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At least 775 records · Page 43Linked to original sources
PubMed1994

Expression of two structurally identical viral superantigens results in thymic elimination at distinct developmental stages.

Mouse mammary tumor virus proviral integrants encode superantigens. Developing thymocytes bearing TCRs with particular V beta elements encounter these endogenous viral superantigens as self molecules in the thymus and are consequently clonally eliminated. To study this mechanism of tolerance induction, we have bred B10.BR-Mtv-1 and B10.BR-Mtv-6 mice, which carry either Mtv-1 or Mtv-6 proviruses but are otherwise genetically identical. The protein products of these mouse mammary tumor virus integrants, vSAG1 and vSAG6, both interact with V beta 3+ T cells and have identical amino acid sequences. Interestingly, vSAG6 expression results in the complete deletion of V beta 3+ peripheral T cells, whereas vSAG1 expression results in only partial deletion. Flow cytometric analyses indicate that B10.BR-Mtv-6 mice delete V beta 3+ thymocytes at the immature CD4+8+ stage, whereas B10.BR-Mtv-1 mice delete only mature CD4+ or CD8+ cells. In addition, the two strains exhibit different time courses of thymic deletion: neonatal B10.BR-Mtv-6 mice eliminate V beta 3+ T cells by day 2, in contrast to B10.BR-Mtv-1 mice in which deletion does not occur until day 15. RNase protection assays demonstrate that B10.BR-Mtv-6 mice have significantly greater thymic vSAG6 mRNA expression levels than vSAG1 levels in B10.BR-Mtv-1 animals, correlating with a more complete deletion of reactive thymocytes at an earlier point in the maturational sequence.

Animals↗
PubMed2006

Visualization of episomal and integrated Epstein-Barr virus DNA by fiber fluorescence in situ hybridization.

For many Epstein-Barr virus (EBV)-associated malignancies, it is still a matter of controversy whether infected cells harbor episomal or chromosomally integrated EBV genomes or both. It is well established that the expression of EBV genes per se carries oncogenic potential, but the discrimination between episomal and integrated forms is of great relevance because integration events can contribute to the oncogenic properties of EBV, whereas host cells that exclusively harbor viral episomes may not carry the risks mediated by chromosomal integration. This notion prompted us to establish a reliable technique that not only allows to unequivocally discriminate episomal from integrated EBV DNA, but also provides detailed insights into the genomic organization of the virus. Here, we show that dynamic molecular combing of host cell DNA combined with fluorescence in situ hybridization (FISH) using EBV-specific DNA probes facilitate unambiguous discrimination of episomal from integrated viral DNA. Furthermore, the detection of highly elongated internal repeat 1 (IR1) sequences provides evidence that this method permits detection of major genomic alterations within the EBV genome. Thus, fiber FISH may also provide valuable insights into the genomic organization of viral genomes other than EBV.

Burkitt Lymphoma↗
PubMed1993

Human immunodeficiency virus type 1 DNA integration: fine structure target analysis using synthetic oligonucleotides.

The target specificity of DNA strand transfer mediated by human immunodeficiency virus type 1 integrase was examined in vitro with synthetic oligonucleotides. Although insertion occurred at most locations in the target, some sites were preferred over others by at least 15-fold. Changing the nucleotide sequence of the target changed the distribution of preferred sites in complex ways, some of which included changes in target preference distant from the sequence alteration. Alignment of target sequences revealed that adenosine is preferred adjacent to the insertion site. Strand transfer occurred to within 2 nucleotides of the 3' end and to within 3 nucleotides of the 5' end of the target. This suggests that only 2 or 3 nucleotides flanking the target site are required for integration; such restricted contact with target DNA would allow integrase to insert the two ends of viral DNA into two closely spaced sites in host DNA, consistent with the concerted in vivo integration reaction that generates a 5-bp target duplication.

Base Sequence↗
PubMed1999

Adeno-associated virus (AAV) site-specific integration: formation of AAV-AAVS1 junctions in an in vitro system.

An in vitro system to study the mechanism of site-specific integration of adeno-associated virus (AAV) was developed. This system is based on two substrates, a linear or circular AAV donor and a circular acceptor containing the preintegration locus AAVS1. In the presence of HeLa extract and the His-Tag-purified Rep68 protein, specific covalent junctions between AAV and AAVS1 were formed and detected by PCR. The majority of the junctions were located within the Rep binding site of both the AAV and the AAVS1 substrates, underlining the involvement of the Rep protein. A limited amount of replication and the presence of nuclear factors promoted the efficiency of the reaction. The process was ATP-dependent, indicating that the helicase activity of Rep may be important in the formation of the junctions. According to current models of integration, the formation of the junctions would represent a first step in the process of AAV integration. This step could be crucial for the site specificity of the recombination event that leads to the integration of AAV into human chromosome 19 in vivo.

Base Sequence↗
PubMed1980

Synthesis and integration of avian sarcoma virus DNA.

In this paper, we have presented data regarding the integration of viral DNA and the persistence of unintegrated viral DNA. We know that integration occurs with specificity with respect to the viral genome, and yet it remains to be established which, if any, of the unintegrated DS DNA species-either the linear or the covalently closed circular forms-is the immediate precursor to the DNA that does become integrated. The results of the present studies indicate that the viral DNA species that are able to persist in an unintegrated state may be transcribed to yield new virions. Furthermore, these species may not be intermediates as far as the integration pathway, but may instead be terminal products of a synthesis reaction that has proceeded beyond the point where integration normally occurs. Varmus et al. (1977) have shown that integration occurs only into newly replicated cellular DNA. Therefore, we would speculate that integration may occur by an interaction between a replication fork of the host cell DNA and an earlier, non-double-strand form of viral DNA.

Alpharetrovirus↗
PubMed1990

Analysis of mutations in the integration function of Moloney murine leukemia virus: effects on DNA binding and cutting.

The 3' terminus of the pol gene of Moloney murine leukemia virus encodes the integration (IN) protein, required for the establishment of the integrated provirus. A series of six linker insertion mutations and two single-base substitutions were generated within the region encoding the IN protein. Mutations were initially generated within an Escherichia coli plasmid expressing the IN protein, and the resulting variants were assayed for DNA-binding activity. Mutations which altered conserved cysteine residues within a potential DNA finger-binding motif resulted in lower or variable DNA binding, which appeared to be the result of variable protein folding. Upon renaturation, these proteins were able to nonspecifically bind DNA in a manner similar to that of the other mutant IN proteins and the parent. When reconstructed back into full-length virus, seven of the eight mutations were lethal. All mutants produced a stable IN protein in virions and mediated normal conversion of the retroviral RNA to its three DNA forms. Fine-structure analysis of the linear double-stranded viral DNA indicated that all seven lethal alterations within the IN protein blocked the formation of the 3' recessed termini that normally precedes integration.

Amino Acid Sequence↗
PubMed1990

Integration of hepatitis B virus DNA into cells of six established human hepatocellular carcinoma cell lines.

The authors successfully established 5 hepatocellular carcinoma cell lines, JHH-1, 2, 4, 5 and 6, derived from hepatitis B surface antigen seronegative patients and one line. JHH-7, from a patient considered to be a hepatitis B virus carrier. In the culture media of any of the JHH cell lines, including JHH-7, hepatitis B surface antigen was not detected by radioimmunoassay. However, in JHH-7, integration of hepatitis B virus DNA was confirmed at two sites on the chromosomes of this line by Southern blot hybridization. In contrast, in other JHH cell lines derived from hepatitis B surface antigen seronegative patients, integration of hepatitis B virus DNA into the chromosomes of cells was not detected. These cell lines will be useful in the investigation of hepatocellular carcinoma development, especially for research into non-A/non-B hepatitis viruses.

Albumins↗
PubMedDate not supplied

[Insertion mutants of the vaccinia virus. The effect of inactivating E7R and D8L genes on the biological properties of the virus].

