《Crick 4 *4 *4 遺傳密碼錶》的起草origin與修訂evolution （二）

Figure 1

The standard genetic code. The codon series are shaded in accordance with the polar requirement scale values (80), which is a measure of an amino acid』s hydrophobicity: the greater hydrophobicity the darker the shading (the stop codons are shaded black).

When considering the evolution of the genetic code, we proceed under several basic assumptions that are worth spelling out. It is assumed that there are only 4 nucleotides and 20 encoded amino acids (with the notable exception of selenocysteine and pyrrolysine, for which subsets of organisms have evolved special coding schemes (19), see also discussion below) and that each codon is a triplet of nucleotides. It has been argued that movement in increments of three nucleotides is a fundamental physical property of RNA translocation in the ribosome so that the translation system originated as a triplet-based machine (20–22). Obviously, this does not rule out the possibility that, e.g., only two nucleotides in each codon are informative (see, e.g., (23–26) for hypotheses on the evolution of the code through a 「doublet」 phase). Questions on why there are four standard nucleotides in the code (27, 28) or why the standard code encodes 20 amino acids (29–31) are fully legitimate. Conceivably, theories on the early phases of the evolution of the code should be constrained by the minimal complexity that is required of a self-replicating system (e.g., (32)). However, this fascinating are of enquiry is beyond the scope of this review, and for the present discussion we adopt the above fundamental numbers as assumptions. With these premises, we here attempt to critically assess and synthesize the main lines of evidence and thinking about the code』s nature and evolution.

The code is evolvable

The code expansion theory proposed in Crick』s seminal paper posits that the actual allocation of amino acids to codons is mainly accidental and 『yet related amino acids would be expected to have related codons』 (6). This concept is known as 『frozen accident theory』 because Crick maintained, following the earlier argument of Hinegardner and Engelberg (2) that, after the primordial genetic code expanded to incorporate all 20 modern amino acids, any change in the code would result in multiple, simultaneous changes in protein sequences and, consequently, would be lethal, hence the universality of the code. Today, there is ample evidence that the standard code is not literally universal but is prone to significant modifications, albeit without change to its basic organization.

Since the discovery of codon reassignment in human mitochondrial genes (33), a variety of other deviations from the standard genetic code in bacteria, archaea, eukaryotic nuclear genomes and, especially, organellar genomes have been reported, with the latest census counting over 20 alternative codes (34–38). All alternative codes are believed to be derived from the standard code (35); together with the observation that many of the same codons are reassigned (compared to the standard code) in independent lineages (e.g., the most frequent change is the reassignment of the stop codon UGA to tryptophan), this conclusion implies that there should be predisposition towards certain changes; at least one of these changes was reported to confer selective advantage (39).

The underlying mechanisms of codon reassignment typically include mutations in tRNA genes, where a single nucleotide substitution directly affects decoding (40), base modification (41), or RNA editing (42) (reviewed in (35)). Another pathway of code evolution is recruitment of non-standard amino acids. The discovery of the 21stamino acid, selenocysteine, and the intricate molecular machinery that is involved in the incorporation of selenocysteine into proteins (43) initially has been considered a proof that the current repertoire of amino acids is extremely hard to change. However, the subsequent discovery of the second non-canonical amino acid, pyrrolysine, and, importantly, the existence of a pyrrolysine-specific tRNA revealed additional malleability of the code (19, 44). In addition to the variations on the standard code discovered in organisms with minimized genomes, many experimental attempts on code modification and expansion have been reported (45). Recently, a general method has been developed to encode the incorporation of unnatural amino acids in genomes by recruiting either one of the stop codons or a subset of a codon series for a particular amino acid and engineering the cognate tRNA and aminoacyl-tRNA synthetase (46). The application of this methodology has already allowed incorporation in E. coli proteins of over 30 unnatural amino acids, in a striking demonstration of the potential malleability of the code (45, 46).

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