Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases

The sequences of known Escherichia coli 16S rRNA:m(2)G1207 methyltransferase (MTase) RsmC and hypothetical 168 rRNA:m(2)G966 MTase encoded by the ygjo open reading frame were used to carry out a database search of other putative m(2)G-generating enzymes in finished and unfinished genomic sequences. Sequence comparison and phylogenetic analysis of 21 close homologs of RsmC and YgjO revealed the presence of the third paralogous lineage in E. coli and other gamma -Proteobacteria, which might correspond to the subfamily of MTases specific for G1516 in 16S rRNA. In addition, the comparative sequence analysis supported by sequence/structure threading suggests that rRNA:m(2)G MTases are very closely related to RNA and DNA:m(6)A MTases and that these two enzyme families share common architecture of the active site and presumably a similar mechanism of methyl group transfer onto the exocyclic amino group of their target bases.-Bujnicki, J. M. Phylogenomic analysis of 16S rRNA (guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases.