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1.
Massimo Di Giulio 《Journal of molecular evolution》2001,53(6):724-732
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.
Received: 21 February 2001 / Accepted: 22 May 2001 相似文献
2.
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.
Received: 4 May 1998 / Accepted: 11 July 1998 相似文献
3.
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. 相似文献
4.
Ramin Amirnovin 《Journal of molecular evolution》1997,44(5):473-476
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 相似文献
5.
We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909–1912, 1975) is
essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code
organization might have passed prior to reaching its current form. The calculation of the minimization level of all these
evolutionary stages leads to the following conclusions. (1) The minimization percentages increased linearly with the number
of amino acids codified in the codes of the various evolutionary stages when only the sense changes are considered in the
analysis. This seems to favor the physicochemical theory of genetic code origin even if, as discussed in the paper, this observation
is also compatible with the coevolution theory. (2) For the first seven evolutionary stages of the genetic code, this trend
is less clear and indeed is inverted when we consider the global optimisation of the codes due to both sense changes and synonymous
changes. This inverse correlation between minimization percentages and the number of amino acids codified in the codes of
the intermediate stages seems to favor neither the physicochemical nor the stereochemical theories of genetic code origin,
as it is in the early and intermediate stages of code development that these theories would expect minimization to have played
a crucial role, and this does not seem to be the case. However, these results are in agreement with the coevolution theory,
which attributes a role to the physicochemical properties of amino acids that, while important, is nevertheless subordinate
to the mechanism which concedes codons from the precursor amino acids to the product amino acids as the primary factor determining
the evolutionary structuring of the genetic code. The results are therefore discussed in the context of the various theories
proposed to explain genetic code origin.
Received: 25 October 1998 / Accepted: 19 February 1999 相似文献
6.
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 相似文献
7.
How did the ``universal' genetic code arise? Several hypotheses have been put forward, and the code has been analyzed extensively
by authors looking for clues to selection pressures that might have acted during its evolution. But this approach has been
ineffective. Although an impressive number of properties has been attributed to the universal code, it has been impossible
to determine whether selection on any of these properties was important in the code's evolution or whether the observed properties
arose as a consequence of selection on some other characteristic. Therefore we turned the question around and asked, what
would a genetic code look like if it had evolved in response to various different selection pressures? To address this question,
we constructed a genetic algorithm. We found first that selecting on a particular measure yields codes that are similar to
each other. Second, we found that the universal code is far from minimized with respect to the effects of mutations (or translation
errors) on the amino acid compositions of proteins. Finally, we found that the codes that most closely resembled real codes
were those generated by selecting on aspects of the code's structure, not those generated by selecting to minimize the effects
of amino acid substitutions on proteins. This suggests that the universal genetic code has been selected for a particular
structure—a structure that confers an important flexibility on the evolution of genes and proteins—and that the particular
assignments of amino acids to codons are secondary.
Received: 29 December 1998 / Accepted: 8 July 1999 相似文献
8.
Massimo Di Giulio 《Biology direct》2008,3(1):37
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. 相似文献9.
We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use
very simple assumptions about translation, mutation, and protein fitness to calculate mutation-selection equilibria of codon
frequencies and fitness in a large asexual population with a given genetic code. We then compute the fitnesses of altered
genetic codes that compete to invade the population by translating its genes with higher fitness. Codes and genes coevolve
in a succession of stages, alternating between genetic equilibration and code invasion, from an initial wholly ambiguous coding
state to a diversified frozen coding state. Our simulations almost always resulted in partially redundant frozen genetic codes.
Also, the range of simulated physicochemical properties among encoded amino acids in frozen codes was always less than maximal.
These results did not require the assumption of historical constraints on the number and type of amino acids available to
codes nor on the complexity of proteins, stereochemical constraints on the translational apparatus, nor mechanistic constraints
on genetic code change. Both the extent and timing of amino-acid diversification in genetic codes were strongly affected by
the message mutation rate and strength of missense selection. Our results suggest that various omnipresent phenomena that
distribute codons over sites with different selective requirements—such as the persistence of nonsynonymous mutations at equilibrium,
the positive selection of the same codon in different types of sites, and translational ambiguity—predispose the evolution
of redundancy and of reduced amino acid diversity in genetic codes.
