Origins of Genetic Coding: Self-Guided Molecular Self-Organisation

Abstract

The origin of genetic coding is characterised as an event of cosmic significance in which quantum mechanical causation was transcended by constructive computation. Computational causation entered the physico-chemical processes of the pre-biotic world by the incidental satisfaction of a condition of reflexivity between polymer sequence information and system elements able to facilitate their own production through translation of that information. This event, which has previously been modelled in the dynamics of Gene-Replication-Translation systems, is properly described as a process of self-guided self-organisation. The spontaneous emergence of a primordial genetic code between two-letter alphabets of nucleotide triplets and amino acids is easily possible, starting with random peptide synthesis that is RNA-sequence-dependent. The evident self-organising mechanism is the simultaneous quasi-species bifurcation of the populations of information-carrying genes and enzymes with aminoacyl-tRNA synthetase-like activities. This mechanism allowed the code to evolve very rapidly to the ~20 amino acid limit apparent for the reflexive differentiation of amino acid properties using protein catalysts. The self-organisation of semantics in this domain of physical chemistry conferred on emergent molecular biology exquisite computational control over the nanoscopic events needed for its self-construction.

Keywords: aminoacyl-tRNA synthetase; computation; genetic coding; mechanistic causation; reflexivity; replication; translation.

Figure 1

Ribosomal protein synthesis. This representation of protein synthesis emphasises the computational role of aminoacyl-tRNA synthetase (aaRS) enzymes in translation. These enzymes (irregular shape, RHS of figure) enforce the rules of the code by specifically matching their amino acid substrate to cognate tRNA molecules, i.e., those bearing nucleotide triplet anticodons (drawn as “legs”) consistent with the codon-to-amino acid rules of the genetic code, shown here as colour-matching. A 4-letter code (different colours for different letter symbols) is depicted. The amino acid added to the growing peptide is a correct (colour-matched) translation of the codon occurring at that point in the genetic message (mRNA).

Figure 2

Replication as autocatalysis. The net reaction, components → X, is catalysed by X, a role shown by (a) adding it to both the reactant and product side of the chemical equation; (b) placing it above the arrow; or (c) indicating catalytic feedback (red arrow).

Figure 3

Reflexive production of assignment catalysts. (a) Two fictional aaRS-encoding genes, AABABAABABBA and BAABABBABABB, are shown as anti-parallel complementary strands of a single base-paired nucleic acid molecule in accordance with the hypothesis of Rodin & Ohno [37,38]. The genes are translated by operation of the coding assignments A→a and B→b between the binary codon alphabet {A, B} and the binary amino acid alphabet {a, b} to produce molecules with amino acid sequences aababaababba and baababbababb representative of two separate classes of aaRS species. (b) The antiparallel genes are depicted in a double helical configuration, and the conserved core structures of the ancestral Class I and II aaRS enzymes are shown.

Figure 4

Gene–Replication–Translation (GRT) system. The genetic information in the nucleic acid G encodes a set of aaRS-type assignment catalysts T = {T₁, T₂ … T_λ} and a nucleic acid replicase R. The set T catalyses the codon-to-amino acid assignments for the system’s genetic code.

Figure 5

Quasi-species bifurcation. Proteins with aaRS-like activity, including weak and non-specific activity, are found throughout a large region of n-dimensional protein sequence space. However, significant activities for the two specific assignments, A→a and B→b, are found within much narrower, separate domains, which are also separate from the domains of the code conflicting A→b and B→a assignments (not shown). Binary coding arises from a symmetry-breaking transition whereby the protein population with aaRS-like activity becomes concentrated from the large, broad domain into the two smaller regions of sequence space.