SEARCH · PubMed Health

Results for “replicative form”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources

PubMed1982

Escherichia coli host factor required specifically for the phi X174 stage III reaction: in vitro identification and partial purification.

A cell-free extract prepared from phi X174-infected Escherichia coli cells sustained in vitro synthesis of viral DNA (stage III reaction) when supplemented with fraction II from uninfected cells. The reaction was dependent upon deoxyribonucleoside triphosphate, ATP, added phi X174 replicative form I DNA template, and the fraction II from uninfected cells. This reaction differed from the stage II reaction (semiconservative replication of duplex replicative form DNA) by the production of stable viral protein-DNA complexes sensitive to anti-phi X174 antiserum. Three types of protein-DNA complexes were identified, 50S, 92S, and a 114S complex that cobanded in CsCl and cosedimented in neutral sucrose gradients with a phi X174 phage marker. The sensitivity of these complexes to anti-phi X174 antiserum and Staphylococcus aureus provided a relatively rapid biochemical assay for direct measurement of the amount of DNA synthesized by the stage III reaction. With this assay, an E. coli factor (SIII) required specifically for the synthesis of viral protein-DNA complexes was identified and purified 200-fold from uninfected E. coli cells. The partially purified SIII factor was required for the synthesis of DNA and viral protein-DNA complexes in the phi X174-infected cell extracts and could not be replaced by rep protein, single-strand binding protein, or DNA polymerase III holoenzyme.

Bacteriophage phi X 174↗

PubMed1979

Highly active template-specific RNA-dependent RNA polymerase from barley leaves infected with brome mosaic virus.

The extraction of a template-dependent and template-specific RNA-dependent RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) from a eukaryotic source is described. The enzyme, extracted from barley leaves infected with brome mosaic virus (BMV), is capable of incorporating high levels of radioactivity into trichloroacetic acid-insoluble products. The purification procedure included solubilization with nonionic detergent and precipitation with polyethylene glycol. The enzyme was more than 50 times more active than was a comparable preparation from mock-inoculated leaves and was stimulated more than 15-fold by the addition of BMV RNA to the reaction. Other viral RNA templates were less than 25% as efficient as was BMV RNA in stimulating UMP incorporation; poly(A), tRNA, and mRNA gave little stimulation and rRNA was inactive. Autoradiographic analysis after electrophoretic separation of the radioactive products from reaction mixtures containing BMV RNA template revealed prominent bands that coelectrophoresed with replicative forms of BMV RNAs. When BMV RNA template was enriched in RNA3 or RNA4, larger proportions of the products were replicative forms of RNA3 or RNA4, respectively.

DNA-Directed RNA Polymerases↗

PubMed1988

Reactivation of hepatitis B virus in anti-HBe-positive chronic active type B hepatitis: molecular and immunohistochemical studies.

The causes of acute clinical exacerbations, and the role of reactivation of hepatitis B virus (HBV) in 16 non-cirrhotic patients with chronic active type B hepatitis (CAH-B) negative for serum hepatitis B e antigen (HBeAg) but positive for anti-HBE, were studied by molecular hybridization and immunohistochemical methods. IgM antibody to hepatitis A virus (anti-HAV IgM) and antibody to delta agent (anti-delta) were negative in all. HBeAg reappeared transiently in only two patients. Serum hepatitis B virus (HBV) DNA levels increased during acute exacerbations in 14 patients (88%), and decreased after the episode. Cytoplasmic hepatitis B core antigen (HBcAg) expression was found in 9 out of 13 patients (69%) during acute exacerbation. By Southern blot hybridization, 5 of 6 (83%) liver tissues obtained during clinical exacerbations had free replicative forms of HBV DNA. In 20 control patients with no exacerbation, serum HBV DNA, HBcAg expression in hepatocytes and free replicative forms of HBV DNA were positive in 15% (3/20), 10% (2/20) and 25% (2/8), respectively--figures significantly lower than those of the group studied. We conclude that acute exacerbations sometimes seen in patients with anti-HBe-positive CAH-B in Taiwan are caused mainly by reactivation of HBV.

Adult↗

PubMed1984

The complex of T4 bacteriophage gene 44 and 62 replication proteins forms an ATPase that is stimulated by DNA and by T4 gene 45 protein.

The bacteriophage T4 genome is believed to encode all of the proteins needed for the replication of its own DNA. Included among these proteins are the "polymerase accessory proteins", the products of T4 genes 44, 62 and 45. The first two of these genes specify the synthesis of the 44/62 protein complex, which is here shown to be a DNA-dependent ATPase, hydrolyzing either ATP or dATP to the corresponding nucleoside diphosphate and releasing inorganic phosphate. This nucleotide hydrolysis is greatly stimulated by addition of the gene 45 protein and by single-stranded DNA termini. A rapid micro DNA-cellulose assay is introduced and used to measure accessory protein binding to the complex of T4 gene 32 protein and single-stranded DNA. In the presence of ATP, the 44/62 protein binds to this complex but not to naked DNA, while the 45 protein requires both the 32 protein and the 44/62 protein for detectable binding.

Adenosine Triphosphatases↗

PubMed2001

An alteration in concatameric structure is associated with efficient segregation of plasmids in transfected Plasmodium falciparum parasites.

Transfection of the human malaria parasite Plasmodium falciparum is currently performed with circularised plasmids that are maintained episomally in parasites under drug selection but which are rapidly lost when selection pressure is removed. In this paper, we show that in instances where gene targeting is not favoured, transfected plasmids can change to stably replicating forms (SRFs) that are maintained episomally in the absence of drug selection. SRF DNA is a large concatamer of the parental plasmid comprising at least nine plasmids arranged in a head-to-tail array. We show as well that the original unstable replicating forms (URFs) are also present as head-to-tail concatamers, but only comprise three plasmids. Limited digestion and gamma irradiation experiments revealed that while URF concatamers are primarily circular, as expected, SRF concatamers form a more complex structure that includes extensive single-stranded DNA. No evidence of sequence rearrangement or additional sequence was detected in SRF DNA, including in transient replication experiments designed to select for more efficiently replicating plasmids. Surprisingly, these experiments revealed that the bacterial plasmid alone can replicate in parasites. Together, these results imply that transfected plasmids are required to form head-to-tail concatamers to be maintained in parasites and implicate both rolling-circle and recombination-dependent mechanisms in their replication.

Animals↗

PubMed1973

Lack of close relationship between three strains of human rhinoviruses as determined by their RNA sequences.

The possible genomic homologies between three serotypes of human rhinoviruses (HRV 1A, HRV 2, and HRV 14) were investigated. First we confirmed that these viruses were unrelated by the criterion of the absence of common antigenic determinants on the surfaces of the native virions, as detected by cross-neutralization of complementfixation. RNA-RNA hybridization was then examined with purified, highly radioactive, double-stranded, replicative-form RNA and excess single-stranded virion RNA. Single-stranded RNA showed 100% homology with the minus strand from the replicative-form RNA of the same type of virus. HRV 1A, HRV 2, and HRV 14 showed low intertypic homologies; these were not significantly greater than those found between the rhinoviruses and polivirus, which were used as a negative control. The immunological relationship and the RNA homology between HRV 1A and HRV 1B were also examined by the above techniques. It was confirmed that HRV 1A and HRV 1B share some surface determinants and it was also found that HRV 1B RNA shares 70% homology with HRV 1A RNA.

Base Sequence↗

PubMed1986

In vivo study of the mechanism of action of antiviral agents against hepadna virus replication in the liver. Resistance of supercoiled viral DNA.

The mode of action of antiviral agents (interferon and adenine arabinoside) was studied in human and in animals chronically infected with hepadna virus. Interferon (36-100 megaunits) was given to 20 carrier patients, and hepatitis B virus (HBV)-DNA replicative forms were studied in pre- and post-treatment biopsies. ARA-A was given intravenously to duck hepatitis B virus (DHBV)-infected ducks. Changes in intrahepatic viral replicative forms were studied by Southern blotting using 32P-labelled HBV or DHBV probe. Our study indicates that both interferon and ARA-A seem to effectively decrease 'mature' forms of viral DNA by an effect on either mRNA or DNA polymerase. However, the supercoiled viral DNA tends to resist the treatment, and may become the transcribing template for a new cycle of viral replication after cessation of the drugs.

Animals↗

PubMed2005

Hepatitis B virus infection in lymphatic tissues in inactive hepatitis B carriers.

BACKGROUND/AIMS: Hepatitis B virus (HBV) infection in extrahepatic tissues is controversial. To clarify whether episomal HBV can infect nonhepatic tissues, we investigated the molecular forms of HBV in the lymphatic cells of inactive HBV carriers who lacked viremia, thus avoiding contamination with HBV genomes originating from the viral particles present in the serum. METHODS: We assessed HBV genome, replicative forms, and viral integrants in the liver, serum, peripheral blood mononuclear cells (PBMC), and lymph nodes of 21 inactive HBV carriers who tested positive for antibodies against the HBV core antigen (anti-HBc). RESULTS: Of the 21 anti-HBc positive individuals, HBV-DNA was detected in liver samples of 15 (71.4%), in the lymph nodes of 11 (52.4%), and in PBMC of three (14.3%). However, none of the detected HBV genomes from lymphatic tissues included the replicative forms of HBV. In one case, integrated HBV was present in the lymphatic tissues and the host-viral junction was present in the intronic sequences of chromosome 17. CONCLUSIONS: These data suggest that human lymphatic tissues cannot support viral replication in anti-HBc positive inactive HBV carriers, while retaining the viral genome as an integrated form.

Adult↗

PubMed1972

Cleavage of bacteriophage fl DNA by the restriction enzyme of Escherichia coli B.

We studied the cleavage of the replicative-form DNA (RF I) of bacteriophage f1 and its SB mutants by purified restriction endonuclease of E. coli B. The results indicate that: (i) Circular replicative forms are broken once to yield full-length linear molecules (RF III). Such linear molecules are less susceptible than RF I to endonuclease R-B. (ii) The genetic sites (SB sites) that confer on the DNA susceptibility to B-restriction are not the actual sites of cleavage. The number of possible cleavage sites is larger than the number of SB sites. We conclude this because an RF III molecule produced by endonuclease R-B from RF I of a mutant that has only one SB site can be circularized by denaturation and renaturation. (iii) The SB site is not modified when the DNA is cleaved, since an SB site can be used repeatedly by endonuclease R-B; the RF III described in ii can be cleaved by the same enzyme after denaturation and renaturation.

Carbon Isotopes↗

PubMed1996

Analysis of the intracellular fate of Legionella pneumophila mutants.

L. pneumophila is a model organism for investigating the mechanisms by which intracellular pathogens acquire the metabolites needed for replication while evading the microbicidal mechanisms of the macrophage. We determined that intracellular L. pneumophila replicate in close association with the endoplasmic reticulum and suggest that L. pneumophila exploits the macrophage autophagy pathway to establish this specialized vacuole. To identify the bacterial factors required at this step as well as the factors important for other stages of the intracellular pathway, we isolated a collection of bacterial mutants that are defective for growth in macrophages. The ability of the mutant strains to evade fusion with the lysosomes and to establish replication vacuoles was examined by fluorescence microscopic localization of markers for the late endosomes (lgp 120), lysosomes (Texas Red-ovalbumin), endoplasmic reticulum (BiP), and L. pneumophila. By this approach, we identified mutants with distinct intracellular fates; one type does not evade the endocytic pathway, another forms replication vacuoles less efficiently than does wild-type, and a third type forms replication vacuoles but replicates poorly. These mutants are likely to facilitate identification and characterization of the bacterial factors required by L. pneumophila to establish a protected niche for intracellular replication.

Animals↗

PubMed1974

Replication of bacteriophage phiX174 DNA in a temperature-sensitive dnaC mutant of escherichia coli C.

Bacteriophage phiX174 cannot grow in a temperature-sensitive dnaC mutant of Escherichia coli C at the nonpermissive temperature. The inability to grow is the result of inhibition of virus DNA synthesis. Parental replicative form synthesis is not temperature sensitive. Single-stranded virus DNA continues to be synthesized for at least 45 min after shifting to the nonpermissive temperature late in infection. In contrast, the replication of the replicative form terminates within 5 min after shifting to the nonpermissive temperature.

Centrifugation, Density Gradient↗

PubMed2003

CTXphi-independent production of the RS1 satellite phage by Vibrio cholerae.

The cholera toxin genes of Vibrio cholerae are encoded by the filamentous phage, CTXphi. Chromosomal CTXphi prophage DNA is often found flanked by copies of a related genetic element designated RS1, and RS1 DNA can be packaged into filamentous phage particles (designated RS1phi) by using the CTXphi morphogenesis genes. RS1phi is a satellite phage that further controls expression and dissemination of CTXphi. Here we describe a CTXphi-independent mechanism for production of RS1phi. A nontoxigenic environmental V. cholerae strain (55V71) was identified that supports production of RS1phi. However, newly infected CTX-negative strains did not produce RS1phi, indicating that additional 55V71 genes were involved in production of RS1phi. Analysis of nucleic acids from phage preparations of 55V71 revealed a 7.5-kb single-stranded DNA, whose corresponding replicative form was found in plasmid preparations. This DNA likely corresponds to the genome of a new filamentous phage, which we have designated KSF-1phi. The replicative form DNA of KSF-1phi was cloned into pUC18, and the resulting construct pKSF-1.1 supported the production of RS1phi particles by CTX-negative V. cholerae strains. RS1phi particles produced in this way infect recipient V. cholerae strains by a mechanism that is independent of the CTXphi receptor, the toxin-coregulated pilus. Thus, KSF-1phi is capable of facilitating the transfer of the RS1 element to strains that do not express toxin coregulated pilus. Given that RS1phi can enhance coproduction of CTXphi particles, KSF-1phi-mediated dissemination of RS1 may indirectly promote the spread of toxin genes among V. cholerae strains. This study also shows that filamentous phages can package diverse DNA elements and thus may play a role in horizontal transfer of more genes than previously appreciated.

Bacteriophages↗

PubMed1972

Replication of Phi-X174 DNA by Escherichia coli polA- in vitro (Phi-X174 DNA-DNA replication-E. coli polA-).

Lysates of an Escherichia coli polA(-) strain convert single-stranded DNA from varphiX174 virus to the double-stranded replicative form with high efficiency on cellophane discs. The initiation of synthesis of the complementary strand appears to be rate limiting; once initiation occurs, the chain is propagated rapidly. Under these conditions, the unsealed replicative form accumulates and is slowly converted to the sealed form; this conversion requires the activity of the DPN-dependent DNA ligase.

Centrifugation, Density Gradient↗

PubMed1991

Zinc(II) protects against metal-mediated free radical induced damage: studies on single and double-strand DNA breakage.

M13 DNA was used as a source for single and double-stranded DNA. Free radical-induced damage to single and double stranded DNA was caused by ascorbate/iron and ascorbate/copper oxidative systems. The degree of breakage was estimated by running samples on an agarose gel and staining with ethidium bromide, followed by photographic analysis. DNA breakage was dependent on time and concentration of iron or copper ions. Zinc ions protected against damage caused by iron/ascorbate both to single-stranded and double-stranded DNA. In contrast, in the copper/ascorbate system zinc ions protected only against the double-stranded DNA (replicative form of M13) breakage, and not against copper-mediated single-stranded DNA breakages. It seemed to amplify the efficiency of breakage. The protection provided to the replicative form in the copper/ascorbate system is much less effective than the protection to DNA in the iron/ascorbate system. These results support the notion that redox-inactive metal ions, that compete for iron or copper binding sites, could provide protection against transition metal-mediated and free radical-induced damage.

Copper↗

PubMed1988

Evidence of restricted viral replication in adult mink infected with Aleutian disease of mink parvovirus.

Strand-specific hybridization probes were used in in situ molecular hybridization specifically to localize cells containing replicative intermediates of Aleutian disease of mink parvovirus (ADV). When adult mink of Aleutian genotype were infected with ADV Utah I, the largest number of cells positive for viral replication (i.e., containing replicative-form DNA and RNA) were found in the mesenteric lymph nodes and spleens at 10 days after infection. The localization of positive cells in the middle of germinal centers suggested that they were B lymphoblasts. Circulating leukocytes and bone marrow cells also contained viral RNA, but the levels of replicative-form DNA were below detectability. The levels of viral DNA and RNA in adult mink cells replicating ADV were decreased compared with those in permissively infected cell cultures or neonatal mink, suggesting that the replication of ADV in adult mink might be semipermissive or restricted at some early stage of viral gene expression. The low level of viral replication and transcription in lymphoid cells might provide a mechanism for the development of immune disorders and for the maintenance of persistent infection. Single-stranded virion DNA was found in other organs, but the strand-specific probes made it possible to show that this DNA represented virus sequestration. In addition, glomerular immune complexes containing virion DNA were detected, suggesting that ADV virions, or perhaps free DNA, may have a role in the development of ADV-induced glomerulonephritis.

Aleutian Mink Disease Virus↗

PubMed1988

Isolation and characterization of thermosensitive mutants from Kilham rat virus, a rodent parvovirus.

Thermosensitive mutants were isolated from nitrous acid-treated Kilham rat virus (KRV). At a restrictive temperature (39.5 degrees C), the mutants tested did not produce appreciable amounts of infectious particles, haemagglutinin or progeny single-stranded DNA. Virus antigen accumulation as detected by immunoperoxidase was reduced. Complementation tests revealed two distinct groups. The three members of complementation group 1 synthesized normal amounts of replicative forms but were restricted in single-stranded DNA production and capsid protein expression, exhibiting phenotypes compatible with cap mutations. The sole representative of group 2, KRV ts6, failed to accumulate replicative forms, displaying a rep- phenotype. These mutants provide new tools to test the role of viral products in the biology of autonomous parvoviruses.

Animals↗

PubMed2003

Enhancement of recombinant adeno-associated virus type 2-mediated transgene expression in a lung epithelial cell line by inhibition of the epidermal growth factor receptor.

Recombinant adeno-associated viruses (rAAVs) have attracted considerable interest as gene delivery systems because they show long-term expression in vivo and transduce numerous cell types. Limitations to successful gene transduction from rAAVs have prompted investigations of a variety of treatments to enhance transgene expression from rAAV vectors. Tyrphostin-1, an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, dramatically enhances rAAV transgene expression. Elegant studies have demonstrated that a single-strand D-sequence-binding protein (ssDBP) is phosphorylated by EGFR and binds to the D sequence element in the AAV terminal repeat (TR). Binding of the Tyr-phosphorylated ssDBP prevents conversion of single-stranded vector DNA to a double-strand conformation. We observed dramatic increases in transgene expression in lung epithelial cells (IB3) with tyrphostin treatment. Gel shift analysis of ssDBP revealed that its DNA binding characteristics were unchanged after tyrphostin treatment or adenovirus infection. Tyrphostin stimulated rAAV transgene expression to a greater extent than adenovirus coinfection. Southern hybridizations revealed that the vector DNA remained in the single-strand conformation in tyrphostin-treated cells but double-stranded replicative form monomer DNA was most abundant in adenovirus-infected cells. Northern analyses revealed that tyrphostin treatment enhanced mRNA accumulation more than in adenovirus-infected cultures even though replicative form DNA was undetectable. Analysis of the JNK, ERK, and p38K mitogen-activated protein kinase pathways revealed that tyrphostin treatment stimulated the activity of JNK and p38K. Our data suggest that tyrphostin-induced alteration of stress response pathways results in dramatic enhancement of transcription on linear vector DNA templates in the IB3 cell line. These results expand the downstream targets of the EGFR in regulating rAAV transduction.

Cell Line, Transformed↗

PubMed1990

The small nonstructural protein (NS2) of the parvovirus minute virus of mice is required for efficient DNA replication and infectious virus production in a cell-type-specific manner.

Seven mutations which affect only the small nonstructural protein NS2 were introduced into the infectious clone of the autonomous parvovirus, minute virus of mice (MVM). The majority of these mutants were severely defective for replication following transfection of normal host murine A9 fibroblasts; however, all were found to replicate more efficiently and produce infectious virus in certain other cell types, including human NB324K. The isolation of viral stocks from NB324K cells permitted a more detailed analysis of the mutant defect on A9 cells. NS2 mutant NS2-2018 was shown to be approximately 10-fold deficient for viral monomer replicative-form DNA production within a single-burst cycle in infected A9 cells and produced a reduced amount of progeny single strand. Mutant NS2-2018 generated wild-type levels of monomer replicative-form DNA on NB324K cells but made reduced levels of progeny single strand and small plaques on these cells. The accumulation of NS1 is reduced late in NS2-2018 infection of A9 cells, but NS1 accumulates to wild-type levels late in NB324K cell infections. NS1 nuclear localization is not dependent on NS2 in A9 or NB324K cells. These results indicate that NS2 participates in MVM DNA replication and is required for efficient viral growth. The requirement for NS2 during MVM replication is also host cell specific. This requirement is significantly more pronounced in the normal host murine A9 cells than in certain other cell types, including NB324K.

Animals↗