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At least 1,153 records · Page 64Linked to original sources
PubMed1996

Two types of defective human T-lymphotropic virus type I provirus in adult T-cell leukemia.

Adult T-cell leukemia (ATL), an aggressive neoplasm of mature helper T cells, is etiologically linked with human T lymphotropic virus type I (HTLV-1). After infection, HTLV-I randomly integrates its provirus into chromosomal DNA. Since ATL is the clonal proliferation of HTLV-I-infected T lymphocytes, molecular methods facilitate the detection of clonal integration of HTLV-I provirus in ATL cells. Using Southern blot analyses and long polymerase chain reaction (PCR) we examined HTLV-I provirus in 72 cases of ATL, of various clinical subtypes. Southern blot analyses revealed that ATL cells in 18 cases had only one long terminal repeat (LTR). Long PCR with LTR primers showed bands shorter than for the complete virus (7.7 kb) or no bands in ATL cells with defective virus. Thus, defective virus was evident in 40 of 72 cases (56%). Two types of defective virus were identified: the first type (type 1) defective virus retained both LTRs and lacked internal sequences, which were mainly the 5' region of provirus, such as gag and pol. Type 1 defective virus was found in 43% of all defective viruses. The second form (type 2) of defective virus had only one LTR, and 5'-LTR was preferentially deleted. This type of defective virus was more frequently detected in cases of acute and lymphoma-type ATL (21/54 cases) than in the chronic type (1/18 cases). The high frequency of this defective virus in the aggressive form of ATL suggests that it may be caused by the genetic instability of HTLV-I provirus, and cells with this defective virus are selected because they escape from immune surveillance systems.

Adult↗
PubMed2002

A 5.9-kb tandem repeat at the euchromatin-heterochromatin boundary of the X chromosome of Drosophila melanogaster.

We present an analysis of a chromosomal walk in the region of the euchromatin-heterochromatin transition at the base of the X chromosome of Drosophila melanogaster. This region is difficult to analyse because of the presence of repeated sequences, and we have used cosmids to walk from the last euchromatic gene, suppressor of forked, towards the pericentric heterochromatin. The proximal 30-kb sequence we have isolated consists of repetitive DNA, including four tandem copies of a 5.9-kb sequence. This tandem repeat is itself a mosaic of other, mostly repeated, sequences, including part of a retrotransposon without long terminal repeats, a simple-sequence region of TAA repeats and part of a retrotransposon with long terminal repeats that has not been previously described. Although sequences homologous to these components are found elsewhere in the genome, this arrangement of repeated sequences is only found at the base of the X chromosome. It is conserved in D. melanogaster strains of different geographic origin, but is not conserved in even closely related species.

Animals↗
PubMed1991

Nucleotide sequence analysis of the unusually long terminal inverted repeats of a giant linear plasmid, SCP1.

SCP1 is a giant linear plasmid of 350 kb coding for the methylenomycin biosynthetic genes in Streptomyces coelicolor. The unusually long terminal inverted repeats present on both ends of SCP1 were analyzed on the nucleotide sequence level. Analysis of six clones containing the terminal 0.35-kb XbaI fragment revealed a slight heterogeneity in the nucleotide sequences of the SCP1 ends. Moreover, it was indicated that this fragment contained seven palindromic inverted repeats and a GT-rich region in the 5'-end strand. The size of the terminal inverted repeats was determined to be 81 kb by the cloning and sequencing of their end-points. An insertion sequence, IS466 was shown to be present just at the end of the right terminal inverted repeat.

Anti-Bacterial Agents↗
PubMed1981

Structure of the baboon endogenous virus genome: cloning of circular virus DNA in bacteriophage lambda.

Linear, small and large circular forms of unintegrated viral DNAs were detected in Hirt supernatant fraction of human cultured cells infected with baboon endogenous virus M7. The circular M7 DNAs were cloned in bacteriophage lambda, Charon 28. Seventeen independent clones were isolated and analyzed by restriction endonuclease mapping. Nine clones were carrying a viral sequence of 8.6 kilobase pairs (kb) with two tandem repeats of 0.6 kb, which correspond to the large circular form of the unintegrated M7 DNA. Eight other clones had the viral insert of 8.0 kb, i. e., the small circular form, and were deleted one of the repeated sequences. The repeated sequences correspond to the long terminal repeats of 0.6 kb, located at both ends of the linear M7 DNA of 8.6 kb. One of the recombinants of the large circular M7 DNA had an inversion of 2.5 kb. One end of the inverted sequence was near the terminus of the long terminal repeats and the other in the gag gene region. The inversion seems to be occurred by integration of a viral DNA within itself during early periods of infection. The mechanism of the processes leading to integration is discussed from the structure of these unintegrated M7 DNAs as the precursors.

