) Defense of genomes against attack by restriction-modification systems.We demonstrated that host attack … More by EcoRII restriction-modification gene complex can be counteracted by Dcm solitary methyltransferase. We also found that site-specific recombination machinery in the chromosome can defend the genome against attack by a restriction-modification system.B. Comparison and informatic analysis of closely related bacterial genomes.(B-1) Staphylococcus aureus.We compared genome sequences of two strains of S. aureus. We listed medium-sized genome polymorphisms and inferred mechanisms of their formation. We identified restriction-modification gene homologues in S. hominis.(B-2) Neisseria.We compared genomes sequences of two strains of N. meningitides and one strain of N. gonorhoeae and identified genome rearrangement mechanisms related to IS and restriction-modification gene complexes.(B-3) Development of tools for genome comparison.We developed a tool for comparison of closely-related genomes.C. A new nomenclature for restriction modification enzymes and their genes.We proposed a new system of nomenclature of restriction enzymes methyltransferases and their genes based on their biological diversity. Less