Symmetry Breaking and Adaptation: The Genetic Code of Retroviral Env Proteins

TL;DR

This paper explores how symmetry breaking in the genetic code, driven by mutation and recombination, influences the adaptation of retroviral Env proteins, with evidence from HIV codon usage patterns.

Contribution

It demonstrates that selective pressures cause symmetry breaking in codon usage, enhancing the virus's ability to produce advantageous mutations.

Findings

Codons prone to mutation are more frequent in HIV env gene.

Symmetry breaking correlates with increased viral adaptability.

Evidence supports mutation-driven symmetry breaking in genetic code.

Abstract

Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of the synonym symmetry by mutation and recombination. We conjecture that this enhances the probability to produce mutants that are well-adapted to the current environment. Evidence is found in the codon frequencies of the HIV {\it env} protein: the codons most likely to mutate and lead to new viruses resistant to the current immunological attack, are found with a greater frequency than their less mutable synonyms.