The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase

As a part of a large-scale project aiming at characterization of a complete set of RNA modification enzymes of model organisms, we have studied the Escherichia coli proteins YibK, LasT, YfhQ, and YbeA for their ability to introduce the last unassigned methylations of ribose at positions 32 and 34 of the tRNA anticodon loop. We found that YfhQ catalyzes the AdoMet-dependent formation of Cm32 or Um32 in tRNASer1 and tRNAGln2 and that an E. coli strain with a disrupted yfhQ gene lacks the tRNA:Cm32/Um32 methyltransferase activity. Thus, we propose to rename YfhQ as TrMet(Xm32) according to the recently proposed, uniform nomenclature for all RNA modification enzymes, or TrmJ, according to the traditional nomenclature for bacterial tRNA MTases.Our results reveal that methylation at position 32 is carried out by completely unrelated TrMet(Xm32) enzymes in eukaryota and prokaryota (RFM superfamily member Trm7 and SPOUT superfamily member TrmJ, respectively), mirroring the scenario observed in the case of the m1G37 modification (introduced by the RFM member Trm5 in eukaryota and archaea, and by the SPOUT member TrmD in bacteria).All mature transfer RNAs (tRNA) molecules, from all known living organisms, contain numerous modified nucleosides at multiple positions [1]. Although other RNA species also contain modified nucleosides, they are less common than in tRNA, where over 80 modifications have been found to occur at typically ~10%, but sometimes even at as many as 25% positions [2]. Recently, owing to the availability of complete genome sequences, there has been a remarkable progress in identification of enzymes that introduce modifications in tRNAs of model organisms Escherichia coli and Saccharomyces cerevisiae (reviews: [3,4]). For instance, as a part of a large-scale project, aiming at identification of the complete repertoire of RNA methyltransferases (MTases) in E. coli by combination of bioinformatics and experimental analyses, we have recently identified the so far