Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase

Abstract

The presence of tricyclic wyosine derivatives 3'-adjacent to anticodon is a hallmark of tRNA(Phe) in eukaryotes and archaea. In yeast, formation of wybutosine (yW) results from five enzymes acting in a strict sequential order. In archaea, the intermediate compound imG-14 (4-demethylwyosine) is a target of three different enzymes, leading to the formation of distinct wyosine derivatives (yW-86, imG, and imG2). We focus here on a peculiar methyltransferase (aTrm5a) that catalyzes two distinct reactions: N(1)-methylation of guanosine and C(7)-methylation of imG-14, whose function is to allow the production of isowyosine (imG2), an intermediate of the 7-methylwyosine (mimG) biosynthetic pathway. Based on the formation of mesomeric forms of imG-14, a rationale for such dual enzymatic activities is proposed. This bifunctional tRNA:m(1)G/imG2 methyltransferase, acting on two chemically distinct guanosine derivatives located at the same position of tRNA(Phe), is unique to certain archaea and has no homologs in eukaryotes. This enzyme here referred to as Taw22, probably played an important role in the emergence of the multistep biosynthetic pathway of wyosine derivatives in archaea and eukaryotes.

Keywords: COG2520; archaea; methyltransferase; modification; transfer RNA.

FIGURE 1.

Biosynthesis of wyosine derivatives in archaeal tRNA^Phe. (A) The chemical structures of the various wyosine derivatives identified in tRNA^Phe of archaea and two selected eukaryotes (fungi). (B) The serial steps leading to the final product wybutosine in S. cerevisiae and T. utilis. (C,D) The sequential biosynthetic steps leading to the various wyosine derivatives found in archaeal tRNA^Phe. The steps catalyzed by the bifunctional tRNA^Phe:m¹G/imG2 methyltransferase are indicated in red (D). The archaea where such bifunctional aTrm5a (now designated Taw22) may function are indicated in red.

FIGURE 2.

Schematic representation of the active sites of selected tRNA methyltransferases acting at guanosine derivatives located on position 37 in precursor tRNA^Phe. Depending on the enzyme considered, transfer of a methyl-group (encircled in red) or a 3-amino-3-carboxypropyl group (encircled in blue) on guanine (G) or 4-demethylwyosine (imG-14) may occur, leading to either m¹G, imG, imG2, or yW-72 guanosine derivatives (see formula in Fig. 1). (A) Methylation of the electron-rich N¹-atom of guanine catalyzed by the multi-tRNA specific aTrm5a, b, or c. In the case of M. jannaschii Trm5b, a glutamic acid (E185) in the active site (indicated as Enz-A⁻), allows abstraction of the proton at the N¹-atom of guanine and the subsequent addition of the methyl group from the sulfonium ion of AdoMet (Christian et al. 2010). However, in Trm5 of a few other archaea, an aspartic acid (D) is found instead (cf. Supplemental Fig. SS7 in de Crécy-Lagard et al. 2010). (B) Methylation or 3-amino-3-carboxypropylation of electron-rich C⁷-atom in the mesomeric form of imG-14 of tRNA^Phe catalyzed by aTrm5a/Taw22 or Taw2, respectively (cf. comments and Fig. 9 in Lin 2011). The amino acid residue in the active site of the enzyme (Enz-A⁻) allowing abstraction of the proton located on the C⁷-atom of imG-14 is probably the same conserved E or D residue as mentioned above in the cases of other aTrm5, including MjTrm5b. As discussed in the text, a certain degree of flexibility of the target base, the AdoMet and/or mobility of the catalytic E or D residue of the active site of the enzyme will probably be required. The S-adenosyl-L-methionine in both A and B is represented in its naturally occurring S,S configuration (Cannon et al. 2002).