In Vitro Detection of the Enzymatic Activity of Folate-Dependent tRNA (Uracil-54,-C5)-Methyltransferase: Evolutionary Implications

Formation of 5-methyluridine (ribothymidine) at position 54 of the T-ψ loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-l-methionine (S-AdoMet). However, in other bacteria, like Enterococcus faecalis and Bacillus subtilis, it was shown that the source of carbon is N⁵,N¹⁰-methylenetetrahydrofolate (CH₂=THF). Recently we have determined that the Bacillus subtilis gid gene (later renamed to trmFO) encodes the folate-dependent tRNA(uracil-54,C5)-MTase. Here, we describe a procedure for overexpression and purification of this recombinant enzyme, as well as detection of its activity in vitro. Inspection of presently available sequenced genomes reveals that trmFO gene is present in most Firmicutes, in all α- and δ-Proteobacteria (except Rickettsiales in which the trmFO gene is missing), Deinococci, Cyanobacteria, Fusobacteria, Thermotogales, Acidobacteria, and in one Actinobacterium. Interestingly, trmFO is never found in genomes containing the gene trmA coding for S-adenosyl-l-methionine-dependent tRNA (uracil-54,C5)-MTase. The phylogenetic analysis of TrmFO sequences suggests an ancient origin of this enzyme in bacteria.