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At least 1,171 records · Page 65Linked to original sources
PubMed1989

Organization of adeno-associated virus DNA in latently infected Detroit 6 cells.

The DNA of a human dependovirus, adeno-associated virus (AAV), integrates into the cellular genome under conditions nonpermissive for viral DNA replication. The AAV DNA can be rescued from the cellular genome by superinfection with a helper virus, e.g., adenovirus. To characterize the organization of the proviral DNA in greater detail, we isolated three proviral subfragments from a latently infected human cell line. Our findings, based on sequence analysis, restriction enzyme mapping, and genomic blots, demonstrate that the viral terminal repeats (trs) are present at or near the cellular/viral DNA junctions, but significant deletions of the tr sequences have occurred. One of the proviral clones has extensive rearrangements which apparently occurred by nonhomologous recombination. The tail-to-tail arrangement of one of the proviral clones is consistent with limited DNA replication prior to integration by a mechanism similar to that seen in a productive infection. Although there are BamH1 fragments in the cell line we have characterized, which are the right size to have come from a head-to-tail tandem repeat, critical double digests show no evidence for the presence of a head-to-tail tandem repeat of wild-type proviral DNA. Use of probes derived from the flanking cellular DNA enabled us to determine that in this cell line the viral DNA had integrated into a site composed of nonrepetitive sequences.

Base Sequence↗
PubMed1992

Simian virus 40 minichromosomes as targets for retroviral integration in vivo.

We present a method for studying multiple retroviral integration events into a small DNA target in vivo. Episomal simian virus 40 (SV40) genomes established by infection of CV-1 cells served as integration targets during subsequent infection with murine leukemia virus (MLV). Using a PCR-based assay for the abundance and distribution of integration events, nonrandom integration of MLV DNA into SV40 DNA is detectable as early as 4 hr and reaches a maximum level by 8 hr after MLV infection. The level of integration but not the distribution of integration sites is sensitive to the stage in the SV40 life cycle at which MLV infection is performed. Using a temperature-sensitive tumor (T) antigen mutant SV40 strain, we observed that active replication of the target DNA is not required for efficient integration in vivo. The distribution of integration sites in vivo is closely approximately by in vitro reactions with isolated SV40 minichromosomes as integration targets. However, the degree of bias between the most and least favored sites is greater in vivo than in vitro.

Animals↗
PubMed1994

Retrovirus insertion into herpesviruses.

Recent studies have indicated that retroviruses can integrate into and mutate the genomes of herpesviruses during co-infection. This interaction has the potential to change the host range and pathogenicity of both viruses and result in novel infectious agents and diseases. This phenomenon also allows genetic material to be exchanged between these viruses and their hosts.

Animals↗
PubMed1995

A novel suicide substrate for DNA topoisomerases and site-specific recombinases.

DNA topoisomerases and DNA site-specific recombinases are biologically important enzymes involved in a diverse set of cellular processes. We show that replacement of a phosphodiester linkage by a 5'-bridging phosphorothioate linkage creates an efficient suicide substrate for calf thymus topoisomerase I and lambda integrase protein (Int). Although the bridging phosphorothioate linkage is cleaved by these enzymes, the 5'-sulfhydryl which is generated is not competent for subsequent ligation reactions. We use the irreversibility of Int-promoted cleavage to explore conditions and factors that contribute to various steps of lambda integrative recombination. The phosphorothioate substrates offer advantages over conventional suicide substrates, may be potent tools for inhibition of the relevant cellular enzymes and represent a unique tool for the study of many other phosphoryl transfer reactions.

Animals↗
PubMed2006

Assessment of the integral membrane protein topology in living cells.

The bimolecular fluorescence complementation (BiFC) phenomenon has been successfully applied for in vivo protein-protein interaction studies and protein tagging analysis. Here we report a novel BiFC-based technique for investigation of integral membrane protein topology in living plant cells. This technique relies on the formation of a fluorescent complex between a non-fluorescent fragment of the yellow fluorescent protein (YFP) targeted into a specific cellular compartment and a counterpart fragment attached to the integral membrane protein N- or C-terminus or inserted into the internal loop(s). We employed this technique for topological studies of beet yellows virus-encoded p6 membrane-embedded movement protein, a protein with known topology, and the potato mop-top virus-encoded integral membrane TGBp2 protein with predicted topology. The results confirm that p6 is a type III integral transmembrane protein. Using a novel method, the central hydrophilic region of TGBp2 was localized into the ER lumen, whereas the N- and C-termini localized to the cytosol. We conclude that the BiFC-based reporter system for membrane protein topology analysis is a relatively fast and efficient method that can be used for high-throughput analysis of proteins integrated into the endoplasmic reticulum in living plant cells.

