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PubMed1991

HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer.

Retroviral DNA integration involves a coordinated set of DNA cutting and joining reactions. Linear viral DNA is cleaved at each 3' end to generate the precursor ends for integration. The resulting recessed 3' ends are inserted into target DNA by a subsequent DNA strand transfer reaction. Purified HIV-1 integration protein carries out both of these steps in vitro. Two novel forms of the dinucleotide cleaved from HIV-1 DNA were identified and one, a cyclic dinucleotide, was used to analyze the stereochemical course of viral DNA cleavage. Both viral DNA cleavage and DNA strand transfer display inversion at chiral phosphorothioates during the course of the reaction. These results suggest that both reactions occur by a one-step mechanism without involvement of a covalent protein-DNA intermediate.

Alkaline Phosphatase↗
PubMedDate not supplied

[Interactions of HIV-1 DNA heterocyclic bases with viral DNA].

Human immunodeficiency virus type 1 integrase is one of three viral enzymes, and it realizes a key process of the viral replication cycle, i.e. viral DNA integration into infected cell genome. Integrase recognizes nucleotide sequences located at the ends of the viral DNA U3 and U5 LTRs and catalyzes 3'-processing and strand transfer reactions. To study the interactions between integrase and viral DNA at present work, we used modified integrase substrates mimicking the terminal U5 LTR sequence and containing non-nucleoside insertions in one or/and both strands. It is shown that the substrate modifications have no influence on the integrase binding rate, while the heterocyclic bases removal in the 5th and 6th substrate positions and in the 3rd position of the substrate processed strand distinctly inhibits the integrase catalytic activity. This fact demonstrates these bases significance for the active enzyme/substrate complex formation. On the contrary, modification of the 3rd position within substrate non-processed strand stimulates 3'-processing. Since heterocyclic base elimination results in disruption of the DNA complementary and staking interactions, this result shows that DNA double helix destabilization close to the cleaved bond promotes the 3'-processing.

DNA, Viral↗
PubMed1976

State of the viral DNA in rat cells transformed by polyoma virus. I. Virus rescue and the presence of nonintergrated viral DNA molecules.

The interaction of polyoma virus with a continuous line of rat cells was studied. Infection of these cells with polyoma did not cause virus multiplication but induced transformation. Transformed cells did not produce infectious virus, but in all clones tested virus was rescuable upon fusion with permissive mouse cells. Transformed rat cells contained, in addition to integrated viral genomes, 20 to 50 copies of nonintegrated viral DNA equivalents per cell (average). "Free" viral DNA molecules were also found in cells transformed by the ts-a and ts-8 polyoma mutants and kept at 33 C. This was not due to a virus carrier state, since the number of nonintegrated viral DNA molecules was found to be unchanged when cells were grown in the presence of antipolyoma serum. Recloning of the transformed cell lines produced subclones, which also contained free viral DNA. Most of these molecules were supercoiled and were found in the muclei of the transformed cells. The nonintegrated viral DNA is infectious. Its specifici infectivity is, however, about 100-fold lower than that of polyoma DNA extracted from productively infected cells, suggesting that these molecules contain a large proportion of defectives.

Animals↗
PubMed1982

The interaction of polyoma virus with F9 embryonal carcinoma cells and chemically induced differentiated progeny: fate of the viral DNA and expression of viral antigens.

Murine embryonal carcinoma (EC) cells fail to express viral T antigen following infection with polyoma (Py) virus, while some differentiated derivatives are fully susceptible to viral infection. The block to expression in EC cells apparently occurs after adsorption and penetration but prior to the synthesis of early viral proteins. The F9 EC cell line was employed to further investigate the failure of Py gene expression in EC cells as well as the viral susceptibility of certain differentiated cell types. F9 cultures treated with retinoic acid (RA) or RA in combination with dibutyryl cAMP (dBcAMP) are quantitatively induced to differentiate to endodermal cell types. When the fate of the viral DNA was examined in F9 EC cells, free viral DNA was observed early after infection but was eventually lost with continued cell growth. Cultures induced to differentiate in the presence of RA demonstrated limited viral susceptibility which increased with prolonged RA exposure. Polyoma sensitivity did not directly parallel basement membrane antigen production, a marker used to distinguish this differentiated endodermal cell type. Viral gene expression could be obtained if Py DNA was introduced into the cells prior to RA induction. In contrast, the endodermal progeny derived from a dual treatment with RA plus dBcAMP appeared highly refractory to Py infection.

