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1.
Masaharu Takemura 《Journal of molecular evolution》2001,52(5):419-425
A number of molecular forms of DNA polymerases have been reported to be involved in eukaryotic nuclear DNA replication, with
contributions from α-, δ-, and ε-polymerases. It has been reported that δ-polymerase possessed a central role in DNA replication
in archaea, whose ancestry are thought to be closely related to the ancestor of eukaryotes. Indeed, in vitro experiment shown
here suggests that δ-polymerase has the potential ability to start DNA synthesis immediately after RNA primer synthesis. Therefore,
the question arises, where did the α-polymerase come from? Phylogenetic analysis based on the nucleotide sequence of several
conserved regions reveals that two poxviruses, vaccinia and variola viruses, have polymerases similar to eukaryotic α-polymerase
rather than δ-polymerase, while adenovirus, herpes family viruses, and archaeotes have eukaryotic δ-like polymerases, suggesting
that the eukaryotic α-polymerase gene is derived from a poxvirus-like organism, which had some eukaryote-like characteristics.
Furthermore, the poxvirus's proliferation independent from the host-cell nucleus suggests the possibility that this virus
could infect non-nucleated cells, such as ancestral eukaryotes. I wish to propose here a new hypothesis for the origin of
the eukaryotic nucleus, posing symbiotic contact of an orthopoxvirus ancestor with an archaebacterium, whose genome already
had a δ-like polymerase gene.
Received: 26 October 2000 / Accepted: 16 January 2001 相似文献
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Austin L. Hughes 《Journal of molecular evolution》2002,54(1):90-101
Phylogenies of gene families including members in both vertebrates and DNA viruses of the poxvirus and/or herpesvirus families
showed that the viral genes originated at widely different times over the history of life. Certain of these viral genes (for
example, the genes encoding the large and small subunits of ribonucleoside–diphosphate reductase) originated before animals
diverged from fungi, while others originated much more recently. The most striking examples of recent origin involved viral
genes encoding the cytokine interleukin-10 (IL-10), which originated independently in viruses at least three times since the
divergence of the orders of eutherian mammals, presumably by viral capture of host genes. In certain domains, viral IL-10
genes showed significantly higher rates of nonsynonymous substitution than their nearest mammalian homologues. Though the
mutation rate in these viral genes is up to 20 times that of the corresponding mammalian genes, a high mutation rate alone
did not account for these differences because they were not seen in all domains. Rather, in certain domains it appears that
functional constraints present in the case of mammalian IL-10 are relaxed in the case of the viral homologues. Furthermore,
a nonrandom pattern of change with respect to amino acid residue charge in the N-terminal portion of the mature protein has
occurred repeatedly in independently derived viral IL-10 genes, strongly suggesting that positive selection has led to divergence
of this functionally important domain in viral IL-10.
Received: 11 January 2001 / Accepted: 23 May 2001 相似文献
5.
Genetic Variability of Natural Populations of Cotton Leaf Curl Geminivirus, a Single-Stranded DNA Virus 总被引:5,自引:0,他引:5
Ana I. Sanz Aurora Fraile Jesus M. Gallego Jose M. Malpica Fernando García-Arenal 《Journal of molecular evolution》1999,49(5):672-681
Reports on the genetic variability and evolution of natural populations of DNA viruses are scarce in comparison with the
abundant information on the variability of RNA viruses. Geminiviruses are plant viruses with circular ssDNA genomes that are
replicated by the host plant DNA polymerases. Whitefly-transmitted geminiviruses (WTG) are the agents of important diseases
of crop plants and best exemplify emerging plant viruses. In this report we have analyzed the genetic diversity of cotton
leaf curl geminivirus (CLCuV), a typical emerging WTG. No genetic differentiation was observed between isolates from different
host plant species or geographic regions. Thus, the analyzed isolates represented a unique, undifferentiated population. Genetic
variability, estimated as nucleotide diversities at synonymous positions in open reading frames (ORFs) for the AC1 (=replication)
protein and coat protein (CP = AV1), was very high, exceeding the values reported for different genes in several plant and
animal RNA viruses. This was unexpected in a virus that uses the DNA replication machinery of its eukaryotic host. Diversities
at nonsynonymous positions, on the other hand, indicated that variability may be constrained in the genome of CLCuV. The ratio
of nonsynonymous-to-synonymous substitutions varied for the different ORFs: they were higher for CP than for AC1 and lower
still for the AC4 and AV2 ORFs, which overlap AC1 and CP ORFs, respectively. Analysis of nucleotide diversities at synonymous
and nonsynonymous positions of the AC4 and AV2 ORFs suggest that their evolution is constrained by AC1 and CP, respectively.
