Identification of Escherichia coli m²G methyltransferases: I. The ycbY Gene Encodes a Methyltransferase Specific for G2445 of the 23 S rRNA

N2-methylguanosine 2445 of the 23 S rRNA is located in a cluster of modified nucleotides concentrated at the peptidyl transferase center of the ribosome. Here we describe the identification of a gene, ycbY, as encoding an enzyme responsible for methylation of G2445. Knock-out of the ycbY gene leads to loss of modification at G2445 as revealed by reverse transcription. The modification is restored in the ycbY knock-out strain if co-transformed with a plasmid expressing the ycbY gene product. Recombinant YcbY protein is able to methylate 23 S rRNA purified from the ycbY knock-out strain in vitro, assembled 50 S subunits are not a substrate for the methylase. Knock-out of the ycbY gene leads to growth retardation. Growth competition with the parental wild-type strain leads to a gradual decrease in the knock-out strain cells proportion in the media. It is likely that the G2445 modification is necessary for prevention of non-functional secondary or tertiary structure formation at the peptidyl transferase center. Based on these results we suggest that YcbY be renamed to RlmL in accordance with the accepted nomenclature for rRNA methyltransferases.