Bacteriophage lambda↗
PubMed1983

Molecular cloning of the unintegrated squirrel monkey retrovirus genome: organization and distribution of related sequences in primate DNAs.

The closed circular form of the endogenous squirrel monkey type D retrovirus (SMRV) was molecularly cloned in a bacteriophage vector. The restriction map of the biologically active clone was determined and found to be identical to that of the parental SMRV linear DNA except for the deletion of one long terminal repeat. Restriction enzyme analysis and Southern blotting indicated that the SMRV long terminal repeat was approximately 300 base pairs long. The SMRV restriction map was oriented to the viral RNA by using a gene-specific probe from baboon endogenous virus. Restriction enzyme digests of a variety of vertebrate DNAs were analyzed for DNA sequence homology with SMRV by using the cloned SMRV genome as a probe. Consistent with earlier studies, multiple copies of SMRV were detected in squirrel monkey DNA. Related fragments were also detected in the DNAs from other primate species, including humans.

Animals↗
PubMed1983

Retrovirus transduction: generation of infectious retroviruses expressing dominant and selectable genes is associated with in vivo recombination and deletion events.

We describe the generation of infectious retroviruses containing foreign genes by an in vivo recombination-deletion mechanism. Cotransfection into mouse cells of chimeric plasmids carrying a murine retrovirus 5' long terminal repeat and either the thymidine kinase (tk) gene of herpesvirus or the dominant selectable bacterial gene for neomycin resistance (neo), along with a clone of Moloney murine leukemia virus, results in the generation of infectious thymidine kinase or neomycin-resistant viruses. Expression of the selectable marker in these viruses can be regulated by the homologous transcriptional promoter of the gene, by the promoter contained within the Friend spleen focus-forming virus long terminal repeat, or by the simian virus 40 early region promoter. In all cases, the rescued viruses appeared to arise by recombination in vivo with Moloney murine leukemia virus sequences, resulting in the acquisition of the Moloney 3' long terminal repeat and variable amounts of the 3' adjacent Moloney genome. In two of the thymidine kinase constructs where tk was inserted 200 base pairs downstream from the long terminal repeat, the rescued viruses acquired a large part of the murine leukemia virus genome, including the region involved in packaging genomic RNA into virions. The generation of infectious neomycin-resistant virus is associated with deletions of simian virus 40 splicing and polyadenylation sequences. These results demonstrate that nonhomologous recombination and deletion events can take place in animal cells, resulting in the acquisition or removal of cis-acting sequences required for, or inhibitory to, retrovirus infectivity.

Adenine Phosphoribosyltransferase↗
PubMed2001

Reporter gene expression in fish following cutaneous infection with pantropic retroviral vectors.

A central issue in gene delivery systems is choosing promoters that will direct defined and sustainable levels of gene expression. Pantropic retroviral vectors provide a means to insert genes into either somatic or germline cells. In this study, we focused on somatic cell infection by evaluating the activity of 3 promoters inserted by vectors into fish cell lines and fish skin using pantropic retroviruses. In bluegill and zebrafish cell lines, the highest levels of luciferase expression were observed from the 5' murine leukemia virus long terminal repeat of the retroviral vector. The Rous sarcoma virus long terminal repeat and cytomegalovirus early promoter, as internal promoters, generated lower levels of luciferase. Luciferase reporter vectors infected zebrafish skin, as measured by the presence of viral DNA, and expressed luciferase. We infected developing walleye dermal sarcomas with retroviral vectors to provide an environment with enhanced cell proliferation, a condition necessary for integration of the provirus into the host genome. We demonstrated a 4-fold to 7-fold increase in luciferase gene expression in tumor tissue over infections in normal walleye skin.

Journal Article↗
PubMed1994

Defective endogenous proviruses are expressed in feline lymphoid cells: evidence for a role in natural resistance to subgroup B feline leukemia viruses.

