Convergent evolution of AUA decoding in bacteria and archaea

Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense codon sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm²C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA^Ile responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA^Ile to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA^Ile with Ile. Despite their similar chemical structures, L and agm²C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).