Biosynthesis of Wyosine Derivatives in tRNA: An Ancient and Highly Diverse Pathway in Archaea

Abstract

Wyosine (imG) and its derivatives such as wybutosine (yW) are found at position 37 of phenylalanine-specific transfer RNA (tRNA(Phe)), 3' adjacent to the anticodon in Eucarya and Archaea. In Saccharomyces cerevisiae, formation of yW requires five enzymes acting in a strictly sequential order: Trm5, Tyw1, Tyw2, Tyw3, and Tyw4. Archaea contain wyosine derivatives, but their diversity is greater than in eukaryotes and the corresponding biosynthesis pathways still unknown. To identify these pathways, we analyzed the phylogenetic distribution of homologues of the yeast wybutosine biosynthesis proteins in 62 archaeal genomes and proposed a scenario for the origin and evolution of wyosine derivatives biosynthesis in Archaea that was partly experimentally validated. The key observations were 1) that four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya, 2) that the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. We also identified 7-aminocarboxypropyl-demethylwyosine (yW-86) and its N4-methyl derivative (yW-72) as final products in tRNAs of several Archaea when these were previously thought to be only intermediates of the eukaryotic pathway. We confirmed that isowyosine (imG2) and 7-methylwyosine (mimG) are two archaeal-specific guanosine-37 derivatives found in tRNA of both Euryarchaeota and Crenarchaeota. Finally, we proposed that the duplication of the trm5 gene in some Archaea led to a change in function from N1 methylation of guanosine to C7 methylation of 4-demethylwyosine (imG-14).

Biosynthesis of wyosine derivatives in tRNAPhe of Archaea: role of a remarkable bifunctional tRNAPhe:m1G/imG2 methyltransferase

“…Comparison of the amino acid sequences of these three families of methyltransferases demonstrates that no essential differences exist in the AdoMet binding motifs, and only small differences are evident in the NPPY motif known to be important in positioning the target nitrogen atom in several amino-methyltransferases (Bujnicki 2000). In contrast, the N-terminal sequences of these enzyme families differ substantially, a small conserved domain designated D1 is always present in both aTrm5b and aTrm5c, whereas it is absent in a majority of aTrm5a (de Crécy-Lagard et al 2010). …”

“…The next biosynthetic step is the complex radical-mediated formation of 4-demethylwyosine (imG-14), catalyzed by the flavin-binding domain of the TYW1 gene product in yeast (Young and Bandarian 2013). In all archaea, except for a few halobacteriales and Cenarchaeum symbiosum, a single homologous gene taw1 is found (de Crécy-Lagard et al 2010). However, at variance with the yeast Tyw1, archaeal Taw1 does not have the flavin-binding domain but contains a second Fe-S cluster instead (Perche-Letuvée et al 2012).…”

“…1C), whereas the N 4 -methyl transferase (Taw3), with the exception of only a few Euryarchaeota, is found mainly in Crenoarchaeota ( Fig. 1C,D Crécy-Lagard et al 2010). Nevertheless, in the case of Crenoarchaeota and a few Euryarchaeota, no obvious candidate gene coding for a methyltransferase capable of adding a methyl group on C 7 -atom of imG-14 to form imG2 derivative has been identified so far (Fig.…”

“…Phyletic distribution of trm5 gene homologs in 62 archaeal genomes allowed identification of three aTrm5 subfamilies: aTrm5a, aTrm5b, and aTrm5c (de Crécy-Lagard et al 2010). The aTrm5b variant is almost ubiquitous in Euryarchaeota, but in Crenoarchaeota it is totally absent.…”

Celebrating wobble decoding: Half a century and still much is new

“…The bulky residue prevents the intraloop hydrogen bond between residues 32 and 37, thus promoting proper pre-structuring of the ASL. 116,117 In mitochondrial tRNAs, imG 37 or its derivatives are commonly replaced by i 6 A 37 or a derivative thereof, or by a methylated purine, therefore suggesting the evolution of an alternative strategy for establishing the same functional properties by using different chemical moieties in RNA modifications. 113,116 …”