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1.
Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances
sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization
protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5′ end of the sperm
bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of
the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates
moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible
to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide
substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald
and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms
observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting
that the polymorphism observed in the 5′ region of S. franciscanus bindin is a result of neutral evolution.
Received: 19 June 1998 / Accepted: 2 August 2000 相似文献
2.
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
3.
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
4.
5.
A maximum-likelihood analysis of selection pressures acting on the attachment (G) glycoprotein gene of respiratory syncytial
virus (RSV) from humans (HRSV) and bovines (BRSV) is presented. Six positively selected sites were identified in both group
A and group B of HRSV, although only one site was common between them, while no positively selected sites were detected in
BRSV. All positively selected sites were located within the ectodomain of the G protein and showed some association with positions
of immunoglobulin (Ig) epitopes and sites of O-glycosylation. These results suggest that immune (antibody)-driven natural
selection is an important determinant of RSV evolution and that this selection pressure differs among strains. The passage
histories of RSV strains were also shown to affect the distribution of positively selected sites, particularly in HRSV B,
and should be considered whenever retrospective analysis of adaptive evolution is undertaken.
Received: 15 August 2000 / Accepted: 2 November 2000 相似文献
6.
Suzuki Y Katayama K Fukushi S Kageyama T Oya A Okamura H Tanaka Y Mizokami M Gojobori T 《Journal of molecular evolution》1999,48(4):383-389
With the aim of elucidating evolutionary features of GB virus C/hepatitis G virus (GBV-C/HGV), molecular evolutionary analyses
were conducted using the entire coding region of this virus. In particular, the rate of nucleotide substitution for this virus
was estimated to be less than 9.0 × 10−6 per site per year, which was much slower than those for other RNA viruses. The phylogenetic tree reconstructed for GBV-C/HGV,
by using GB virus A (GBV-A) as outgroup, indicated that there were three major clusters (the HG, GB, and Asian types) in GBV-C/HGV,
and the divergence between the ancestor of GB- and Asian-type strains and that of HG-type strains first took place more than
7000–10,000 years ago. The slow evolutionary rate for GBV-C/HGV suggested that this virus cannot escape from the immune response
of the host by means of producing escape mutants, implying that it may have evolved other systems for persistent infection.
Received: 2 June 1998 / Accepted: 8 August 1998 相似文献
7.
The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular
clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio
test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately
inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood
method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were
also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important
insights on HCV origin and evolution.
Received: 13 January 2001 / Accepted: 21 June 2001 相似文献
8.
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
9.
Protease cascades and their inhibitors are a common feature of many biological regulatory systems, and the various components
of such cascades have been subjected to a long and concerted evolution. We present here evidence that in the coagulation cascade,
the sequence of the protease-binding reactive-site loop of antithrombin has evolved such that the majority of its residues
has been acquired not for the efficient inhibition of its target proteases, thrombin and factor Xa, but to avoid the inhibition
of activated protein C (APC). We substituted residues of the reactive-site loop of antithrombin into α1-antitrypsin and tested the chimeras against thrombin, factor Xa, and APC. With respect to factor Xa and thrombin, the difference
in association rate between the fastest and the slowest inhibitors was 5.5- and 88-fold, respectively. However, with respect
to APC the difference was 12,500-fold. While most of the variation in the inhibition rates of thrombin could be accounted
for by P2 Gly-to-Pro substitutions, for APC almost every residue had an effect on inhibition. In 22 of 25 direct comparisons
of antitrypsin residues with antithrombin residues, either singly or in blocs, the antithrombin residues caused a decrease
in the rate of inhibition of APC. The antithrombin residue Asn393, at position P′3, emerged as particularly important for
avoiding the inhibition of APC, however, its 190-fold effect was seen only when in conjunction with antithrombin P7 to P′2
residues. Cooperative effects among residues of the reactive-site loop thus emerged as critical for restricting the activity
of this sequence against APC.
Received: 15 November 1999 / Accepted: 2 August 2000 相似文献
10.
A Monte Carlo method was used to test the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta
virus. This analysis revealed that there is insufficient sequence similarity among these pathogens to support the hypothesis
that they have a common evolutionary origin. Furthermore, while definite patterns of sequence similarity were observed among
some viroids, there was a clear lack of overall similarity, indicating that a monophyletic origin for even this group cannot
be reliably supported from sequence data alone.
Received: 30 April 1999 / Accepted: 24 August 1999 相似文献
11.
