Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase

Antimicrob Agents Chemother. 2013 Aug;57(8):4019-26. doi: 10.1128/AAC.00448-13. Epub 2013 Jun 10.


The cfr gene encodes the Cfr methyltransferase that primarily methylates C-8 in A2503 of 23S rRNA in the peptidyl transferase region of bacterial ribosomes. The methylation provides resistance to six classes of antibiotics of clinical and veterinary importance. The rlmN gene encodes the RlmN methyltransferase that methylates C-2 in A2503 in 23S rRNA and A37 in tRNA, but RlmN does not significantly influence antibiotic resistance. The enzymes are homologous and use the same mechanism involving radical S-adenosyl methionine to methylate RNA via an intermediate involving a methylated cysteine in the enzyme and a transient cross-linking to the RNA, but they differ in which carbon atom in the adenine they methylate. Comparative sequence analysis identifies differentially conserved residues that indicate functional sequence divergence between the two classes of Cfr- and RlmN-like sequences. The differentiation between the two classes is supported by previous and new experimental evidence from antibiotic resistance, primer extensions, and mass spectrometry. Finally, evolutionary aspects of the distribution of Cfr- and RlmN-like enzymes are discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Consensus Sequence
  • Databases, Protein
  • Drug Resistance, Bacterial / genetics*
  • Drug Resistance, Microbial / genetics
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Genes, Bacterial
  • Genetic Variation
  • Methylation
  • Methyltransferases / genetics
  • Methyltransferases / metabolism*
  • Microbial Sensitivity Tests
  • Molecular Sequence Data
  • Phylogeny
  • Plasmids / genetics
  • Plasmids / metabolism
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal, 23S / genetics
  • RNA, Ribosomal, 23S / metabolism
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Staphylococcus / enzymology
  • Staphylococcus / genetics


  • Bacterial Proteins
  • CFR protein, Staphylococcus sciuri
  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Ribosomal, 23S
  • Methyltransferases
  • RlmN protein, E coli