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1.
Molecular parasites that utilize the replication machinery of cells or of in vitro amplification reactions have previously
been characterized. By and large, these parasites have been smaller than the viruses or amplicons that gave rise to them.
This is likely because shorter genomes can be replicated more quickly. In contrast, we have identified and characterized parasites
of an isothermal amplification reaction that are longer than their parental molecules yet replicate much more efficiently.
These results raise interesting questions regarding whether the optimal size of replicators reflects a trade-off between the
information encoded in a parasite and the information encoded in the machinery replicating that parasite.
Received: 9 February 1999 / Accepted: 7 June 1999 相似文献
2.
P. A. Sansberro H. Y. Rey L. A. Mroginski M. M. Collavino 《Journal of Plant Growth Regulation》1998,17(2):101-105
The effects of benzyladenine (BAP), kinetin (KIN), zeatin (ZEA), isopentenyladenine (2iP), and thidiazuron (TDZ) were studied
on in vitro growth of rudimentary embryos of Ilex paraguariensis St. Hil. Heart stage zygotic embryos were removed from seeds of immature, light green fruits and cultured aseptically on
quarter-strength Murashige and Skoog medium containing 3% sucrose, 0.65% agar, and supplemented with or without three concentrations
of BAP, KIN, ZEA, 2iP, or TDZ. Cultures were incubated in darkness at 27 ± 2°C. Media containing 4.4 × 10−6
m BAP, 4.6 × 10−6
m KIN, or 4.9 × 10−6
m 2iP were totally ineffective in inducing embryo growth after culture for 28 days. However, lower concentrations of these
compounds (4.4 × 10−8
m BAP, 4.6 × 10−8
m KIN, 4.5 × 10−8
m ZEA, or 4.9 × 10−8
m 2iP) promoted embryo growth. TDZ at 9.9 × 10−9
m, 9.9 × 10−8
m, or 9.9 × 10−7
m induced embryo growth at similar rates. The maximum percentage of embryos converted to seedlings was achieved when the medium
was supplemented with 4.5 × 10−7
m ZEA.
Received August 1, 1997; accepted February 19, 1998 相似文献
3.
Zelus D Robinson-Rechavi M Delacre M Auriault C Laudet V 《Journal of molecular evolution》2000,51(3):234-244
Interleukin-2 (IL-2) is a cytokine involved in induction and regulation of the immune response in mammals. There have been
numerous reports about the search for IL-2 in species other than mammals, and recently an IL-2-like gene has been isolated
in chicken. Using PCR, we searched for IL-2 gene sequences in a wide variety of mammals, including marsupials and monotremes,
as well as in birds. Although we can readily amplify IL-2 gene fragments in placental mammals, no amplification was obtained
in other species. This is best explained by very high substitution rates. This suggest that strategies to isolate IL-2 homologous
genes outside mammals should involve functional assays, as for the chicken gene, and not hybridization-based techniques. Nonsynonymous
substitution rates are especially high in ruminants, due to positive selection acting on regions important in term of structure-function.
We suggest that, although globally similar, the immune response of various mammals is not identical, mainly at the level of
cytokine-mediated regulations.
Received: 27 July 1999 / Accepted: 15 April 2000 相似文献
4.
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
5.
Retrotransposons are mobile genetic elements that are ubiquitous components of eukaryotic genomes. The evolutionary success
of retrotransposons is explained by their ability to replicate faster than the host genomes in which they reside. Elements
with higher rates of genomic replication possess a selective advantage over less active elements. Retrotransposon populations,
therefore, are shaped largely by selective forces acting at the genomic level between elements. To evaluate rigorously the
effects of selective forces acting on retrotransposons, detailed information on the patterns of molecular variation within
and between retrotransposon families is needed. The sequencing of the Saccharomyces cerevisiae genome, which includes the entire genomic complement of yeast retrotransposons, provides an unprecedented opportunity to
access and analyze such data. In this study, we analyzed in detail the patterns of nucleotide variation within the open reading
frames of two parental (Ty1 and Ty2) and one hybrid (Ty1/2) family of yeast retrotransposons. The pattern and distribution
of nucleotide changes on the phylogenetic reconstructions of the three families of Ty elements reveal evidence of negative
selection on both internal and external branches of the Ty phylogenies. These results indicate that most, if not all, Ty elements
examined represent active or recently active retrotransposon lineages. We discuss the relevance of these findings with respect
to the coevolutionary dynamic operating between genomic element populations and the host organisms in which they reside.
Received: 5 November 1998 / Accepted: 17 March 1999 相似文献
6.
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
7.
Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree 总被引:6,自引:0,他引:6
We propose a new type of unsupervised, growing, self-organizing neural network that expands itself by following the taxonomic
relationships that exist among the sequences being classified. The binary tree topology of this neutral network, contrary
to other more classical neural network topologies, permits an efficient classification of sequences. The growing nature of
this procedure allows to stop it at the desired taxonomic level without the necessity of waiting until a complete phylogenetic
tree is produced. This novel approach presents a number of other interesting properties, such as a time for convergence which
is, approximately, a lineal function of the number of sequences. Computer simulation and a real example show that the algorithm
accurately finds the phylogenetic tree that relates the data. All this makes the neural network presented here an excellent
tool for phylogenetic analysis of a large number of sequences.
Received: 14 May 1996 / Accepted: 6 August 1996 相似文献
8.
Shuji Shigenobu Hidemi Watanabe Yoshiyuki Sakaki Hajime Ishikawa 《Journal of molecular evolution》2001,53(4-5):377-386
Endosymbiotic bacteria live in animal cells and are transmitted vertically at the time of the host's reproduction. In view
of their small and asexual populations with infrequent chances of recombination, these endocellular bacteria are expected
to accumulate mildly deleterious mutations. Previous studies showed that the DNA sequences of these bacteria evolved faster
than those of free-living bacteria. In this study, we compared all the ORFs of Buchnera, an endocellular bacterial symbiont of aphids, with those of 34 other prokaryotic organisms and estimated the effect of the
accelerated evolution of Buchnera on the functions of its proteins. It was revealed that Buchnera proteins contain many mutations at the sites where sequences are conserved in their orthologues in many other organisms.
In addition, amino acid replacements at the conserved sites are mostly changes to physicochemically different amino acids.
These results suggest that functions and conformations of Buchnera proteins have been seriously impaired or strongly modified. Indeed, extensive loss of functional motifs was observed in some
Buchnera proteins. In many Buchnera proteins mutations were not detected evenly throughout each molecule but tended to accumulate in some functional units, possibly
leading to loss of specific functions. As Buchnera has an unusual and limited gene repertory, it is conceivable that the manner of interactions among its proteins has been
changed, and thus, functional constraints over their amino acid residues have also been changed during evolution. This may
account for the loss of some functional units only in the Buchnera proteins. We obtained evidence that amino acid replacements in Buchnera were not always deleterious, but neutral or, in some cases, even positively selected.
Received: 14 December 2000 / Accepted: 12 March 2001 相似文献
9.
To date, the small nuclear 4.5SI RNA has only been studied in the rat (Rattus norvegicus). Combining PCR and hybridization analyses, we have revealed 4.5SI RNA homologues sequences in the genomes of four myomorph rodent families (Muridae, Cricetidae, Spalicidae, and Rhizomyidae),
and not in other myomorph families (Dipodidae, Zapodidae, Geomyidae, and Heteromyidae) or sciuromorph and caviomorph rodents.
By Northern-hybridization, 4.5SI RNA has been detected in the common rat (R. norvegicus, Muridae), golden hamster (Mesocricetus auratus, Cricetidae), and Russian mole rat (Spalax microphthalmus, Spalacidae), but not in the related great jerboa (Allactaga jaculus, Dipodidae) or in four non-myomorph rodent species tested. cDNA derived from 4.5SI RNA of M. auratus and S. microphthalmus has been cloned and sequenced. The hamster RNA is found to differ from rat 4.5SI RNA by only one nucleotide substitution. For the mole rat, two variants of 4.5SI RNA are detected: short (S) and long (L) with length 101 and 108 nt, respectively. The L variant differs from the S variant
as well as from murid and cricetid 4.5SI RNAs by both a 7 nt insertion and a varying number of nucleotide substitutions. The sequence similarity between the spalacid
S-variant and murid/crecitid variants of 4.5SI RNA is 90%. Judging from species distribution, 4.5SI RNA genes emerged during the same period of time as the related short interspersed element B2 arose. This occurred after
the divergence of Dipodidae lineage but before the branching of Spalicidae/Rhizomyidae lineage from a common myomorph rodent
stem. S variant genes seemed to emerge in a common ancestor of spalacids and rhizomyds whereas L variant genes formed in spalacids
following the divergence of these two families. The low rate of evolutionary changes of 4.5SI RNA, at least, in murids and cricetids (6 × 10−4 substitutions per site per million years), suggests that this RNA is under selection constraint and have a function. This
is a remarkable fact if the recent origin and narrow species distribution range of 4.5SI RNA genes is taken into account. Genes with narrow species distribution are proposed to be referred to as stenogenes.
Received: 11 December 2000 / Accepted: 27 August 2001 相似文献
10.
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages 总被引:8,自引:0,他引:8
Brian R. Morton 《Journal of molecular evolution》1998,46(4):449-459
In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study
the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each
gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons
based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared
to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias
is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among
the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation
efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities
in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity
among the various genomes are discussed.
Received: 6 June 1997 / Accepted: 24 July 1997 相似文献
11.
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
12.
There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having
12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of
human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore
used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions.