Endoplasmic Reticulum↗
PubMed1997

Integration specificities of two lambdoid phages (21 and e14) that insert at the same attB site.

It was shown previously that phage 21 and the defective element e14 integrate at the same site within the icd gene of Escherichia coli K-12 but that 21 integrase and excisionase excise e14 in vivo very infrequently compared to excision of 21. We show here that the reverse is also true: e14 excises itself much better than it excises an adjacent 21 prophage. In vitro integrase assays with various attP substrates delimit the minimal attP site as somewhere between 366 and 418 bp, where the outer limits would include the outermost repeated dodecamers suggested as arm recognition sites by S. J. Schneider (Ph.D. dissertation, Stanford University, Stanford, Calif., 1992). We speculate that the reason 21 attP is larger than lambda attP (240 bp) is because it must include a 209-bp sequence homologous to the 3' end of the icd transcript in order to allow icd expression in lysogens. Alteration of portions of 21 attP to their e14 counterparts shows that 21 requires both the arm site and core site sequences of 21 but that replacements by e14 sequences function in some positions. Consistent with Schneider's in vivo results, and like all other known integrases from lambdoid phages, 21 requires integration host factor for activity.

Bacterial Proteins↗
PubMed1977

[Oncogenic virus induction by halogenated pyrimidines (author's transl)].

Oncongenic DNA and RNA Viruses are integrated into the cell genome of vertebrates. Physical, chemical and biological agents, among them the halogenated pyrimidines ododeoxyuridine (IdU) and bromodeoxyuridine (BdU) cause the induction of these viruses in cells of many species. In this review the action of IdU and BdU in certain cell differentiation systems chondrogenesis, myogenesis and others) and on activation of oncogenic viruses, first of all of type C-RNA viruses, is described and some possible mechanisms of induction are discussed.

Animals↗
PubMed2006

Evaluation of immune effects of fowlpox vaccine strains and field isolates.

The immune effects of fowlpox virus (FPV) field isolates and vaccine strains were evaluated in chickens infected at the age of 1 day and 6 weeks. The field isolates and the obsolete vaccine strain (FPV S) contained integrated reticuloendotheliosis virus (REV) provirus, while the current vaccine strain (FPVST) carries only REV LTR sequences. An indirect antibody ELISA was used to measure the FPV-specific antibody response. The non-specific humoral response was evaluated by injection of two T-cell-dependent antigens, sheep red blood cells (SRBC) and bovine serum albumin (BSA). There was no significant difference in the antibody response to FPV between chickens infected with FPV various isolates and strains at either age. In contrast, antibody responses to both SRBC and BSA were significantly lower in 1-day-old chickens inoculated with field isolates and FPV S at 2-3 weeks post-inoculation. Furthermore, cell-mediated immune (CMI) responses measured by in vitro lymphocyte proliferation assay and in vivo using a PHA-P skin test were significantly depressed in chickens inoculated with field isolates and FPV S at the same periods. In addition, thymus and bursal weights were lower in infected chickens. These immunosuppressive effects were not observed in chickens inoculated with the current vaccine strain, FPVST, at any time. The results of this study suggest that virulent field isolates and FPV S have immunosuppressive effects when inoculated into young chickens, which appeared in the first 3 weeks post infection. REV integrated in the FPV field isolates and FPV S may have played a central role in the development of immunosuppression.

Animals↗
PubMed1998

The regional integration of retroviral sequences into the mosaic genomes of mammals.