Animals↗
PubMed1984

Deletion of cellular DNA at site of viral DNA insertion in the adenovirus type 12-induced mouse tumor CBA-12-1-T.

The adenovirus type 12 (Ad12)-induced mouse tumor CBA-12-1-T contains greater than 30 copies of viral DNA integrated into cellular DNA. One of the sites of linkage between the left terminus of Ad12 DNA and mouse DNA was cloned, mapped and sequenced by using conventional techniques. The preinsertion sequence was also cloned from normal CBA/J mouse DNA and sequenced. The sequence data and blotting analyses demonstrated that at the site of linkage nine nucleotide pairs of viral DNA and at least 1500 to 1600 nucleotide pairs of cellular DNA were deleted. Up to the site of linkage, the cellular DNA sequence in CBA-12-1-T tumor DNA and the preinsertion sequence in CBA/J mouse cells were identical. The site of Ad12 DNA integration was found to be located close to a site of transition from unique to repetitive cellular DNA sequences. The nucleotide sequence at the site of linkage and at the preinsertion site revealed palindromic stretches of 5 and 10 nucleotides pairs, respectively. Scattered patch homologies (8-10 nucleotide pairs long) were observed between adenoviral and cellular DNAs. A hypothetical model for DNA arrangements at the site of recombination is presented.

Adenoviridae↗
PubMed1984

Rearrangements of host and viral DNA in mouse cells transformed by simian virus 40.

We have determined the structure of host DNA and viral DNA at the site of integration of Simian virus 40 (SV40) in a line of transformed Balb/c-3T3 cells (SVB400) isolated by single cell cloning after virus infection. Recombinant phage containing integrated viral DNA and flanking host DNA were purified from a genomic library and, in conjunction with restriction endonuclease cleavage analysis of the transformed cell DNA, were used to determine the organization of the integrated viral sequences. There is heterogeneity in the arrangement of the viral sequences resulting from tandem duplications of all or part of the SV40 genome with preservation of the viral-host junctions. The predominant arrangement is the result of tandem duplication of 41% of the SV40 genome from 0.64 to 0.23. Analysis of the structure of integrated viral DNA in SVB400 at different passage numbers and in single cell clones derived from the 20th passage indicated that rearrangements of viral DNA occur after the integration event and continue with passage of the cells. The organization of host sequences before and after the integration of SV40 was determined by restriction endonuclease cleavage analysis of parental 3T3 DNA and SVB400 DNA, and by analysis of recombinant phage isolated from genomic libraries. A deletion of at least 15 X 10(3) bases of host DNA occurred at the site of integration, which indicates that viral integration was not a result of a simple insertion of SV40. Nucleotide sequence analysis of the virus-host junctions showed that retained SV40 sequences were colinear with the viral genome, and that the junctions with SV40 DNA occurred at nucleotide numbers 1377 and 3610. There was no evidence of duplications of viral or host sequences at the junctions, and a comparison of the flanking mouse sequences with the deleted SV40 sequences revealed no significant homology at the point of joining of the two genomes.

Animals↗
PubMed1976

Quantitation of bovine papilloma viral DNA in viral-induced tumors.

Bovine papilloma virus (BPV) DNA was labeled in vitro under conditions of repair synthesis and subsequently used as a "probe" in DNA-DNA reassociation studies to detect BPV-specific DNA sequences in a viral-induced calf meningioma and hamster fibroma. In vitro labeled BPV DNA had denaturation characteristics expected for duplex DNA and denatured DNA reassociated with apparent second-order kinetics. Analysis of in vitro labeled BPV DNA reassociation rates in the presence of excess tumor DNA revealed that the calf meningioma contained approximately 700 to 800 BPV genome equivalents per diploid cell whereas the hamster fibroma contained about 150 incomplete BPV genome equivalents per diploid cell. Thermal denaturation of in vitro labeled BPV DNA which reassociated in the presence of the two tumor DNA preparations indicated less than 1.5% base pair mismatching.

Animals↗
PubMed1984

Characterization of an aphidicolin-resistant mutant of herpes simplex virus type 2 which induces an altered viral DNA polymerase.

The replication of wild-type herpes simplex virus type 2 (HSV-2) was very sensitive to aphidicolin, a specific inhibitor of eukaryotic alpha-type DNA polymerases; viral DNA synthesis was strongly inhibited by 1 microgram/ml of aphidicolin, but the synthesis of early viral polypeptides was not affected. Using aphidicolin as the selective agent, aphidicolin-resistant ( Aphr ) viruses were isolated from HSV-2 strain 186. All of these plaque isolates induced altered viral DNA polymerases which were more resistant to aphidicolin than wild-type polymerase. These results clearly indicate that viral DNA polymerase is a target of aphidicolin in vivo and suggest that host cell DNA polymerase alpha may be not involved in the replication of HSV-2. Partially purified mutant polymerase exhibited a 7.5-fold lower apparent Km for dCTP and a 3-fold lower apparent Km for dTTP than similarly purified wild-type enzyme. The apparent Ki value for aphidicolin of the mutant polymerase was 6.5-fold higher than that of the wild-type enzyme. Moreover, all Aphr viruses isolated were also resistant to thymine-1-beta-D-arabinofuranoside (ara-T). While, they were as sensitive as wild-type virus to cytosine-1-beta-D-arabinofuranoside (ara-C), adenine-9-beta-D-arabinofuranoside (ara-A), and acycloguanosine (acyclo-G). Interestingly these Aphr isolates were more sensitive to phosphonoacetic acid (PAA) than the wild-type. In contrast, PAA-resistant ( PAAr ) viruses of HSV-2 were more sensitive to aphidicolin and were more resistant to all of four nucleoside analogs than the parental wild-type virus. These results suggest that the aphidicolin-binding site of HSV DNA polymerase may be very close to the binding sites for dCTP and dTTP and it functionally correlates with that for pyrophosphate group.

Antiviral Agents↗
PubMed1999

Persistent Hz-1 virus infection in insect cells: evidence for insertion of viral DNA into host chromosomes and viral infection in a latent status.

Persistent/latent viral infections of insect cells are a prominent though poorly understood phenomenon. In this study, the long-term association between the Hz-1 virus and insect host cells, conventionally referred to as persistent viral infection, is described. With the aid of a newly developed fluorescent cell-labeling system, we found that productive viral replication occurs by spontaneous viral reactivation in fewer than 0.2% of persistently infected cell lines over a 5-day period. Once viral reactivation takes place, the host cell dies. The persistently infected cells contain various amounts of viral DNA, and, in an extreme case, up to 16% of the total DNA isolated from infected cells could be of viral origin. Both pulsed-field gel electrophoresis and in situ hybridization experiments showed that some of these viral DNA molecules are inserted into the host chromosomes but that the rest of viral DNA copies are free from host chromosomes. Thus, Hz-1 virus is the first nonretroviral insect virus known to insert its genome into the host chromosome during the infection process. These data also suggest that the previously described persistent infection of Hz-1 virus in insect cells should be more accurately referred to as latent viral infection.

Animals↗
PubMed1995

Turnover of circulating virion RNA and of cell-associated viral DNA reflects active viral replication in human immunodeficiency virus type 1-infected individuals.

A quantitative assessment of human immunodeficiency virus type 1 turnover in patient cell-free virion and infected-cell compartments under the dynamic conditions imposed by an effective antiviral therapy was performed. The turnover was rapid, and following a temporal lag, the extent of viral population replacement was eventually similar in both compartments. Each compartment therefore reflects considerable active virus replication.

Antiviral Agents↗
PubMed1976

Unintegrated viral DNA is synthesized in the cytoplasm of avian sarcoma virus-transformed duck cells by viral DNA polymerase.

We have examined the location, structure, and mechanism of synthesis of unintegrated viral DNA present in fully transformed cultures of avian sarcoma virus-infected duck cells. De novo synthesis of the unintegrated forms several weeks after the initial infection was documented by labeling unintegrated DNA in both strands with 5-bromodeoxyuridine. The unintegrated DNA is synthesized in, and probably confined to, the cytoplasm, and it consists of duplexes of short "plus" strands (ca. 0.5 X 10(6) to 1.0 X 10(6) daltons) and "minus" strands the length of a subunit of the viral genome (ca. 2.5 X 10(6) to 3.0 X 10(6) daltons). The structure of the duplex and the mode of incorporation of density label support the hypothesis that the unintegrated DNA is synthesized from an RNA templated by virus-coded DNA polymerase.

Animals↗
PubMed1971

Heterogeneity of murine leukemia virus in vitro DNA; detection of viral DNA in mammalian cells.

Kinetic analysis of the reassociation of DNA synthesized in vitro by a murine leukemia virus DNA polymerase revealed two classes of double-stranded product representative of 25 and 100 percent of viral genetic information. The DNA product representing the smaller portion of the viral genome comprised 85 percent of the double-stranded DNA generated in vitro and was extensively duplicated in the genomes of both normal cells and cells containing RNA tumor virus.