After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each
branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly
higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher
nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection.
Received: 16 March 1999 / Accepted: 17 June 1999 相似文献
13.
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
14.
15.
Continuous in vitro evolution methods were used to study the behavior of an evolving population of RNA ligase ribozymes in response to selection pressures involving conditions of extreme pH. The starting population consisted of randomized variants of a ribozyme that had been optimized for activity at pH 8.5. The ribozymes were subjected to repeated rounds of selective amplification under progressively more acidic or more alkaline conditions. The two final evolved populations of ribozymes were able to operate at either pH 5.8 or pH 9.8, respectively. Representative individuals from the two final populations were isolated and characterized. The low-pH ribozyme exhibited a 10-fold increase in catalytic rate at pH 5.8 compared to the starting molecule. The high-pH ribozyme retained its structural integrity and activity at pH 9.8, whereas the starting molecule was denatured under this condition. These findings demonstrate that a population of functional macromolecules can adapt to stringent environmental conditions through the acquisition of relatively few mutations. The results establish continuous in vitro evolution as a useful model system for exploring the evolution of enzymatic function in extreme environments.
Present address (Henriette Kühne): Cardinal Health, 2950 Trade Place, San Diego, CA 92126, USA 相似文献
16.
Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection 总被引:7,自引:0,他引:7
Héctor Musto Héctor Romero Alejandro Zavala Kamel Jabbari Giorgio Bernardi 《Journal of molecular evolution》1999,49(1):27-35
We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly
biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among
genes. At one end genes display codon choices determined mainly by the extreme genome composition of this parasite, and very
probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a particular subset
of codons, many of which are C-ending. Since the majority of these few genes is putatively highly expressed, we postulate
that the increased C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compositional constraints, a small number of genes exhibit translational selection.
Received: 10 November 1998 / Accepted: 28 January 1999 相似文献
17.
AbstractIsolation of genes encoding catalysts for defined chemical reactions should be facilitated by selection of proteins for catalysis from molecular repertoires. Display of proteins on phage allows the coupling between a protein and its gene. Furthermore, if the reaction product can be linked to the phage enzyme catalyzing the reaction, affinity chromatography for the product yields the protein catalyzing the reaction and its gene. One main advantage of this selection method is that it can be in principle generalized to most chemical reactions.Here, iterative in vitro selections for polymerase activity were used to isolate a single phage-polymerase among more than 108 phage particles. Three to five selection cycles were required depending on the fraction of infectious phage-polymerases in the initial phage population. This is the first report quantifying the enrichment over iterative selection rounds for the isolation of rare catalysts displayed on phage. 相似文献
18.
Isolation of genes encoding catalysts for defined chemical reactions should be facilitated by selection of proteins for catalysis from molecular repertoires. Display of proteins on phage allows the coupling between a protein and its gene. Furthermore, if the reaction product can be linked to the phage enzyme catalyzing the reaction, affinity chromatography for the product yields the protein catalyzing the reaction and its gene. One main advantage of this selection method is that it can be in principle generalized to most chemical reactions.
Here, iterative in vitro selections for polymerase activity were used to isolate a single phage-polymerase among more than 108 phage particles. Three to five selection cycles were required depending on the fraction of infectious phage-polymerases in the initial phage population. This is the first report quantifying the enrichment over iterative selection rounds for the isolation of rare catalysts displayed on phage. 相似文献
Here, iterative in vitro selections for polymerase activity were used to isolate a single phage-polymerase among more than 108 phage particles. Three to five selection cycles were required depending on the fraction of infectious phage-polymerases in the initial phage population. This is the first report quantifying the enrichment over iterative selection rounds for the isolation of rare catalysts displayed on phage. 相似文献
19.
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
20.
To determine whether the persistent nature of hepatitis C infection is related to the emergence of antigenic variants driven
by immune selection, we examined the sequence heterogeneity in a portion of the hepatitis C virus (HCV) nonstructural 3 (NS3)
gene of a patient infected over the course of more than 2 years. By PCR amplification, cloning, and sequencing, we observed
several variable and conserved regions in the NS3 segment of the HCV genome. All variable regions had higher ratios of nonsynonymous/synonymous
mutations and encompassed immunodominant epitopes, and their locations were not essential to maintain the known function of
HCV RNA helicase. In contrast, the regions that are critical for HCV RNA helicase activity were found to be conserved with
lower heterogeneity or lower ratios of nonsynonymous/synonymous mutations, and none except one of these regions was encoded
within immunodominant epitopes. Our results are consistent with immune selection of viral variants at the epitope and molecular
levels that may enable HCV to evade host defenses over time. Plotting the relatedness of sequence variants revealed a star
topology suggesting that a wild-type HCV sequence is maintained, unlike HIV.
Received: 2 November 2000 / Accepted: 1 October 2001 相似文献