The joint evolution of defence and inducibility against natural enemies

The aminoacyl-tRNA synthetases (aaRSs) ensure the fidelity of the translation of the genetic code, covalently attaching appropriate amino acids to the corresponding nucleic acid adaptor molecules-tRNA. The fundamental role of aminoacylation reaction catalysed by aaRSs implies that representatives of the family are thought to be among the earliest proteins to appear. Based on sequence analysis and catalytic domain structure, aaRSs have been partitioned into two classes of 10 enzymes each. However, based on the structural and sequence data only, it will not be easily understood that the present partitioning is not governed by chance. Our findings suggest that organization of amino acid biosynthetic pathways and clustering of aaRSs into different classes are intimately related to one another. A plausible explanation for such a relationship is dictated by early link between aaRSs and amino acids biosynthetic proteins. The aaRSs catalytic cores are highly relevant to the ancient metabolic reactions, namely, amino acids and cofactors biosynthesis. In particular we show that class II aaRSs mostly associated with the primordial amino acids, while class I aaRSs are usually related to amino acids evolved lately. Reasoning from this we propose a possible chronology of genetic code evolution.     

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.     

Evolution of the Genetic Code by Incorporation of Amino Acids that Improved or Changed Protein Function

Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids—valine, alanine, aspartic acid, and glycine—were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.     

An extension of the coevolution theory of the origin of the genetic code

Background  

The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors.     

Evolution of the biosynthesis of the branched-chain amino acids

The origin of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threonine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from -ketoisovaleric acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use of the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.     

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     

The Level and Landscape of Optimization in the Origin of the Genetic Code

We consider a model of the origin of genetic code organization incorporating the biosynthetic relationships between amino acids and their physicochemical properties. We study the behavior of the genetic code in the set of codes subject both to biosynthetic constraints and to the constraint that the biosynthetic classes of amino acids must occupy only their own codon domain, as observed in the genetic code. Therefore, this set contains the smallest number of elements ever analyzed in similar studies. Under these conditions and if, as predicted by physicochemical postulates, the amino acid properties played a fundamental role in genetic code organization, it can be expected that the code must display an extremely high level of optimization. This prediction is not supported by our analysis, which indicates, for instance, a minimization percentage of only 80%. These observations can therefore be more easily explained by the coevolution theory of genetic code origin, which postulates a role that is important but not fundamental for the amino acid properties in the structuring of the code. We have also investigated the shape of the optimization landscape that might have arisen during genetic code origin. Here, too, the results seem to favor the coevolution theory because, for instance, the fact that only a few amino acid exchanges would have been sufficient to transform the genetic code (which is not a local minimum) into a much better optimized code, and that such exchanges did not actually take place, seems to suggest that, for instance, the reduction of translation errors was not the main adaptive theme structuring the genetic code.     

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.     

The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code

Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code. Received: 10 September 1996 / Accepted: 3 March 1997     

Multiple nutritional requirements of lactobacilli: genetic lesions affecting amino acid biosynthetic pathways.

Genetic lesions responsible for amino acid requirements in several species of multiple auxotrophic lactobacilli were investigated. Systematic attempts were made to isolate mutants that could grow in the absence of each of the amino acids required by the parental strains of Lactobacillus plantarum, L. casei, L. helveticus, and L. acidophilus. After treatment with appropriate mutagens, such mutants could be obtained with respect to many but not all required amino acids. Successful isolation of mutants for a given amino acid means that a minor genetic lesion reparable by single-step mutations affects its biosynthesis; a failure to isolate mutants suggests the involvement of more extensive lesions. Analysis of these results as well as the specific requirements exhibited by the parental strains revealed certain regularities; some of the biosynthetic pathways for individual amino acids were virtually unaffected by more extensive lesions in at least species tested, whereas others were affected by more extensive lesions in at least some species. Both the number and the kind of pathways affected by extensive lesions differed appreciably among different species. Furthermore, the growth response of the parental strains to some putative amino acid precursors revealed a clear correlation between the extent of genetic lesions and the occurrence and location of a genetic block(s) for a given pathway. These findings are discussed in relation to the phylogeny, ecology, and evolution of lactic acid bacteria.     

