24 Dynamics of the Genetic Code

Abstract

Shape is crucial for catalysis. In the hypothetical RNA World, the replicative RNAs, which constituted the hereditary information, also functioned as the “shapes” for catalysis. There was no need for decoding. When decoding originated, presumably discrimination between alternate coding possibilities was initially weak, but once one mode became predominant, there would have been selection to lock it in with increasing efficiency. Nontriplet translocation and nonstandard meaning of code words presumably generally approached a minimum compatible with speed and energy use optimization. In the present day, nonstandard decoding alternatives generally just contribute to a low level of translational errors, of which frameshifting errors (Atkins et al. 1972; Kurland 1992) are a grave type. However, some unknown proportion of genes in probably all organisms has special sites where efficient decoding alternatives are programmed into the mRNA. The group of mechanisms involved in redirection of decoding is called “recoding” (Gesteland et al. 1992). Either the evolution of the ability to perform recoding was coincident with evolution of the ability of the decoding apparatus to perform standard decoding, or it is a later sophistication. Of course, the answer is unknown, but the conservation of the required mRNA signals presented below indicates that recoding has been part of the decoding repertoire for at least several hundred million years and must therefore be favored by evolution. This is clearly distinct from the error rate that is a trade-off between energy expenditure, speed, and accuracy. In the latter case, evolution has optimized the balance as a whole.