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PubMed1982

An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

Animals↗

PubMed1982

Symmetry characteristics of the genetic code.

The symmetric pattern of codon degeneracies is discussed by using empirical arguments processed within a group-theoretic framework. It is reasoned that the genetic code is a relation rather than a mapping, and the symmetry of a relation defined on the codons is investigated. The principal results are (i) a new extraction of the basic symmetry inherent in the standard genetic code; (ii) the unification of the symmetry of ambiguous codon assignments with that of the standard genetic code; and (iii) the primacy of the concept of a biological context as that device which degenerates the code relation to a mapping.

Codon↗

PubMed1989

How old is the genetic code? Statistical geometry of tRNA provides an answer.

The age of the molecular organization of life as expressed in the genetic code can be estimated from experimental data. Comparative sequence analysis of transfer RNA by the method of statistical geometry in sequence space suggests that about one-third of the present transfer RNA sequence divergence was present at the urkingdom level about the time when archaebacteria separated from eubacteria. It is concluded that the genetic code is not older than, but almost as old as our planet. While this result may not be unexpected, it was not clear until now that interpretable data exist that permit inferences about such early stages of life as the establishment of the genetic code.

Anticodon↗

PubMed1990

The genetic code in mitochondria and chloroplasts.

The universal genetic code is used without changes in chloroplasts and in mitochondria of green plants. Non-plant mitochondria use codes that include changes from the universal code. Chloroplasts use 31 anticodons in translating the code; a number smaller than that used by bacteria, because chloroplasts have eliminated 10 CNN anticodons that are found in bacteria. Green plant mitochondria (mt) obtain some tRNAs from the cytosol, and genes for some other tRNAs have been acquired from chloroplast DNA. The code in non-plant mt differs from the universal code in the following usages found in various organisms: UGA for Trp, AUA for Met, AGR for Ser and stop, AAA for Asn, CUN for Thr, and possibly UAA for Tyr. CGN codons are not used by Torulopsis yeast mt. Non-plant mt, e.g. in vertebrates, may use a minimum of 22 anticodons for complete translation of mRNA sequences. The following possible causes are regarded as contributing to changes in the non-plant mt: directional mutation pressure, genomic economization, changes in charging specificity of tRNAs, loss of release factor RF2, changes in RF1, changes in anticodons, loss of lysidine-forming enzyme system, and disappearance of codons from coding sequences.

Animal Population Groups↗

PubMed2001

Topological nature of the genetic code.

A model for topological coding of proteins is proposed. The model is based on the capacity of hydrogen bonds (property of connectivity) to fix conformations of protein molecules. The protein chain is modeled by an n -arc graph with the following elements: vertices (alpha -carbon atoms), structural edges (peptide bonds) and connectivity edges (virtual edges connecting non-adjacent atoms). It was shown that 64 conformations of the 4-arc graph can be described in the binary system by matrices of six variables which form a supermatrix containing four blocks. On the basis of correspondences between the pairs of variables in matrices and four letters of the genetic code matrices and supermatrix are converted, respectively, into the triplets and the table of the genetic code. An algorithm admitting computer programming is proposed for coding the n -arc graph and protein chain. Connectivity operators (polar amino acids) are assigned to blocks of triplets coding for cyclic conformations (G, A-in the second position), while anti-connectivity operators (non-polar amino acids) correspond to blocks of triplets coding for open conformations (C, U-in the second position). Amino acids coded by triplets differing by the first base have different structures. The third base for C, U and G, A is degenerated. Properties of the real genetic code are in full agreement with the model. The model provides an insight into the topological nature of the genetic code and can be used for development of algorithms for the prediction of the protein structure.

Algorithms↗

PubMed2006

Genetic code from tRNA point of view.

The possible codon-anticodon pairings follow the standard genetic code, yet in a different mode. The corresponding rules for decoding sequence of the codons in mRNA with tRNA may be called "tRNA code". In this paper we analyse the mutational and translational stability of such tRNA code. Our approach is based on the model of "ambiguous intermediate" and on the study of underlying block structure and Eulerean graph technique. It is shown that the wobble rules and the reduced number of tRNA anticodons strongly affect the mutational and translational stability of the code. The selection of tRNA anticodons, besides the optimization of translation, also ensures the more reliable start and, to a lesser extent, the stop of translation. The attribution of tRNA anticodons to the groups [WWW, WWS, SWW, SWS] and [SSS, SSW, WSS, WSW] as well as [MMM, MMK, KMM, KMK] and [KKK, KKM, MKK, MKM] clearly correlates with class I and class II aminoacyl-tRNA synthetases and obeys the principle of the optimal coding in both cases. Both W-S and M-K groupings also refer to the encoding of amino acids with the large and small side-chain volumes, which may provide such an attribution. The higher variability of tRNA code agrees with the suggestions that the variations in an assignment of tRNA anticodons may serve as the driving force generating the different variants of the genetic code.