Development of the genetic code: Insights from a fungal codon reassignment

The high conservation of the genetic code and its fundamental role in genome decoding suggest that its evolution is highly restricted or even frozen. However, various prokaryotic and eukaryotic genetic code alterations, several alternative tRNA-dependent amino acid biosynthesis pathways, regulation of tRNA decoding by diverse nucleoside modifications and recent in vivo incorporation of non-natural amino acids into prokaryotic and eukaryotic proteins, show that the code evolves and is surprisingly flexible. The cellular mechanisms and the proteome buffering capacity that support such evolutionary processes remain unclear. Here we explore the hypothesis that codon misreading and reassignment played fundamental roles in the development of the genetic code and we show how a fungal codon reassignment is enlightening its evolution.     

Selection, history and chemistry: the three faces of the genetic code.

The genetic code might be a historical accident that was fixed in the last common ancestor of modern organisms. 'Adaptive', 'historical' and 'chemical' arguments, however, challenge such a 'frozen accident' model. These arguments propose that the current code is somehow optimal, reflects the expansion of a more primitive code to include more amino acids, or is a consequence of direct chemical interactions between RNA and amino acids, respectively. Such models are not mutually exclusive, however. They can be reconciled by an evolutionary model whereby stereochemical interactions shaped the initial code, which subsequently expanded through biosynthetic modification of encoded amino acids and, finally, was optimized through codon reassignment. Alternatively, all three forces might have acted in concert to assign the 20 'natural' amino acids to their present positions in the genetic code.     

大肠杆菌高效合成L-苯甘氨酸的研究进展

自然界存在着多种氨基酸,除用于蛋白质合成的20种外,大量用于合成具有生物活性的物质,广泛应用于食品、医药等多个领域.其中,非天然芳香族氨基酸L-苯甘氨酸作为一种重要的组成单元广泛的应用于盘尼西林、维吉霉素S、原始霉素Ⅰ等β-内酰胺类抗生素的生物合成当中.目前L苯甘氨酸主要通过化学法合成,但该方法合成收率低、污染大,且不...     

Biological role of the general control of amino acid biosynthesis in Saccharomyces cerevisiae.

The biological role of the "general control of amino acid biosynthesis" has been investigated by analyzing growth and enzyme levels in wild-type, bradytrophic, and nonderepressing mutant strains of Saccharomyces cerevisiae. Amino acid limitation was achieved by using either bradytrophic mutations or external amino acid imbalance. In the wild-type strain noncoordinate derepression of enzymes subject to the general control has been found. Derepressing factors were in the order of 2 to 4 in bradytrophic mutant strains grown under limiting conditions and only in the order of 1.5 to 2 under the influence of external amino acid imbalance. Nonderepressing mutations led to slower growth rates under conditions of amino acid limitation, and no derepression of enzymes under the general control was observed. The amino acid pools were found to be very similar in the wild type and in nonderepressing mutant strains under all conditions tested. Our results indicate that the general control affects all branched amino acid biosynthetic pathways, namely, those of the aromatic amino acids and the aspartate family, the pathways for the basic amino acids lysine, histidine, and arginine, and also the pathways of serine and valine biosyntheses.     

Amino Acid Biosynthesis in the Halophilic Archaeon Haloarcula hispanica

Biosynthesis of proteinogenic amino acids in the extremely halophilic archaeon Haloarcula hispanica was explored by using biosynthetically directed fractional 13C labeling with a mixture of 90% unlabeled and 10% uniformly 13C-labeled glycerol. The resulting 13C-labeling patterns in the amino acids were analyzed by two-dimensional 13C,1H correlation spectroscopy. The experimental data provided evidence for a split pathway for isoleucine biosynthesis, with 56% of the total Ile originating from threonine and pyruvate via the threonine pathway and 44% originating from pyruvate and acetyl coenzyme A via the pyruvate pathway. In addition, the diaminopimelate pathway involving diaminopimelate dehydrogenase was shown to lead to lysine biosynthesis and an analysis of the 13C-labeling pattern in tyrosine indicated novel biosynthetic pathways that have so far not been further characterized. For the 17 other proteinogenic amino acids, the data were consistent with data for commonly found biosynthetic pathways. A comparison of our data with the amino acid metabolisms of eucarya and bacteria supports the theory that pathways for synthesis of proteinogenic amino acids were established before ancient cells diverged into archaea, bacteria, and eucarya.     

