The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu.
Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.
Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
Raghuvaran
R
Shanmugam
Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA.
Muktak
M
Aklujkar
Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany.
Matthias
M
Schäfer
Max-Planck-Genomzentrum, 50829 Köln, Germany.
Richard
R
Reinhardt
Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany.
Olaf
O
Nickel
Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany.
Gunter
G
Reuter
Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA.
Derek R
DR
Lovley
Institute of Biology, Humboldt University, 10115 Berlin, Germany.
Ann
A
Ehrenhofer-Murray
Department of Genetics, University of Kassel, 34132 Kassel, Germany.
Wolfgang
W
Nellen
Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel.
Serge
S
Ankri
Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany.
Mark
M
Helm
Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
Tomasz P
TP
Jurkowski
Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany albert.jeltsch@ibc.uni-stuttgart.de.
Albert
A
Jeltsch
D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism*; D045302:Geobacter / Q000201:enzymology*; D006801:Humans; D008745:Methylation; D051379:Mice; D009690:Nucleic Acid Conformation; D012349:RNA, Transfer, Asp / Q000737:chemistry / Q000378:metabolism; D012352:RNA, Transfer, Glu / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity; D012359:tRNA Methyltransferases / Q000378:metabolism*
D001426:Bacterial Proteins; D012349:RNA, Transfer, Asp; D012352:RNA, Transfer, Glu; D012359:tRNA Methyltransferases