We identified the presence of genes for methanogenesis from methanol and also from dimethylsulfide and methylamines in the two other sequenced genomes ("Candidatus Methanomethylophilus alvus" , "Candidatus Methanomassiliicoccus intestinalis" ), together with the Pyl-coding genes and in-frame amber codon in the mtmB, mtbB, and mttB genes of these three species.
These include, for the three genomes available and analyzed to date, at least the global presence of all the genes for Pyl synthesis, charging and cotranslational incorporation, in cooccurrence with all the genes for methylotrophic methanogenesis from methylamines, that is, those coding for methylamines-corrinoid protein methyltransferases (MT) genes (mtmB, mtbB, and mttB) all bearing an in-frame amber codon. It is interesting to note that, as a nonsense (stop) codon, the amber codon is used with a low frequency, this value being maximal in the M.
Taking together these pieces of evidence, it is likely that, in the archaeal domain, the Pyl system arose in a methanogenic euryarchaeote, in correspondence to the emergence of the genes coding for methylamines-corrinoid protein methyltransferases (MT) (mtmB, mtbB, and mttB) that all bear an in-frame amber codon, allowing the use of new substrates (mono-, di-, and trimethylamine, resp.).
Krzycki, "The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain inframe and read- through amber codons," Journal of Bacteriology, vol.
The scientists' altered tRNA, however, reads the amber codon
as if it were glutamine and adds that amino acid, enabling the protein to grow to its normal length.