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PubMed1992

The evolution of aminoacyl-tRNA synthetases, the biosynthetic pathways of amino acids and the genetic code.

In this paper the partition metric is used to compare binary trees deriving from (i) the study of the evolutionary relationships between aminoacyl-tRNA synthetases, (ii) the physicochemical properties of amino acids and (iii) the biosynthetic relationships between amino acids. If the tree defining the evolutionary relationships between aminoacyl-tRNA synthetases is assumed to be a manifestation of the mechanism that originated the organization of the genetic code, then the results appear to indicate the following: the hypothesis that regards the genetic code as a map of the biosynthetic relationships between amino acids seems to explain the organization of the genetic code, at least as plausibly as the hypotheses that consider the physicochemical properties of amino acids as the main adaptive theme that lead to the structuring of the code.

Amino Acids↗
PubMed2005

Coevolution theory of the genetic code at age thirty.

The coevolution theory of the genetic code, which postulates that prebiotic synthesis was an inadequate source of all twenty protein amino acids, and therefore some of them had to be derived from the coevolving pathways of amino acid biosynthesis, has been assessed in the light of the discoveries of the past three decades. Its four fundamental tenets regarding the essentiality of amino acid biosynthesis, role of pretran synthesis, biosynthetic imprint on codon allocations and mutability of the encoded amino acids are proven by the new knowledge. Of the factors that guided the evolutionary selection of the universal code, the relative contributions of Amino Acid Biosynthesis: Error Minimization: Stereochemical Interaction are estimated to first approximation as 40,000,000:400:1, which suggests that amino acid biosynthesis represents the dominant factor shaping the code. The utility of the coevolution theory is demonstrated by its opening up experimental expansions of the code and providing a basis for locating the root of life.

Amino Acids↗
PubMed2003

Translocation properties of primitive molecular machines and their relevance to the structure of the genetic code.

We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a follow-up to our previous work (Aldana et al., 1998, Martínez-Mekler et al., 1999a,b), we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles (rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi-one-dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present-day genetic sequences, we show that the above property is enhanced for coding regions. Intergenic sequences display a behavior closer to the random situation. We argue that this dynamical property could be one of the underlying causes for the three-base codon structure of the genetic code

Animals↗
PubMed1989

The distribution of amino acids in the genetic code.

By introducing a mutational deterioration function MD and a principle of approximate minimum of the function, we have deduced the distribution of amino acids in genetic code, which includes the degeneracy rule of codons, the global extreme of genetic code from codon interactions and the hydrophobicity domain of the prevalent (standard) code.

Amino Acids↗
PubMed1994

Compositional frequencies of amino acids in the proteins and the genetic code.

It was found that amino acid compositional frequencies in proteins demonstrate a pseudosymmetry pattern in respect of the genetic code arrangement as we discussed in earlier papers (Siemion and Stefanowicz, 1992a, BioSystems, 27, 77-84; Siemion and Stefanowicz, 1992b, Bull. Pol. Acad. Sci., Chem. 40, 11-20; Siemion, 1994, BioSystems, 32, 25-35). The type of pseudosymmetry observed is very similar to that found in the changes of Chou-Fasman P alpha conformational parameters within the genetic code arrangement. It is also shown that the compositional frequencies of amino acids belonging to the 'G' and 'C' families of codons (excluding UCN Ser codons) change linearly with the sequence of the one-step mutations expected by our arrangement of proper codons.

Amino Acid Sequence↗
PubMed2001

A blind empiricism against the coevolution theory of the origin of the genetic code.

Ronneberg et al. (Proc Natl Acad Sci USA 97:13690-13695, 2000) recently suggested abandoning the coevolution theory of genetic code origin on the basis of two pieces of evidence. They (1) criticize the use of several pairs of amino acids in a precursor-product relationship to support this theory and (2) suggest a new set of codes in which to investigate the statistical bases of the coevolution theory, reaching the conclusion that this theory is not statistically validated in this set. In this paper I critically analyze the robustness of these conclusions. Observations and arguments lead to the belief that the pairs of amino acids in a precursor-product relationship originally used by the coevolution theory are such, or may at least be interpreted as such, and are therefore a manifestation of this theory. Furthermore, the new set of codes that Ronneberg et al. suggest is open to criticism and is thus substituted by the set of amino acid permutation codes, in which even the pairs of amino acids they favor end up by supporting the coevolution theory. Overall, the analysis seems to show that the paper by Ronneberg et al. is of minor scientific value while the coevolution theory seems to be one of the best theories at our disposal for explaining the evolutionary organisation of the genetic code and is, contrary to their claims, statistically well validated.

Base Pairing↗
PubMed2000

From amino acid landscape to protein landscape: analysis of genetic codes in terms of fitness landscape.

