Tracing the Origin of the Genetic Code to Dipeptide Sequences in Proteomes

The safekeeping of the genetic code has been entrusted, for the most part, to interactions between aminoacyl-tRNA synthetases and their cognate tRNA. In a previous phylogenomic study, chro-nologies of RNA substructures, protein domains and dipeptide sequences uncovered the early emergence of an ‘operational’ code in the acceptor arm of tRNA prior to the implementation of the 'standard' genetic code in the anticodon loop of the molecule. This history likely originated in synthetase urzymes capable of aminoacylation and peptide bond formation, but was driven by episodes of molecular co-evolution and recruitment that promoted flexibility and folding of pri-mordial proteins. Here, we show that dipeptide sequences offer deep time insight into the chro-nology of code emergence. A phylogeny describing the evolution of the repertoire of 400 canonical dipeptides reconstructed from an analysis of 4.3 trillion dipeptide sequences across 1,561 prote-omes revealed the overlapping temporal emergence of dipeptides containing Leu, Ser and Tyr, followed by those containing Val, Ile, Met, Lys, Pro, and Ala, all of which supported the opera-tional RNA code. Our study uncovers a hidden evolutionary link between a protein code of di-peptides – arising from the structural demands of emerging proteins – and an early operational code shaped by co-evolution, editing, catalysis and specificity.