Animals↗
PubMed1993

Viral DNA and a viral peptide can act as cofactors of adenovirus virion proteinase activity.

Human adenovirus (Ad2), like many other viruses, contains a virion-associated proteinase essential for the synthesis of infectious virus particles. We observed proteinase activity in wild-type virus but not in the ts-1 virus, which contains a mutation in the Ad2 L3 endoprotease gene that confers temperature-sensitive processing of virion precursor proteins. Unexpectedly, we did not observe proteinase activity with purified recombinant endoprotease protein (M(r) 23 K). Purified recombinant endoprotease protein, however, complemented the mutation in ts-1 virions, restoring proteinase activity when mixed together. This implied that cofactors may be required. Here we reconstitute proteinase activity in vitro with three purified viral components: (1) the recombinant endoprotease protein; (2) an 11-amino-acid peptide that originates from the carboxy terminus of pVI, the precursor to virion component VI; and (3) adenovirus DNA. The use of DNA for a proteinase activity is unprecedented.

Adenoviruses, Human↗
PubMed2000

Prevalence of TT viral DNA in italian blood donors with and without elevated serum ALT levels: molecular characterization of viral DNA isolates.

BACKGROUND AND OBJECTIVE: A novel non-enveloped DNA virus, called TT virus (TTV), has been reported to be associated with post-transfusion hepatitis of unknown etiology. Although its clinical role still remains obscure, its presence in blood donations might cause problems. It, therefore, appeared of interest to investigate TTV prevalence in voluntary blood donors. DESIGN AND METHODS: A total of 595 Italian blood donors with and without elevated serum alanine aminotransferase (ALT) levels were tested by polymerase chain reaction using two sets of semi-nested primers that amplify the well-known region in the N22 clone. The amplified products were then sequenced to assess the genotype by phylogenetic and restriction fragment length polymorphism analyses. RESULTS: The prevalence of TTV in blood donors was 5+/-1.9% (25 out of 500) with a 95% confidence limit. A similar prevalence was found in 95 selected blood donors with increased ALT levels. A viral load of 10(3)-10(4) viral DNA molecules/mL was found, thus indicating a rather narrow range of variability. A phylogenetic tree built up on the basis of 210 base sequences of ORF1 allowed isolates to be classified into 2 groups corresponding, at least, to two of the putatives TTV genotypes, group 1 and group 2 of Okamoto's classification. A similar classification was also obtained by site restriction enzyme analysis. INTERPRETATION AND CONCLUSIONS: The results show that TTV infection is present among Italian blood donors. No significant difference in prevalence of TTV infection was found between patients with normal and increased ALT, making the association between TTV infection and human hepatitis questionable.

Adolescent↗
PubMed1974

The presence of unique DNA sequences after viral induction of leukemia in mice. (RNA tumor virus-nucleic acid hybridization-insertion of viral DNA).

From previous studies, lymphocyte DNA from human leukemias and DNA from involved tissues of patients with Hodgkin's disease or Burkitt's lymphoma contain sequences that are absent from their normal counterparts. These sequences are related to those found in particulate elements associated with these neoplasias and possessing biochemical properties characteristic of RNA tumor viruses. Similar observations have been made of unique sequences related to those of the feline virus RD-114 and found in spontaneous mastocytomas in cats. Here we extend these results to the classical murine model of virus-induced leukemias. Splenic DNA from BALB/c mice with leukemia induced by Rauscher leukemia virus (RLV) possess some RLV-related sequences that do not exist in normal BALB/c DNA. Furthermore, these leukemia-specific sequences were absent in all other mouse strains examined, including AKR, a strain with a high incidence of spontaneous leukemia. The DNA of all noninfected mouse strains possesses considerable homology with the RLV genome. Temperature denaturation studies indicate, however, that although the RLV-related sequences found in all normal mice are similar to each other, they are not exactly homologous with RLV sequences. We conclude that RLV-induced leukemia in BALB/c results in the insertion of RLV sequences into cellular DNA that itself possesses only partial homology with the RLV genome.

Animals↗
PubMed1978

Specific labelling of replicating SPP1 DNA: analysis of viral DNA synthesis and identification of phage DNA-genes.

Specific labelling of replicating bacteriophage SPP1 DNA can be achieved by infection at nonpermissive temperature of a B. subtilis strain carrying the initation mutation dnaB ts134. Under these conditions host DNA synthesis is reduced by 90 to 95%. This technique was used to identify cistrons of SPP1 involved in phage DNA synthesis and to define intermediates in SPP1 replication.

Bacillus subtilis↗