Novel m4C modification in type I restriction-modification systems

Nucleic Acids Res. 2016 Nov 2;44(19):9413-9425. doi: 10.1093/nar/gkw743. Epub 2016 Aug 31.


We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized Type I systems use two identical copies of a single methyltransferase (MTase) subunit, with one bound at each half site of the specificity (S) subunit to form the MTase. The new m4C-producing Type I systems we describe have two separate yet highly similar MTase subunits that form a heterodimeric M1M2S MTase. The MTase subunits from these systems group into two families, one of which has NPPF in the highly conserved catalytic motif IV and modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying cytosine to m4C. The high degree of similarity among their cytosine-recognizing components (MTase and S) suggest they have recently evolved, most likely from the far more common m6A Type I systems. Type I enzymes that modify cytosine exclusively were formed by replacing the adenine target recognition domain (TRD) with a cytosine-recognizing TRD. These are the first examples of m4C modification in Type I RM systems.

MeSH terms

  • Adenine / metabolism
  • Amino Acid Sequence
  • Catalysis
  • Computational Biology / methods
  • Cytosine / metabolism*
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Restriction-Modification Enzymes / chemistry
  • DNA Restriction-Modification Enzymes / genetics
  • DNA Restriction-Modification Enzymes / metabolism*
  • Methylation
  • Methyltransferases / chemistry
  • Methyltransferases / metabolism
  • Mutation
  • Nucleotide Motifs
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Substrate Specificity


  • DNA Restriction-Modification Enzymes
  • Protein Subunits
  • Cytosine
  • DNA
  • Methyltransferases
  • Adenine