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The genetic code is primarily implemented by aminoacyl-tRNA synthetases (aaRSs), cognate tRNA adapters, the ribosomal decoding site, and the atomic structure of proteins. Its origin and evolution are here elucidated by integrating evidence from phylogenies of tRNA, evolutionary timelines of protein structural domains, and the deep history of dipeptide sequences in proteomes within a biocommunication and coevolutionary framework. Phylogenetic analyses of tRNA sequence and structure reveal that aminoacylation specificities for Sec, Tyr, Ser, and Leu are ancient, whereas those for Asn, Met, and Arg are evolutionarily derived. These timelines highlight early reliance on the second and then first codon bases, the antiquity of Ala and Pro codons, and major evolutionary takeovers associated with structural innovations such as the loss of the long variable arm of tRNA. Complementary chronologies of the structural domains of aaRSs show that an operational RNA code embedded in the tRNA acceptor arm emerged well before the standard anticodon-based code and that early aaRSs with architectures homologous to modern TyrRS and SerRS likely catalyzed both aminoacylation and peptide bond formation. These interactions exemplify early molecular biocommunication, in which primitive peptides and tRNA cofactors evolved by fostering catalytic efficiency, editing accuracy, specificity, and structural recruitment to improve folding and protein flexibility. Independent support for this early operational code comes from a global phylogeny of 400 canonical dipeptides reconstructed from billions of sequences across thousands of proteomes. Dipeptides containing Leu, Ser, and Tyr emerged first, followed by Val, Ile, Met, Lys, Pro, and Ala, reflecting overlapping timelines of amino acid entry into the code. The parallel emergence of dipeptide–antidipeptide pairs further supports an ancient bidirectional (sense-antisense) coding system previously revealed by synthetic biology studies. Together, these findings offer a unified retrodictive view linking early protein structural constraints, coevolutionary signaling processes, and the rise of the genetic code.

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The Proteomic and Coevolutionary Roots of the Genetic Code

  • 章节

  • 发表日期：

    2026年

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  • Gustavo Caetano-Anollés

摘要

The genetic code is primarily implemented by aminoacyl-tRNA synthetases (aaRSs), cognate tRNA adapters, the ribosomal decoding site, and the atomic structure of proteins. Its origin and evolution are here elucidated by integrating evidence from phylogenies of tRNA, evolutionary timelines of protein structural domains, and the deep history of dipeptide sequences in proteomes within a biocommunication and coevolutionary framework. Phylogenetic analyses of tRNA sequence and structure reveal that aminoacylation specificities for Sec, Tyr, Ser, and Leu are ancient, whereas those for Asn, Met, and Arg are evolutionarily derived. These timelines highlight early reliance on the second and then first codon bases, the antiquity of Ala and Pro codons, and major evolutionary takeovers associated with structural innovations such as the loss of the long variable arm of tRNA. Complementary chronologies of the structural domains of aaRSs show that an operational RNA code embedded in the tRNA acceptor arm emerged well before the standard anticodon-based code and that early aaRSs with architectures homologous to modern TyrRS and SerRS likely catalyzed both aminoacylation and peptide bond formation. These interactions exemplify early molecular biocommunication, in which primitive peptides and tRNA cofactors evolved by fostering catalytic efficiency, editing accuracy, specificity, and structural recruitment to improve folding and protein flexibility. Independent support for this early operational code comes from a global phylogeny of 400 canonical dipeptides reconstructed from billions of sequences across thousands of proteomes. Dipeptides containing Leu, Ser, and Tyr emerged first, followed by Val, Ile, Met, Lys, Pro, and Ala, reflecting overlapping timelines of amino acid entry into the code. The parallel emergence of dipeptide–antidipeptide pairs further supports an ancient bidirectional (sense-antisense) coding system previously revealed by synthetic biology studies. Together, these findings offer a unified retrodictive view linking early protein structural constraints, coevolutionary signaling processes, and the rise of the genetic code.