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Fitting the standard genetic code into its triplet table
Wednesday, 2021/09/15 | 09:48:22

Michael Yarus

Fig. Prof. Mike Yarus, Molecular, Cellular & Developmental Biology | University of Colorado Boulder

 

PNAS September 7, 2021 118 (36) e2021103118

Significance

The standard genetic code (SGC) is common to all sufficiently explored Earth biota, suggesting a common origin for protein biosynthesis in every known organism. The ancient events leading to this near-universal biological characteristic are manifestly of scientific importance. The accompanying text presents a detailed pathway for formation of the SGC, as well as a method for identifying essential origin events. Significantly, the SGC can evolve using only well-characterized chemical, biochemical, and physical mechanisms, paralleling other known evolutionary transitions.

Abstract

Minimally evolved codes are constructed here; these have randomly chosen standard genetic code (SGC) triplets, completed with completely random triplet assignments. Such “genetic codes” have not evolved, but retain SGC qualities. Retained qualities are basic, part of the underpinning of coding. For example, the sensitivity of coding to arbitrary assignments, which must be < ∼10%, is intrinsic. Such sensitivity comes from the elementary combinatorial properties of coding and constrains any SGC evolution hypothesis. Similarly, assignment of last-evolved functions is difficult because of late kinetic phenomena, likely common across codes. Census of minimally evolved code assignments shows that shape and size of wobble domains controls the code’s fit into a coding table, strongly shifting accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while fitting a highly ordered, degenerate code into a preset three-dimensional space. Three-dimensional late Crick wobble in a genetic code assembled by lateral transfer between early partial codes satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, this origin can yield shortened evolution to SGC-level order and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies previously studied chemical, biochemical, and wobble order in amino acid assignment, including a stereochemical minority of triplet–amino acid associations. Finally, fusion of intermediates into the final SGC is credible, mirroring broadly accepted later cellular evolution.

 

See: https://www.pnas.org/content/118/36/e2021103118

 

Fig. 5. A unified SGC from three-dimensional late Crick wobble. Three-dimensional coding tables are shown with standard assignments: first nucleotide variation UCAG back to front, second nucleotide variation Left to Right, and third nucleotide variation Top plane to Bottom plane in UCAG order. Colors on triplet tiles correspond to those in Fig. 4, explained in the text. Standard three-letter abbreviations for the amino acids identify each codon assignment. Small white symbols are coding triplets exceptionally concentrated in cognate-selected RNA–amino acid binding sites (25). Anticodon concentrations are marked with white *, codon concentrations are marked with white °. The three-dimensional coding table on the Left is a possible nonwobble, uniquely assigned, precursor of the complete SGC on the Right, where coding after adoption of late Crick wobble is shown.

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