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1.
Yves Van de Peer John S. Taylor Ingo Braasch Axel Meyer 《Journal of molecular evolution》2001,53(4-5):436-446
The duplication of genes and even complete genomes may be a prerequisite for major evolutionary transitions and the origin
of evolutionary novelties. However, the evolutionary mechanisms of gene evolution and the origin of novel gene functions after
gene duplication have been a subject of many debates. Recently, we compiled 26 groups of orthologous genes, which included
one gene from human, mouse, and chicken, one or two genes from the tetraploid Xenopus and two genes from zebrafish. Comparative analysis and mapping data showed that these pairs of zebrafish genes were probably
produced during a fish-specific genome duplication that occurred between 300 and 450 Mya, before the teleost radiation (Taylor
et al. 2001). As discussed here, many of these retained duplicated genes code for DNA binding proteins. Different models have
been developed to explain the retention of duplicated genes and in particular the subfunctionalization model of Force et al.
(1999) could explain why so many developmental control genes have been retained. Other models are harder to reconcile with
this particular set of duplicated genes. Most genes seem to have been subjected to strong purifying selection, keeping properties
such as charge and polarity the same in both duplicates, although some evidence was found for positive Darwinian selection,
in particular for Hox genes. However, since only the cumulative pattern of nucleotide substitutions can be studied, clear indications of positive
Darwinian selection or neutrality may be hard to find for such anciently duplicated genes. Nevertheless, an increase in evolutionary
rate in about half of the duplicated genes seems to suggest that either positive Darwinian selection has occurred or that
functional constraints have been relaxed at one point in time during functional divergence.
Received: 4 January 2001 / Accepted: 29 March 2001 相似文献
2.
Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide
choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures.
In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding
first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform
to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that
genes from different genomes can be separated with a high degree of accuracy, according to these distance values.
In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their
poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides,
we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects.
Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene
present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking
correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.
Received: 16 January 2001 / Accepted: 30 August 2001 相似文献
3.
Akiko Kashiwagi Wataru Noumachi Masato Katsuno Mohammad T. Alam Itaru Urabe Tetsuya Yomo 《Journal of molecular evolution》2001,52(6):502-509
A simplified experimental evolution encompassing the essence of natural one was designed in an attempt to understand the
involved mechanism. In our system, molecular evolution was observed through three serial cycles of consecutive random mutagenesis
of the glutamine synthetase gene and chemostat culture of the transformed Escherichia coli cells containing the mutated genes. Selection pressure was imposed solely on the glutamine synthetase gene when varieties
of mutant genes compete in an unstructured environment of the chemostat. The molecular phylogeny and population dynamics were
deduced from the nucleotide sequences of the genes isolated from each of the chemostat runs. An initial mutant population
in each cycle, comprised of diversified closely-related genes, ended up with several varieties of mutants in a state of coexistence.
Competition between two mutant genes in the final population of the first cycle ascertained that the observed coexisting state
is not an incidental event and that cellular interaction via environmental nutrients is a possible mechanism of coexistence.
In addition, the mutant gene once extinct in the previous passage was found to have the capacity to reinvade and constitute
the gene pool of the later cycle of molecular evolution. These results, including the kinetic characteristics of the purified
wild-type and mutant glutamine synthetases in the phylogenetic tree, revealed that the enzyme activity had diverged, rather
than optimized, to a fittest value during the course of evolution. Here, we proposed that the plasticity of gene fitness in
consequence of cellular interaction via the environment is an essential mechanism governing molecular evolution.
Received: 29 August 2000 / Accepted: 25 January 2001 相似文献
4.
