Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
Highlights
The origin of the genetic code and translation remains amongst the greatest conundrums of Life despite more than 50 years of research [1]
One of the key features of the standard genetic code is its capacity to minimize the deleterious effects of mutations, making it optimized for translation [8,9,10,11]
Our findings suggest that the genetic code shows a certain preference towards nonextremophiles, that is, the codon usage of these organisms is expected to be more robust against mutations
Summary
The origin of the genetic code and translation remains amongst the greatest conundrums of Life despite more than 50 years of research [1]. One of the key features of the standard genetic code (i.e., the nearly universal mapping of amino acids to codons) is its capacity to minimize the deleterious effects of mutations, making it optimized for translation [8,9,10,11]. The basis for this argument is the average fitness cost of replacing one amino acid with another due to mutation, measuring the change on a scale of amino acid physicochemical properties (e.g., hydrophobicity or polarity) that should correspond to the risks of misfold and loss of function in proteins [8,9]. The inherent structure of the genetic code defines the probability of which codon i mutates into codon j given the occurrence of a transition or a transversion; these are denoted by terms P (ci → cj |ti) and
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