Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code

The aminoacyl-tRNA synthetases exist as two enzyme families which were apparently generated by divergent evolution from two primordial synthetases. The two classes of enzymes exhibit intriguing familial relationships, in that they are distributed nonrandomly within the codon-amino acid matrix of the genetic code. For example, all XCX codons code for amino acids handled by class II synthetases, and all but one of the XUX codons code for amino acids handled by class I synthetases. One interpretation of these patterns is that the synthetases coevolved with the genetic code. The more likely explanation, however, is that the synthetases evolved in the context of an already-established genetic code—a code which developed earlier in an RNA world. The rules which governed the development of the genetic code, and led to certain patterns in the coding catalog between codons and amino acids, would also have governed the subsequent evolution of the synthetases in the context of a fixed code, leading to patterns in synthetase distribution such as those observed. These rules are (1) conservative evolution of amino acid and adapter binding sites and (2) minimization of the disruptive effects on protein structure caused by codon meaning changes.     

The triplet genetic code had a doublet predecessor

Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and anticodons GNN. Evidence for this scenario is presented based on the properties of aminoacyl-tRNA synthetases, amino acids and nucleotide bases.     

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     

On the origin and evolution of the genetic code

Two ideas have essentially been used to explain the origin of the genetic code: Crick's frozen accident and Woese's amino acid-codon specific chemical interaction. Whatever the origin and codon-amino acid correlation, it is difficult to imagine the sudden appearance of the genetic code in its present form of 64 codons coding for 20 amino acids without appealing to some evolutionary process. On the contrary, it is more reasonable to assume that it evolved from a much simpler initial state in which a few triplets were coding for each of a small number of amino acids. Analysis of genetic code through information theory and the metabolism of pyrimidine biosynthesis provide evidence that suggests that the genetic code could have begun in an RNA world with the two letters A and U grouped in eight triplets coding for seven amino acids and one stop signal. This code could have progressively evolved by making gradual use of letters G and C to end with 64 triplets coding for 20 amino acids and three stop signals. According to proposed evidence, DNA could have appeared after the four-letter structure was already achieved. In the newborn DNA world, T substituted U to get higher physicochemical and genetic stability.     

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.     

Molecular basis for the genetic code

Summary It was found by using the CPK molecular model that holes on the complexes of four nucleotides (C4N) on the tRNAs, namely complexes of the anticodon bases with the discriminator base at 4th position of 3 end, had lock and key relations to the corresponding protein amino acids. Various general features of the universal and mitochondrial genetic codes were easily explained in terms of the C4N model. The recognition mechanism of the tRNA by the aminoacyl-tRNA-synthetase is closely correlated with the formation of the C4N on the Rossmann fold on the synthetase. The meaning of the hypermodification of the tRNA base next to the third anticodon base and other phenomena were also discussed.     

Structure,function and evolution of seryl-tRNA synthetases: Implications for the evolution of aminoacyl-tRNA synthetases and the genetic code

Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNA^ser in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 Amnoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3 end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence. Correspondence to: S. CusackBased on a presentation made at a workshop-Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code-held at Berkeley, CA, July 17–20, 1994     

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.     

Experimental investigation on the origin of the genetic code

Summary One of the essential relationships between nucleic acids and amino acids in present biological systems, and perhaps in precursors to these systems is expressed in binding interactions. Such interactions depend on the size, composition and conformation of the interacting species. A simplified model of such complex systems was tested in an attempt to assess first the compositional effect, i.e., the binding behavior of monomeric nucleic acid and protein components. Nine representative amino acids were immobilized individually on a prepared chromatographic support by the formation of an amide linkage. Selective binding of ribonucleoside 5-phosphates was exhibited by these amino acids under standardized conditions and the binding was characterized by a site-binding model. It was found that binding behavior was dependent of the nature of the base and the nature of the amino acid. Basic information is thus provided which should be useful in the interpretation of more complex nucleic acid-protein systems and the study of their role in the evolution of the cell.     

