Local stability and evolution of the genetic code

TL;DR

This study investigates how small modifications to the standard genetic code influence its robustness, revealing that the code is non-random and shaped by both natural selection and stochastic factors during evolution.

Contribution

It provides a detailed analysis of the stability of the genetic code, demonstrating its non-random structure and the effects of small modifications on its robustness.

Findings

Standard code is significantly less robust than random codes.

Distribution of stability variations shows abrupt drops beyond one standard deviation.

Binary block structure is essential for code robustness.

Abstract

The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function, the negative variations of which correspond to a more robust code. The fraction of more robust codes obtained under small modifications appeared to be unexpectedly high, ranged from 0.1 to 0.4 depending on the choice of stability function and code modifications, yet significantly lower than the corresponding fraction in the random codes (about a half). In this sense the standard code ought to be considered distinctly non-random in accordance with previous observations. The distribution of the negative variations of stability function revealed very abrupt drop beyond one standard deviation, much sharper than for Gaussian distribution or for the random codes with the same number of codons in the sets coding for amino acids or stop-codons. This behavior holds for both the standard code as a whole and its binary NRN-NYN, NWN-NSN, and NMN-NKN blocks. Previously, it has been proved that such binary block structure is necessary for the robustness of a code and is inherent to the standard genetic code. The modifications of the standard code corresponding to more robust coding may be related to the different variants of the code. These effects may also contribute to the rates of replacements of amino acids. The observed features demonstrate the joint impact of random factors and natural selection during evolution of the genetic code.