Data suggest that AC4 and AV2 are new genes that may have originated by overprinting on the preexistent AC1 and CP genes.
Evidence for recombination was found for the AC1 and CP ORFs and for the noncoding intergenic region (IR). Data indicate that
the origin of replication is a major recombination point in the IR, but not the only one. Analyses of the IR also suggest
that recombinants may be frequent in the population and that recombination may have an important role in the generation of
CLCuV variability.
Received: 26 February 1999 / Accepted: 31 May 1999 相似文献
6.
Bacteriophage T7 was challenged with either of two toxic genes expressed from plasmids. Each plasmid contained a different
gene downstream of a T7 promoter; cells harboring each plasmid caused an infection by wild-type T7 to abort. T7 evolved resistance
to both inhibitors by avoidance of the plasmid expression system rather than by blocking or bypassing the effects of the specific
toxic gene product. Resistance was due to a combination of mutations in the T7 RNA polymerase and other genes expressed at
the same time as the polymerase. Mutations mapped to sites that are unlikely to alter polymerase specificity for its cognate
promoter but the basis for discrimination between phage and plasmid promoters in vivo was not resolved. A reporter assay indicated that, relative to wild-type phage, gene expression from the plasmid was diminished
several-fold in cells infected by the evolved phages. A recombinant phage, derived from the original mutant but lacking a
mutation in the gene for RNA polymerase, exhibited intermediate activity in the reporter assay and intermediate resistance
to the toxic gene cassettes. Alterations in both RNA polymerase and a second gene are thus responsible for resistance. These
findings have broad evolutionary parallels to other systems in which viral inhibition is activated by viral regulatory signals
such as defective-interfering particles, and they may have mechanistic parallels to the general phenomena of position effects
and gene silencing.
Received: 18 July 2000 / Accepted: 8 February 2001 相似文献
7.
RNA viruses and retroviruses fix substitutions approximately 1 million-fold faster than their hosts. This diversification
could represent an inevitable drift under purifying selection, the majority of substitutions being phenotypically neutral.
The alternative is to suppose that most fixed mutations are beneficial to the virus, allowing it to keep ahead of the host
and/or host population. Here, relative sequence diversification of different proteins encoded by viral genomes is found to
be linear. The examples encompass a wide variety of retroviruses and RNA viruses. The smoothness of relative divergence spans
quasispeciation following clonal infection, to variation among different isolates of the same virus, to viruses from different
species or those associated with different diseases, indicating that the majority of fixed mutations likely reflects drift.
This held for both mammalian and plant viruses, indicating that adaptive immunity doesn't necessarily shape the relative accumulation
of amino acid substitutions. When compared to their hosts RNA viruses evolution appears conservative.
Received: 16 November 1999 / Accepted: 10 March 2000 相似文献
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9.
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
10.
The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from phycodnavirus (which infects microalgae) as the basis of this analysis, as it represents a virus of a primitive eukaryote. We show that it has significant similarity with replicative DNA polymerases of eukaryotes and certain of their large DNA viruses. Sequence alignment confirms this similarity and establishes the presence of highly conserved domains in the polymerase amino terminus. Subsequent reconstruction of a phylogenetic tree indicates that these algal viral DNA polymerases are near the root of the clade containing all eukaryotic DNA polymerase delta members but that this clade does not contain the polymerases of other DNA viruses. We consider arguments for the polarity of this relationship and present the hypothesis that the replication genes of DNA viruses gave rise to those of eukaryotes and not the reverse direction. 相似文献
11.
Jocelyne DiRuggiero James R. Brown Allison P. Bogert Frank T. Robb 《Journal of molecular evolution》1999,49(4):474-484
DNA repair in the Archaea is relevant to the consideration of genome maintenance and replication fidelity in the last universal
common ancestor (LUCA) from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features.
Second, DNA repair proteins would have been essential in LUCA to maintain genome integrity, regardless of the environmental
temperature. Yet we know very little of the basic molecular mechanisms of DNA damage and repair in the Archaea in general.
Many studies on DNA repair in archaea have been conducted with hyperthermophiles because of the additional stress imposed
on their macromolecules by high temperatures. In addition, of the six complete archaeal genome sequences published so far,
five are thermophilic archaea. We have recently shown that the hyperthermophile Pyrococcus furiosus has an extraordinarily high capacity for repair of radiation-induced double-strand breaks and we have identified and sequenced
several genes involved in DNA repair in P. furiosus. At the sequence level, only a few genes share homology with known bacterial repair genes. For instance, our phylogenetic
analysis indicates that archaeal recombinases occur in two paralogous gene families, one of which is very deeply branched,
and both recombinases are more closely related to the eukaryotic RAD51 and Dmc1 gene families than to the Escherichia coli recA gene. We have also identified a gene encoding a repair endo/exonuclease in the genomes of several Archaea. The archaeal sequences
are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are
known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and protein
sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal
set of genes thought to represent the genome of the LUCA. 相似文献
12.
