A genetic code change in progress: tRNA-Leu(CAG) is conserved in mostSaccharomycopsisyeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation

Abstract

AbstractIn the yeast generaSaccharomycopsisandAscoidea, nuclear genes use a non-standard genetic code in which CUG codons are translated as serine instead of leucine, due to a tRNA-Ser with the unusual anticodon CAG. However, some species in this ‘CUG-Ser2’ clade also contain an ancestral tRNA-Leu gene with the same anticodon. One of these species,Ascoidea asiatica, has been shown to have a stochastic proteome in which proteins contain approximately 50% Ser and 50% Leu at CUG codon sites, whereas previously examinedSaccharomycopsisspecies translate CUG only as Ser. Here, we investigated the presence, conservation, and possible functionality of the tRNA-Leu(CAG) gene in the genusSaccharomycopsis. We analyzed the genomes of 33 strains, including almost all known species ofSaccharomycopsis, and found that most of them contain both tRNA-Ser(CAG) and tRNA-Leu(CAG) genes. The tRNA-Leu(CAG) gene is evolving faster than tRNA-Ser(CAG) and it has been lost in two species,S. microsporaandS. synnaedendra. We deleted the single tRNA-Leu(CAG) gene inS. capsularisand found that it is not essential. Bioinformatic analysis suggested that some CUG codon sites inSaccharomycopsisspecies may be translated as Leu, specifically in genes with functions in meiosis or sporulation, but mass spectrometry of sporulatingS. capsularisandS. fermentanscultures showed only CUG-Ser translation. Cloverleaf structures of tRNA-Leu(CAG) from allSaccharomycopsisspecies contain mutations that are likely to make them non-functional in translation, but the evolutionary conservation of the gene leads us to propose that it has been retained for an unknown non-translational role.