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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

Bioinformatics Unit, International Institute of Molecular and Cell Biology, 02–109 Warsaw, Poland; and Molecular Biology Research Program, Henry Ford Health System, Detroit, Michigan 48202, USA

¹Correspondence: Bioinformatics Unit, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02–109 Warsaw, Poland. E-mail: iamb{at}bioinfo.pl

The sequences of known Escherichia coli 16S rRNA:m²G1207 methyltransferase (MTase) RsmC and hypothetical 16S rRNA:m²G966 MTase encoded by the ygjo open reading frame were used to carry out a database search of other putative m²G-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 -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:m²G MTases are very closely related to RNA and DNA:m⁶A 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.

Key Words: RNA modification • sequence alignment • molecular evolution • structure prediction

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