title: Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.
abstract: The restriction-modification systems use epigenetic modification to distinguish between self and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily with half-pipe fold has DNA glycosylase activity that excises an adenine base in the recognition sequence (5'-GTAC). We now found a second activity in this enzyme: at the resulting apurinic/apyrimidinic (AP) (abasic) site (5'-GT#C, # = AP), its AP lyase activity generates an atypical strand break. Although the lyase activity is weak and lacks sequence specificity, its covalent DNA-R.PabI reaction intermediates can be trapped by NaBH4 reduction. The base excision is not coupled with the strand breakage and yet causes restriction because the restriction enzyme action can impair transformation ability of unmethylated DNA even in the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation of the target adenine base. These findings expand our understanding of genetic and epigenetic processes linking those in prokaryotes and eukaryotes.
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Fukuyo
authors.affiliation: Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Nakano
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Yingbiao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Furuta
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Ishikawa
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Miki
authors.initials: M
authors.lastname: Watanabe-Matsui
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Yano
authors.affiliation: Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Hamakawa
authors.affiliation: Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ide
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan ikobaya@ims.u-tokyo.ac.jp.
authors.forename: Ichizo
authors.initials: I
authors.lastname: Kobayashi
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004249:DNA Damage; D045647:DNA Glycosylases / Q000378:metabolism; D004260:DNA Repair; D004262:DNA Restriction Enzymes / Q000378:metabolism; D015280:DNA Restriction-Modification Enzymes / Q000378:metabolism*; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D008780:Methyltransferases / Q000378:metabolism; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D043903:Pyrococcus abyssi / Q000201:enzymology; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D015280:DNA Restriction-Modification Enzymes; D009841:Oligonucleotides; D004247:DNA; D008780:Methyltransferases; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); D004262:DNA Restriction Enzymes; D045647:DNA Glycosylases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase