Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities

Masaki Fukuyo, Toshiaki Nakano, Yingbiao Zhang, Yoshikazu Furuta, Ken Ishikawa, Miki Watanabe-Matsui, Hirokazu Yano, Takeshi Hamakawa, Hiroshi Ide, Ichizo Kobayashi

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2841-2852
Number of pages12
JournalNucleic acids research
Volume43
Issue number5
DOIs
Publication statusPublished - 2015 Mar 11

ASJC Scopus subject areas

  • Genetics

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    Fukuyo, M., Nakano, T., Zhang, Y., Furuta, Y., Ishikawa, K., Watanabe-Matsui, M., Yano, H., Hamakawa, T., Ide, H., & Kobayashi, I. (2015). Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities. Nucleic acids research, 43(5), 2841-2852. https://doi.org/10.1093/nar/gkv116