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PubMed1987

Information theory and the genetic code.

The genetic code, which directs the protein biosynthesis, is an information system. Although all its details are not known at present, its essential characteristics are elucidated, as well for the replication or transcription as for the translation of the genetic message. A coherent picture now appears, which reveals the existence of an universal structure, the most fundamental features of which seem to obey some logic. A systematic approach has been devised, which aims to their integration in a theorectical scheme: many features of the code table can thus be interpreted as resulting from a unique principle of best resistance against the effects of mutations. Any group of triplets or amino-acids can be considered along this line. It is more difficult however, to analyse the coexistence of two (or more) different groups. In this work, we propose to extend our optimization principle into a more general one, which includes the notion of information as defined by Shannon. We explore some consequences of this new principle in the most simple models that one can build for the origin and evolution of the genetic code.

Genetic Code↗
PubMed1983

[The genetic code and cyclic codes].

The genetic code can be considered as degenerated from a minimal cyclic code, whose maximal chain is given. We study the relation of this code with the cyclic code corresponding to the 64 triplets. Finally we compare the minimal code to that obtained from a binary cyclic code.

Adenine↗
PubMedDate not supplied

[Asymmetry in the symmetric structure of the genetic code].

The genetic code is characterized by hidden symmetry. Amino acids possessing common antiamino acids are located symmetrically in the graphic models of the code. There is only one exception--apolar amino acids V, M, I, L and F are asymmetrically arranged. Asymmetric disposition of these amino acids is apparently due to divergence in the course of structural evolution of amino acid families as a result of inclusion of new members into the coding system.

Algorithms↗
PubMed2001

Molecular evolution: Please release me, genetic code.

The genetic code is no longer universal, even in non-mitochondrial genomes. Recent studies have implicated the eukaryotic release factor eRF1 in mediating coding changes that are not as inconceivable as once thought. Specific residues in eRF1 proteins can be correlated with specific code changes in a wide variety of taxa.

Animals↗
PubMed2005

A mechanism for the association of amino acids with their codons and the origin of the genetic code.

The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.

Amino Acids↗
PubMed2026

Reading another hidden message in the genetic code.

The genetic code determines not only the amino acid sequences of proteins but also mRNA stability. How is this hidden message read? Hia and colleagues have now identified human DHX29 as a reader of the mRNA stability code carried by codons, providing new mechanistic insights into translation-coupled gene regulation.

Genetic Code↗
PubMed1992

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.

Base Sequence↗
PubMed2003

Death, taxes, and the genetic code?

The genetic code is an enduring feature of biology: only rare circumstances result in changes to translation of the code, at least in nature. Researchers are devising methods to engineer ribosome-synthesized polypeptides containing novel and potentially useful amino acids.

Amino Acids↗
PubMed1983

The significance of redundancy in the genetic code.

The genetic code has an inherent bias towards some amino acids because of the variable number of synonymous codons per amino acid. In proteins generally, this bias is expressed in the relative proportions of the twenty amino acids. It is suggested that even though neutral mutation may be responsible for the expression of this bias, the latter could be providing a positive advantage by directing mutation to introduce chemically simpler and more immutable amino acids where selective criteria have become relaxed.

Amino Acid Sequence↗
PubMedDate not supplied

Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity.

Characteristic features of tRNA such as the anticodon sequence and modified nucleotides in the anticodon loop are thought to be crucial effectors for promoting or restricting codon reassignment. Our recent findings on basepairing rules between anticodon and codon in various metazoan mitochondria suggest that the complete loss of a codon is not necessarily essential for codon reassignment to take place. We postulate that a possible competition between two tRNAs with cognate anticodon sequences towards the relevant codon to be varied has a potential role in codon reassignment. Our proposition can be viewed as an expanded version of the codon capture theory proposed by Osawa and Jukes (J Mol Evol 28: 271-278, 1989).

Animals↗
PubMed2002

The impact of message mutation on the fitness of a genetic code.

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness "load" that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code.

Amino Acids↗
PubMed2005

On the coevolution of genes and genetic code.

The canonical genetic code acts efficiently in minimizing the effects of mistranslations and point mutations. In the work presented we have also considered the effects of single nucleotide insertions and deletions on the optimality of the genetic code. Our results suggest that the canonical genetic code compensates for the ins/del mutations as well as mistranslations and point mutations. On the other hand, we highlighted the point that ins/del mutations have a lesser impact on the selected genes of Saccharomyces cerevisiae compared to randomly generated ones. We hypothesized that the codon usage preferences in S. cerevisiae genes are responsible for the higher efficiency of translation machinery in this organism. Our results support the conjecture that codon usage preferences render the genetic code more effective in minimizing the effects of ins/del mutations.

Animals↗
PubMed2004

Symmetry preservation in the evolution of the genetic code.

The standard genetic code is found to exhibit an exact symmetry under a finite group of order 4 known in mathematics as the Klein group. The same symmetry is also present in almost all non-standard codes, mitochondrial as well as nuclear. Analysis of the phylogenetic tree for the evolution of the mitochondrial codes reveals that all changes along the main line of evolution preserve this symmetry, with a tendency towards symmetry enhancement. In the side branches of the evolutionary tree, the majority of changes also respect the symmetry. The few exceptional cases where it is broken correspond to reassignments that appear to be unstable or incomplete. Since the Klein group emerges naturally from the symplectic model for the prebiotic evolution that has led to the standard code, we interpret these results as lending support to the hypothesis that this symmetry has been selected during the evolution of the genetic code, not only before but also after establishment of the standard code.

Animals↗
PubMed2006

Is there a twenty third amino acid in the genetic code?

The universal genetic code includes 20 common amino acids. In addition, selenocysteine (Sec) and pyrrolysine (Pyl), known as the twenty first and twenty second amino acids, are encoded by UGA and UAG, respectively, which are the codons that usually function as stop signals. The discovery of Sec and Pyl suggested that the genetic code could be further expanded by reprogramming stop codons. To search for the putative twenty third amino acid, we employed various tRNA identification programs that scanned 16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals. Our data suggest that the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely.

Amino Acids↗
PubMed2004

Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code.

The expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties.

Aequorin↗
PubMed2004

Evolving new genetic codes.

Although the genetic code is almost universal, natural variations exist that have caused evolutionary biologists to speculate about codon evolution. There are two predominant hypotheses that specify either a gradual (ambiguous intermediate) or stochastic (codon capture) change in the code. These hypotheses are similar to two biotechnology techniques that have been used to engineer the genetic code: a 'top down' approach, in which the whole organism is evolved for the ability to incorporate unnatural amino acids, and a 'bottom up' approach, in which aminoacyl-tRNA synthetases and their cognate tRNAs are engineered. The biotechnology experiments provide insights into natural codon evolution, and a combination of these approaches should enable the evolution of organisms that can incorporate unnatural amino acids throughout their proteomes.

Journal Article↗