线粒体遗传密码及基因组遗传密码的对称分析

病毒、细菌和真核生物的氨基酸编码都使用相同的遗传密码,表明它们可能有共同的来源。但人和牛的线粒体的遗传密码和基因组的遗传密码相比,出现以下不同;（1）ATA编码甲硫氮酸M而不是异亮氨酸I。（2）TGA不再是终止密码子X而编码色氨酸W。（3）AGA和AGG不再是精氨酸R的密码子而变为终止密码子X。应用高维空间拓扑分析的方法,对线粒体遗传密码和基因组遗传密码的6维编码空间进行对称性分析,得到如下结果：（1）线粒体遗传密码的起始密码子是2个而不是1个。（2）线粒体遗传密码的终止密码子是4个而不是3个。（3）线粒体遗传密码空间只有2、4、6三种偶数简并度而没1、3两种奇数简并度,表明其对称度较高。（4）线粒体遗传密码空间除丝氨酸S分成两个平行的子空间之外,终止密码子X亦分成两个平行的子空间,表明其连通度较低。（5）线粒体遗传密码一基因组遗传密码相比,共有3个简并平面出现变异,即：1001λλ（M和I）,011λ1λ（W和X）,以及1011λλ（S和X或S和R）。（6）基因组遗传密码的1、3两种奇数简并度可能来源于线粒体遗传密码的1001λλ平面和011λ1λ平面的对称性破缺。对线粒体遗传密码变异的生物学意义及遗传密码的起源进行了分析和讨论。     

On the information content of the genetic code

In living organisms 20 amino acids along with the terminator value(s) are encoded by 64 codons giving a degeneracy of the codons as described by the genetic code. A basic theoretical problem of genetic codes is to explain the particular distribution of degeneracies of partitions involved in the codes. In this work the degeneracy problem is considered in the framework of information theory. It is shown by direct numerical evaluation of a certain degeneracy information function associated with the genetic code that the degeneracy of the codes is observed to be related to the optimization of this function.     

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10⁻¹⁰ per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC.     

The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA

The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the past ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.     

Block structure and stability of the genetic code

It is known that different codons may be unified into larger groups related to the hierarchical structure, approximate hidden symmetries, and evolutionary origin of the universal genetic code. Using a simplified evolutionary motivated two-letter version of genetic code, the general principles of the most stable coding are discussed. By the complete enumeration in such a reduced code it is strictly proved that the maximum stability with respect to point mutations and shifts in the reading frame needs the fixation of the middle letters within codons in groups with different physico-chemical properties, thus, explaining a key feature of the universal genetic code. The translational stability of the genetic code is studied by the mapping of code onto de Bruijn graph providing both the compact visual representation of mutual relationships between different codons as well as between codons and protein coding DNA sequence and a powerful tool for the investigation of stability of protein coding. Then, the results are extended to four-letter codes. As is shown, the universal genetic code obeys mainly the principles of optimal coding. These results demonstrate the hierarchical character of optimization of universal genetic code with strictly optimal coding being evolved at the earliest stages of molecular evolution. Finally, the universal genetic code is compared with the other natural variants of genetic codes.     

Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon

In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammalian ribosomes, we show that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher the UGA codon, which encodes cysteine in this organism. This result strongly suggests that in ciliates with variant genetic codes eRF1 does not recognize the reassigned codons. Recent hypotheses describing stop codon discrimination by eRF1 are not fully consistent with the set of eRF1 sequences available so far and require direct experimental testing.     

Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix

The genetic code is one of the most highly conserved characters in living organisms. Only a small number of genomes have evolved slight variations on the code, and these non-canonical codes are instrumental in understanding the selective pressures maintaining the code. Here, we describe a new case of a non-canonical genetic code from the oxymonad flagellate Streblomastix strix. We have sequenced four protein-coding genes from S.strix and found that the canonical stop codons TAA and TAG encode the amino acid glutamine. These codons are retained in S.strix mRNAs, and the legitimate termination codons of all genes examined were found to be TGA, supporting the prediction that this should be the only true stop codon in this genome. Only four other lineages of eukaryotes are known to have evolved non-canonical nuclear genetic codes, and our phylogenetic analyses of alpha-tubulin, beta-tubulin, elongation factor-1 alpha (EF-1 alpha), heat-shock protein 90 (HSP90), and small subunit rRNA all confirm that the variant code in S.strix evolved independently of any other known variant. The independent origin of each of these codes is particularly interesting because the code found in S.strix, where TAA and TAG encode glutamine, has evolved in three of the four other nuclear lineages with variant codes, but this code has never evolved in a prokaryote or a prokaryote-derived organelle. The distribution of non-canonical codes is probably the result of a combination of differences in translation termination, tRNAs, and tRNA synthetases, such that the eukaryotic machinery preferentially allows changes involving TAA and TAG.     

