Excision of the doubly methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins

Philos Trans R Soc Lond B Biol Sci. 2018 Jun 5;373(1748):20170337. doi: 10.1098/rstb.2017.0337.


Cytosine (C) in DNA is often modified to 5-methylcytosine (m5C) to execute important cellular functions. Despite the significance of m5C for epigenetic regulation in mammals, damage to m5C has received little attention. For instance, almost no studies exist on erroneous methylation of m5C by alkylating agents to doubly or triply methylated bases. Owing to chemical evidence, and because many prokaryotes express methyltransferases able to convert m5C into N4,5-dimethylcytosine (m N4,5C) in DNA, m N4,5C is probably present in vivo We screened a series of glycosylases from prokaryotic to human and found significant DNA incision activity of the Escherichia coli Nei and Fpg proteins at m N4,5C residues in vitro The activity of Nei was highest opposite cognate guanine followed by adenine, thymine (T) and C. Fpg-complemented Nei by exhibiting the highest activity opposite C followed by lower activity opposite T. To our knowledge, this is the first description of a repair enzyme activity at a further methylated m5C in DNA, as well as the first alkylated base allocated as a Nei or Fpg substrate. Based on our observed high sensitivity to nuclease S1 digestion, we suggest that m N4,5C occurs as a disturbing lesion in DNA and that Nei may serve as a major DNA glycosylase in E. coli to initiate its repair.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.

Keywords: 5-methylcytosine methylation damage; DNA base excision repair; N4,5-dimethylcytosine; epigenetics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / metabolism*
  • Cytosine / analogs & derivatives*
  • Cytosine / metabolism
  • DNA-Formamidopyrimidine Glycosylase / genetics*
  • DNA-Formamidopyrimidine Glycosylase / metabolism
  • Deoxyribonuclease (Pyrimidine Dimer) / genetics*
  • Deoxyribonuclease (Pyrimidine Dimer) / metabolism
  • Epigenesis, Genetic*
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Humans
  • Methylation


  • Escherichia coli Proteins
  • N4,5-dimethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • Deoxyribonuclease (Pyrimidine Dimer)
  • Nei protein, E coli
  • DNA-Formamidopyrimidine Glycosylase
  • DNA-formamidopyrimidine glycosylase, E coli

Associated data

  • figshare/0.6084/m9.figshare.c.4024486