Assigning the values of a certain physicochemical property for individual amino acids to the corresponding codons, we can make an amino acid property "landscape" on a four valued three dimensional sequence space from a genetic code table. Eleven property landscapes made from the standard genetic code (SGC) were analyzed. The evaluation of correlation for each landscape is done by theta value, which represents the ratio of the mean slope (as an additive term) to the degree of roughness (as a nonadditive term). The theta-values for hydropathy indices, polarity, specific heat, and beta-sheet propensity were considerably large with respect to SGC. This implies that the additivity of the contribution from each letter holds for these properties. To clarify the meaning of the so-called mutational robustness of SGC, we next examined correlations between the amino acid property and the actual "site fitnesses" of a protein. The site fitnesses were derived from a set of binding preference scores of amino acid residues at every site in MHC class I molecule binding peptides (Udaka et al. in press). We found that the SGC's theta value for an amino acid property is correlated with the significance of the property in the protein function. Adaptive walk simulation on fitness (= affinity) landscapes in a base sequence space for these model peptides confirmed better evolvability due to the introduction of SGC.

Amino Acids↗
PubMed1986

Comparative rates of esterification of 5'-AMP with hydrophobic amino acids: relevance to the genetic-code assignments.

We have continued our program aimed at understanding the origin and evolution of the genetic code and the process of protein synthesis by comparing the rates of esterification of 5'-AMP by a series of hydrophobic N-acetylamino acids. The reaction clearly shows differences in reaction rate (AcPhe greater than AcLeu greater than AcVal greater than AcIle) among the amino acids having A as middle letter of their anticodons. However, there were no significant differences in reaction rate between AcLeu, AcNorleu, and Ac-alpha-aminobutyric acid, and AcGly reacted faster than all of these and AcPhe. Consequently, this simple reaction with AMP can distinguish only among those amino acids that actually have A as the middle anticodonic nucleotide. The relevance of these studies to the origins of the process of protein synthesis and of the genetic code is discussed in conjunction with results from other studies of a similar nature.

Acetylation↗
PubMed2001

Aminoacyl-tRNA synthetases: potential markers of genetic code development.

Aminoacylation of tRNAs, catalyzed by 20 aminoacyl-tRNA synthetases, is responsible for establishing the genetic code. The enzymes are divided into two classes on the basis of the architectures of their active sites. Members of the two classes also differ in that they bind opposite sides of the tRNA acceptor stem. Importantly, specific pairs of synthetases--one from each class--can be docked simultaneously onto the acceptor stem. This article relates these specific pairings to the organization of the table of codons that defines the universal genetic code.

Amino Acyl-tRNA Synthetases↗
PubMed1984

Genetic code and optimal resistance to the effects of mutations.

This paper deals with the notion of resistance of the genetic code to the effects of mutations. We measure the resistance of a group of t codons as the number of pairs of those which differ from each other in only one of their three bases. We find for each value of t the maximum possible value of the resistance and we describe some groups of codons giving this value. Important examples of such configurations are found in the genetic code, among these are the groups of synonymous codons, as observed elsewhere, and the cluster of codons which have an hydrophobic amino acid for translation.

Base Sequence↗
PubMed2006

The evolution of the genetic code took place in an anaerobic environment.

We have compared orthologous proteins from an aerobic organism, Cytophaga hutchinsonii, and from an obligate anaerobe, Bacteroides thetaiotaomicron. This comparison allows us to define the oxyphobic ranks of amino acids, i.e. a scale of the relative sensitivity to oxygen of the amino acid residues. The oxyphobic index (OI), which can be simply obtained from the amino acids' oxyphobic ranks, can be associated to any protein and therefore to the genetic code, if the number of synonymous codons attributed to the amino acids in the code is assumed to be the frequency with which the amino acids appeared in ancestral proteins. Sampling of the OI variable from the proteins of obligate anaerobes and aerobes has established that the OI value of the genetic code is not significantly different from the mean OI value of anaerobe proteins, while it is different from that of aerobe proteins. This observation would seem to suggest that the terminal phases of the evolution of genetic code organization took place in an anaerobic environment. This result is discussed in the framework of hypotheses suggested to explain the timing of the evolutionary appearance of the aerobic metabolism.

Amino Acid Substitution↗
PubMed1975

Amino acid composition of proteins: Selection against the genetic code.

Distribution of amino acids in 68 representative proteins is compared with their distribution among 61 codons of the genetic code. Average amounts of lysine, aspartic acid, glutamic acid, and alanine are above the levels anticipated from the genetic code, and arginine, serine, leucine, cysteine, proline, and histidine are below such levels. Arginine plus lysine account for 11.0 percent of codons and aspartic acid plus glutamic acid account for 11.3 percent; thus the average charge is roughly neutral.

