Protein Sequences Recapitulate Genetic Code Evolution

Hervé Seligmann

doi:10.1016/j.csbj.2018.05.001

Abstract

Several hypotheses predict ranks of amino acid assignments to genetic code's codons. Analyses here show that average positions of amino acid species in proteins correspond to assignment ranks, in particular as predicted by Juke's neutral mutation hypothesis for codon assignments. In all tested protein groups, including co- and post-translationally folding proteins, ‘recent’ amino acids are on average closer to gene 5′ extremities than ‘ancient’ ones. Analyses of pairwise residue contact energies matrices suggest that early amino acids stereochemically selected late ones that stablilize residue interactions within protein cores, presumably producing 5′-late-to-3′-early amino acid protein sequence gradients. The gradient might reduce protein misfolding, also after mutations, extending principles of neutral mutations to protein folding. Presumably, in self-perpetuating and self-correcting systems like the genetic code, initial conditions produce similarities between evolution of the process (the genetic code) and ‘ontogeny’ of resulting structures (here proteins), producing apparent teleonomy between process and product.

Highlights

The structure of biological molecules includes imprints of ancient evolution at life's dawn
For each of the 20 amino acid species A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y, the mean position of residues belonging to a given amino acid species is calculated, based on the ranks of the residues in the sequence, from position 1 corresponding to the 5′ initiation codon to position k, the last codon before the termination codon
In an early phase of the genetic code, recruited amino acids were structurally simple amino acids that are frequently spontaneously synthesized as shown by Miller's experiment and amino acids found in meteorites

Summary

Introduction

The structure of biological molecules includes imprints of ancient evolution at life's dawn. The ribosome's structure testifies to even more ancient events: ribosomal protein amino acids interact preferentially with ribosomal RNA trinucleotides that correspond to that amino acid's assigned anticodon (s) according to the standard genetic code [42]. This striking fossilization of the process that determined some codon-amino acid assignments in the ribosome's structure confirms that at least some codonamino acid assignments result from stereochemical affinities between. Structurally simple amino acids tend to associate with rRNA nucleotide triplets corresponding to their genetic code codon assignments, while complex amino acids associate with their anticodons (stereochemical complexity according to Dufton [19]). This indicates a primary phase of direct codon-amino acid contact, and secondarily evolution of mRNA, anticodon and from there the proto-tRNA [97]

Methods

Results

Conclusion