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Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes 总被引:21,自引:0,他引:21
Michael J. McLean Kenneth H. Wolfe Kevin M. Devine 《Journal of molecular evolution》1998,47(6):691-696
Variation in GC content, GC skew and AT skew along genomic regions was examined at third codon positions in completely sequenced
prokaryotes. Eight out of nine eubacteria studied show GC and AT skews that change sign at the origin of replication. The
leading strand in DNA replication is G-T rich at codon position 3 in six eubacteria, but C-T rich in two Mycoplasma species. In M. genitalium the AT and GC skews are symmetrical around the origin and terminus of replication, whereas its GC content variation has been
shown to have a centre of symmetry elsewhere in the genome. Borrelia burgdorferi and Treponema pallidum show extraordinary extents of base composition skew correlated with direction of DNA replication. Base composition skews
measured at third codon positions probably reflect mutational biases, whereas those measured over all bases in a sequence
(or at codon positions 1 and 2) can be strongly affected by protein considerations due to the tendency in some bacteria for
genes to be transcribed in the same direction that they are replicated. Consequently in some species the direction of skew
for total genomic DNA is opposite to that for codon position 3.
Received: 2 February 1998 / Accepted: 15 June 1998 相似文献
3.
Jenkins GM Pagel M Gould EA de A Zanotto PM Holmes EC 《Journal of molecular evolution》2001,52(4):383-390
The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined
in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary
with arthropod association in the genus Flavivirus, a major source of disease in humans and animals. Flaviviruses are transmitted by mosquitoes, by ticks, or directly between
vertebrate hosts. Those viruses associated with ticks were found to have a significantly lower G+C content than non-vector-borne
flaviviruses and this difference was present throughout the genome at all amino acids and codon positions. In contrast, mosquito-borne
viruses had an intermediate G+C content which was not significantly different from those of the other two groups. In addition,
biases in dinucleotide and codon usage that were independent of base composition were detected in all flaviviruses, but these
did not covary with arthropod association. However, the overall effect of these biases was slight, suggesting only weak selection
at synonymous sites. A preliminary analysis of base composition, codon usage, and vector specificity in other RNA virus families
also revealed a possible association between base composition and vector specificity, although with biases different from
those seen in the Flavivirus genus.
Received: 29 August 2000 / Accepted: 19 December 2000 相似文献
4.
Cristian Cañestro Ricard Albalat Lars Hjelmqvist Laura Godoy Hans Jörnvall Roser Gonzàlez-Duarte 《Journal of molecular evolution》2002,54(1):81-89
The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized
three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon–intron distribution,
and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million
years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary
rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including
the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis
and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform
burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in
early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in
favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning
of the drifting of major land masses from the Pangea.
Received: 10 April 2001 / Accepted: 23 May 2001 相似文献
5.
Francesco Frati Chris Simon Jack Sullivan David L. Swofford 《Journal of molecular evolution》1997,44(2):145-158
The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic
levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic
relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all
insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the
basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions
appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in
some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels
observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or
exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity
of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information
was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical
support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well
supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from
an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.
Received: 12 January 1996 / Accepted: 10 August 1996 相似文献
6.
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
7.
The aldo-keto reductase enzymes comprise a functionally diverse gene family which catalyze the NADPH-dependant reduction
of a variety of carbonyl compounds. The protein sequences of 45 members of this family were aligned and phylogenetic trees
were deduced from this alignment using the neighbor-joining and Fitch algorithms. The branching order of these trees indicates
that the vertebrate enzymes cluster in three groups, which have a monophyletic origin distinct from the bacterial, plant,
and invertebrate enzymes. A high level of conservation was observed between the vertebrate hydroxysteroid dehydrogenase enzymes,
prostaglandin F synthase, and ρ-crystallin of Xenopus laevis. We infer from the phylogenetic analysis that prostaglandin F synthase may represent a recent recruit to the eicosanoid biosynthetic
pathway from the hydroxysteroid dehydrogenase pathway and furthermore that, in the context of gene recruitment, Xenopus laevisρ-crystallin may represent a shared gene.
Received: 26 August 1996 / Accepted: 5 June 1997 相似文献
8.