Amino Acyl-tRNA Synthetases↗

PubMedDate not supplied

A model for the coevolution of the genetic code and the process of protein synthesis: Review and assessment.

The contemporary genetic code and the process of protein biosynthesis most assuredly evolved from a simpler code and process. We believe that there was obligatory coevolution of the two and that the earlier code and process must have involved a more direct linkage between the amino acids and the information macromolecule. We propose that an early form of translating existed in which amino acids were attached directly to the 'messenger' RNA along the backbone as 2'OH aminoacyl esters. These esters then condensed with each other on the RNA backbone yielding a peptide covalently attached to the RNA, without the use of tRNA's and ribosomes. THis presentation is concerned with experimental data which indicate that such a simple translation system is possible and must have involved the following steps: (1) formation of the aminoacyl adenylate anhydride, (2) transfer of the amino acid from the adenylate to immidazole, (3) transfer of the amino acid from imidazole to 2'OH groups along the backbone of RNAs, (4) condensation of the amino acids to yield peptides. Steps (1)-(3) have been confirmed in chemical systems. Our preliminary evidence indicates step (4) is also possible. The aminoacylation of polyribonucleotides and the subsequent formation of peptides is a dynamic and experimentally accessible system for studying genetic coding specfities and our present studies are now concentrated on step (4), looking for such specifities.

Acylation↗

PubMed1983

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.

Base Sequence↗

PubMed1981

First approximation of a stereochemical rationale for the genetic code based on the topography and physicochemical properties of "cavities" constructed from models of DNA.

To examine the question of whether or not the genetic code has a stereochemical basis, we used artificial constructs of the topography and physicochemical features of unique "cavities" formed by removal of the second codon base in B-DNA. The effects of base changes on the stereochemistry of the cavities are consistent with the pattern of the genetic code. Fits into the cavities of the side chains of the 20 L amino acids involved in protein synthesis can be demonstrated by using conventional physicochemical principles of hydrogen bonding and steric constraints. The specificity of the fits is remarkably consistent with the genetic code.

Amino Acids↗

PubMed1996

The genetic code and cyclic codes.

We proposed previously a cyclic code made of 22 triplets, which we now call the AB code. It is made up of the following chain: AUGGUGCCAUUCAAGACUAUGA. The letters A, U, C, G represent the classical symbols of the (purine and pyrimidine) bases of the genetic code. This chain presents the following features: (1) when it is in cyclic form, it begins with the initiation codon AUG, ends with the termination codon UGA, and it can be read triplet after triplet by choosing 1 and only 1 representative of each synonymy class in the classical degenerate genetic code made of 64 triplets. The chain, therefore, possesses 1 and only 1 codon for each amino-acid; (2) except for the doublet CG, triplets of the chain begin with the 15 other possible doublets of bases (satisfying the "wobble" hypothesis presented by Crick); (3) it corresponds (except for 1 base) to the "loop" part of the CEnothera mitochondrial Gly-tRNA; (4) it can be modified, without loss of the properties (1) and (2), in such a way as to have 15 bases in common with the loop part of other mitochondrial tRNA's considered as primitive, like Ala-, Pro- and Arg-tRNA; (5) it contains the most frequent triplets, but not the most rare ones, appearing in the genome of numerous species; (6) it exhibits a coherent internal structure with respect to the molecular weight of its triplets. This structure, also found in the loop part of mitochondrial tRNA's, contains an excess of AU bases with respect to GC bases. This fact has no explanation in the classical probabilistic model of the tRNA's. Therefore, we propose the cyclic AB code as a primitive genetic structure with the essential coding properties of the present genetic code.

Codon↗

PubMed2004

Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire.

Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.

Amino Acids↗

PubMed2003

The case for an error minimizing standard genetic code.

Since discovering the pattern by which amino acids are assigned to codons within the standard genetic code, investigators have explored the idea that natural selection placed biochemically similar amino acids near to one another in coding space so as to minimize the impact of mutations and/or mistranslations. The analytical evidence to support this theory has grown in sophistication and strength over the years, and counterclaims questioning its plausibility and quantitative support have yet to transcend some significant weaknesses in their approach. These weaknesses are illustrated here by means of a simple simulation model for adaptive genetic code evolution. There remain ill explored facets of the 'error minimizing' code hypothesis, however, including the mechanism and pathway by which an adaptive pattern of codon assignments emerged, the extent to which natural selection created synonym redundancy, its role in shaping the amino acid and nucleotide languages, and even the correct interpretation of the adaptive codon assignment pattern: these represent fertile areas for future research.

Amino Acids↗

PubMed1982

Thermodynamic approach to a possible theory of the evolution of a genetic code.

