Abstract
The rules that specify how the information contained in DNA is translated into amino acid "language" during protein synthesis are called "the genetic code", commonly called the "Standard" or "Universal" Genetic Code Table. As a matter of fact, this coding table is not at all "universal": in addition to different genetic code tables used by different organisms, even within the same organism the nuclear and mitochondrial genes may be subject to two different coding tables. Results In an attempt to understand the advantages and disadvantages these coding tables may bring to an organism, we have decided to analyze various coding tables on genes subject to mutations, and have estimated how these genes "survive" over generations. We have used this as indicative of the "evolutionary" success of that particular coding table. We find that the "standard" genetic code is not actually the most robust of all coding tables, and interestingly, Flatworm Mitochondrial Code (FMC) appears to be the highest ranking coding table given our assumptions. Conclusions It is commonly hypothesized that the more robust a genetic code, the better suited it is for maintenance of the genome. Our study shows that, given the assumptions in our model, Standard Genetic Code is quite poor when compared to other alternate code tables in terms of robustness. This brings about the question of why Standard Code has been so widely accepted by a wider variety of organisms instead of FMC, which needs to be addressed for a thorough understanding of genetic code evolution.
Highlights
How the genetic code evolved has been a matter of interest for many researchers over the past decades – Crick [1] had postulated the coevolution and frozen accident hypotheses, where similar amino acids would end up using similar codons as a result of coevolution of coding tables and genes, and remain “frozen” at an optimum coding that reduces deleterious effects of mutations
One of the important properties of a genetic code is its robustness to error, which means that if a mutation occurs in a gene, the amino acid substitution ideally renders a functionally similar protein, a robust code reduces the deleterious effects of mutations
The alternate coding tables are believed to have arisen from the evolution of the standard genetic code through codon reassignments, and most studies on possible mechanisms of this evolution start out by the assumption that the changes resulting in codon reassignment would be strongly disadvantegous and get eliminated from the system [3,4]
Summary
How the genetic code evolved has been a matter of interest for many researchers over the past decades – Crick [1] had postulated the coevolution and frozen accident hypotheses, where similar amino acids would end up using similar codons as a result of coevolution of coding tables and genes, and remain “frozen” at an optimum coding that reduces deleterious effects of mutations (reviewed in [2]). One of the important properties of a genetic code is its robustness to error, which means that if a mutation occurs in a gene, the amino acid substitution ideally renders a functionally similar protein, a robust code reduces the deleterious effects of mutations. The alternate coding tables are believed to have arisen from the evolution of the standard genetic code through codon reassignments, and most studies on possible mechanisms of this evolution start out by the assumption that the changes resulting in codon reassignment would be strongly disadvantegous and get eliminated from the system [3,4]. Our present study aims to compare the possible “evolutionary” advantages of these different genetic codes in terms of robustness and resilience to mutations
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