Michael Kruse Sally P. Leys Isabel M. Müller Werner E.G. Müller 《Journal of molecular evolution》1998,46(6):721-728
Recent analyses of genes encoding proteins typical for multicellularity, especially adhesion molecules and receptors, favor
the conclusion that all metazoan phyla, including the phylum Porifera (sponges), are of monophyletic origin. However, none
of these data includes cDNA encoding a protein from the sponge class Hexactinellida. We have now isolated and characterized
the cDNA encoding a protein kinase C, belonging to the C subfamily (cPKC), from the hexactinellid sponge Rhabdocalyptus dawsoni. The two conserved regions, the regulatory part with the pseudosubstrate site, the two zinc fingers, and the C2 domain, as
well as the catalytic domain were used for phylogenetic analyses. Sequence alignment and construction of a phylogenetic tree
from the catalytic domains revealed that the yeast Saccharomyces cerevisiae and the protozoan Trypanosoma brucei are at the base of the tree, while the hexactinellid R. dawsoni branches off first among the metazoan sequences; the other two classes of the Porifera, the Calcarea (the sequence from Sycon raphanus was used) and the Demospongiae (sequences from Geodia cydonium and Suberites domuncula were used), branch off later. The statistically robust tree also shows that the two cPKC sequences from the higher invertebrates
Drosophila melanogaster and Lytechinus pictus are most closely related to the calcareous sponge. This finding was also confirmed by comparing the regulatory part of the
kinase gene. We suggest, that (i) within the phylum Porifera, the class Hexactinellida diverged first from a common ancestor
to the Calcarea and the Demospongiae, which both appeared later, and (ii) the higher invertebrates are more closely related
to the calcareous sponges.
Received: 6 August 1997 / Accepted: 24 October 1997 相似文献
12.
Regulation of Na-K-ATPase Activity in the Proximal Tubule: Role of the Protein Kinase C Pathway and of Eicosanoids 总被引:4,自引:0,他引:4
To evaluate further the signal transduction mechanisms involved in the short-term modulation of Na-K-ATPase activity in the
mammalian kidney, we examined the role of phospholipase C-protein kinase C (PLC-PKC) pathway and of various eicosanoids in
this process, using microdissected rat proximal convoluted tubules. Dopamine (DA) and parathyroid hormone (either synthetic
PTH1-34 or PTH3-34) inhibited Na-K-ATPase activity in dose-dependent manner; this effect was reproduced by PKC530-558 fragment and blocked by the specific PKC inhibitor calphostin C, as well as by the PLC inhibitors neomycin and U-73122. Pump
inhibition by DA, PTH, or arachidonic acid, and by PKC activators phorbol dibutyrate (PDBu) or dioctanoyl glycerol (DiC8)
was abolished by ethoxyresorufin, an inhibitor of the cytochrome P450-dependent monooxygenase pathway, but was unaffected
by indomethacin or nordihydroguaiaretic acid, inhibitors of the cyclooxygenase and lipoxygenase pathways of the arachidonic
acid cascade, respectively. Furthermore, each of the three monooxygenase products tested (20-HETE, 12(R)-HETE, or 11,12-DHT)
caused a dose-dependent inhibition of the pump. The effect of DA, PTH, PDBu or DiC8, as well as that of 20-HETE was not altered
when sodium entry was blocked with the amiloride analog ethylisopropyl amiloride or increased with nystatin.
We conclude that short-term regulation of proximal tubule Na-K-ATPase activity by dopamine and parathyroid hormone occurs
via the PLC-PKC signal transduction pathway and is mediated by cytochrome P450-dependent monooxygenase products of arachidonic
acid metabolism, which may interact with the pump rather than alter sodium access to it.
Received: 7 January 1996/Revised: 24 April 1996 相似文献
13.
Lacaz-Vieira F 《The Journal of membrane biology》2000,178(2):151-161
The present study aimed to characterize the role of protein kinase C (PKC) on the dynamics of tight junction (TJ) opening
and closing in the frog urinary bladder. The early events of TJ dynamics were evaluated by the fast Ca++ switch assay (FCSA), which consisted in opening the TJs by removing basolateral Ca++ ([Ca++]
bl
), and closing them by returning [Ca++]
bl
to normal values. Changes in TJ permeability can be reliably gauged through changes of transepithelial electrical conductance
(G) determined in the absence of apical Na+. The FCSA allows the appraisal of drugs and procedures acting upon the mechanism controlling the TJs. The time courses of
TJ opening and closing in an FCSA were shown to follow single exponential time courses. PKC inhibition by H7 (100 μm) caused a reduction of the rate of junction opening in response to removing [Ca++]
bl
, without affecting junction closing, indicating that PKC is a key element in the control of TJ opening dynamics in this preparation.
