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

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.