The idea that the pattern of point mutation in Drosophila has remained constant during the evolution of the genus has recently been challenged. A study of the nucleotide composition
focused on the Drosophila
saltans group has evidenced unsuspected nucleotide composition differences among lineages. Compositional differences are associated
with an accelerated rate of amino acid replacement in functionally less constrained regions. Here we reassess this issue from
a different perspective. Adopting a maximum-likelihood estimation approach, we focus on the different predictions that mutation
and selection make about the nonsynonymous-to-synonymous rate ratio. We investigate two gene regions, alcohol dehydrogenase
(Adh) and xanthine dehydrogenase (Xdh), using a balanced data set that comprises representatives from the melangaster, obscura, saltans, and willistoni groups. We also consider representatives of the Hawaiian picture-winged group. These Hawaiian species are known to have experienced
repeated bottlenecks and are included as a reference for comparison. Our results confirm patterns previously detected. The
branch ancestral to the fast-evolving willistoni/saltans lineage, where most of the change in GC content has occurred, exhibits an excess of synonymous substitutions. The shift in
mutation bias has affected the extent of the rate variation among sites in Xdh.
Received: 4 May 1999 / Accepted: 26 July 1999 相似文献
9.
Jon P. Anderson Allen G. Rodrigo Gerald H. Learn Yang Wang Hillard Weinstock Marcia L. Kalish Kenneth E. Robbins Leroy Hood James I. Mullins 《Journal of molecular evolution》2001,53(1):55-62
Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide
frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy
of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating
model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers.
Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates,
however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested
using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen
in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution
rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals
from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific
for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States.
The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence
evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1
subtype B env sequences.
Received: 4 October 2000 / Accepted: 1 March 2001 相似文献
10.
The extracellular hemoglobins of cladocerans derive from the aggregation of 12 two-domain globin subunits that are apparently
encoded by four genes. This study establishes that at least some of these genes occur as a tandem array in both Daphnia magna and Daphnia exilis. The genes share a uniform structure; a bridge intron separates two globin domains which each include three exons and two
introns. Introns are small, averaging just 77 bp, but a longer sequence (2.2–3.2 kb) separates adjacent globin genes. A survey
of structural diversity in globin genes from other daphniids revealed three independent cases of intron loss, but exon lengths
were identical, excepting a 3-bp insertion in exon 5 of Simocephalus. Heterogeneity in the extent of nucleotide divergence was marked among exons, largely as a result of the pronounced diversification
of the terminal exon. This variation reflected, in part, varying exposure to concerted evolution. Conversion events were frequent
in exons 1–4 but were absent from exons 5 and 6. Because of this difference, the results of phylogenetic analyses were strongly
affected by the sequences employed in this construction. Phylogenies based on total nucleotide divergence in exons 1–4 revealed
affinities among all genes isolated from a single species, reflecting the impact of gene conversion events. In contrast, phylogenies
based on total nucleotide divergence in exons 5 and 6 revealed affinities among orthologous genes from different taxa.
Received: 8 March 1999 / Accepted: 14 July 1999 相似文献
11.
12.
Drosophila nuclear introns are commonly assumed to change according to a single rate of substitution, yet little is known about the
evolution of these non-coding sequences. The hypothesis of a uniform substitution rate for introns seems to be at odds with
recent findings that the nucleotide composition of introns varies at a scale unknown before, and that their base content variation
is correlated with that of the adjacent exons. However, no direct attempt at comparing substitution rates in introns seems
to have been addressed so far. We have studied the rate of nucleotide substitution over a region of the Xdh gene containing two adjacent short, constitutively spliced introns, in several species of Drosophila and related genera. The two introns differ significantly in base composition and substitution rate, with one intron evolving
at least twice as fast as the other. In addition, the substitution pattern of the introns is positively associated with that
of the surrounding coding regions, evidencing that the molecular evolution of these introns is impacted by the region in which
they are embedded. The observed differences cannot be attributed to selection acting differently at the level of the secondary
structure of the pre-mRNA. Rather, they are better accounted for by locally heterogeneous patterns of mutation.