Linda Baumann Paul Baumann Nancy A. Moran Jonas Sandström Mylo Ly Thao 《Journal of molecular evolution》1999,48(1):77-85
The prokaryotic endosymbionts (Buchnera) of aphids are known to provision their hosts with amino acids that are limiting in the aphid diet. Buchnera from the aphids Schizaphis graminum and Diuraphis noxia have plasmids containing leuABCD, genes that encode enzymes of the leucine biosynthetic pathway, as well as genes encoding proteins probably involved in plasmid
replication (repA1 and repA2) and an open reading frame (ORF1) of unknown function. The newly reported plasmids closely resemble a plasmid previously described in Buchnera of the aphid Rhopalosiphum padi [Bracho AM, Martínez-Torres D, Moya A, Latorre A (1995) J Mol Evol 41:67–73]. Nucleotide sequence comparisons indicate conserved
regions which may correspond to an origin of replication and two promoters, as well as inverted repeats, one of which resembles
a rho-independent terminator. Phylogenetic analyses based on amino acid sequences of leu gene products and ORF1 resulted in trees identical to those obtained from endosymbiont chromosomal genes and the plasmid-borne
trpEG. These results are consistent with a single evolutionary origin of the leuABCD-containing plasmid in a common ancestor of Aphididae and the lack of plasmid exchange between endosymbionts of different
aphid species. Trees for ORF1 and repA (based on both nucleotides and amino acids) are used to examine the basis for leu plasmid differences between Buchnera of Thelaxes suberi and Aphididae. The most plausible explanation is that a single transfer of the leu genes to an ancestral replicon was followed by rearrangements. The related replicon in Buchnera of Pemphigidae, which lacks leuABCD, appears to represent the ancestral condition, implying that the plasmid location of the leu genes arose after the Pemphigidae diverged from other aphid families. This conclusion parallels previously published observations
for the unrelated trpEG plasmid, which is present in Aphididae and absent in Pemphigidae. Recruitment of amino acid biosynthetic genes to plasmids
has been ongoing in Buchnera lineages after the infection of aphid hosts.
Received: 9 March 1998 / Accepted: 18 May 1998. 相似文献
13.
Helen F Schmidt Eric G Sakowski Shannon J Williamson Shawn W Polson KEric Wommack 《The ISME journal》2014,8(1):103-114
Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton. 相似文献
14.
On the fidelity of DNA replication: herpes DNA polymerase and its associated exonuclease. 总被引:1,自引:0,他引:1
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Procaryotic DNA polymerases contain an associated 3'----5' exonuclease activity which provides a proofreading function and contributes substantially to replication fidelity. DNA polymerases of the eucaryotic herpes-type viruses contain similar associated exonuclease activities. We have investigated the fidelity of polymerases purified from wild type herpes simplex virus, as well as from mutator and antimutator strains. On synthetic templates, the herpes enzymes show greater relative exonuclease activities, and greater ability to excise a terminal mismatched base, than procaryotic DNA polymerases which proofread. On a phi X174 natural DNA template, the herpes enzymes are more accurate than purified eucaryotic DNA polymerases; the error rate is similar to E. coli polymerase I. However, conditions which abnegate proofreading by E. coli polymerase I have little effect on the herpes enzymes. We conclude that either these viral polymerases are accurate in the absence of proofreading, or the conditions examined have little effect on proofreading by the herpes DNA polymerases. 相似文献
15.
In many bacterial genomes, the leading and lagging strands have different skews in base composition; for example, an excess
of guanosine compared to cytosine on the leading strand. We find that Chlamydia genes that have switched their orientation relative to the direction of replication, for example by inversion, acquire the
skew of their new ``host' strand. In contrast to most evolutionary processes, which have unpredictable effects on the sequence
of a gene, replication-related skews reflect a directional evolutionary force that causes predictable changes in the base
composition of switched genes, resulting in increased DNA and amino acid sequence divergence.
Received: 27 April 2000 / Accepted: 1 August 2000 相似文献
16.
The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages. 相似文献
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18.