H7 at 250 μm almost completely inhibits TJ opening in response to basolateral Ca++ withdrawal. Subsequent H7 removal caused a prompt inhibition release characterized by a sharp G increase which, however, once started cannot be stopped by H7 reintroduction, Ca++ being necessary to allow TJ recovery. A step rise of apical Ca++ concentration ([Ca++]
ap
) causes a reduction of the rate of TJ opening in a FCSA, an effect that is believed to be mediated by apical Ca++ entering the open TJs. The specific condition of having Ca++ only in the apical solution and the TJs located midway between the Ca++ source (apical solution) and the Ca++-binding sites presumably located at the zonula adhaerens, might configure a situation in which a control feedback loop is set up. A rise of [Ca++]
ap
during the phase of G increase in an FCSA causes a transient recovery of G followed by a subsequent escape phase where G increases again. Oscillations of G also appear in response to a rise of apical Ca++. Both escape and oscillations result from the properties of the TJ regulatory feedback loop. In conclusion, the present results
indicate that PKC plays a key role in TJ opening in response to extracellular Ca++ withdrawal without major effect on the reverse process. In addition, PKC inhibition by H7 not only prevents TJ opening in
response to basolateral Ca++ removal but induces a prompt blockade of TJ oscillations induced by apical Ca++, oscillations which reappear again when H7 is removed.
Received: 9 May 2000/Revised: 30 August 2000 相似文献
14.
Pavesi A 《Journal of molecular evolution》2000,50(3):284-295
In viruses an increased coding ability is provided by overlapping genes, in which two alternative open reading frames (ORFs)
may be translated to yield two distinct proteins. The identification of signature sequences in overlapping genes is a topic
of particular interest, since additional out-of-frame coding regions can be nested within known genes. In this work, a novel
feature peculiar to overlapping coding regions is presented. It was detected by analysis of a sample set of 21 virus genomic
sequences and consisted in the repeated occurrence of a cluster of basic amino acid residues, encoded by a frame, combined
to a stretch of acidic residues, encoded by the corresponding overlapping frame. A computer scan of an additional set of virus
sequences demonstrated that this feature is common to several other known overlapping ORFs and led to prediction of a novel
overlapping gene in hepatitis G virus (HGV). The occurrence of a bifunctional coding region in HGV was also supported by its
extremely lower rate of synonymous nucleotide substitutions compared to that observed in the other gene regions of the HGV
genome. Analysis of the amino acid sequence that was deduced from the putative overlapping gene revealed a high content of
basic residues and the presence of a nuclear targeting signal; these characteristics suggest that a core-like protein may
be expressed by this novel ORF.
Received: 21 July 1999 / Accepted: 26 October 1999 相似文献
15.
A detailed analysis of the evolutionary history of hepatitis B virus (HBV) was undertaken using 39 mammalian hepadnaviruses
for which complete genome sequences were available, including representatives of all six human genotypes, as well as a large
sample of small S gene sequences. Phylogenetic trees of these data were ambiguous, supporting no single place of origin for
HBV, and depended heavily on the underlying model of DNA substitution. In some instances genotype F, predominant in the Americas,
was the first to diverge, suggesting that the virus arose in the New World. In other trees, however, sequences from genotype
B, prevalent in East Asia, were the most divergent. An attempt was also made to determine the rate of nucleotide substitution
in the C open reading frame and then to date the origin of HBV. However, no relationship between time and number of substitutions
was found in two independent data sets, indicating that a reliable molecular clock does not exist for these data. Both the
pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct
the past spread of this virus.
Received: 5 December 1998 / Accepted: 23 February 1999 相似文献
16.
António M. Baptista Per Harald Jonson Edward Hough Steffen B. Petersen 《Journal of molecular evolution》1998,47(3):353-362
The trypsin family of serine proteases is one of the most studied protein families, with a wealth of amino acid sequence
information available in public databases. Since trypsin-like enzymes are widely distributed in living organisms in nature,
likely evolutionary scenarios have been proposed. A novel methodology for Fourier transformation of biological sequences (FOTOBIS)
is presented. The methodology is well suited for the identification of the size and extent of short repeats in protein sequences.
In the present paper the trypsin family of enzymes is analyzed with FOTOBIS and strong evidence for tandem gene duplication
is found. A likely evolutionary path for the development of present-day trypsins involved an intrinsic extensive tandem gene
duplication of a small DNA fragment of 15–18 nucleotides, corresponding to five or six amino acids. This ancestral trypsin
gene was subsequently duplicated, leading to the earliest version of a full-sized trypsin, from which the contemporary trypsins
have developed.
Received: 22 November 1997 / Accepted: 26 January 1998 相似文献
17.