One of the distinctive features of a biological system is its remoteness from equilibrium: for the treatment of the information exchanged by these systems with the external world the concept of information amount is not sufficient because for nonequilibrium systems we need further specifications about information, i.e. its value. We defined the information value for a genetic code. The comparison of the results we had applying such a definition to the three genetic codes found in nature shows that our definition described the system of transmission and reception of information in a biological organism very well and that the information value of a genetic code can be considered as an index of its efficiency, i.e. of its ability to minimize the effects of a mutation of the genotype on the phenotype. Otherwise, our results show that the information value, and hence the efficiency of the three known codes is the same and suggest that the prerequisite of the evolution of the codes is the preservation of this value.

Biological Evolution↗

PubMed2001

Genview and Gencode : a pair of programs to test theories of genetic code evolution.

GENVIEW: and GENCODE: are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. GENVIEW: provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. GENVIEW: is a graphical user interface (GUI) program which runs on Linux, Unix and Microsoft Windows platforms and is based on the GTKf + toolkit. GENVIEW: outputs ASCII configuration files which are interpreted by GENCODE: to perform an analysis. GENCODE: is available for the same platforms as GENVIEW.

Evolution, Molecular↗

PubMed1985

A hardware interpretation of the evolution of the genetic code.

A quantitative rationale for the evolution of the genetic code is developed considering the principle of minimal hardware. This principle defines an optimal code as one that minimizes for a given amount of information encoded, the product of the number of physical devices used by the average complexity of each device. By identifying the number of different amino acids, number of nucleotide positions per codon and number of base types that can occupy each such position with, respectively, the amount of information, number of devices and the complexity, we show that optimal codes occur for 3, 7 and 20 amino acids with codons having a single, two and three base positions per codon, respectively. The advantage of a code of exactly 4 symbols is deduced, as well as a plausible evolutionary pathway from a code of doublets to triplets. The present day code of 20 amino acids encoded by 64 codons is shown to be the most optimal in an absolute sense. Using a tetraplet code further evolution to a code in which there would be 55 amino acids is in principle possible, but such a code would deviate slightly more than the present day code from the minimal hardware configuration. The change from a triplet code to a tetraplet code would occur at about 32 amino acids. Our conclusions are independent of, but consistent with, the observed physico-chemical properties of the amino acids and codon structures. These correlations could have evolved within the constrains imposed by the minimal hardware principle.

Amino Acids↗

PubMed2002

Genetic code origin: are the pathways of type Glu-tRNA(Gln) --> Gln-tRNA(Gln) molecular fossils or not?

A logical-evolutionary analysis is conducted to clarify whether or not pathways of type Glu-tRNA(Gln) --> Gln-tRNA(Gln) are molecular fossils of the mechanism that gave rise to the evolutionary organization of the genetic code. The result of this analysis is that these pathways are most likely a manifestation of this mechanism. This provides strong evidence in favor of the coevolution theory of genetic code origin, as this theory is based on the amino acid biosynthetic transformation taking place on tRNA-like molecules which imprinted the genetic code structuring. Comments on the different interpretations of these pathways found in the literature are also provided.

Evolution, Molecular↗

PubMed1983

[Genetic code: codon bases--the symbols of amino acid synthesis and catabolism pathways].

The correlations between genetic codes of amino acids and pathways of synthesis and catabolism of carbon backbone of amino acids are considered. Codes of amino acids which are synthesized from oxoacids of glycolysis, the Krebs cycle and glyoxalic cycle via transamination without any additional chemical reactions, are initiated with guanine (alanine, glutamic and aspartic acids, glycine). Codons of amino acids which are formed on the branches of glycolysis at the level of compounds with three carbon atoms, begin with uracil (phenylalanine, serine, leucine, tyrosine, cysteine, tryptophan). Codes of amino acids formed from aspartate begin with adenine (methionine, isoleucine, threonine, asparagine, lysine, serine), while those of the amino acids formed from the compounds with five carbon atoms (glutamic acid and phosphoribosyl pyrophosphate) begin with cytosine (arginine, proline, glutamine, histidine). The second letter of codons is linked to catabolic pathways of amino acids: most of amino acids entering glycolysis and the Krebs cycle through even-numbered carbon compounds, have adenine and uracil at the second position of codes (A-U type); most of amino acids entering the glycolysis and the Krebs cycle via odd-numbered carbon compounds, have codons with guanine and cytidine at the second position (G-C type). The usage of purine and pyrimidine as the third letter of weak codones in most of amino acids is linked to the enthropy of amino acid formation. A hypothesis claiming that the linear genetic code was assembled from the purine and pyrimidine derivatives which have acted as participants of primitive control of amino acid synthesis and catabolism, is suggested.

Amino Acid Sequence↗

PubMed1989

The extension reached by the minimization of the polarity distances during the evolution of the genetic code.

The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization of the polarity distances, by the genetic code during its formation.

Amino Acids↗