Evolution of the Genetic Code.
Until the variant codes were discovered, most felt that the genetic code must have been established early in the history of life and then, by necessity, remained inviolate. Any mutations that altered the code, it was argued, would have such detrimental effects on proteins as to render such mutations lethal. How then are we to explain the existence of so much variation in the genetic code? Syozo Osawa has written a fascinating book which provides a compelling answer in the form of the "Osawa-Jukes codon capture theory." However, the book goes beyond the codon capture theory, summarizing much of what is known about the genetic code and those aspects of translation that help understand codon usage, G-C percentage, and code evolution.
For Osawa, the primal force driving code evolution is "directional mutation pressure." In his earlier work, Osawa surveyed the genomic G+C content of a variety of bacteria and discover that it could be as low as 25% in species like Mycoplasma capricolum and as high as 75% in species like Micrococcus luteus. Additionally, there is variation within the genome of a species for G+C content. In all species, the G+C content in the second position of codons is approximately 40%. By contrast, the variation in the third position of codons is even more extreme than for entire genomes, ranging from 10% to 90%. In Mycoplasma, for example, codons ending in A or U are used almost exclusively whenever the degeneracy of the code allows. In Osawa's view, G+C content itself is a neutral trait. The variation in G+C content at silent sites in coding regions and in spacer DNA is due to directional mutation pressure. In some species, the mutation spectrum pushes the nucleotide composition toward high A+T, in other species, to high G+C.
The codon capture theory follows almost immediately. In species with highly biased base frequencies, certain codons will not be used at all. In fact, in some of these species not only are certain codons not used, but the genes for the corresponding transfer RNAs appear to be missing as well. These unassigned codons could be used for new amino acids without any negative consequences for other proteins. Osawa fills in the intermediate steps in a detailed discussion of the evolution of new tRNAs and synthetases by gene duplications and subsequent change of function. Ironically, this theory uses a neutral trait, G+C content, to drive the evolution of the most critical of all traits. the genetic code.
The codon capture theory is very appealing as it allows for the evolution of the code without the horrors of amino acid substitutions in a large number of proteins. Osawa is so convinced of the ease of codon capture that he gives a nonparsimonious phylogeny of yeasts that involves first a switch of CUG form leucine to serine, and then a switch back. Others who feel the code is difficult to change might have argued for a phylogeny with only a single switch in the use of CUG.
Evolution of the Genetic Code is an interesting book, but it is not an easy read. The book is dripping with information, yet has little in the way of helpful illustrations as learning aids. If, like me, you have trouble memorizing genetic codes and a plethora of organism-specific wobble rules, you will be constantly referring back to tables for these particulars. Nonetheless, the book is quite clear, if terse, and at no time did I find the prose ambiguous. However, the editing is atrocious. There are many typographical errors, in one case the caption was left off a table, and the grammar and style should have had the careful attention of a good editor. Oxford University Press should be ashamed for charging $115 for a 205-page book without investing more resources in its production.
Scientifically, the book glosses over some points that will be of particular interest to the readers of Evolution. Perhaps the most conspicuous of these is the nature of the directed mutation pressure. In Osawa's view, G+C content is a neutral trait that reflects the mutation spectum. The mutation spectrum itself must vary between species, presumably because of variation in the nature of the DNA repair enzymes. Whatever evolutionary forces are shaping the repair enzymes, the effects of that evolution on the genomic G+C content must be irrelevant. Surprisingly, Osawa does not discuss the evolution of the mutation pressure at all, so we cannot know precisely why he thinks it varies so much between species or what forces are causing the evolution.
Alternatively, G+C content may be a selected phenotype. Support for this view comes from the oft stated "fact" that bacteria living at higher temperatures have higher G+C content (I have not been able to verify this as a generality) and the fact that the G+C content of third positions is more extreme than that of spacer DNA (see figure 4.3 of Osawa's book). Whether G+C content is selected or not has little relevance to the codon capture theory but is worthy of investigation in its own right.
Perhaps the greatest weakness of the book is its discussion of the evolution of codon usage. In Osawa's view. much of the variation in codon usage between species is due to mutation pressure. He does not discuss or even cite any of the work of Michael Bulmer, Adam Eyre-Walker, Paul Sharp, Hiroshi Akashi, and others, which has shown that codon usage evolution is quite complex, involving translation efficiency, accuracy, and various pleiotropic effects collectively called "conficting selection" by Eyre-Walker. If codon usage is selected, then mutation pressure will not be the sole determinate of base composition in third positions, and the story told by Osawa becomes more complicated.
Oh yes, there is a chapter on the origin of the code and no, it is still not known how the earliest codes were established. Osawa does describe an interesting theory due to Maizels and Weiner and summarizes the supporting observations. While the "true" sequence of events may not be known, the sophistication of the discussion has gone far beyond the early stereochemical and frozen-accident theories and makes interesting reading. Osawa's own contributions focus on the more approachable problems of the refinements of the code.
Even with its faults, this book is well worth reading. Although not light reading, the richness of the phenomenology and the profundity of the theories make the effort worthwhile.
CHANGING CIPHERS, Evolution of the Genetic Code. Syozo Osawa. 1995. Oxford University Press, New York. 205 pp. ISBN 0-19-854781-1. HB $115.00.
John H. Gillespie, Section of Evolution and Ecology, University of California, Davis. California 95616 E-mail: email@example.com
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|Author:||Gillespie, John H.|
|Article Type:||Book Review|
|Date:||Aug 1, 1996|
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