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.     

A new noncanonical nuclear genetic code: translation of UAA into glutamate

Deviant genetic codes reported in ciliates share the same feature: one (UGA) or two (UAR) of the three canonical stop codons are translated into one particular amino acid. In many genera, such as Oxytricha, Paramecium, and Tetrahymena, UAR codons are translated into glutamine. UGA is translated into cysteine in Euplotes or into tryptophan in Colpoda inflata and Blepharisma americanum. Here, we show that three peritrich species (Vorticella microstoma, Opisthonecta henneguyi, and Opisthonecta matiensis) translate UAA into glutamate and that at least UAA in O. matiensis is decoded through a mutant suppressor-like tRNA. This kind of genetic code has never been reported for any living organism. Phylogenetic analysis with alpha-tubulin sequences corroborates that peritrichs, peniculines (Paramecium), and hymenostomates (Tetrahymena) form a monophyletic group (class Oligohymenophorea). The differential translation (glu/gln) of UAR codons, the monophyly of the Oligohymenophorea, and the common evolutionary origin of glutamate and glutamine suggest that deviant genetic codes of present-day oligohymenophoreans could have the same origin.     

A mathematical model accounting for the organization in multiplets of the genetic code

A model using suitable mathematical operators in the crystal basis model of the genetic code is presented. This model retains a requirement for stability of the genetic code against misreading or translation errors. The main features (including number of encoded amino-acids, nucleotide content, and synonymous codons multiplet dimension) are described for mitochondrial and eukaryotic genetic codes.     

Translation termination factor eRF1 of the ciliate <Emphasis Type="Italic">Blepharisma japonicum</Emphasis> recognizes all three stop codons

In species with variant genetic codes, one or two stop codons encode amino acid residues and are not recognized by the intrinsic class I translation termination factor (eRF1). Ciliata include a large number of species with variant genetic codes. The stop codon specificity of the Blepharisma japonicum translation termination factor eRF1 was determined in an in vitro eukaryotic translation system and in an in vivo assay (a dual reporter system). It was shown that eRF1 of B. japonicum retained specificity to all three stop codons, although the efficiency of peptydyl-tRNA hydrolysis in the presence of UGA was reduced in the in vitro assay. Since Heterotrichea (including B. japonicum) are the earliest diverged lineage in the phylogenetic tree of ciliates, B. japonicum probably possesses a universal genetic code similar to the putative ciliate ancestor group.     

Some theoretical aspects of reprogramming the standard genetic code

Reprogramming of the standard genetic code to include non-canonical amino acids (ncAAs) opens new prospects for medicine, industry, and biotechnology. There are several methods of code engineering, which allow us for storing new genetic information in DNA sequences and producing proteins with new properties. Here, we provided a theoretical background for the optimal genetic code expansion, which may find application in the experimental design of the genetic code. We assumed that the expanded genetic code includes both canonical and non-canonical information stored in 64 classical codons. What is more, the new coding system is robust to point mutations and minimizes the possibility of reversion from the new to old information. In order to find such codes, we applied graph theory to analyze the properties of optimal codon sets. We presented the formal procedure in finding the optimal codes with various number of vacant codons that could be assigned to new amino acids. Finally, we discussed the optimal number of the newly incorporated ncAAs and also the optimal size of codon groups that can be assigned to ncAAs.     

The logic of the genetic code: Synonyms and optimality against effects of mutations

The groups of codons which correspond to the same amino-acid in the genetic code (synonyms) are compared to theoretical codes constructed so as to resist best to the effects of mutations. The analysis shows that the genetic code presents synonymy structures which are optimized against translation errors.     

