《Crick 4 *4 *4 遺傳密碼錶》的起草origin與修訂evolution （一）

IUBMB Life. Author manuscript; available in PMC 2012 Mar 5.

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IUBMB Life. 2009 Feb; 61(2): 99–111.

doi: 10.1002/iub.146

PMCID: PMC3293468

NIHMSID: NIHMS78555

PMID: 19117371

Origin and evolution of the genetic code: the universal enigma

Eugene V. Koonin* and Artem S. Novozhilov

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Abstract

The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physico-chemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code』s evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, i.e., the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.

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Introduction

Shortly after the genetic code of Escherichia coli was deciphered (1), it was recognized that this particular mapping of 64 codons to 20 amino acids and two punctuation marks (start and stop signals) is shared, with relatively minor modifications, by all known life forms on earth (2, 3). Even a perfunctory inspection of the standard genetic code table (Fig. 1) shows that the arrangement of amino acid assignments is manifestly nonrandom (4–7). Generally, related codons (i.e., the codons that differ by only one nucleotide) tend to code for either the same or two related amino acids, i.e., amino acids that are physico-chemically similar (although there are no unambiguous criteria to define physicochemical similarity). The fundamental question is how these regularities of the standard code came into being, considering that there are more than 1084 possible alternative code tables if each of the 20 amino acids and the stop signal are to be assigned to at least one codon. More specifically, the question is, what kind of interplay of chemical constraints, historical accidents, and evolutionary forces could have produced the standard amino acid assignment, which displays many remarkable properties. The features of the code that seem to require a special explanation include, but are not limited to, the block structure of the code, which is thought to be a necessary condition for the code』s robustness with respect to point mutations, translational misreading, and translational frame shifts (8); the link between the second codon letter and the properties of the encoded amino acid so that codons with U in the second position correspond to hydrophobic amino acids (9, 10); the relationship between the second codon position and the class of aminoacyl-tRNA synthetase (11), the negative correlation between the molecular weight of an amino acid and the number of codons allocated to it (12, 13); the positive correlation between the number of synonymous codons for an amino acid and the frequency of the amino acid in proteins (14, 15); the apparent minimization of the likelihood of mistranslation and point mutations (16, 17); and the near optimality for allowing additional information within protein coding sequences (18).

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