The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA

RNA. 2008 Jan;14(1):98-106. doi: 10.1261/rna.814408. Epub 2007 Nov 19.


A2503 in 23S rRNA of the gram-negative bacterium Escherichia coli is located in a functionally important region of the ribosome, at the entrance to the nascent peptide exit tunnel. In E. coli, and likely in other species, this adenosine residue is post-transcriptionally modified to m2A. The enzyme responsible for this modification was previously unknown. We identified E. coli protein YfgB, which belongs to the radical SAM enzyme superfamily, as the methyltransferase that modifies A2503 of 23S rRNA to m2A. Inactivation of the yfgB gene in E. coli led to the loss of modification at nucleotide A2503 of 23S rRNA as revealed by primer extension analysis and thin layer chromatography. The A2503 modification was restored when YfgB protein was expressed in the yfgB knockout strain. A similar protein was shown to catalyze post-transcriptional modification of A2503 in 23S rRNA in gram-positive Staphylococcus aureus. The yfgB knockout strain loses in competition with wild type in a co-growth experiment, indicating functional importance of A2503 modification. The location of A2503 in the exit tunnel suggests its possible involvement in interaction with the nascent peptide and raises the possibility that its post-transcriptional modification may influence such an interaction.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine / metabolism*
  • Amino Acid Sequence
  • Base Sequence
  • DNA Modification Methylases / chemistry
  • DNA Modification Methylases / metabolism*
  • DNA Primers
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism*
  • Molecular Sequence Data
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism*
  • RNA, Ribosomal, 23S / chemistry
  • RNA, Ribosomal, 23S / metabolism*
  • Sequence Homology, Nucleic Acid
  • Staphylococcus aureus / genetics


  • DNA Primers
  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Ribosomal, 23S
  • DNA Modification Methylases
  • Adenosine