Searching tRNA sequences for relatedness to aminoacyl-tRNA synthetase families

tRNA sequences were analyzed for sequence features correlated with known classes of aminoacyl-tRNA synthetase enzymes. The tRNAs were searched for distinguishing nucleotides anywhere in their sequences. The analyses did not find nucleotides predictive of synthetase class membership. We conclude that such nucleotides never existed in tRNA sequences or that they existed and were lost from many of the tRNA sequences during evolution.Based on a presentation made at a workshop—Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code—held at Berkeley, CA, July 17–20, 1994 Correspondence to: H.B. Nicholas, Jr.     

Chemogenetic and optogenetic control of post-translational modifications through genetic code expansion

Post-translational modifications (PTMs) of proteins extensively diversify the biological information flow from the genome to the proteome and thus have profound pathophysiological implications. Precise dissection of the regulatory networks of PTMs benefits from the ability to achieve conditional control through external optogenetic or chemogenetic triggers. Genetic code expansion provides a unique solution by allowing for site-specific installation of functionally masked unnatural amino acids (UAAs) into proteins, such as enzymes and enzyme substrates, rendering them inert until rapid activation through exposure to light or small molecules. Here, we summarize the most recent advances harnessing this methodology to study various forms of PTMs, as well as generalizable approaches to externally control nodes-of-interest in PTM networks.     

Arithmetic inside the universal genetic code

The first information system emerged on the earth as primordial version of the genetic code and genetic texts. The natural appearance of arithmetic power in such a linguistic milieu is theoretically possible and practical for producing information systems of extremely high efficiency. In this case, the arithmetic symbols should be incorporated into an alphabet, i.e. the genetic code. A number is the fundamental arithmetic symbol produced by the system of numeration. If the system of numeration were detected inside the genetic code, it would be natural to expect that its purpose is arithmetic calculation e.g., for the sake of control, safety, and precise alteration of the genetic texts. The nucleons of amino acids and the bases of nucleic acids seem most suitable for embodiments of digits. These assumptions were used for the analyzing the genetic code.

The compressed, life-size, and split representation of the Escherichia coli and Euplotes octocarinatus code versions were considered simultaneously. An exact equilibration of the nucleon sums of the amino acid standard blocks and/or side chains was found repeatedly within specified sets of the genetic code. Moreover, the digital notations of the balanced sums acquired, in decimal representation, the unique form 111, 222, …, 999. This form is a consequence of the criterion of divisibility by 037. The criterion could simplify some computing mechanism of a cell if any and facilitate its computational procedure. The cooperative symmetry of the genetic code demonstrates that possibly a zero was invented and used by this mechanism. Such organization of the genetic code could be explained by activities of some hypothetical molecular organelles working as natural biocomputers of digital genetic texts.

It is well known that if mutation replaces an amino acid, the change of hydrophobicity is generally weak, while that of size is strong. The antisymmetrical correlation between the amino acid size and the degeneracy number is known as well. It is shown that these and some other familiar properties may be a physicochemical effect of arithmetic inside the genetic code.

The “frozen accident” model, giving unlimited freedom to the mapping function, could optimally support the appearance of both arithmetic symbols and physicochemical protection inside the genetic code.     

An algebraic hypothesis about the primeval genetic code architecture

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, A, C, G, U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G ≡ C and A = U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B³)^N of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.     

Speculations on the evolution of the genetic code

An evolutionary scheme is postulated in which the bases enter the genetic code in a definite temporal sequence and the correlated amino acids are assigned definite functions in the evolving system.The scheme requires a singlet code (guanine coding for glycine) evolving into a doublet code (guanine-cytosine doublet coding for gly (GG), ala (GC), arg (CG), pro (CC)). The doublet code evolves into a triplet code. Polymerization of nucleotides is thought to have been by block polymerization rather than by a template mechanism. The proteins formed at first were simple structural peptides. No direct nucleotide-amino acid stereo-chemical interaction was required. Rather an adaptor-type indirect mechanism is thought to have been functioning since the origin.     

A statistical test of hypotheses on the organization and origin of the genetic code

Summary Theories of the origin of the genetic code assign different weights to amino acid properties such as polarity and precursor-product relationship. Previous statistical work on the origin of the genetic code has produced controversial results. We analyze relationships between various amino acid and tRNA properties by one and the same statistical method. It is shown that polarities as well as precursor-product relationships are both likely to have been important in shaping the genetic code, together with codon swapping that left protein sequences intact.     

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.