The integrative plasmids with the expressive marker gene for beta-galactosidase were constructed for insertional inactivation of nonessential genes E7R and D8L of vaccinia virus located in the central region of the viral genome. Inactivation of the D8L gene in the strains WR and LIVP results in smaller viral plaques in the culture of chicken embryo cells, decreases the viral ability to propagate in mouse brain and has no effect on the size and character of damage in intracutaneous infection of rabbits. Inactivation of E7R gene did not affect the known biological properties of the virus. The existence of the nonessential genes in the central region of the viral genome, inactivation of which does not result in viral attenuation, can be used for increase of antigenic activity of the live attenuated vaccines.

Animals↗
PubMed1995

Different roles of bases within the integration signal sequence of human immunodeficiency virus type 1 in vitro.

To investigate the roles of bases near the tips of each strand of the long terminal repeat of the human immunodeficiency virus type 1 in the integration reaction, we examined the efficiencies of both binding and integration activities of staggered-ended substrates and mismatched mutant substrates by the integration assay and the UV cross-linking assay. Our results suggest that some bases of the human immunodeficiency virus type 1 long terminal repeat are required primarily for binding, whereas others are more critical for later reaction steps in vitro.

Base Sequence↗
PubMed1990

Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro.

Normal replication of Moloney murine leukemia virus (MoMLV) requires the integration of a DNA copy of the viral RNA genome into a chromosome of the host. In this work, we characterize the DNA sequences at the ends of the linear proviral precursor that are required for integration in the presence of MoMLV integration protein in vitro. We found that nine bases of MoMLV DNA at each end of a linear model substrate were sufficient for near-maximal levels of integration and that four bases of MoMLV DNA at each end were sufficient for low levels of correct integration. We also found that a 3'-terminal A residue was preferred for integration. We infer from the limited DNA sequence requirements for integration that factors in addition to DNA sequence direct integration protein to act at the ends of the viral DNA.

Base Sequence↗
PubMed2026

Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.

BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan. RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts. CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.

Animals↗
PubMed1985

Integration of spleen focus-forming virus proviruses in Friend tumor cells.

Using the Southern blot procedure, we studied the presumed spleen focus-forming virus (SFFV) provirus integration sites in the genome of the premalignant and the malignant cells isolated during the course of Friend erythroleukemia. Two restriction endonucleases, PstI and BamHI, discriminated the presumed integrated SFFV proviruses from the endogenous xenotropic-mink cell focus-forming viral sequences. No SFFV integration sites were detectable in the premalignant cells, suggesting a random integration of SFFV proviruses in the genome of these cells. In contrast, SFFV proviruses were detected at a single or very few sites in the genome of all malignant cells we analyzed. These results indicate that the event leading to the malignant transformation in acute Friend leukemia is clonal. In two of the six animals examined, tumors cells isolated from the spleens and the livers of individual mice showed identical SFFV integration patterns. This last result suggests that in some cases different tumors in a same leukemic animal could be derived from a unique clonal event.

Animals↗
PubMed2003

Molecular and genetic determinants of rous sarcoma virus integrase for concerted DNA integration.

Site-directed mutagenesis of recombinant Rous sarcoma virus (RSV) integrase (IN) allowed us to gain insights into the protein-protein and protein-DNA interactions involved in reconstituted IN-viral DNA complexes capable of efficient concerted DNA integration (termed full-site). At 4 nM IN, wild-type (wt) RSV IN incorporates approximately 30% of the input donor into full-site integration products after 10 min of incubation at 37 degrees C, which is equivalent to isolated retrovirus preintegration complexes for full-site integration activity. DNase I protection analysis demonstrated that wt IN was able to protect the viral DNA ends, mapping approximately 20 bp from the end. We had previously mapped the replication capabilities of several RSV IN mutants (A48P and P115S) which appeared to affect viral DNA integration in vivo. Surprisingly, recombinant RSV A48P IN retained wt IN properties even though the virus carrying this mutation had significantly reduced integrated viral DNA in comparison to wt viral DNA in virus-infected cells. Recombinant RSV P115S IN also displayed all of the properties of wt RSV IN. Upon heating of dimeric P115S IN in solution at 57 degrees C, it became apparent that the mutation in the catalytic core of RSV IN exhibited the same thermolabile properties for 3' OH processing and strand transfer (half-site and full-site integration) activities consistent with the observed temperature-sensitive defect for integration in vivo. The average half-life for inactivation of the three activities were similar, ranging from 1.6 to 1.9 min independent of the IN concentrations in the assay mixtures. Wt IN was stable under the same heat treatment. DNase I protection analysis of several conservative and nonconservative substitutions at W233 (a highly conserved residue of the retrovirus C-terminal domain) suggests that this region is involved in protein-DNA interactions at the viral DNA attachment site. Our data suggest that the use of recombinant RSV IN to investigate efficient full-site integration in vitro with reference to integration in vivo is promising.

