The Triplet Code From First Principleshttp://www.jbsdonline.comAbstractTemporal order (“chronology”) of appearance of amino acids and their respective codons onevolutionary scene is reconstructed. A consensus chronology of amino acids is built on thebasis of 60 different criteria each offering certain temporal order. After several steps of fil-tering the chronology vectors are averaged resulting in the consensus order: G, A, D, V, P,S, E, (L, T), R, (I, Q, N), H, K, C, F, Y, M, W. It reveals two important features: the aminoacids synthesized in imitation experiments of S. Miller appeared first, while the amino acidsassociated with codon capture events came last. The reconstruction of codon chronology isbased on the above consensus temporal order of amino acids, supplemented by the stabilityand complementarity rules first suggested by M. Eigen and P. Schuster, and on the earlierestablished processivity rule. At no point in the reconstruction the consensus amino-acidchronology was in conflict with these three rules. The derived genealogy of all 64 codonssuggested several important predictions that are confirmed. The reconstruction of the originand evolutionary history of the triplet code becomes, thus, a powerful research tool formolecular evolution studies, especially in its early stages.Key words: Amino acids; Code origin; Codon capture; Codon history; Codons;Complementarity; Earliest genes; Earliest proteins; Early evolution; First codons; Molecularchronology; Origin of Life; Processivity.IntroductionResearch on the origin and evolution of the early life is an area of elaborate spec-ulations of which almost none became a theory proper, that is complemented bytestable and subsequently confirmed predictions. An important exception is pre-diction by S. Miller that some biologically relevant substances could have been abi-otically produced in the atmosphere of the early Earth. The prediction was spec-tacularly confirmed in the imitation experiments (1, 2) [see also (3)] that yielded asmany as ten different natural amino acids, thus, laying the foundation of the theo-ry of the origin of life and early evolution. Eigen and Schuster noted (4) that ala-nine and glycine, the highest yield amino acids in the experiments of Miller, areencoded today by (G+C)-rich complementary triplets GCC and GGC. They putforward the hypothesis on the importance of complementarity and thermostabilityin the evolution of the triplet code.Many hypothetical scenarios of this evolution are discussed in literature. It is com-monly believed that 20 amino acids of present-day proteins did not appear simul-taneously on the evolutionary scene. Rather, some amino acids entered at earlierstages while others are comparatively late. Many factors may have influenced thetemporal order of engagement of the amino acids and codons in the triplet code. Inthis work total of 60 various criteria for the amino-acid chronology are summarizedin a consensus chronology that reveals two fundamental features: the amino acidsof Miller are first in the list, while the amino acids associated with codon capture,especially those for which codon assignments are not yet fully stabilized, appearJournal of Biomolecular Structure &Dynamics, ISSN 0739-1102Volume 22, Issue Number 1, (2004)©Adenine Press (2004)Edward N. TrifonovGenome Diversity CenterInstitute of EvolutionUniversity of HaifaHaifa 31905, Israel1Phone: +972 4 828 8096Fax: +972 4 824 6554Email: [email protected] in the chronology. The order of appearance of the amino acids suggests aunique order of engagement of the respective codons. A complete reconstructionof the genealogy of all 64 codons is described. It follows strictly the rules of com-plementarity and thermostability, of Eigen and Schuster. A new rule of processiv-ity (5) is confirmed whereby new codons are not introduced de novo but ratherappear progressively as simple point change derivatives and complementary copiesof those engaged earlier, starting with a single ancestral codon pair GCC·GGC.The reconstructed stages of evolution of the triplet code are, thus, uniquely definedby five most basic principles: I. Abiotic start, II. Complementarity, III.Thermostability, IV. Processivity, and V. Codon capture at the end.ResultsAmino-acid ChronologyAn early version of the consensus amino-acid chronology has been derived on thebasis of 40 different criteria (5). In this section the updated amino acid chronolo-gy is presented, built on 60 criteria. A more advanced data filtering is applied. Inthe derivation of the chronology no specific theory is given preference. Instead alldiverse knowledge and thoughts accumulated during decades are thoroughly takeninto account and expressed in form of the consensus temporal order.Every theory or viewpoint that suggests certain temporal order for the amino acidsis taken as a contribution to the consensus order, in form of a specific detailed orapproximate ranking of the amino acids, the earliest first. 60 rankings for 60 dif-ferent criteria are used for the derivation of the consensus. Many of the criteria areapparently independent while some are related. To avoid any bias such related cri-teria were combined in groups. Each group was represented by a single (average)ranking for the group. The criteria then were divided in two non-mixible classes:single-factor and multi-factor criteria. The single-factor criteria are all independent.When a positive correlation between respective chronological orders is observed itreflects only the fact that they express some common trend, presumably related tothe amino-acid chronology we are aiming to. On the contrary, the multi-factor cri-teria, that is various synthetic hypotheses on the origin and evolution of the tripletcode, are interdependent. Each one of them is built on several basic ideas, fre-quently common for different combined criteria, but in different combinations andwith different priorities, depending on the expertise and intuition of their author(s).Essentially, the multi-factor criteria are individually biased opinions on the samematter. The two classes of the criteria are used in this work for separate reconstruc-tions of the amino-acid chronology. One is result of equal weight averaging of inde-pendent temporal orders (single-factor criteria), while another one corresponds tothe consensus of opinions, also taken with equal
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