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Open Access Research article

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

Elzbieta Purta12, Françoise van Vliet3, Karolina L Tkaczuk14, Stanislaw Dunin-Horkawicz1, Hirotada Mori5, Louis Droogmans6 and Janusz M Bujnicki17*

Author Affiliations

1 Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland

2 Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland

3 Institut de Recherches Microbiologiques Wiame, avenue E. Gryson 1, B-1070 Bruxelles, Belgium

4 Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland

5 Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan

6 Laboratoire de Microbiologie, Université Libre de Bruxelles, Institut de Recherches Microbiologiques Wiame, avenue E. Gryson 1, B-1070 Bruxelles, Belgium

7 Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland

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BMC Molecular Biology 2006, 7:23  doi:10.1186/1471-2199-7-23

Published: 18 July 2006

Abstract

Background

Naturally occurring tRNAs contain numerous modified nucleosides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process. In model organisms Escherichia coli and Saccharomyces cerevisiae most enzymes involved in this process have been identified. Interestingly, it was found that tRNA methylation, one of the most common modifications, can be introduced by S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) that belong to two structurally and phylogenetically unrelated protein superfamilies: RFM and SPOUT.

Results

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.

Conclusion

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).