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

限制性修饰基因复合物在细菌基因组多样性产生中的作用

• 批准号: 12470034
• 负责人: KOBAYASHI Ichizo
• 金额: $ 9.22万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2000
• 资助国家: 日本
• 起止时间: 2000 至 2002
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-12470034/
• 关键词: pathogenic bacteria; bacterial genomes; genome polymorphism; genome instability; genome evolution; genome comparison; pathogenicity; toxin; ゲノム生物学; バイオテクノロジー; ゲノム内コンフリクト; システム・バイオロジー; 制限酵素; ゲノム再編; 病原菌; ピロリ菌; 極限環境微生物; バイオインフォーマティクス

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

A.基因组动力学实验分析。（a -1）限制性修饰基因复合体的增殖。在这里，我们发现了限制性修饰基因复合物的扩增。插入到芽孢杆菌染色体上的BamHI基因复合物显示出对同源DNA片段替代的抗性。这种增殖发生在具有天然DNA释放、吸收和转化能力的细菌中，可能有助于RM基因复合物在病毒样生命周期中的传播。（a -2）限制性修饰基因复合物的基因组内运动。当试图从细胞中清除限制性修饰基因复合体时，我们检测到它在细胞内的运动。从这些产物的序列测定中，我们讨论了限制性修饰基因复合物、IS和宿主同源重组功能之间潜在的合作机制。（A-3）保护基因组免受限制性修饰系统的攻击。我们发现EcoRII限制性修饰基因复合物对宿主的攻击可以被Dcm单独甲基转移酶抵消。我们还发现染色体上的位点特异性重组机制可以保护基因组免受限制性修饰系统的攻击。近缘细菌基因组比较与信息学分析。（B-1）金黄色葡萄球菌。我们比较了两株金黄色葡萄球菌的基因组序列。我们列出了中型基因组多态性，并推断了它们的形成机制。我们在人链球菌中鉴定了限制性修饰基因同源物。奈瑟氏菌属(b - 2)。我们比较了两株脑膜炎奈瑟菌和一株淋病奈瑟菌的基因组序列，确定了与IS和限制性修饰基因复合物相关的基因组重排机制。（B-3）基因组比较工具的开发。我们开发了一种比较近亲基因组的工具。限制性内切修饰酶及其基因的新命名。基于限制性内切酶、甲基转移酶及其基因的生物多样性，提出了一种新的命名体系。少

项目成果

小林一三: "ゲノム比較:ゲノムつくり換えていた制限酵素修飾酵素遺伝子"蛋白質核酸酵素、臨時増刊号「ゲノムサイエンスの新たなる挑戦」. 46. 2393-2399 (2001)

小林一三：“基因组比较：重建基因组的限制性酶修饰酶基因”，蛋白质核酸酶，特刊“基因组科学的新挑战”46。2393-2399（2001）

An Escherichia coli strain, BJ5183, that shows highly efficient conservative (two-progeny) DNA double-strand break repair of restriction breaks

大肠杆菌菌株 BJ5183，显示出对限制性断裂的高效保守（双子代）DNA 双链断裂修复

• 发表时间: 2003
• 期刊: Gene 303
• 作者: A.Ino;I.Kobayashi;A.Ino;I.Kobayashi;K.Kusano;N.Handa;Y.Katayama;R.J.Roberts;M.Sadykov;I.Kobayashi;N.Takahashi
• 通讯作者: N.Takahashi

A mechanism for restriction-modification-mediated gene mobility suggested from comparison of two complete bacterial genomes

两个完整细菌基因组的比较表明限制性修饰介导的基因迁移机制

• 发表时间: 2000
• 期刊: Gene 259
• 作者: A.Ino;I.Kobayashi;A.Ino;I.Kobayashi;K.Kusano;N.Handa;Y.Katayama;R.J.Roberts;M.Sadykov;I.Kobayashi;N.Takahashi;N.Handa;Y.Katayama;M.Sadykov;I.Kobayashi;N.Takahashi;A.Ino;N.Takahashi;I.Kobayashi;M.Kuroda;N.Handa;N.Handa;A.Chinen;A.Nobusato
• 通讯作者: A.Nobusato

Takami, H., Takaki, Y., Uchiyama, I.: "Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments"Nucleic Acids Res.. 30. 3927-3935 (2002)

Takami, H.、Takaki, Y.、Uchiyama, I.：“从 Iheya Ridge 分离的 Oceanobacillus iheyensis 的基因组序列及其对极端环境的意外适应能力”Nucleic Acids Res.. 30. 3927-3935 (2002)

Y.Fujitani: "A reaction-diffusion model for interference in meiotic crossing-over"Genetics. (in press).

Y.Fujitani：“减数分裂交叉干扰的反应扩散模型”遗传学。