Possible evolutionary steps in the genetic code

In mammalian mitochondrial codes, fourfold codons wobble-pair with UNN anticodons so that U wobbles with U, C, A and G. Twofold pyrimidine-terminated codons pair with GNN and twofold purine-terminated codons pair with UNN. These properties enable a prediction to be made for evolution of the universal genetic code. It was postulated (1) that an archetypal code of 16 quartets coded for 15 amino acids. If this code used UNN anticodons, then duplication of tRNA genes, followed by mutations in the anticodons and aminoacylation sites, would give rise to the present universal code.     

An Analysis of the Metabolic Theory of the Origin of the Genetic Code

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature. Received: 8 August 1996 / Accepted: 26 December 1996     

Genetic code development by stop codon takeover

A novel theoretical consideration of the origin and evolution of the genetic code is presented. Code development is viewed from the perspective of simultaneously evolving codons, anticodons and amino acids. Early code structure was determined primarily by thermodynamic stability considerations, requiring simplicity in primordial codes. More advanced coding stages could arise as biological systems became more complex and precise in their replication. To be consistent with these ideas, a model is described in which codons become permanently associated with amino acids only when a codon-anticodon pairing is strong enough to permit rapid translation. Hence all codons are essentially chain-termination or "stop" codons until tRNA adaptors evolve having the ability to bind tightly to them. This view, which draws support from several lines of evidence, differs from the prevalent thinking on code evolution which holds that codons specifying newer amino acids were derived from codons encoding older amino acids.     

Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria

Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm(5)U) at the anticodon wobble positions of tRNA(Met)(AUR), tRNA(Trp)(UGR), and tRNA(Gly)(AGR), suggesting that τm(5)U plays a critical role in the accurate deciphering of all four non-universal codes by preventing the misreading of pyrimidine-ending near-cognate codons (NNY) in their respective family boxes. Acquisition of the wobble modification appears to be a prerequisite for the genetic code alteration.     

How translation termination factor eRF1 Euplotes does not recognise UGA stop codon

In universal-code eukaryotes, a single class-1 translation termination factor eRF1 decodes all three stop codons, UAA, UAG, and UGA. In some ciliates with variant genetic codes one or two stop codons are used to encode amino acid(s) and are not recognized by eRF1. In Stylonychia, UAG and UAA codons are reassigned as glutamine codons, and in Euplotes, UGA is reassigned as cysteine codon. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of eRF1. Because variant-code ciliates most likely evolved from universal code ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. To find out amino acid residues which confer UAR-only specificity to Euplotes aediculatus eRF1, eRFI chimeras were constructed by swapping eRF1 E. aediculatus N-terminal domain sequences with the matching ones from the human protein. In these chimeras the MC-domain was from human eRF1. Functional analysis of these chimeric eRFI highlighted the crucial role of the two regions (positions 38-50 and 123-145) in the N-terminal domain of E. aediculatus eRF1 that restrict E. aediculatus eRF1 specificity toward UAR codons. Possibly, restriction of eRF1 specificity to UAR codons might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UGA to sense codons.     

Was Wright Right? The Canonical Genetic Code is an Empirical Example of an Adaptive Peak in Nature; Deviant Genetic Codes Evolved Using Adaptive Bridges

The canonical genetic code is on a sub-optimal adaptive peak with respect to its ability to minimize errors, and is close to, but not quite, optimal. This is demonstrated by the near-total adjacency of synonymous codons, the similarity of adjacent codons, and comparisons of frequency of amino acid usage with number of codons in the code for each amino acid. As a rare empirical example of an adaptive peak in nature, it shows adaptive peaks are real, not merely theoretical. The evolution of deviant genetic codes illustrates how populations move from a lower to a higher adaptive peak. This is done by the use of “adaptive bridges,” neutral pathways that cross over maladaptive valleys by virtue of masking of the phenotypic expression of some maladaptive aspects in the genotype. This appears to be the general mechanism by which populations travel from one adaptive peak to another. There are multiple routes a population can follow to cross from one adaptive peak to another. These routes vary in the probability that they will be used, and this probability is determined by the number and nature of the mutations that happen along each of the routes. A modification of the depiction of adaptive landscapes showing genetic distances and probabilities of travel along their multiple possible routes would throw light on this important concept.