Endogenous feline leukemia virus (FeLV)-related sequences (enFeLV) are a family of proviral elements found in domestic cats and their close relatives. These elements can recombine with exogenous, infectious FeLVs of subgroup A (FeLV-A), giving rise to host range variants of FeLV-B. We found that a subset of defective enFeLV proviruses is highly expressed in lymphoma cell lines and in a variety of primary tissues, including lymphoid tissues from healthy specific-pathogen-free cats. At least two RNA species were detected, a 4.5-kb RNA containing gag, env, and long terminal repeat sequences and a 2-kb RNA containing env and long terminal repeat sequences. Cloning of enFeLV cDNA from two FeLV-free lymphoma cell lines (3201 and MCC) revealed a long open reading frame (ORF) encoding a truncated env gene product corresponding to the N-terminal portion of gp70env. Interestingly, all of three natural FeLV-B isolates include 3' env sequences which are missing from the highly transcribed subset and hence must be derived from other enFeLV elements. The enFeLV env ORF cDNA clones were closely similar to a previously characterized enFeLV provirus, CFE-16, but were polymorphic at a site corresponding to an exogenous FeLV neutralization epitope. Site-specific antiserum raised to a C-terminal 30-amino-acid peptide of the enFeLV env ORF detected an intracellular product of 35 kDa which was also shed from cells in stable form. Expression of the 35-kDa protein correlated with enFeLV RNA levels and was negatively correlated with susceptibility to infection with FeLV-B. Cell culture supernatant containing the 35-kDa protein specifically blocked infection of permissive fibroblast cells with FeLV-B isolates. We suggest that the truncated env protein mediates resistance by receptor blockade and that this form of enFeLV expression mediates the natural resistance of cats to infection with FeLV-B in the absence of FeLV-A.

Animals↗
PubMed2003

A long terminal repeat-containing retrotransposon of Schizosaccharomyces pombe expresses a Gag-like protein that assembles into virus-like particles which mediate reverse transcription.

The Tf1 element of Schizosaccharomyces pombe is a long terminal repeat-containing retrotransposon that encodes functional protease, reverse transcriptase, and integrase proteins. Although these proteins are known to be necessary for protein processing, reverse transcription, and integration, respectively, the function of the protein thought to be Gag has not been determined. We present here the first electron microscopy of Tf1 particles. We tested whether the putative Gag of Tf1 was required for particle formation, packaging of RNA, and reverse transcription. We generated deletions of 10 amino acids in each of the four hydrophilic domains of the protein and found that all four mutations reduced transposition activity. The N-terminal deletion removed a nuclear localization signal and inhibited nuclear import of the transposon. The two mutations in the center of Gag destabilized the protein and resulted in no virus-like particles. The C-terminal deletion caused a defect in RNA packaging and, as a result, low levels of cDNA. The electron microscopy of cells expressing a truncated Tf1 showed that Gag alone was sufficient for the formation of virus-like particles. Taken together, these results indicate that Tf1 encodes a Gag protein that is a functional equivalent of the Gag proteins of retroviruses.

Amino Acid Sequence↗
PubMed1984

Expression of xenotropic-like env RNA sequences in normal DBA/2 and NZB mouse tissues.

Using a DNA probe prepared from cloned env gene sequences of Friend spleen focus-forming viruses, we detected the differential expression of multiple RNA species in uninfected DBA/2 fibroblasts and in various tissues from adult DBA/2 and NZB mice. The size of the major RNA species detected was estimated to be 24S . The 24S RNA species was enriched in polyadenylate-selected preparations and thus may represent a message for endogenous viral envelope glycoproteins. The viral origin of the 24S RNA was further characterized by its hybridization to DNA probes containing the long terminal repeats of Harvey murine sarcoma virus, mouse mammary tumor virus, or the U3 region of an endogenous xenotropic virus. Although the env-related 24S RNA failed to react with either Harvey murine sarcoma virus or mouse mammary tumor virus long terminal repeat probes, it hybridized well with the xenotropic virus long terminal repeat probe. Therefore, it is likely that the RNA detected with the Friend spleen focus-forming virus env probe reflects transcription of xenotropic envelope sequences in uninfected tissues. Our finding that the level of 24S RNA varied in different organs indicated some tissue specificity in the expression of these xenotropic-like env proteins.

Animals↗
PubMed2000

Cutting edge: activation of HIV-1 transcription by the MHC class II transactivator.

Both macrophages and activated CD4+ T cells can be productively infected by HIV-1, and both cell types express MHC class II molecules. Expression of MHC class II proteins in these cells is regulated by a specific transcriptional coactivator, the class II transactivator (CIITA). In this study, we report for the first time that CIITA expression profoundly influences HIV-1 replication. Stable expression of CIITA in Jurkat cells markedly increased 1) HIV-1 replication as assessed by the p24 Ag production and 2) luciferase expression after transfection with full-length provirus or long terminal repeat constructs. Similarly, transient expression of CIITA increased provirus expression as well as long terminal repeat promoter activity in 293 and HeLa-T4 cells. In contrast, mutant forms of CIITA did not increase HIV-1 expression. This study shows that expression of CIITA increases HIV-1 replication through a transcriptional mechanism.

Cell Line↗
PubMed1982

Molecular cloning of circular unintegrated DNA of two types of the SEATO strain of gibbon ape leukemia virus.

Closed circular unintegrated DNA of the SEATO strain of gibbon ape leukemia virus (GaLV-S) was isolated from canine thymus fibroblasts after cocultivation with chronically infected bat lung fibroblasts. Restriction endonuclease HindIII cleaves GaLV-S DNA once, thus allowing isolation and cloning of HindIII-digested unintegrated DNA in a permitted form. Two clones isolated in the vector, Charon 21A, were nearly identical by restriction enzyme mapping to each of the two types of GaLV-S previously observed. These two types differ at a single SalI site. Unlike previous maps of GaLV-S proviral DNA, however, both clones lack SstI sites in the long-terminal-repeat units. Both the GaLV-S clones and the major species of GaLV-S proviral DNA contain an EcoRI site in the long-terminal-repeat units. The presence of this EcoRI site and the absence of an SstI site in the GaLV-S long-terminal-repeat units differentiate it from all other known GaLV strains and from the closely related nononcogenic simian sarcoma-associated virus. Heteroduplex comparisons of each of the two clones to clones of simian sarcoma-associated virus show no obvious deletion or substitution loops. This suggests that the ability of GaLV-S to induce myeloid leukemia in gibbon apes in not due to an acquired onc gene.

Animals↗
PubMed1990

Identification of a long stretch of homopurine.homopyrimidine sequence in a cluster of retroposons in the human genome.

A cluster of nine retroposons of four different types in a 6221 base EcoRI DNA fragment was isolated from a human fetal liver genomic library using a human nucleophosmin (B23) cDNA as a probe. These retroposons are: (1) a solitary HERV-K long terminal repeat upstream from; (2) a nucleophosmin processed pseudogene; (3) six Alu repeated sequences interspersed in both directions; and (4) a truncated Kpn repeated sequence integrated by an Alu monomer and the HERV-K long terminal repeat. Sequence analysis shows that the nucleophosmin pseudogene contains a long stretch (135 base-pairs) of homopurine.homopyrimidine (Pur.Pyr) sequence. S1 and P1 nuclease digestion indicated that this sequence was able to adopt a non-B-DNA triplex structure under either acidic or neutral conditions. This finding is the first example of the association of a potential DNA triplex structure with a cluster of retroposons.

Base Sequence↗
PubMed2004

The fugitive LTR retrotransposon from the genome of the human blood fluke, Schistosoma mansoni.

Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 [Le Paslier, M.C., Pierce, R.J., Merlin, F., Hirai, H., Wu, W., Williams, D.L., Johnston, D., LoVerde, P.T., Le Paslier, D., 2000. Construction and characterization of a Schistosoma mansoni bacterial artificial chromosome library. Genomics 65, 87-94] from chromosome 1 of the genome of Schistosoma mansoni (GenBank ) revealed the likely presence of a proviral form of a novel schistosome retrotransposon. The novel element, which we named the fugitive, belonged to the mag-like family of the gypsy-Ty3 clade of long terminal repeat retrotransposons. It was closely related to the mag-like retrotransposon Gulliver from Schistosoma japonicum, but was dissimilar to several other long terminal repeat retrotransposons known from S. mansoni including Boudicca, Saci-1, Saci-2 and Saci-3. The full length fugitive element was 4811 bp constituted of a single read-through open reading frame of 4134 bp flanked at both ends by identical long terminal repeat sequences of 273 bp. The open reading frame encoded retroviral-like gag, with a distinctive double Cys-His motif, and pol polyprotein, with a pol domain order of protease, reverse transcriptase, RNaseH and integrase. Examination of schistosome transcriptome sequences in the public domain revealed that the fugitive was transcribed in at least six developmental stages of S. mansoni, while bioinformatics approaches and Southern hybridisation analysis indicated that as many as 2000 copies of the fugitive were interspersed throughout the schistosome genome.