Received: 21 December 2000 / Accepted: 12 March 2001 相似文献
10.
We have previously proposed an SNS hypothesis on the origin of the genetic code (Ikehara and Yoshida 1998). The hypothesis
predicts that the universal genetic code originated from the SNS code composed of 16 codons and 10 amino acids (S and N mean
G or C and either of four bases, respectively). But, it must have been very difficult to create the SNS code at one stroke
in the beginning. Therefore, we searched for a simpler code than the SNS code, which could still encode water-soluble globular
proteins with appropriate three-dimensional structures at a high probability using four conditions for globular protein formation
(hydropathy, α-helix, β-sheet, and β-turn formations). Four amino acids (Gly [G], Ala [A], Asp [D], and Val [V]) encoded by
the GNC code satisfied the four structural conditions well, but other codes in rows and columns in the universal genetic code
table do not, except for the GNG code, a slightly modified form of the GNC code. Three three-amino acid systems ([D], Leu
and Tyr; [D], Tyr and Met; Glu, Pro and Ile) also satisfied the above four conditions. But, some amino acids in the three
systems are far more complex than those encoded by the GNC code. In addition, the amino acids in the three-amino acid systems
are scattered in the universal genetic code table. Thus, we concluded that the universal genetic code originated not from
a three-amino acid system but from a four-amino acid system, the GNC code encoding [GADV]-proteins, as the most primitive
genetic code.
Received: 11 June 2001 / Accepted: 11 October 2001 相似文献
11.
Thomas Cavalier-Smith 《Journal of molecular evolution》2001,53(4-5):555-595
I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects.
Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution
required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore
a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic
acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes
initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level
reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection
in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes
consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified
lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose
from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second
key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by
membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the
outer surface of an `inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids
and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve
replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to
signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation
evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells,
to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble
enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup,
causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially:
GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition
particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex
autotrophic, anaerobic green bacterium.
Received: 19 February 2001 / Accepted: 9 April 2001 相似文献
12.
Di Giulio M 《Journal of theoretical biology》2001,209(3):345-349
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. 相似文献
13.
Jeffrey Tze-Fei Wong 《Origins of life and evolution of the biosphere》2007,37(4-5):403-408
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. 相似文献
14.
Konecny J Schöniger M Hofacker I Weitze MD Hofacker GL 《Journal of molecular evolution》2000,50(3):238-242
Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins.
We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted
to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point
mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one
strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical
properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure.
We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient
search for new variants on the protein level.
Received: 4 June 1999 / Accepted: 12 October 1999 相似文献
15.
Radu Popa 《Journal of molecular evolution》1997,44(2):121-127
A sequential model is proposed regarding the origin of biological chirality. Three major stages are presumed: a symmetry
breaking (prebiotic chiral disruption in enantiomeric mixtures of monomers), a chiral amplification (prebiotic increase of
the chiral character of the monomers affected first by the symmetry breaking), and a chiral expansion (proto biological increase
of the chiral character and spread of the chirality to molecules which were less affected by prebiotic chiralizations). As
a symmetry-breaking mechanism, the model proposed by Deutsch (1991) is used, which involves a dissymmetric exposure of amino
acids (AA) to ultraviolet circularly polarized light (UV-CPL) on evaporative seashores. It is presumed that the chiral amplification,
up to a protobiologic significance, was influenced by a periodic overlapping of two abiotic events, a synchronization between
tidal-based hydrous–anhydrous cycles, and littoral asymmetric photolysis cycles. This long-term astronomic asymmetry acted
around 3.8–4.2 billion years ago and was unique to the Earth in our solar system. It is also presumed that the abiotic symmetry
breaking is heterogenous, that only a few l-AAs were used in the beginning, and that the chirality expanded later to all 20 AAs based on a coevolutionary strategy of
the genetic code and on a physiological relationship between AAs. In this scenario the d-chirality of pentoses in polynucleotides was attributed to both d-pentose/l-AA relationships and to a structural evolution.
Received: 10 May 1996 / Accepted: 13 August 1996 相似文献
16.