Wang B 《Journal of molecular evolution》2001,53(3):244-250
Genes with atypical G+C content and pattern of codon usage in a certain genome are possibly of exotic origin, and this idea
has been applied to identify horizontal events. In this way, it was postulated that a total of 755 genes in the E. coli genome are relics of horizontal events after the divergence of E. coli from the Salmonella lineage 100 million years ago (Lawrence and Ochman, 1998). In this paper we propose a new way to study sequence composition
more thoroughly. We found that although the 755 genes differ in composition from other genes in the E. coli genome, the difference is minor. If we accepted that these genes are horizontally transferred, then (1) it would be more
likely that they were transferred from genomes evolutionarily closely related to E. coli; but (2) the dating method used by Lawrence and Ochman (1997, 1998) largely underestimated the average age of introduced sequences
in the E. coli genome, in particular, most of the 755 genes should be introduced into E. coli before, instead of after, the divergence of E. coli from the Salmonella lineage. Our study reveals that atypical G+C content and pattern of codon usage are not reliable indicators of horizontal
gene transfer events.
Received: 27 September 2000 / Accepted: 9 April 2001 相似文献
5.
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
6.
Pont-Kingdon G Vassort CG Warrior R Okimoto R Beagley CT Wolstenholme DR 《Journal of molecular evolution》2000,51(4):404-415
The 3231-nucleotide-pair (ntp) sequence of one end of one of the two linear mitochondrial (mt) DNA molecules of Hydra attenuata (phylum Cnidaria, class Hydrozoa, order Anthomedusae) has been determined. This segment contains complete genes for tRNAf-Met, l-rRNA, tRNATrp, subunit 2 of cytochrome c oxidase (COII), subunit 8 of ATP synthetase (ATPase8), and the 5′ 136 ntp of ATPase6. These genes are arranged in the order
given and are transcribed from the same strand of the molecule. As in two other cnidarians, the hexacorallian anthozoan Metridium senile and the octocorallian anthozoan Sarcophyton glaucum, the mt-genetic code of H. attenuata is near standard. The only modification appears to be that TGA specifies tryptophan rather than termination. Also as in M. senile and S. glaucum, the encoded H. attenuata mt-tRNAf-Met has primary and secondary structural features resembling those of Escherichia coli initiator tRNAt-Met. As the encoded mt-tRNATrp cannot be folded into a totally orthodox secondary structure, two alternative forms are suggested. The encoded H. attenuata mt-l-rRNA is 1738 nt, which is 451 nt shorter than the M. senile mt-l-rRNA. Comparisons of secondary structure models of these two mt-l-rRNAs indicate that most of the size difference results
from loss of nucleotides in the H. attenuata molecule at a minimum of 46 locations, which includes elimination of six distinct helical elements.
Received: 9 March 2000 / Accepted: 24 July 2000 相似文献
7.
The common assumption of operons as composed of genes that cooperate in a biological process is confirmed here by showing
that Escherichia coli operons tend to be composed of genes that belong to the same general class of cellular function. Furthermore, the comparison
between the genomic organization of E. coli and that of Bacillus subtilis shows that the genes that are homologous to genes that belong to experimentally characterized E. coli operons tend to cluster in neighboring regions of the genome. This tendency is greater for the subset of E. coli operons whose genes belong to a single functional class. These observations indicate strong evolutionary pressure that, translated
into functional constraints, leads to the inclusion of many essential functions in conserved operons and clusters in these
two distant species. 相似文献
8.
Syvanen M 《Journal of molecular evolution》2002,54(2):258-266
The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gram− bacteria,
Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four
groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal
tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea,
Eukaryota) (Gram+, Gram−) topology, two genes supported the one where Gram− and Eukaryota form a clade, and one gene supported
the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing
the two central nodes into a single node. These are referred to as star phylogenies.
I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger
than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star
phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that
the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely
related species. This implies that the genes under comparison experience comparable functional constraint. However, when the
genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint
this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is
that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one
another. They presumably spread through life by horizontal gene transfer.
Received: 12 July 2001 / Accepted: 27 July 2001 相似文献
9.
Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms
to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force,
so there is a balance between mutation, selection, and drift; (2) at some sites there is no selection on codon usage, so some
synonymous sites are unaffected by translational selection; and (3) translationally sub-optimal codons are favored by alternative
selection pressures at certain synonymous sites. We find that when all the data is considered, model 1 is supported and both
models 2 and 3 are rejected as sole explanations for the existence of translationally sub-optimal codons. However, we find
evidence in favor of both models 2 and 3 when the data is partitioned between groups of amino acids and between regions of
the genes. Thus, all three mechanisms appear to contribute to the existence of translationally sub-optimal codons in E. coli.
Received: 18 July 2000 / Accepted: 17 April 2001 相似文献
10.
Langenkämper G Fung RW Newcomb RD Atkinson RG Gardner RC MacRae EA 《Journal of molecular evolution》2002,54(3):322-332
We present phylogenetic analyses to demonstrate that there are three families of sucrose phosphate synthase (SPS) genes present
in higher plants. Two data sets were examined, one consisting of full-length proteins and a second larger set that covered
a highly conserved region including the 14-3-3 binding region and the UDPGlu active site. Analysis of both datasets showed
a well supported separation of known genes into three families, designated A, B, and C. The genomic sequences of Arabidopsis thaliana include a member in each family: two genes on chromosome 5 belong to Family A, one gene on chromosome 1 to Family B, and
one gene on chromosome 4 to Family C. Each of three Citrus genes belong to one of the three families. Intron/exon organization of the four Arabidopsis genes differed according to phylogenetic analysis, with members of the same family from different species having similar
genomic organization of their SPS genes. The two Family A genes on Arabidopsis chromosome 5 appear to be due to a recent duplication. Analysis of published literature and ESTs indicated that functional
differentiation of the families was not obvious, although B family members appear not to be expressed in roots. B family genes
were cloned from two Actinidia species and southern analysis indicated the presence of a single gene family, which contrasts to the multiple members of
Family A in Actinidia. Only two family C genes have been reported to date.
Received: 17 April 2001 / Accepted: 27 August 2001 相似文献
11.
Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these
interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus
adhesion molecules might be under multiple forms of selection including selection to constrain functional interactions or
evolve novel epitopes to avoid recognition. We address these issues by studying genetic diversity in the Escherichia coli type-1 fimbrial major subunit, fimA. Overall, sequence diversity in fimA is high (π= 0.07) relative to that in other E. coli genes. High diversity is a function of positive diversifying selection, as detected by d
N/d
S ratios higher than 1.0, and amino acid residuces subject to diversifying selection are nonrandomly clustered on the exterior
surface of the peptide. In addition, McDonald and Kreitman tests suggest that there has been historical but not current directional
selection at fimA between E. coli and Salmonella. Finally, some regions of the fimA peptide appear to be under strong structural constraint within E. coli, particularly the interior regions of the molecule that is involved in subunit to subunit interaction. Recombination also
plays a major role contributing to E. coli fimA allelic variation and estimates of recombination (2N
e
c) and mutation (2N
eμ) are about the same. Recombination may act to separate the diverse evolutionary forces in different regions of the fimA peptide.
Received: 13 April 2000 / Accepted: 28 October 2000 相似文献
12.
To characterize the coding-sequence divergence of closely related genomes, we compared DNA sequence divergence between sequences
from a Brassica rapa ssp. pekinensis EST library isolated from flower buds and genomic sequences from Arabidopsis thaliana. The specific objectives were (i) to determine the distribution of and relationship between K
a and K
s, (ii) to identify genes with the lowest and highest K
a:K
s values, and (iii) to evaluate how codon usage has diverged between two closely related species. We found that the distribution
of K
a:K
s was unimodal, and that substitution rates were more variable at nonsynonymous than synonymous sites, and detected no evidence
that K
a and K
s were positively correlated. Several genes had K
a:K
s values equal to or near zero, as expected for genes that have evolved under strong selective constraint. In contrast, there
were no genes with K
a:K
s >1 and thus we found no strong evidence that any of the 218 sequences we analyzed have evolved in response to positive selection.