Received: 26 July 1999 / Accepted: 21 August 1999 相似文献
13.
Janet L. Siefert Kirt A. Martin Fadi Abdi William R. Widger George E. Fox 《Journal of molecular evolution》1997,45(5):467-472
Five complete bacterial genome sequences have been released to the scientific community. These include four (eu)Bacteria,
Haemophilus influenzae, Mycoplasma genitalium, M. pneumoniae, and Synechocystis PCC 6803, as well as one Archaeon, Methanococcus jannaschii. Features of organization shared by these genomes are likely to have arisen very early in the history of the bacteria and
thus can be expected to provide further insight into the nature of early ancestors. Results of a genome comparison of these
five organisms confirm earlier observations that gene order is remarkably unpreserved. There are, nevertheless, at least 16
clusters of two or more genes whose order remains the same among the four (eu)Bacteria and these are presumed to reflect conserved
elements of coordinated gene expression that require gene proximity. Eight of these gene orders are essentially conserved
in the Archaea as well. Many of these clusters are known to be regulated by RNA-level mechanisms in Escherichia coli, which supports the earlier suggestion that this type of regulation of gene expression may have arisen very early. We conclude
that although the last common ancestor may have had a DNA genome, it likely was preceded by progenotes with an RNA genome.
Received: 10 March 1996 / Accepted: 20 May 1997 相似文献
14.
In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging
to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of
the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin:
The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles
and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor
BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont
algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded
by the well-supported successive divergence of labyrinthulomycetes and bicosoecids.
On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching
order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae,
and several smaller groups of organisms remains largely unresolved.
When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution
rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving
sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic
grouping in most distance trees.
Received: 11 June 1997 / Accepted: 21 July 1997 相似文献
15.
In translation, separate aminoacyl-tRNA synthetases attach the 20 different amino acids to their cognate tRNAs, with the
exception of glutamine. Eukaryotes and some bacteria employ a specific glutaminyl-tRNA synthetase (GlnRS) which other Bacteria,
the Archaea (archaebacteria), and organelles apparently lack. Instead, tRNAGln is initially acylated with glutamate by glutamyl-tRNA synthetase (GluRS), then the glutamate moiety is transamidated to glutamine.
Lamour et al. [(1994) Proc Natl Acad Sci USA 91:8670–8674] suggested that an early duplication of the GluRS gene in eukaryotes
gave rise to the gene for GlnRS—a copy of which was subsequently transferred to proteobacteria. However, questions remain
about the occurrence of GlnRS genes among the Eucarya (eukaryotes) outside of the ``crown' taxa (animals, fungi, and plants),
the distribution of GlnRS genes in the Bacteria, and their evolutionary relationships to genes from the Archaea. Here, we
show that GlnRS occurs in the most deeply branching eukaryotes and that putative GluRS genes from the Archaea are more closely
related to GlnRS and GluRS genes of the Eucarya than to those of Bacteria. There is still no evidence for the existence of
GlnRS in the Archaea. We propose that the last common ancestor to contemporary cells, or cenancestor, used transamidation
to synthesize Gln-tRNAGln and that both the Bacteria and the Archaea retained this pathway, while eukaryotes developed a specific GlnRS gene through
the duplication of an existing GluRS gene. In the Bacteria, GlnRS genes have been identified in a total of 10 species from
three highly diverse taxonomic groups: Thermus/Deinococcus, Proteobacteria γ/β subdivision, and Bacteroides/Cytophaga/Flexibacter.
Although all bacterial GlnRS form a monophyletic group, the broad phyletic distribution of this tRNA synthetase suggests that
multiple gene transfers from eukaryotes to bacteria occurred shortly after the Archaea–eukaryote divergence. 相似文献
16.
The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been
demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained
within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous
gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in
a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different
species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence
of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that
there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted
evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically
by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on
species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese
hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency
of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes.
Received: 18 January 2000 / Accepted: 26 April 2000 相似文献
17.