Amino Acid Sequence↗
PubMed1994

On the origin of the genetic code.

A series of stages in the evolution of the genetic code is postulated, representing a chain of logical steps that leads to the present-day code. The stages described are based on translation machinery between the RNA world and that of amino acids, a model that consists of an RNA assembler strand along which RNA hairpin molecules are lined up, forming a picket-fence-like aggregate. Each hairpin carries an amino acid at the bottom of one of its legs, and the mutual proximity of amino acids achieved in this way facilitates their linkage into oligopeptides, in a sequence governed by the nucleotide sequence along the assembler strand, the code. The order in which amino acids are introduced into the code is in the approximate order of their availability, tempered by polarity and structural considerations.

Amino Acid Sequence↗
PubMed1978

Aminoacyl-tRNA synthetase families and their significance to the origin of the genetic code.

A correlation of various aspects of the protein structures and substrate and mechanistic specificities of the aminoacyl-tRNA synthetases has led to the identification of at least one family of enzymes probably derived from a common ancestral synthetase. While strong correlations exist only in one part of the array of 64 codons comprising the Genetic Code, this itself may be interpreted as a meaningful pattern, most consistent with a development of the present code from earlier codes containing fewer amino acids and fewer available codons. Specifically, strong correlations in the enzymes whose cognate tRNAs respond to codons containing a central pyrimidine, including the enzyme family of Ile-, Phe-, Val-, Met-, and Leu-tRNA synthetases, suggests that these enzymes evolved last, and that, therefore, an earlier version of the Genetic Code was comprised solely of codons containing a central purine. It is suggested that further study of the historical interrelationships of these enzymes could lead to a fairly detailed picture of how the Genetic Code developed.

Amino Acyl-tRNA Synthetases↗
PubMed1999

Relationships among isoacceptor tRNAs seems to support the coevolution theory of the origin of the genetic code.

A new method for looking at relationships between nucleotide sequences has been used to analyze divergence both within and between the families of isoaccepting tRNA sets. A dendrogram of the relationships between 21 tRNA sets with different amino acid specificities is presented as the result of the analysis. Methionine initiator tRNAs are included as a separate set. The dendrogram has been interpreted with respect to the final stage of the evolutionary pathway with the development of highly specific tRNAs from ambiguous molecular adaptors. The location of the sets on the dendrogram was therefore analyzed in relation to hypotheses on the origin of the genetic code: the coevolution theory, the physicochemical hypothesis, and the hypothesis of ambiguity reduction of the genetic code. Pairs of 16 sets of isoacceptor tRNAs, whose amino acids are in biosynthetic relationships, occupied contiguous positions on the dendrogram, thus supporting the coevolution theory of the genetic code.

Codon↗
PubMed1997

Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins?

The synonym quotas within the genetic code for the 20 common amino acids are examined in relation to the ways in which these amino acids can be marshalled into different sets on the basis of shared physico-chemical properties. This reveals which shared properties are encouraged or discouraged during the course of protein evolution by the arrangement of the code. A dominant theme is that the synonym quotas are allocated in favour of small and chemically uncomplicated residues, and to the disadvantage of large and chemically prominent ones. From amongst the various measurements that can be considered to quantitatively express aspects of amino acid residue "size and complexity" (e.g. side chain volume, bulkness and formula weight), formula weight has the highest correlation with the synonym quota for each amino acid. However, the correlation is weak. A specially derived "size/complexity" scale for the amino acids based on their relative atomic composition improved the correlation only marginally. The existence of another weak correlation between the synonym quotas and the general amino acid composition of proteins prompted an investigation of the correlations between this composition and the previously considered amino acid properties. Again, the highest correlations are with amino acid formula weight and "size/complexity", but in this instance the correlations are high enough to be truly significant. It is suggested that the biased synonym quotas in the genetic code are intended to ensure that proteins as a whole maintain a certain amino acid composition, even to the extent that the quotas include compensatory biases to counter opposing influences upon this composition caused by the processes of natural selection for protein function. It is the need for these compensatory biases that prevents a simple correlation between the quotas and measures of amino acid complexity. The final outcome, in which amino acids are deployed in functional proteins in approximate proportion to their chemical complexity may serve both as a means of minimising the negative consequences of random genetic mutation (by reducing the chance appearance of the more "disruptive" types of side chain in proteins) and as a means of ensuring the most economic use of biosynthetic resources. According to this reasoning, the code is not a "frozen accident"; it is universally appropriate because it provides the best compromise that can be achieved between biosynthetic cost and biological return in respect of the rate of protein evolution.

Amino Acids↗
PubMed1997

Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum.

Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae, on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla. We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two, Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms, especially when it is considered with the results obtained through a molecular phylogenetic tree.

DNA, Mitochondrial↗