We detected a stronger codon bias but a lower frequency of GC at synonymous sites in A. thaliana than B. rapa. Moreover, there has been a shift in the profile of most commonly used synonymous codons since these two species diverged
from one another. This shift in codon usage may have been caused by stronger selection acting on codon usage or by a shift
in the direction of mutational bias in the B. rapa phylogenetic lineage. 相似文献
13.
The ubiquitous glyoxalase system, which is composed of two enzymes, removes cellular cytotoxic methylglyoxal (MG). In an
effort to identify critical residues conserved in the evolution of the first enzyme in this system, glyoxalase I (GlxI), as
well as the structural implications of sequence alterations in this enzyme, a search of the National Center for Biotechnology
Information (NCBI) database of unfinished genomes was undertaken. Eleven putative GlxI sequences from pathogenic organisms
were identified and analyses of these sequences in relation to the known and previously identified GlxI enzymes were performed.
Several of these sequences show a very high similarity to the Escherichia coli GlxI sequence, most notably the 79% identity of the sequence identified from Yersinia pestis, the causative agent of bubonic plague. In addition to the conservation of residues critical to binding the catalytic metal
in all of the proposed GlxI enzymes, four regions in the Homo sapiens GlxI enzyme are absent in all of the bacterial GlxI sequences, with the exception of Pseudomonas putida. Removal of these regions may alter the active-site conformation of the bacterial enzymes in relation to that of the H. sapiens. These differences may be targeted for the development of inhibitors selective to the bacterial enzymes.
Received: 13 October 1999 / Accepted: 17 January 2000 相似文献
14.
Gwenaël Piganeau Dominique Mouchiroud Laurent Duret Christian Gautier 《Journal of molecular evolution》2002,54(1):129-133
The relationship between the silent substitution rate (K
s) and the GC content along the genome is a focal point of the debate about the origin of the isochore structure in vertebrates.
Recent estimation of the silent substitution rate showed a positive correlation between K
s and GC content, in contradiction with the predictions of both the regional mutation bias model and the selection or biased
gene conversion model. The aim of this paper is to help resolve this contradiction between theoretical studies and data. We
analyzed the relationship between K
s and GC content under (1) uniform mutation bias, (2) a regional mutation bias, and (3) mutation bias and selection. We report
that an increase in K
s with GC content is expected under mutation bias because of either nonequilibrium of the isochore structure or an increasing
mutation rate from AT toward GC nucleotides in GC-richer isochores. We show by simulations that CpG deamination tends to increase
the mutation rate with GC content in a regional mutation bias model. We also demonstrate that the relationship between K
s and GC under the selectionist or biased gene conversion model is positive under weak selection if the mutation selection
equilibrium GC frequency is less than 0.5.
Received: 28 March 2001 / Accepted: 16 May 2001 相似文献
15.
Wei Wu Morris Goodman Margaret I. Lomax Lawrence I. Grossman 《Journal of molecular evolution》1997,44(5):477-491
Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory
chain on the mitochondrial inner membrane. Up to 13 subunits encoded by both the mitochondrial (subunits I, II, and III) and
nuclear genomes occur in eukaryotic organisms ranging from yeast to human. Previously, we observed a high number of amino
acid replacements in the human COX IV subunit compared to mouse, rat, and cow orthologues. Here we examined COX IV evolution
in the two groups of anthropoid primates, the catarrhines (hominoids, cercopithecoids) and platyrrhines (ceboids), as well
as one prosimian primate (lorisiform), by sequencing PCR-amplified portions of functional COX4 genes from genomic DNAs. Phylogenetic analysis of the COX4 sequence data revealed that accelerated nonsynonymous substitution rates were evident in the early evolution of both catarrhines
and, to a lesser extent, platyrrhines. These accelerated rates were followed later by decelerated rates, suggesting that positive
selection for adaptive amino acid replacement became purifying selection, preserving replacements that had occurred. The evidence
for positive selection was especially pronounced along the catarrhine lineage to hominoids in which the nonsynonymous rate
was first faster than the synonymous rate, then later much slower. The rates of three types of ``neutral DNA' nucleotide
substitutions (synonymous substitutions, pseudogene nucleotide substitutions, and intron nucleotide substitutions) are similar
and are consistent with previous observations of a slower rate of such substitutions in the nuclear genomes of hominoids than
in the nuclear genomes of other primate and mammalian lineages.
Received: 22 May 1996 / Accepted: 24 November 1996 相似文献
16.
We compared the codon usage of sequences of transposable elements (TEs) with that of host genes from the species Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens. Factorial correspondence analysis showed that, regardless of the base composition of the genome, the TEs differed from the
genes of their host species by their AT-richness. In all species, the percentage of A + T on the third codon position of the
TEs was higher than that on the first codon position and lower than that in the noncoding DNA of the genomes. This indicates
that the codon choice is not simply the outcome of mutational bias but is also subject to selection constraints. A tendency
toward higher A + T on the third position than on the first position was also found in the host genes of A. thaliana, C. elegans, and S. cerevisiae but not in those of D. melanogaster and H. sapiens. This strongly suggests that the AT choice is a host-independent characteristic common to all TEs. The codon usage of TEs
generally appeared to be different from the mean of the host genes. In the AT-rich genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Saccharomyces cerevisiae, the codon usage bias of TEs was similar to that of weakly expressed genes. In the GC-rich genome of D. melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest
that selection acts on TEs and that TEs may display specific behavior within the host genomes.
Received: 2 May 2001 / Accepted: 29 October 2001 相似文献
17.
While globin genes ctt-2β and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless. We analyzed four globin genes
linked to the two intron-bearing genes in C. th. thummi. Three have a single intron at the same position as ctt-2β and ctt-9.1; the fourth is intronless and lies between intron bearing genes. Finally, in addition to its intron, one gene (ctt-13RT) was recently interrupted by retrotransposition. Phylogenetic analyses show that the six genes in C. th. thummi share common ancestry with five globin genes in the distantly related species C. tentans, and that a 5-gene ancestral cluster predates the divergence of the two species. One gene in the ancestral cluster gave rise
to ctn-ORFB in C. tentans, and duplicated in C. th. thummi to create ctt-11 and ctt-12. From parsimonious calculations of evolutionary distances since speciation, ctt-11, ctt-12, and ctn-ORFB evolved rapidly, while ctn-ORFE in C. tentans evolved slowly compared to other globin genes in the clusters. While these four globins are under selective pressure, we
suggest that most chironomid globin genes were not selected for their unique function. Instead, we propose that high gene
copy number itself was selected because conditions favored organisms that could synthesize more hemoglobin. High gene copy
number selection to produce more of a useful product may be the basis of forming multigene families, all of whose members
initially accumulate neutral substitutions while retaining essential function. Maintenance of a large family of globin genes
not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into
as many as 5000 species.
Received: 31 December 1996 / Accepted: 16 May 1997 相似文献
18.
Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A 总被引:1,自引:0,他引:1
Yang Z 《Journal of molecular evolution》2000,51(5):423-432
Algorithmic details to obtain maximum likelihood estimates of parameters on a large phylogeny are discussed. On a large tree,
an efficient approach is to optimize branch lengths one at a time while updating parameters in the substitution model simultaneously.
Codon substitution models that allow for variable nonsynonymous/synonymous rate ratios (ω=d
N/d
S) among sites are used to analyze a data set of human influenza virus type A hemagglutinin (HA) genes. The data set has 349
sequences. Methods for obtaining approximate estimates of branch lengths for codon models are explored, and the estimates
are used to test for positive selection and to identify sites under selection. Compared with results obtained from the exact
method estimating all parameters by maximum likelihood, the approximate methods produced reliable results. The analysis identified
a number of sites in the viral gene under diversifying Darwinian selection and demonstrated the importance of including many
sequences in the data in detecting positive selection at individual sites.
Received: 25 April 2000 / Accepted: 24 July 2000 相似文献
19.
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