Di Giulio M 《Journal of molecular evolution》2002,55(5):616-622
A logical-evolutionary analysis is conducted to clarify whether or not pathways of type Glu-tRNAGln \rightarrow Gln-tRNAGln
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. 相似文献
17.
We studied 10 protein-coding mitochondrial genes from 19 mammalian species to evaluate the effects of 10 amino acid properties
on the evolution of the genetic code, the amino acid composition of proteins, and the pattern of nonsynonymous substitutions.
The 10 amino acid properties studied are the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric
point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation. The genetic code appears to have evolved toward
minimizing polarity and hydropathy but not the other seven properties. This can be explained by our finding that the presumably
primitive amino acids differed much only in polarity and hydropathy, but little in the other properties. Only the chemical
composition (C) and isoelectric point (IE) appear to have affected the amino acid composition of the proteins studied, that
is, these proteins tend to have more amino acids with typical C and IE values, so that nonsynonymous mutations tend to result
in small differences in C and IE. All properties, except for hydroxythiolation, affect the rate of nonsynonymous substitution,
with the observed amino acid changes having only small differences in these properties, relative to the spectrum of all possible
nonsynonymous mutations.
Received: 2 January 1998 / Accepted: 25 April 1998 相似文献
18.
Massimo Di Giulio 《Origins of life and evolution of the biosphere》1995,25(6):549-564
An extensive analysis of the evolutionary relationships existing between transfer RNAs, performed using parsimony algorithms, is presented. After building up an estimate of the tRNA ancestral sequences, these sequences are then compared using certain methods. The results seem to suggest that the coevolution hypothesis (Wong, J.T., 1975, Proc. Natl. Acad. Sci. USA 72, 1909–1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids is further supported by these results, as compared to the hypotheses that see the physicochemical properties of amino acids as the main adaptative theme that led to the structuring of the genetic code. 相似文献
19.
Edward N. Trifonov Alla Kirzhner Valery M. Kirzhner Igor N. Berezovsky 《Journal of molecular evolution》2001,53(4-5):394-401
Evolution of proteins encoded in nucleotide sequences began with the advent of the triplet code. The chronological order
of the appearance of amino acids on the evolution scene and the steps in the evolution of the triplet code have been recently
reconstructed (Trifonov, 2000b) on the basis of 40 different ranking criteria and hypotheses. According to the consensus chronology,
the pair of complementary GGC and GCC codons for the amino acids alanine and glycine appeared first. Other codons appeared
as complementary pairs as well, which divided their respective amino acids into two alphabets, encoded by triplets with either
central purines or central pyrimidines: G, D, S, E, N, R, K, Q, C, H, Y, and W (Glycine alphabet G) and A, V, P, S, L, T, I, F, and M (Alanine alphabet A). It is speculated that the earliest polypeptide chains were very short, presumably of uniform length, belonging to two alphabet
types encoded in the two complementary strands of the earliest mRNA duplexes. After the fusion of the minigenes, a mosaic
of the alphabets would form. Traces of the predicted mosaic structure have been, indeed, detected in the protein sequences
of complete prokaryotic genomes in the form of weak oscillations with the period 12 residues in the form of alteration of
two types of 6 residue long units. The next stage of protein evolution corresponded to the closure of the chains in the loops
of the size 25–30 residues (Berezovsky et al., 2000). Autocorrelation analysis of proteins of 23 complete archaebacterial
and eubacterial genomes revealed that the preferred distances between valine, alanine, glycine, leucine, and isoleucine along
the sequences are in the same range of 25–30 residues, indicating that the loops are primarily closed by hydrophobic interactions
between the ends of the loops. The loop closure stage is followed by the formation of typical folds of 100–200 amino acids,
via end-to-end fusion of the genes encoding the loop-size chains. This size was apparently dictated by the optimal ring closure
for DNA. In both cases the closure into the ring (loop) rendered evolutionarily advantageous stability to the respective structures.
Further gene fusions lead to the formation of modern multidomain proteins. Recombinational gene splicing is likely to have
appeared after the DNA circularization stage.
Received: 21 December 2000 / Accepted: 28 February 2001 相似文献
20.
Massimo Di Giulio 《Origins of life and evolution of the biosphere》1992,22(5):309-319
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. 相似文献