Abstract
A variety of RNA methyltransferases act during ribosomal RNA maturation to modify nucleotides in a site-specific manner. However, of the 10 base-methylated nucleotides present in the small ribosomal subunit of
Escherichia coli
, only three enzymes responsible for modification of four bases are known. Here, we show that the protein encoded by
yggJ
, a member of the uncharacterized DUF558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at U1498 in 16S rRNA. The gene is well-conserved across bacteria and plants, and likely performs the same function in other organisms. A
yggJ
deletion strain lacks the methyl group at U1498 as well as the specific methyltransferase activity. Moreover, purified recombinant YggJ specifically methylates m
3
U1498 in vitro. The deletion strain was unaffected in exponential growth in rich or minimal media at multiple temperatures, but it was defective when grown in competition with isogenic wild-type cells. Based on these data, we conclude that
yggJ
is the founding member of a family of RNA base methyltransferases, and propose that it be renamed
rsmE
.
