Restriction glycosylases: involvement of endonuclease activities in the restriction process.
All restriction enzymes examined are phosphodiesterases generating 3΄-OH and 5΄-P ends, but one restriction enzyme (restriction glycosylase) excises unmethylated bases from its recognition sequence. Whether its restriction activity involves endonucleolytic cleavage remains unclear. One report on this enzyme, R.PabI from a hyperthermophile, ascribed the breakage to high temperature while another showed its weak AP lyase activity generates atypical ends. Here, we addressed this issue in mesophiles. We purified R.PabI homologs from Campylobacter coli (R.CcoLI) and Helicobacter pylori (R.HpyAXII) and demonstrated their DNA cleavage, DNA glycosylase and AP lyase activities in vitro at 37°C. The AP lyase activity is more coupled with glycosylase activity in R.CcoLI than in R.PabI. R.CcoLI/R.PabI expression caused restriction of incoming bacteriophage/plasmid DNA and endogenous chromosomal DNA within Escherichia coli at 37°C. The R.PabI-mediated restriction was promoted by AP endonuclease action in vivo or in vitro. These results reveal the role of endonucleolytic DNA cleavage in restriction and yet point to diversity among the endonucleases. The cleaved ends are difficult to repair in vivo, which may indicate their biological significance. These results support generalization of the concept of restriction–modification system to the concept of self-recognizing epigenetic system, which combines any epigenetic labeling and any DNA damaging.
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Yingbiao
Y
Zhang
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima, Japan.
Tomoyuki
T
Matsuzaka
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.|Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.|Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
Hirokazu
H
Yano
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.|Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.
Yoshikazu
Y
Furuta
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima, Japan.
Toshiaki
T
Nakano
National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
Ken
K
Ishikawa
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.
Masaki
M
Fukuyo
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.|Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.
Noriko
N
Takahashi
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Yutaka
Y
Suzuki
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
Sumio
S
Sugano
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima, Japan.
Hiroshi
H
Ide
Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.|Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.|Graduate School of Life Sciences, Tohoku University, Sendai, Japan.|Faculty of Medicine, Kyorin University, Mitaka, Tokyo, Japan.|Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.|Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
Ichizo
I
Kobayashi
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D017000:Campylobacter coli / Q000235:genetics / Q000378:metabolism; D045647:DNA Glycosylases / Q000235:genetics / Q000378:metabolism*; D004260:DNA Repair; D004262:DNA Restriction Enzymes / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D004262:DNA Restriction Enzymes; D045647:DNA Glycosylases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase