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Results for “replicative form”

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PubMed1992

Characterization of viral DNAs from cells infected with chicken anaemia agent: sequence analysis of the cloned replicative form and transfection capabilities of cloned genome fragments.

The viral DNAs induced by the unclassified animal virus, chicken anaemia agent (CAA), during replication in MDCC-MSB 1 cells have been investigated. Analyses after S1 nuclease, restriction endonuclease and denaturation treatments indicated that infected cell extracts contained genome-size, single-stranded DNA (M(r) 2.3 kb), closed and open circular, double-stranded replicative form (RF) DNAs (M(r) 2.3 kbp) and a population of smaller double-stranded DNAs (M(r) 0.8 kbp). Recombinant plasmids containing 2.3 kbp CAA RF fragments cloned at the PstI, BamHI and EcoRI sites failed to transfect MDCC-MSB 1 cells. However, one plasmid, which contained two 2.3 kbp CAA RF fragments ligated in tandem at the PstI site, and cloned 2.3 kbp PstI, BamHI and EcoRI fragments, excised from their respective plasmids by restriction endonuclease digestion, were capable of transfection. The nucleotide sequence of the circular genome (2298 bp) of the Cux-1 isolate of CAA has indicated the presence of three overlapping open reading frames (ORFs) of 52 kDa, 24 kDa and 13 kDa on one strand. The existence of these ORFs was corroborated by analyses of partial sequences from three other isolates. The non-coding region of the CAA genome contained sequences with putative regulatory function. These results are discussed in relation to the "rolling circle" model of DNA replication.

Amino Acid Sequence↗

PubMed1993

Construction and characterization of a phage-plasmid hybrid (phagemid), pCAK1, containing the replicative form of viruslike particle CAK1 isolated from Clostridium acetobutylicum NCIB 6444.

A bacteriophage-plasmid hybrid (phagemid) designated pCAK1 was constructed by ligating 5-kbp Escherichia coli plasmid pAK102 (AprEmr) and the 6.6-kbp HaeIII-linearized replicative form of the CAK1 viruslike particle from Clostridium acetobutylicum NCIB 6444. Phagemid pCAK1 (11.6 kbp) replicated via the ColE1 replication origin derived from pAK102 in E. coli. Single-stranded DNA (ssDNA) molecules complexed with protein in a manner which protected ssDNA from nucleases were recovered from the supernatant of E. coli DH11S transformants containing pCAK1 in the absence of cell lysis. This suggests that the viral-strand DNA synthesis replication origin of CAK1 and associated gene expression are functional in E. coli DH11S. The single-stranded form of pCAK1 isolated from E. coli supernatant was transformed into E. coli DH5 alpha' or DH11S by electroporation. Isolation of ampicillin-resistant E. coli transformants following transformation suggests that the complementary-strand DNA synthesis replication origin of CAK1 is also functional in E. coli. The coat proteins associated with ssDNA of pCAK1 demonstrated sensitivity to proteinase K and various solvents (i.e., phenol and chloroform), similar to the results obtained previously with CAK1. Following phagemid construction in E. coli, pCAK1 was transformed into C. acetobutylicum ATCC 824 and C. perfringens 13 by intact cell electroporation. Restriction enzyme analysis of pCAK1 isolated from erythromycin-resistant transformants of both C. acetobutylicum and C. perfringens suggested that it was identical to that present in E. coli transformants.

Bacteriophages↗

PubMed1969

Synthesis of replicative form deoxyribonucleic acid and messenger ribonucleic acid by gene IV mutants of bacteriophage S13.

Gene IV mutants of bacteriophage S13 are known to be blocked in infectious replicative form (RF) DNA synthesis, producing only a small fraction of the RF formed by wild-type phage. This investigation shows that gene IV mutants form only parental RF and are blocked in the synthesis of any progeny RF, either infectious or noninfectious. This was determined by density labeling of RF in cells treated with mitomycin C to suppress host deoxyribonucleic acid (DNA) synthesis. RF synthesis was also studied in untreated cells, using methylated albumin columns to separate RF from host DNA. In this case it was also found that synthesis of progeny RF by gene IV mutants is negligible. It has been found by DNA-ribonucleic acid (RNA) hybridization experiments that gene IV mutants form at least as much or more messenger RNA than wild-type phage. Therefore, parental RF alone can form messenger RNA in appreciable amounts.

Bacteriophages↗

PubMed1979

Host cell DNA chain initiation protein requirements for replication of bacteriophage G4 replicative-form DNA.

Bacteriophages G4ev1 and G4bs1 are simple temperature-resistant derivatives of wild-type G4 as demonstrated by restriction endonuclease analyses. The rate of replication of the duplex replicative-form DNA of these phages was normal in dnaB and dnaC mutants of the host, whereas the rate was markedly reduced in a dnaG host mutant at the restrictive temperature. We conclude that G4 duplex DNA replication requires the host cell dnaG protein, but not the dnaB and dnaC proteins. The reasons for the differences between our conclusions and those based on previously published data are documented and discussed.

Bacterial Proteins↗

PubMed1987

Localization of Escherichia coli RNA polymerase-binding sites on bacteriophage S13 replicative form I DNA by protection of restriction enzyme cleavage sites.

Protection of restriction endonuclease cleavage sites by Escherichia coli RNA polymerase bound to the replicative form I of bacteriophage S13 DNA has been used to identify a number of regions of RNA polymerase binding. Digestion with HincII, AluI, HinfI, or HaeIII, under conditions optimized for "open" complex formation, revealed 12 regions of RNA polymerase binding. Based on differential salt sensitivities, five of the regions were classified as strong or tight binding sites. These were located before genes A (two sites), B, and D and at the 5' end of gene F. The seven regions which exhibited weaker binding were located at the 5' end of gene C (two sites), in the middle of gene D, just before and at the 3' end of gene F, at the 5' end of gene G, and in the middle of gene H. The sites before genes B and D coincide with sites previously identified as promoters in bacteriophage phi X174. One of the sites before gene A, that at nucleotides 5175-5211, represents a new putative promoter site in bacteriophage S13 and phi X174 located before the previously identified A gene promoter at nucleotides 10-45.

Base Sequence↗

PubMed1993

Optimization of methods for transfecting Spiroplasma citri strain R8A2 HP with the spiroplasma virus SpV1 replicative form.

Seven methods for the transfection of bacteria were compared and optimized for use in Spiroplasma citri strain HP using the spiroplasma virus SpV1 R8A2 B replicative form (RF). These methods included both chemical-mediated protocols [CaCl2, RbCl/CaCl2, polyethylene glycol (PEG)], liposome-mediated transfection, electroporation, freeze/thaw cycling, and natural competence. The best protocols were those which utilized PEG or electroporation, yielding transfection frequencies of 1.4 x 10(-4) and 9.1 x 10(-4) transfectants/colony-forming unit (CFU), respectively. For both of these protocols, transfection frequencies were higher using CsCl-purified, covalently closed, circular DNA. In the PEG-mediated protocol, Sigma 8000 brand PEG at a final concentration of 44%, and the presence of carrier DNA proved to be optimal with a PEG exposure time of 2 min. Using electroporation, a 1-2 ms pulse of a 6.5 kV/cm electric field was best; washing the host cell pellet prior to electroporation enhanced efficiencies by 50%. Linearization of the DNA resulted in lower transfection efficiencies by either method.

Bacteriophages↗

PubMed1984

Aphidicolin inhibition of the production of replicative-form DNA during bovine parvovirus infection.

Since parvoviruses apparently do not possess a DNA polymerase activity, one or more of the host cell DNA polymerases must be responsible for replicating the single-stranded DNA genome. We have focused on determining which polymerase, alpha, beta, or gamma (pol alpha, pol beta, or pol gamma, respectively), is responsible for the first step in bovine parvoviral DNA replication: conversion of the single-stranded DNA genome to a parental replicative form (RF). In this study, we used aphidicolin, a specific inhibitor of DNA pol alpha, to assay for the requirement of pol alpha activity in parental RF formation in vivo. Synchronized cell cultures were infected with bovine parvovirus with or without aphidicolin, and the products of viral replication were separated on agarose gels and identified by Southern blot analysis. We found that complete inhibition of viral DNA synthesis resulted when 20 microM aphidicolin was present throughout the infection. In addition, viral DNA synthesis was inhibited by as little as 1 microM aphidicolin, whereas lower concentrations (0.1 and 0.01 microM) resulted in partial inhibition of the replication process. Using 32P-labeled bovine parvovirus as the input virus we differentiated parental RF from daughter RF and progeny DNA synthesis. We conclude that DNA pol alpha is required for the production of RF during bovine parvovirus replication in vivo and that this requirement is most likely for the conversion of bovine parvovirus input single-stranded DNA to parental RF. These results do not rule out a possible role for DNA pol gamma in the first step, nor do they rule out a role for pol alpha or pol gamma in later stages of the replication cycle.

Animals↗

PubMed1976

Effect of ultraviolet irradiation of bacteriophage f1 DNA on its conversion to replicative form by extracts of Escherichia coli.

