Recent evidence for evolution of the genetic code.

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.     

Recent advances in genetic code engineering in Escherichia coli

The expansion of the genetic code is gradually becoming a core discipline in Synthetic Biology. It offers the best possible platform for the transfer of numerous chemical reactions and processes from the chemical synthetic laboratory into the biochemistry of living cells. The incorporation of biologically occurring or chemically synthesized non-canonical amino acids into recombinant proteins and even proteomes via reprogrammed protein translation is in the heart of these efforts. Orthogonal pairs consisting of aminoacyl-tRNA synthetase and its cognate tRNA proved to be a general tool for the assignment of certain codons of the genetic code with a maximum degree of chemical liberty. Here, we highlight recent developments that should provide a solid basis for the development of generalist tools enabling a controlled variation of chemical composition in proteins and even proteomes. This will take place in the frame of a greatly expanded genetic code with emancipated codons liberated from the current function or with totally new coding units.     

Mistranslation of the genetic code

During mRNA decoding at the ribosome, deviations from stringent codon identity, or “mistranslation,” are generally deleterious and infrequent. Observations of organisms that decode some codons ambiguously, and the discovery of a compensatory increase in mistranslation frequency to combat environmental stress have changed the way we view “errors” in decoding. Modern tools for the study of the frequency and phenotypic effects of mistranslation can provide quantitative and sensitive measurements of decoding errors that were previously inaccessible. Mistranslation with non-protein amino acids, in particular, is an enticing prospect for new drug therapies and the study of molecular evolution.     

Working of the genetic code

The genetic code is used differently by different kinds of species. Each type of genome has a particular coding strategy, that is, choices among degenerate bases are consistently similar for all genes therein. This uniformity in the selection between degenerate bases within each taxonomic group has been discovered by applying new methods to the study of coding variability. It is now possible to calculate relative distances between genomes, or genome types, based on use of the codon catalog by the mRNAs therein.     

Study of the genetic code adaptability by means of a genetic algorithm

We used simulated evolution to study the adaptability level of the canonical genetic code. An adapted genetic algorithm (GA) searches for optimal hypothetical codes. Adaptability is measured as the average variation of the hydrophobicity that the encoded amino acids undergo when errors or mutations are present in the codons of the hypothetical codes. Different types of mutations and point mutation rates that depend on codon base number are considered in this study. Previous works have used statistical approaches based on randomly generated alternative codes or have used local search techniques to determine an optimum value. In this work, we emphasize what can be concluded from the use of simulated evolution considering the results of previous works. The GA provides more information about the difficulty of the evolution of codes, without contradicting previous studies using statistical or engineering approaches. The GA also shows that, within the coevolution theory, the third base clearly improves the adaptability of the current genetic code.     

Evolution of a genetic code simulated with the computer

A simple selforganizing model system of molecules is considered and it is demonstrated by a computer simulation, that a genetic code of 16 elements (aminoacids) can gradually be formed by such a system in the course of many generations. By a number of rare chance events, each suppressing other events of equal a priori probability, a single code results out of an immense number of possible codes of the same a priori probability. The result is discussed in relation to the uniqueness of the genetic code in living systems. The computer simulation emphasizes a particular step in a model pathway discussed elsewhere consisting of many assumed physicochemical steps leading to a genetic apparatus.     

Development of the genetic code: Insights from a fungal codon reassignment

The high conservation of the genetic code and its fundamental role in genome decoding suggest that its evolution is highly restricted or even frozen. However, various prokaryotic and eukaryotic genetic code alterations, several alternative tRNA-dependent amino acid biosynthesis pathways, regulation of tRNA decoding by diverse nucleoside modifications and recent in vivo incorporation of non-natural amino acids into prokaryotic and eukaryotic proteins, show that the code evolves and is surprisingly flexible. The cellular mechanisms and the proteome buffering capacity that support such evolutionary processes remain unclear. Here we explore the hypothesis that codon misreading and reassignment played fundamental roles in the development of the genetic code and we show how a fungal codon reassignment is enlightening its evolution.     

