A Unified Theory on Construction and Evolution of the Genetic Code

TL;DR

This paper presents a comprehensive quantitative theory explaining the construction and evolution of the genetic code through mutational deterioration minimization, revealing fundamental principles behind codon redundancy, amino acid distribution, and code symmetry.

Contribution

It introduces the concept of mutational deterioration minimization as a unifying framework for understanding genetic code structure and evolution, including the Yin-Yang duality symmetry.

Findings

Codon redundancy obeys MD minimization.

Amino acid hydrophilic-hydrophobic distribution minimizes GMD.

Standard genetic code is derived from GMD minimization.

Abstract

A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the redundancy distribution of codons in the genetic code obeys MD minimization principle; 2, the hydrophilic-hydrophobic distribution of amino acids on the code table is global MD (GMD) minimal; 3, the standard genetic code can be deduced from the adaptive minimization of GMD; 4, the variants of the standard genetic code can be explained quantitatively by use of GMD formalism and the general trend of the evolution is GMD non-increasing which reflects the selection on the code. We have demonstrated that the redundancy distribution of codons and the hydrophobic-hydrophilic (H-P) distribution of amino acids are robust in the code relative to the mutational parameter, and indicated that the GMD can be looked as a non-fitness function on the adaptive landscape. Finally, an important aspect on the symmetry of the code construction, the Yin-Yang duality is investigated. The Yin-Yang duality among codons affords a sound basis for understanding the H-P structure in the genetic code.