Amino Acid Sequence↗
PubMed1985

Screening for amplification of specific DNA sequences in cultured mammalian cells.

Carcinogen- or herpes virus-induced amplification of integrated simian virus 40 DNA in transformed cell lines has been demonstrated previously by Southern blot analyses, dot hybridizations, and dispersed cell assays. Although these methods are quite reliable, large series of experiments require a considerable amount of time and effort. Therefore, an alternative method has been developed that allows one to carry out great numbers of separate gene-amplification experiments in the 96 wells of microtiter plates and to analyze the DNAs of the treated cells simultaneously after "replica blotting" onto membrane filters by hybridization with a cloned DNA probe.

Animals↗
PubMed1988

A beneficial effect of trypsin on the purification of turnip mosaic virus (TuMV) and other potyviruses.

The effects of treatment with trypsin during the purification of turnip mosaic virus (TuMV), on virus yield, infectivity and integrity of virus coat protein were examined. Trypsin increased yield markedly, and at a low concentration, increased infectivity. These effects were probably due to reduced aggregation of virus particles. At higher concentrations of trypsin, there was some degradation of virus coat protein, and infectivity was reduced. Treatment with trypsin at the optimum concentration can significantly improve purification of TuMV; more limited experiments suggest that it can also be applied to other potyviruses.

Capsid↗
PubMed1984

A mouse DNA sequence that mediates integration and excision of polyoma virus DNA.

In mouse cells transformed by a temperature-sensitive polyoma virus (Py) genome, the integrated viral genome recombines with adjacent chromosomal DNA to yield a small cyclic molecule (RmI) with defined viral and cellular components. We have cloned the cellular component (Ins), determined its sequence, and examined its distribution in normal mouse DNA. The sequence of Ins displays several homologies with that surrounding the replication origin (ori) of Py or SV40 DNA.

Animals↗
PubMed1991

The human homolog of the mouse common viral integration region, FLI1, maps to 11q23-q24.

FLI1 is a common mouse viral integration region in virus-induced leukemias and lymphomas. Using an evolutionarily conserved mouse probe and Southern hybridization to (rodent x human) somatic cell hybrid DNAs, the human homolog of FLI1 has been shown to lie on a fragment of chromosome 11 flanked on the centromeric side by the acute lymphoblastic leukemia-associated t(4;11)(q21;q23) translocation breakpoint and on the telomeric side by the Ewing- and neuroepithelioma-associated t(11;22) (q24;q12) breakpoint.

Animals↗
PubMed1990

Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma.

Loss of heterozygosity on chromosome 16 is a common genetic alteration in human hepatocellular carcinoma (HCC). To clarify the pathogenetic significance of allele loss on chromosome 16, we performed restriction fragment length polymorphism analysis of 70 surgically resected tumors by using 15 polymorphic DNA markers for chromosome 16. Loss of heterozygosity on chromosome 16 was detected in 36 (52%) of 69 informative cases, and the common region of allele loss in these 36 tumors was located between the HP locus (16q22.1) and the CTRB locus (16q22.3-q23.2). These losses occurred more frequently in HCCs of poor differentiation, of larger size, and with metastasis, whereas they were not detected in HCC at the earliest stage. In addition, these losses were not associated with presence or absence of hepatitis B virus DNA integration or hepatitis C virus infection. These results show that loss of heterozygosity on chromosome 16 is a late event occurring after hepatocarcinogenesis and strongly suggest that this phenomenon is involved in enhancement of tumor aggressiveness during progression of HCC.

Alleles↗