Optimization and the genetic code

The present paper will focus on the relation between the structure of the table of the genetic code and the evolution of primitive organisms: it will be shown that the organization of the code table according to an optimization principle based on the notion of resistance to errors can provide a criterium for selection. The ordered aspect of the genetic code table makes this result a plausible starting point for studies of the origin and evolution of the genetic code: these could include, besides a more refined optimization principle at the logical level, some effects more directly related to the physico-chemical context, and the construction of realistic models incorporating both aspects.     

Hemoglobin and the genetic code

Summary One-half of the twenty amino acids of the genetic code are just one mutational step away from the chain-terminator codons UAA, UAG, and UGA. It is postulated that somatic mutation to terminator is a hazard to which the organism has had to respond by adjusting certain proteins in the direction of fewer mutable residues. This view is supported by calculations based on the primary structure of five of the human hemoglobin chains. Each chain is scored for mutability to terminator in accord with the numbers and kinds of amino acids present. Among the adult chains, the most essential one, the alpha, has lowest mutability. The beta and delta follow, and in order of the presumed harm to the organism of a shortage of chain copies. Ante-natal chains tend to have higher mutabilities, supporting the view that cumulative mutational change in DNA can do little harm if the gene ceases to transcribe early in life. Two other predictions based on the supposition of effective selection against mutability to terminator are also met: chain length of polypeptides is negatively correlated with their scores for mutability to terminator, and examination of the recently determined sequence of beta messenger RNA shows preferential use of codons that are not readily mutable to terminator.Supported in part by the National Institutes of Health, Grant HL-16005     

The non-universality of the genetic code: the universal ancestor was a progenote

The coevolution theory of genetic code origin (Wong, J.T. 1975, Proc. Natl Acad. Sci. U.S.A.72, 1909-1912) is assumed here to be substantially correct. This theory is based on the strict parallelism of the biosynthetic relationships between amino acids and the organization of the genetic code and postulates that these relationships were mediated by tRNA-like molecules on which the biosynthetic transformations between precursor and product amino acids took place. These transformations underlay the mechanism that gave rise to genetic code organization. One of the pathways which represents these transformations found in current organisms, and which are thus probably molecular fossils, is the Met-tRNA(fMet)-->fMet-tRNA(fMet)pathway. This pathway is present only in the Bacteria domain. This along with other observations and arguments leads us to believe that this pathway is a clear violation of the universality of the genetic code. Furthermore, the presence of this pathway only in the Bacteria domain seems to imply that the translation apparatus was still rapidly evolving when this pathway was fixed. This, in turn, appears to imply that the last universal common ancestor was a progenote. Finally, the implications that the finding of this pathway has for the stereochemical theory of genetic code origin are discussed.     

Noise immunity of the genetic code

Error detection and correction properties are fundamental for informative codes. Hamming's distance allows us to study this noise resistance. We present codes characterized by the resistance optimization to nonsense mutational effects. The calculation of the cumulated Hamming's distance allowing to determine the number of optimal codes and their structure can be detailed. The principle of these laws of optimization of resistance consists of choosing constituent codons connected by mutational neighbouring in such a way that random application of mutations on such a code minimize the occurrence of nonsense n-uplets or terminators. New coding symmetries are then described and screened using Galois's polynomials properties and Baudot's code. Such a study can be applied to any length of the codons. Here we present the principles of this optimization for the most simple doublet codes. Another constraint is discussed: the distribution of optimal subcodes for synonymity and the frequencies of utilization of the different codons.We compare these results to those of the present genetic code, and we observe that all coded amino acids (except the particular case of SER) are using optimal sub-codes of synonymity.This work suggests that the appearance of the genetic code was provoked by mutations while optimizing on several levels its resistance to their effects. Thus genetic coding would have been the best automata that could be produced in prebiotic conditions.