When DNA of phage chiX174 or phage f1 is used as a template after exposure to ultraviolet radiation, the conversion of single-stranded DNA to replicative form by cell-free extracts of Escherichia coli is inhibited. The extend of synthesis is proportional to the distance of a pyrimidine dimer from a specific origin of replication as calculated from the random location of dimers at various UV doses. The results therefore indicate that the initiation of DNA synthesis on these phage DNAs occurs normally at a specific site, and that chain elongation is blocked when replication reaches a photo product in the template. Reinitiation of DNA synthesis distal to the lesion does not occur.

Centrifugation, Density Gradient↗

PubMed1976

Rhinovirus multistranded RNA: dependence of the replicative form on the presence of actinomycin D.

The multistranded and double-stranded RNAs synthesized in HeLa cells infected with rhinovirus in the presence and in the absence of actinomycin D have been characterized by polyacrylamide gel electrophoresis and hybridization studies. The replicative form is only found in infected cells treated with actinomycin D, whereas the replicative intermediate is found in both the presence and the absence of the drug. The significance of these results is discussed.

Dactinomycin↗

PubMed1998

ToxR-independent expression of cholera toxin from the replicative form of CTXphi.

The ctxAB operon, which encodes cholera toxin, resides in the genome of CTXphi, a filamentous bacteriophage. Within Vibrio cholerae cells, the CTXphi genome can exist either as a replicating plasmid or as a prophage integrated into the chromosome. Previous work established that ToxR is required for chromosomal ctxAB expression. We have learned that strains harboring the CTXphi replicative form produce cholera toxin under all conditions tested, independently of ToxR. During passage of CTXphi lysogens through the infant mouse intestine, transduction of CTXphi to a recipient strain can be detected, indicating that phage excision and replication occur in vivo. These results suggest that phage induction might provide a novel mechanism for the regulation of cholera toxin production.

Animals↗

PubMed1991

The minute virus of mice capsid specifically recognizes the 3' hairpin structure of the viral replicative-form DNA: mapping of the binding site by hydroxyl radical footprinting.

The terminal hairpin structures of the DNA of minute virus of mice (MVM) are essential for viral replication. Here we show that the hairpin 3' terminus of MVM replicative-form DNA binds specifically to empty MVM capsids. Binding of the same terminal DNA sequence in its linear double-stranded (extended) conformation was not observed. After heat denaturation and quick cooling of 3'-terminal extended-form fragments, not only the virion strand but also the complementary strand was found to bind to the capsid, presumably because each strand re-formed a similar hairpin structure. No binding affinity for the capsid was found to be associated with hairpin or extended 5' termini or with any other region of the viral DNA. Hydroxyl radical footprinting analyses revealed three protected nucleotide stretches forming a binding site at the branch point of the two 3'-terminal hairpin arms looping out from the DNA stem (T structure). Single base changes within this site did not affect the binding. In band shift experiments, specific binding to the T structure was demonstrated for VPI but not for VP2.

Base Sequence↗

PubMed1988

Effects of SOS and MucAB functions on reactivation and mutagenesis of M13 replicative form DNA bearing bulky lesions.

We have previously determined the specificity of -1 frameshifts induced by aflatoxin-B1-2,3-dichloride (AFB1C12) in phage M13 double-strand replicative form (RF) DNA. The system consists of: (i) in vitro adduction of RF DNA of BK8, a lacZ + 1 frameshift derivative of phage M13mp8; (ii) transfection into unirradiated or UV-irradiated bacterial host cells; (iii) scoring and sequencing of revertants (i.e., -1 frameshifts). The previous data had shown that induction of SOS functions enhanced mutagenesis. However, this increase in mutagenesis is not accompanied by enhanced survival in a majority of the strains tested. Here, we present evidence to show that the lack of SOS reactivation is a specific property of the RF DNA system rather than a specific property of the lesion. A model mechanism based on the replicative strategy of transfected RF DNA can account for these observations. In addition, we have calculated individual Weigle mutagenesis factors at 8 major mutagen induced sites reported previously. Analysis of these data indicates that, within a restricted subset of possible mutational events (i.e., -1 frameshifts), Weigle mutagenesis is affected by both the DNA sequence environment of the mutation site as well as the repair phenotype of the cell.

Aflatoxin B1↗

PubMed1970

Greater vulnerability of the infecting viral strand of replicative-form deoxyribonucleic acid of bacteriophage phi X174.

