Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity

Modifications of rRNAs are clustered in functional regions of the ribosome. In Helix 74 of Escherichia coli 23S rRNA, guanosines at positions 2069 and 2445 are modified to 7-methylguanosine(m⁷G) and N²- methylguanosine(m²G), respectively. We searched for the gene responsible for m⁷G2069 formation, and identified rlmL, which encodes the methyltransferase for m²G2445, as responsible for the biogenesis of m⁷G2069. In vitro methylation of rRNA revealed that rlmL encodes a fused methyltransferase responsible for forming both m⁷G2069 and m²G2445. We renamed the gene rlmKL. The N-terminal RlmL activity for m²G2445 formation was significantly enhanced by the C-terminal RlmK. Moreover, RlmKL had an unwinding activity of Helix 74, facilitating cooperative methylations of m⁷G2069 and m²G2445 during biogenesis of 50S subunit. In fact, we observed that RlmKL was involved in the efficient assembly of 50S subunit in a mutant strain lacking an RNA helicase deaD.