We have reviewed here three sets of data concerning the integration of retroviral sequences in the mammalian genome: (i) our experimental localization of a number of proviruses integrated in isochores characterized by different GC levels; (ii) results from other laboratories on the localization of retroviral sequences in open chromatin regions and/or next to CpG islands; and (iii) our compositional analysis of genes located in the neighborhood of integrated retroviral sequences. The three sets of data have provided a very consistent picture in that a compartmentalized, isopycnic integration of expressed proviruses appears to be the rule ('isopycnic' refers to the compositional match between viral and host sequences around the integration site). The results reviewed here suggest that: (i) integration of proviral sequences is targeted initially towards 'open chromatin regions'; while these exist in both GC-rich and GC-poor isochores, the 'open chromatin regions' of GC-rich isochores are the main targets for integration of retroviral sequences because of their much greater abundance; (ii) isopycnicity is associated with stability of integration; indeed, even non-expressed integrated retroviral sequences tend to show an isopycnic localization in the genome; (iii) transcription of integrated viral sequences (like transcription of host genes) appears to be associated, as a rule, with an isopycnic localization, as indicated by transcribed sequences that show an isopycnic integration and act in trans; (iv) selection plays a role in the choice of specific sites within an isopycnic region; in exceptional cases [such as mouse mammary tumor virus (MMTV) activating GC-rich oncogenes], selection may override isopycnicity.

Animals↗
PubMed1996

Human immunodeficiency virus type-1 Tat is an integral component of the activated transcription-elongation complex.

The human immunodeficiency virus type 1 transactivator protein, Tat, stimulates transcriptional elongation from the viral long terminal repeat. To test whether Tat associates directly with activated transcription complexes, we have used the lac repressor protein (LacR) to "trap" elongating RNA polymerases. The arrested transcription complexes were purified by binding biotinylated templates to streptaviridin-coated magnetic beads. Transcription complexes were released from the magnetic beads following cleavage of the templates with restriction enzymes and were immunoblotted with antibodies to Tat, LacR and RNA polymerase II. The Tat protein copurified with RNA polymerase bound to wild-type templates but did not copurify with transcription complexes prepared by using templates carrying mutations in the transactivation response element (TAR) RNA. We conclude that Tat and cellular cofactors become attached to the transcription complex during its transit through TAR.

Base Sequence↗
PubMed1988

Pausing in simian virus 40 DNA replication by a sequence containing (dG-dA)27.(dT-dC)27.

A 200 bp sequence including a stretch of 54 base pairs of alternating guanosine and adenosine nucleotide residues [(dG-dA)27.(dT-dC)27] was cloned in the simian virus 40 (SV40) genome between the KpnI and HpaII sites. This sequence was discovered earlier as part of a region limiting the amplification of sequences adjacent to an integrated polyoma virus in a transformed rat cell line. The newly constructed DNA was transfected into African Green monkey kidney CV1 cells and the variant virus was isolated by plaque-purification. The insertion was stably maintained and the variant virus grew more slowly than the wild type, had lower titers and gave smaller plaques. In mixed infection experiments, the variant was found to be stable, though the wild type replicated more rapidly. Pulse labeling experiments indicated that the unusual inserted sequence acts as a pause site for fork progression during DNA replication, as evidenced by the rate of incorporation of radioactively labeled nucleotides into various regions of the SV40 genome. Statistical fit of the experimental curves with theoretically generated curves suggested the pause of fork progression to be about one minute.

Animals↗
PubMed1997

Efficient recovery and regeneration of integrated retroviruses.

We report a rapid and efficient PCR-based rescue procedure for integrated recombinant retroviruses. Full-length proviral DNA is amplified by long-range PCR using a pair of primers derived from the long terminal repeats (LTR), and virus is regenerated by transfecting retrovirus-packaging cells with the PCR-derived provirus. The viral yield from the PCR product is similar to that from the retroviral plasmid vector, and the representation of different inserts is accurately maintained in the recovered retroviral population. This procedure is suitable for expression cloning from retroviral libraries and should be applicable to the analysis of natural retrovirus populations.

Cloning, Molecular↗
PubMed2004

Unusually long target site duplications flanking some of the long terminal repeats of human endogenous retrovirus K in the human genome.

Human endogenous retroviruses (HERVs) make up a substantial part of the human genome. HERVs and solitary long terminal repeats (solo LTRs) are usually flanked by 4-6 nt short direct repeats through the well-known mechanism of their integration. A number of solo LTRs flanked by unusually long direct repeats were detected in the human genome. These unusual structures might be a product of an alternative virus insertion mechanism.

Endogenous Retroviruses↗