Amino Acid Sequence↗
PubMed1993

Oxidoreductive regulation of nuclear factor kappa B. Involvement of a cellular reducing catalyst thioredoxin.

We have investigated an oxidoreductive regulatory pathway for the DNA binding activity of a pleiotropic cellular transcription factor, nuclear factor kappa B (NF kappa B), has been investigated by using NF kappa B prepared from the nucleus and the cytosol of the primary human T lymphocytes. We show that a cellular reducing catalyst thioredoxin (Trx) plays a major role in activation of the DNA binding of NF kappa B in vitro and stimulation of transcription from the NF kappa B-dependent gene expression. We demonstrate evidence suggesting that redox regulation of NF kappa B by Trx might be exerted at a step after dissociation of the inhibitory molecule I kappa B, a cytosolic-anchoring protein for NF kappa B. To examine the effect of Trx in intact cells, we performed transient assay with a chloramphenicol acetyltransferase-expressing plasmid under the control of human immunodeficiency virus (HIV) long terminal repeat and an effector plasmid expressing human Trx. The promoter activity from HIV long terminal repeat was greatly augmented by co-transfecting the Trx-expressing plasmid, whose effect was dependent on the NF kappa B-binding sites. These findings have suggested that cysteine residue(s) of NF kappa B might be involved in the DNA-recognition by NF kappa B and that the redox control mechanism mediated by Trx might have a regulatory role in the NF kappa B-mediated gene expression. These results may also provide a clue to understanding of the molecular process of AIDS pathogenesis and its possible biochemical intervention.

Amino Acid Sequence↗
PubMed1995

Transcriptional silencing of human immunodeficiency virus type 1 long terminal repeat-driven gene expression by the Krüppel-associated box repressor domain targeted to the transactivating response element.

The evolutionarily conserved protein domain, called the Krüppel-associated box (KRAB), present in the amino termini of a large number of Krüppel-type zinc finger proteins is a strong repressor domain. In order to develop novel strategies to control human immunodeficiency virus type 1 (HIV-1) gene expression, we constructed a series of expression vectors expressing the wild-type Tat or Tat transdominant negative mutants fused to the KRAB repressor domain. We found that the KRAB domain tethered to the transactivating response element is able to suppress both basal and Tat-mediated activity of HIV-1 long terminal repeat-driven gene expression. These results suggest that the KRAB repressor domain fused to the Tat transdominant negative mutants can be successfully employed to control HIV-1 gene expression.

Amino Acid Sequence↗
PubMed1985

Sequence comparisons of the anemia- and polycythemia-inducing strains of Friend spleen focus-forming virus.

A nucleotide sequence analysis carried out on the envelope gene of the anemia-inducing strain of the Friend spleen focus-forming virus (F-SFFVA) reveals that its product has some unique features in common with previously described polycythemia-inducing strains of F-SFFV (F-SFFVP). (i) It contains an amino terminus that is highly related to the gp70 of mink cell focus-inducing viruses, (ii) it is a fusion protein containing the amino terminus of gp70 and the carboxy terminus of p15E, and (iii) it lacks the R-peptide normally found at the carboxy end of the p15E region. Although the envelope genes of F-SFFVA and F-SFFVP are quite similar overall, they do show sequence variation, particularly at the 3' end in the p15E-related region. These variations may contribute to previously observed differences in the response of F-SFFVP- and F-SFFVA-infected erythroid cells to regulatory hormone or to differences in the way the envelope glycoproteins are processed. The long terminal repeat regions of F-SFFVA and the Lilly-Steeves strain of F-SFFVP were also sequenced and compared with each other and with a previously published sequence of another F-SFFVP long terminal repeat. The sequences were found to be reasonably similar to each other but different from their ecotropic parent, Friend murine leukemia virus, as a result of a deletion of one copy of the direct tandem repeat in the enhancer regions. The observation that all SFFVS have this common change in the long terminal repeat enhancer region raises the possibility that it is required for pathogenicity.

Amino Acid Sequence↗