Factors affecting PCR-mediated recombination 总被引:2,自引:0,他引:2
Shafikhani S 《Environmental microbiology》2002,4(8):482-486
In the past decade, polymerase chain reaction (PCR) has become an important tool for the identification of previously unknown microorganisms and the analysis of environmental microbial diversity. Several studies published during recent years, however, have demonstrated that products obtained after PCR using Taq or Vent DNA polymerases will contain hybrid molecules when several homologous target sequences such as multigene families, alleles, or RNA viruses are co-amplified. In this report, we examined the recombination frequency and the extent of template switching during PCR using Taq, Pfu and RTth/Vent DNA polymerases. As a test system we constructed a series of plasmids carrying between one and three frame shift mutations in the gene coding for the protease subtilisin or deletions of approximately 100 bp in the lacZ alpha. Highest recombination frequencies were observed when these mutants were co-amplified with Taq followed by RTth/Vent DNA polymerases. Pfu DNA polymerase displayed no discernable recombination activity under normal PCR conditions. Data also suggest that in vivo repair of heteroduplex DNA molecules in Escherichia coli by a RecA-independent mechanism, perhaps the mismatch repair, results in the formation of chimeric molecules. Using Bacillus subtilis as the host, however, can significantly diminish non-PCR RecA-independent in vivo recombination, owing to the fact that transforming DNA molecules enter B. subtilis as single strands. Combined, these results suggest that using Pfu DNA polymerase for amplification and B. subtilis as the host for transformation may significantly reduce chimera formation. 相似文献
19.
The φ29-like phage genus of Podoviridae family contains phages B103, BS32, GA-1, M2, Nf, φ15, φ29, and PZA that all infect
Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNA of approximately 20 kb. The nucleotide
sequences of individual genomes or their parts determined thus far show that these phages evolved from a common ancestor.
A terminal protein (TP) that is covalently bound to the DNA 5′-end primes DNA replication of these phages. The same mechanism
of DNA replication is used by the Cp-1 related phages (also members of the Podoviridae family) and by the phage PRD1 (member
of the Tectoviridae family). Based on the complete or partial genomic sequence data of these phages it was possible to analyze
the evolutionary relationship within the φ29-like phage genus as well as to other protein-primed replicating phages. Noncoding
regions containing origins of replication were used in the analysis, as well as amino acid sequences of DNA polymerases, and
with the φ29-like phages also amino acid sequences of the terminal proteins and of the gene 17 protein product, an accessory
component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of these phage
DNAs with the prophages present in the Bacillus subtilis genome. Based on this complex analysis we define and describe in more detail the evolutionary branches of φ29-like phages,
one branch consisting of phages BS32, φ15, φ29, and PZA, the second branch composed of phages B103, M2, and Nf, and the third
branch having phage GA-1 as its sole member. In addition, amino acid sequences of holins, proteins involved in phage lysis
were used to extend the evolutionary study to other phages infecting Gram-positive bacteria. The analysis based on the amino
acid sequences of holins showed several weak points in present bacteriophage classification.
Received: 14 April 1998 / Accepted: 31 July 1998 相似文献
20.
Dadbeh Rouhbakhsh Chi-Yung Lai Carol D. von Dohlen Marta A. Clark Linda Baumann Paul Baumann Nancy A. Moran David J. Voegtlin 《Journal of molecular evolution》1996,42(4):414-421
The bacterial endosymbionts (Buchnera) from the aphids Rhopalosiphum padi, R. maidis, Schizaphis graminum, and Acyrthosiphon pisum contain the genes for anthranilate synthase (trpEG) on plasmids made up of one or more 3.6-kb units. Anthranilate synthase is the first as well as the rate-limiting enzyme
in the tryptophan biosynthetic pathway. The amplification of trpEG on plasmids may result in an increase of enzyme protein and overproduction of this essential amino acid, which is required
by the aphid host. The nucleotide sequence of trpEG from endosymbionts of different species of aphids is highly conserved, as is an approximately 500-bp upstream DNA segment
which has the characteristics of an origin of replication. Phylogenetic analyses were performed using trpE and trpG from the endosymbionts of these four aphids as well as from the endosymbiont of Schlechtendalia chinensis, in which trpEG occurs on the chromosome. The resulting phylogeny was congruent with trees derived from sequences of two chromosome-located
bacterial genes (part of trpB and 16S ribosomal DNA). In turn, trees obtained from plasmid-borne and bacterial chromosome-borne sequences were congruent
with the tree resulting from phylogenetic analysis of three aphid mitochondrial regions (portions of the small and large ribosomal
DNA subunits, as well as cytochrome oxidase II). Congruence of trees based on genes from host mitochondria and from bacteria
adds to previous support for exclusively vertical transmission of the endosymbionts within aphid lineages. Congruence with
trees based on plasmid-borne genes supports the origin of the plasmid-borne trpEG from the chromosomal genes of the same lineage and the absence of subsequent plasmid exchange among endosymbionts of different
species of aphids.
Received: 22 August 1995 / Accepted: 6 September 1995 相似文献