The non-universality of the genetic code: the universal ancestor was a progenote

The coevolution theory of genetic code origin (Wong, J.T. 1975, Proc. Natl Acad. Sci. U.S.A.72, 1909-1912) is assumed here to be substantially correct. This theory is based on the strict parallelism of the biosynthetic relationships between amino acids and the organization of the genetic code and postulates that these relationships were mediated by tRNA-like molecules on which the biosynthetic transformations between precursor and product amino acids took place. These transformations underlay the mechanism that gave rise to genetic code organization. One of the pathways which represents these transformations found in current organisms, and which are thus probably molecular fossils, is the Met-tRNA(fMet)-->fMet-tRNA(fMet)pathway. This pathway is present only in the Bacteria domain. This along with other observations and arguments leads us to believe that this pathway is a clear violation of the universality of the genetic code. Furthermore, the presence of this pathway only in the Bacteria domain seems to imply that the translation apparatus was still rapidly evolving when this pathway was fixed. This, in turn, appears to imply that the last universal common ancestor was a progenote. Finally, the implications that the finding of this pathway has for the stereochemical theory of genetic code origin are discussed.     

Evolutionary processes possibly limiting the kinds of amino acids in protein to twenty: a review.

Only 20 of more than 250 biosynthetic amino acids are common (coded) constituents of contemporary protein. In this paper, several stages of evolution, both prebiotic and biotic, are examined for means by which other (non-proteinous) amino acids may have been selected against. Simulated prebiotic experiments indicate that some non-proteinous amino acids were present prebiotically, that they could be incorporated during the formation of prebiotic protein, and that they would function in such protein. Biotic selection is thus indicated.Non-proteinous amino acids currently are available via biosynthetic pathways for potential incorporation into bioprotein. Codon-anticodon interaction, peptidyl transferases, and elongation and termination factors of protein synthesis do not show the specificity needed to preclude non-proteinous amino acids. Highly specific recognition among amino acids, tRNAs, and activating enzymes is concluded to be why the kinds of amino acids in contemporary protein are limited to twenty.Some of several theories concerning the origin, nature and evolution of the genetic code can readily accommodate non-proteinous amino acids. Some evidence suggests that such amino acids were eventually eliminated from protein because they were less suitable than related proteinous amino acids. However, deterministic or “direct interaction” theories currently lack sufficient experimental support to answer how non-proteinous amino acids were precluded; such theories, being testable, probably have the most potential for providing an answer.     

A Realistic Model Under Which the Genetic Code is Optimal

The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the mean square measure as a function quantifying error robustness, a value can be obtained for a genetic code which reflects the error robustness of that code. By comparing this value with a distribution of values belonging to codes generated by random permutations of amino acid assignments, the level of error robustness of a genetic code can be quantified. We present a calculation in which the standard genetic code is shown to be optimal. We obtain this result by (1) using recently updated values of polar requirement as input; (2) fixing seven assignments (Ile, Trp, His, Phe, Tyr, Arg, and Leu) based on aptamer considerations; and (3) using known biosynthetic relations of the 20 amino acids. This last point is reflected in an approach of subdivision (restricting the random reallocation of assignments to amino acid subgroups, the set of 20 being divided in four such subgroups). The three approaches to explain robustness of the code (specific selection for robustness, amino acid–RNA interactions leading to assignments, or a slow growth process of assignment patterns) are reexamined in light of our findings. We offer a comprehensive hypothesis, stressing the importance of biosynthetic relations, with the code evolving from an early stage with just glycine and alanine, via intermediate stages, towards 64 codons carrying todays meaning.     

Question 6: Coevolution Theory of the Genetic Code: A Proven Theory

The coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the four fundamental tenets of the theory, thus solving the riddle of the structure of the universal genetic code. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.