Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

Abstract

Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5'-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.

Keywords: Dnmt2; Pmt1; anticodon modification; epitranscriptomics; queuine; queuosine; tRNA cleavage; translation.

Figure 1

Stimulation of Dnmt2 activity in S. pombe (Pmt1) by prior Q incorporation. Dnmt2/Pmt1 shows low activity on non-Q-modified tRNA^Asp (dashed arrow), but is highly active on Q-modified tRNA^Asp. Right, possible consequences of dual Q and m⁵C38 modification. eTGT: eukaryotic TGT enzyme.

Figure 2

tRNA^Asp with the GUC (left) or QUC (right) anticodon decodes both aspartate codons, GAC (left) and GAU (right). The sequence of the anticodon stem-loop of tRNA^Asp from S. pombe is given.

Figure 3

Base pairing between guanine, queuine and cytosine or uracil. Watson-Crick base pairing (top) and wobble base pairing (bottom) are shown. R: ribose.

Figure 4

Effects of Q modification on mistranslation in bacteria [56]. Codon-anticodon pairs of tRNA^Asp and tRNA^Tyr are shown with the codon at the top and the anticodon at the bottom. The respective amino acid is indicated in the corner. First row, cognate codons for tRNA^Asp and tRNA^Tyr. Second row, base mismatches at the second codon position that showed significant misreading in vivo [46]. Third row, wobble mismatches that showed significant misreading in vivo. Red color indicates that the codon showed increased misreading when the respective tRNA was not Q-modified. If the respective codon showed strongly or moderately decreased misreading in the absence of Q modification, the boxes are colored in dark green or light green, respectively. Grey, no effect of Q modification on misreading.