Four types of phiX-infected cells of Escherichia coli CR, a thymine-requiring strain of E. coli C, were prepared in which the parental replicative-form deoxyribonucleic acid (RF DNA) was labeled with same specific amounts of bromouracil in (i) both strands, (ii) only the infecting viral strand, (iii) only the complementary strand, and (iv) neither strand. The sensitivity of each type of infected cell toward irradiation by ultraviolet light, visible light, and X rays was measured. The results indicate that a certain amount of radiation damage in the infecting viral strand of the parental RF was more inhibitory to the production of progeny phage than when the damage was in the complementary strand. Similar conclusions were also drawn from "suicide" experiments of the phage-infected complexes containing (32)P of the same specific activity on either strand of the parental RF DNA. The results suggest that the beta decay occurring in the infecting viral strand was more effective in inactivating the plaque-forming ability of the complex.

Bromine↗

PubMed1982

A comparison of experimental and theoretical melting maps for replicative form of phi X174 DNA.

A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoretical melting maps obtained in (4) and (6). This comparison clearly shows that only rigorous calculations (4) and not the ones proposed by Azbel (6,7) correctly predict the course of RF III melting.

Bacteriophage phi X 174↗

PubMed1969

Host specificity of DNA produced by Escherichia coli. XI. In vitro modification of phage fd replicative form.

An enzymatic activity, having the properties expected of a B-specific host-controlled modification enzyme, has been purified from an extract of Escherichia coli strain B. This activity renders the unmodified replicative form of phage fd resistant to B-specific restriction and is only present in strains carrying intact genes for type B modification. In phosphate buffer, the enzyme acts optimally at pH 6 and is dependent upon a single cofactor, S-adenosylmethionine.

Chromatography↗

PubMed1992

Detection of replicative form of hepatitis C virus RNA in peripheral blood mononuclear cells.

Paired samples of plasma and peripheral blood mononuclear cells (PBMC) from 7 patients with posttransfusion hepatitis C were collected and studied for the presence of replicative forms of hepatitis C virus (HCV). RNA was extracted and tested for both positive and negative strands of HCV RNA by polymerase chain reaction. Positive-strand RNA of HCV was found in both plasma and PBMC of all 7 patients. However, negative-strand RNA was found in PBMC of 3 patients while none was found in the plasma. Levels of negative-strand RNA were about 10-100 times less than those of positive-strand RNA by semiquantification with serial dilution of viral cDNA. The results suggest that active infection and replication of HCV in PBMC is present in patients with posttransfusion hepatitis C and implicate the extrahepatic infection of HCV.

Adult↗

PubMed1991

Cell-free translation and identification of the replicative form of Nudaurelia beta virus RNA.

Larvae of the pine emperor moth, Nudaurelia cytherea capensis, infected with Nudaurelia beta virus (N beta V) consistently contained one species of dsRNA. This dsRNA was the correct size to be the replicative form of the N beta V genome and, in Northern blots, it hybridized with 32P-end-labelled virion RNA. Other smaller dsRNAs were obtained in a non-reproducible manner but these had no sequences in common with the genomic probe; no dsRNAs were observed in extracts from virus-free larvae. Cell-free translation of N beta V RNA resulted in the synthesis of only one major polypeptide, of Mr about 71,000, which could not be precipitated by an anti-N beta V serum.

Animals↗

PubMed1985

Proteins tightly associated with the termini of replicative form DNA of Kilham rat virus, an autonomous parvovirus.

Revie et al. [Revie, D., Tseng, B. Y., Grafstrom, R. H. & Goulian, M. (1979) Proc. Natl. Acad. Sci. USA 76, 5539-5543] have proposed that the double-stranded replicative form (RF) DNA of the autonomous rodent parvovirus H-1 has protein of 60 kDa covalently bound at its 5' termini. We present evidence that the RF DNA of a similar rodent parvovirus, Kilham rat virus (KRV), also has covalently bound protein. NaDodSO4/polyacrylamide gel electrophoresis of purified, 125I-labeled RF DNA shows that proteins of 68-72, 66, 64, and 55 kDa copurify with the DNA during velocity and equilibrium sedimentation in the presence of detergents and 4 M guanidine HCl. Phenol extraction in the presence of 2-mercaptoethanol removes the 68- to 72-kDa proteins, but the 66-, 64-, and 55-kDa proteins remain tightly, but noncovalently, bound. The latter polypeptides also appear to associate with protease-treated RF DNA when mixed with uninfected cell extract. Following removal of these proteins by electrophoresis in NaDodSO4/agarose gels, two proteins (called RF TP-90 and RF TP-40), of about 90 and 40 kDa, become evident. These remain bound to the DNA and are released only after nuclease digestion of the DNA. These two proteins, apparently not of viral origin, are associated with terminal restriction fragments of the RF DNA and appear to be covalently bound to the 5' termini of both strands.

DNA Replication↗