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1.
Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes 总被引:28,自引:0,他引:28
Zhang J 《Journal of molecular evolution》2000,50(1):56-68
To understand the process and mechanism of protein evolution, it is important to know what types of amino acid substitutions
are more likely to be under selection and what types are mostly neutral. An amino acid substitution can be classified as either
conservative or radical, depending on whether it involves a change in a certain physicochemical property of the amino acid.
Assuming Kimura's two-parameter model of nucleotide substitution, I present a method for computing the numbers of conservative
and radical nonsynonymous (amino acid altering) nucleotide substitutions per site and estimate these rates for 47 nuclear
genes from mammals. The results are as follows. (1) The average radical/conservative rate ratio is 0.81 for charge changes,
0.85 for polarity changes, and 0.49 when both polarity and volume changes are considered. (2) The radical/conservative rate
ratio is positively correlated with the nonsynonymous/synonymous rate ratio for charge changes or when both polarity and volume
changes are considered. (3) Both the conservative/synonymous rate ratio and the radical/synonymous rate ratio are lower in
the rodent lineage than in the primate or artiodactyl lineage, suggesting more intense purifying selection in the rodent lineage,
for both conservative and radical nonsynonymous substitutions. (4) Neglecting transition/transversion bias would cause an
underestimation of both radical and conservative rates and the ratio thereof. (5) Transversions induce more dramatic genetic
alternations than transitions in that transversions produce more amino acid altering changes and among which, more radical
changes.
Received: 6 April 1999 / Accepted: 16 August 1999 相似文献
2.
A quantitative measure of error minimization in the genetic code 总被引:7,自引:0,他引:7
Summary We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code. 相似文献
3.
Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of
codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation:
erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one
that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient
in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption
that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition
errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation
biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational
environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency
of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then
only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only
that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects
biases in these errors, as might be expected were the code the product of selection.
Received: 25 July 1997 / Accepted: 9 January 1998 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.
In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences
were found to be larger for a human–killifish pair than a human–lamprey pair. This indicates that some protein sequence convergence
may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions
separately for several species pairs and found that the transitions tend to be saturated in the distantly related species
pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary
time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure
and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of
the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test
showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back
to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60–70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.
Received: 5 October 2001 / Accepted: 24 October 2001 相似文献
6.
In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between
codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural
selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the
fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy,
we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino
acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon
bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not
the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring
the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key
question of codon usage.
Received: 18 June 2000 / Accepted: 10 November 2000 相似文献
7.
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
8.
de Miranda AB Alvarez-Valin F Jabbari K Degrave WM Bernardi G 《Journal of molecular evolution》2000,50(1):45-55
Mycobacterium tuberculosis and Mycobacterium leprae are the ethiological agents of tuberculosis and leprosy, respectively. After performing extensive comparisons between genes
from these two GC-rich bacterial species, we were able to construct a set of 275 homologous genes. Since these two bacterial
species also have a very low growth rate, translational selection could not be so determinant in their codon preferences as
it is in other fast-growing bacteria. Indeed, principal-components analysis of codon usage from this set of homologous genes
revealed that the codon choices in M. tuberculosis and M. leprae are correlated not only with compositional constraints and translational selection, but also with the degree of amino acid
conservation and the hydrophobicity of the encoded proteins. Finally, significant correlations were found between GC3 and synonymous distances as well as between synonymous and nonsynonymous distances.
Received: 30 October 1998 / Accepted: 16 August 1999 相似文献
9.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献
10.
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
11.
In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent
biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we
consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In
particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered.
Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary
conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that
strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably
between genomes.
Received: 6 May 1999 / Accepted: 29 October 1999 相似文献
12.
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
13.
The frequencies of ATG triplets in the genomes of various species were systematically analyzed, and the frequency of ATG
triplets was significantly low around start codons in both prokaryotic and eukaryotic genomes. In eukaryotes, however, the
frequency decrease before the start codon is much more evident than that after the start codon. In prokaryotes, on the other
hand, the ATG frequency pattern around the start codon is less evident, and—more importantly—symmetric.
We also computed average distances between a start codon and its nearest upstream-located ATG triplet and found a general
tendency for the average distances to be longer in higher organisms.
Received: 2 April 1998 / Accepted: 12 August 1998 相似文献
14.
15.
A survey of the patterns of synonymous codon preference in the HIV env gene reveals a correlation between the codon bias and the mutability requirements of different regions of the protein. At
hypervariable regions in gp120 one finds a greater proportion of codons that tend to mutate nonsynonymously, but to a target
that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective
pressure placed on the virus by the induced immune response, which favors amino acid substitutions in the complementarity
determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein.
Received: 9 June 1997 / Accepted: 25 May 1998 相似文献
16.
The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes 总被引:12,自引:0,他引:12
The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly
on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total
of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other
families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to
transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized
clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were
composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood
mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement
with the well-established phylogeny of cichlid fish.
Received: 11 October 2000 / Accepted: 26 February 2001 相似文献
17.
18.
Characteristics of Nucleotide Substitution in the Hepatitis C Virus Genome: Constraints on Sequence Change in Coding Regions at Both Ends of the Genome 总被引:19,自引:0,他引:19
Comparison of complete genome sequences for different variants of hepatitis C virus (HCV) reveals several different constraints
on sequence change. Synonymous changes are suppressed in coding regions at both 5′ and 3′ ends of the genome. No evidence
was found for the existence of alternative reading frames or for a lower mutation frequency in these regions. Instead, suppression
may be due to constraints imposed by RNA secondary structures identified within the core and NS5b genes. Nonsynonymous substitutions
are less frequent than synonymous ones except in the hypervariable region of E2 and, to a lesser extent, in E1, NS2, and NS5b.
Transitions are more frequent than transversions, particularly at the third position of codons where the bias is 16:1. In
addition, nucleotide substitutions may not occur symmetrically since there is a bias toward G or C at the third position of
codons, while T ↔ C transitions were twice as frequent as A ↔ G transitions. These different biases do not affect the phylogenetic
analysis of HCV variants but need to be taken into account in interpreting sequence change in longitudinal studies.
Received: 9 September 1996 / Accepted: 20 April 1997 相似文献
19.
Codon Usage Bias and tRNA Abundance in Drosophila 总被引:5,自引:0,他引:5
Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development.
We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception
of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference
for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with ``optimal' codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose
major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA
pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude
that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance.
Received: 5 December 1996 / Accepted: 14 June 1997 相似文献
20.
On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses 总被引:1,自引:0,他引:1
Angelo Pavesi Bettina De Iaco Maria Ilde Granero Alfredo Porati 《Journal of molecular evolution》1997,44(6):625-631
In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region
of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging
to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap
a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the
nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and
plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both
types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation
between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses,
indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage
correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison
of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine,
leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed
as a way with which they may expand their coding ability and gain new, specialized functions.
Received: 28 October 1996 / Accepted: 29 January 1997 相似文献