Singhania NA Dyer KD Zhang J Deming MS Bonville CA Domachowske JB Rosenberg HF 《Journal of molecular evolution》1999,49(6):721-728
The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase
3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs
of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of
eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine
counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have
occurred at these loci recently, sometime after the divergence of these two rodent species (∼10–15 million years ago). Nonsynonymous
substitutions per site (d
N) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated
rates, and comparisons of nonsynonymous to synonymous substitution (d
N / d
S) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures
promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain,
our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.
Received: 8 April 1999 / Accepted: 22 June 1999 相似文献
18.
Analysis of the 18S rDNA sequences of five species of the family Dugesiidae (phylum Platyhelminthes, suborder Tricladida,
infraorder Paludicola) and eight species belonging to families Dendrocoelidae and Planaridae and to the infraorder Maricola
showed that members of the family Dugesiidae have two types of 18S rDNA genes, while the rest of the species have only one.
The duplication event also affected the ITS-1, 5.8S, ITS-2 region and probably the 28S gene. The mean divergence value between
the type I and the type II sequences is 9% and type II 18S rDNA genes are evolving 2.3 times more rapidly than type I. The
evolutionary rates of type I and type II genes were calibrated from biogeographical data, and an approximate date for the
duplication event of 80–120 million years ago was calculated. The type II gene was shown, by RT-PCR, to be transcribed in
adult individuals of Schmidtea polychroa, though at very low levels. This result, together with the fact that most of the functionally important positions for small-subunit
rRNA in prokaryotes have been conserved, indicates that the type II gene is probably functional.
Received: 24 March 1998 / Accepted: 17 March 1999 相似文献
19.
Aurora M. Nedelcu 《Journal of molecular evolution》2001,53(6):670-679
This study provides a phylogenetic/comparative approach to deciphering the processes underlying the evolution of plastid
rRNA genes in genomes under relaxed functional constraints. Nonphotosynthetic green algal taxa that belong to two distinct
classes, Chlorophyceae (Polytoma) and Trebouxiophyceae (Prototheca), were investigated. Similar to the situation described previously for plastid 16S rRNA genes in nonphotosynthetic land plants,
nucleotide substitution levels, extent of structural variations, and percentage AT values are increased in nonphotosynthetic
green algae compared to their closest photosynthetic relatives. However, the mutational processes appear to be different in
many respects. First, with the increase in AT content, more transversions are noted in Polytoma and holoparasite angiosperms, while more transitions characterize the evolution of the 16S rDNA sequences in Prototheca. Second, although structural variations do accumulate in both Polytoma and Prototheca (as well as holoparasitic plastid 16S rRNAs), insertions as large as 1.6 kb characterize the plastid 16S rRNA genes in the
former, whereas significantly smaller indels (not exceeding 24 bp) seem to be more prevalent in the latter group. The differences
in evolutionary rates and patterns within and between lineages might be due to mutations in replication/repair-related genes;
slipped-strand mispairing is likely the mechanism responsible for the expansion of insertions in Polytoma plastid 16S rRNA genes.
Received: 29 December 2000 / Accepted: 18 May 2001 相似文献
20.
Sequence data of mitochondrial 16S ribosomal DNA (mt-rDNA) and nuclear 28S ribosomal DNA (nuc-rDNA) were compared in two
honeybee species (Apis mellifera and Apis dorsata) and a selection of 22 wasp species (Vespidae) with different levels of sociality. The averge substitution rates in mt-rDNA
and nuc-rDNA were almost-equal in solitary species. In species with larger nests, however, the difference between the nuclear
and the mitochondrial substitution rate significantly increased. The average substitution ratio, ψ (nucleotide substitutions
in mt-rDNA/nucleotide substitutions in nuc-rDNA) was 1.48 ± 0.12 (SE) among the solitary Eumeninae, 3.70 ± 0.15 among five
primitive social Stenogastrinae species, 3.24 ± 0.20 among five Polistinae species, 5.76 ± 0.33 among nine highly eusocial
Vespinae, and 12.7 in the two Apis species. The high egg-laying rate and the effective population size skew between the sexes may contribute to the rise of
the substitution ratio in the highly eusocial species. Drift and bottleneck effects in the mitochondrial DNA pool during speciation
events as well as polyandry may further enhance this phenomenon.
Received: 12 January 1998 / Accepted: 28 April 1998 相似文献