Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding

Abstract

We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, Iσ; an impedance parameter, Z; and an effective alphabet size, neff; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small.

High-Resolution, Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-modular ‘Coupling

“…The scaffold fasta file was then partitioned along lines of the experimental deconstruction of the Class I aaRS superfamily [14] into the disjointed segments of the Urzyme, separated by structurally conserved segments from CP1. Finally, because the Urzyme (83) and CP1 (20) partitions of the scaffold MSAs have different sequence lengths, seven subsets comprising 20 sequence positions distributed throughout the Urzyme were selected arbitrarily by a balanced, randomized procedure [69] to test the effect of sequence length on our phylogenetic signatures.…”

“…Because of their high catalytic proficiency in both essential reactions, these and similar cores derived from Class II aaRS were called "Urzymes", from the German prefix "Ur" = original, authentic. Class I and II Urzymes differentiate between amino acids from the two sets of substrates, with Class I Urzymes activating Class I, in preference to Class II amino acids by ~1.0 kcal/mole, and conversely [18][19][20].…”

Reciprocally-coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis

“…Any change in the dimension of the genetic coding alphabet must be followed by a round of equilibration, as new possibilities are introduced to optimize the catalytic and specificity of the extant aaRSs. Finally, minimizing the dissipation of information similarly constrains optimal aaRS precision according to the frequency of replication and transcription errors in large part because of changes in coding redundancy [14].…”

“…(iv) Expansion of the genetic code from a binary alphabet to the current 20 letters likely obeyed a variational principle minimizing dissipation of information and free energy, and aaRS evolution converted the former type of dissipation into the latter to enhance fidelity [14]. Errors could be reduced if and only if they became more energetically costly, but making errors energetically costly could be achieved if and only if errors were less frequent.…”

“…(v) The coding alphabet itself could expand if and only if there were enhancements in aaRS specificity; yet aaRS specificity could increase if and only if the alphabet size expanded [14].…”