Positive Darwinian Selection Promotes Heterogeneity Among Members of the Antifreeze Protein Multigene Family 总被引:9,自引:0,他引:9
A variety of organisms have independently evolved proteins exhibiting antifreeze activity that allows survival at subfreezing
temperatures. The antifreeze proteins (AFPs) bind ice nuclei and depress the freezing point by a noncolligative absorption–inhibition
mechanism. Many organisms have a heterogeneous suite of AFPs with variation in primary sequence between paralogous loci. Here,
we demonstrate that the diversification of the AFP paralogues is promoted by positive Darwinian selection in two independently
evolved AFPs from fish and beetle. First, we demonstrate an elevated rate of nonsynonymous substitutions compared to synonymous
substitutions in the mature protein coding region. Second, we perform phylogeny-based tests of selection to demonstrate a
subset of codons is subjected to positive selection. When mapped onto the three-dimensional structure of the fish antifreeze
type III antifreeze structure, these codons correspond to amino acid positions that surround but do not interrupt the putative
ice-binding surface. The selective agent may be related to efficient binding to diverse ice surfaces or some other aspect
of AFP function.
Received: 27 February 2001 / Accepted: 12 September 2001 相似文献
18.
To investigate the causes and functional significance of rapid sex-determining protein evolution we compared three Caenorhabditis elegans genes encoding members of the protein phosphatase 2C (PP2C) family with their orthologs from another Caenorhabditis species (strain CB5161). One of the genes encodes FEM-2, a sex-determining protein, while the others have no known sex-determining
role. FEM-2's PP2C domain was found to be more diverged than the other PP2C domains, supporting the notion that sex-determining
proteins are subjected to selective pressures that allow for or cause rapid divergence. Comparison of the positions of amino
acid substitutions in FEM-2 with a solved three-dimensional structure suggests that the catalytic face of the protein is highly
conserved among C. elegans, CB5161, and another closely related species C. briggsae. However, the non-conserved regions of FEM-2 cannot be said to lack functional importance, since fem-2 transgenes from the other species were unable to rescue the germ-line defect caused by a C. elegans fem-2 mutation. To test whether fem-2 functions as a sex-determining gene in the other Caenorhabditis species we used RNA-mediated interference (RNAi). fem-2 (RNAi) in C. elegans and C. briggsae caused germ-line feminization, but had no noticeable effect in CB5161. Thus the function of fem-2 in CB5161 remains uncertain.
Received: 11 April 2001 / Accepted: 6 August 2001 相似文献
19.
Benoit Cousineau Fabrice Leclerc Robert Cedergren 《Journal of molecular evolution》1997,45(6):661-670
Sequence similarity has given rise to the proposal that IF-2, EF-G, and EF-Tu are related through a common ancestor. We evaluate
this proposition and whether the relationship can be extended to other factors of protein synthesis. Analysis of amino acid
sequence similarity gives statistical support for an evolutionary affiliation among IF-1, IF-2, IF-3, EF-Tu, EF-Ts, and EF-G
and suggests further that this association is a result of gene duplication/fusion events. In support of this mechanism, the
three-dimensional structures of IF-3, EF-Tu, and EF-G display a predictable domain structure and overall conformational similarity.
The model that we propose consists of three consecutives duplication/fusion events which would have taken place before the
divergence of the three superkingdoms: eubacteria, archaea, and eukaryotes. The root of this protein superfamily tree would
be an ancestor of the modern IF-1 gene sequence. The repeated fundamental motif of this protein superfamily is a small RNA
binding domain composed of two α-helices packed along side of an antiparallel β-sheet.
Received: 17 October 1996 / Accepted: 10 June 1997 相似文献
20.
应用PCR技术从含有丙型肝炎病毒(HCV)全长开放阅读框的质粒pBRTM/HCV1~3011中获得NS5A全长基因片段,利用基因重组技术将其克隆至真核表达载体pcDNA3.1(-)中。通过酶切、PCR及测序鉴定证实,NS5A基因已正确插入到pcDNA3.1(-)中。再利用脂质体介导转染Huh7细胞,30h后收获细胞,经Western blot验证,证实HCV的NS5A基因在Huh7细胞中已经获得表达。在培养条件完全一致的条件下,表达NS5A基因的Huh7细胞与pcDNA3.1(-)转染的细胞在转染30h后被收集起来,乙醇固定,PI染色后利用流式细胞仪检测细胞周期变化。G0/G1期由60.6%下降到49.7%,S期由23.9%上升到32.7%,而转染pcDNA3.1(-)细胞的细胞周期与正常的Huh7细胞则差别不大。从而证明HCV NS5A蛋白对Huh7细胞周期具有调节作用。 相似文献