title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins.
abstract: SET and RING-finger-associated (SRA) domain is involved in establishment and maintenance of DNA methylation in eukaryotes. Proteins containing SRA domains exist in mammals, plants, even microorganisms. It has been established that mammalian SRA domain recognizes 5-methylcytosine (5mC) through a base-flipping mechanism. Here, we identified and characterized two SRA domain-containing proteins with the common domain architecture of N-terminal SRA domain and C-terminal HNH nuclease domain, Sco5333 from Streptomyces coelicolor and Tbis1 from Thermobispora bispora. Both sco5333 and tbis1 cannot establish in methylated Escherichia coli hosts (dcm(+)), and this in vivo toxicity requires both SRA and HNH domain. Purified Sco5333 and Tbis1 displayed weak DNA cleavage activity in the presence of Mg(2+), Mn(2+) and Co(2+) and the cleavage activity was suppressed by Zn(2+). Both Sco5333 and Tbis1 bind to 5mC-containing DNA in all sequence contexts and have at least a preference of 100 folds in binding affinity for methylated DNA over non-methylated one. We suggest that linkage of methyl-specific SRA domain and weakly active HNH domain may represent a universal mechanism in competing alien methylated DNA but to maximum extent minimizing damage to its own chromosome.
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
authors.forename: Tiesheng
authors.initials: T
authors.lastname: Han
authors.affiliation: New England BioLabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Megumu
authors.initials: M
authors.lastname: Yamada-Mabuchi
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
authors.forename: Gong
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Engineering Research Center of Industrial Microbiology (Ministry of Education), College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, China.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
authors.forename: Guang
authors.initials: G
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Ou
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.affiliation: New England BioLabs, Inc., 240 County Road, Ipswich, MA 01938, USA xyhe@sjtu.edu.cn.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China xyhe@sjtu.edu.cn.
authors.forename: Xinyi
authors.initials: X
authors.lastname: He
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism*; D000192:Actinomycetales; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D002413:Cations, Divalent; D053837:DNA Cleavage; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D048372:Streptomyces coelicolor
chemical_list: D001426:Bacterial Proteins; D002413:Cations, Divalent; D004268:DNA-Binding Proteins; D044503:5-Methylcytosine; D004706:Endodeoxyribonucleases