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Mates JM, Kumar SB, Bazan J, Mefford M, Voronkin I, Handelman S, Mwapasa V, Ackerman W, Janies D, Kwiek JJ. Genotypic and phenotypic heterogeneity in the U3R region of HIV type 1 subtype C. AIDS Res Hum Retroviruses 2014; 30:102-12. [PMID: 23826737 PMCID: PMC3887403 DOI: 10.1089/aid.2013.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Approximately 20% of all HIV-1 mother-to-child transmission (MTCT) occurs in utero (IU). In a chronic HIV infection, HIV-1 exists as a complex swarm of genetic variants, and following IU MTCT, viral genomic diversity is restricted through a mechanism that remains to be described. The 5' U3R region of the HIV-1 long terminal repeat (LTR) contains multiple transcription factor (TF) binding sites and regulates viral transcription. In this study, we tested the hypothesis that sequence polymorphisms in the U3R region of LTR are associated with IU MTCT. To this end, we used single template amplification to isolate 517 U3R sequences from maternal, placental, and infant plasma derived from 17 HIV-infected Malawian women: eight whose infants remained HIV uninfected (NT) and nine whose infants became HIV infected IU. U3R sequences show pairwise diversities ranging from 0.2% to 2.3%. U3R sequences from one participant contained two, three, or four putative NF-κB binding sites. Phylogenetic reconstructions indicated that U3R sequences from eight of nine IU participants were consistent with placental compartmentalization of HIV-1 while only one of eight NT cases was consistent with such compartmentalization. Specific TF sequence polymorphisms were not significantly associated with IU MTCT. To determine if replication efficiency of the U3R sequences was associated with IU MTCT, we cloned 90 U3R sequences and assayed promoter activity in multiple cell lines. Although we observed significant, yet highly variable promoter activity and TAT induction of promoter activity in the cell lines tested, there was no association between measured promoter activity and MTCT status. Thus, we were unable to detect a promoter genotype or phenotype associated with IU MTCT.
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Affiliation(s)
- Jessica M. Mates
- Department of Microbiology, The Ohio State University, Columbus, Ohio
| | - Surender B. Kumar
- College of Veterinary Biosciences and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
| | - Jose Bazan
- The Division of Infectious Diseases, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Megan Mefford
- Center for Microbial Interface Biology, Department of Microbial Infection and Immunity, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
| | - Igor Voronkin
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Samuel Handelman
- Department of Pharmacology, The Ohio State University, Columbus, Ohio
| | - Victor Mwapasa
- Department of Community Health, Malawi College of Medicine, Blantyre, Malawi
| | - William Ackerman
- Department of Obstetrics and Gynecology (Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research), The Ohio State University, Columbus, Ohio
| | - Daniel Janies
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Jesse J. Kwiek
- Center for Microbial Interface Biology, Department of Microbial Infection and Immunity, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
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2
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Cojocariu M, St-Louis MC, Archambault D. Bovine immunodeficiency virus: identification of a long terminal repeat sequence with enhanced promoter activity. Arch Virol 2009; 154:1163-7. [PMID: 19547911 DOI: 10.1007/s00705-009-0411-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
We previously identified a new bovine immunodeficiency virus (BIV) trans-activator factor of transcription (Tat236) that was derived from a variant of BIV. Here, we report a new BIV long terminal repeat (LTR) sequence (LTRn) that was obtained by PCR from the DNA of cells infected with the BIV variant mentioned above. Sequence analysis indicated that the LTRn U3 region harbors three nucleic acid mutations at residue positions -194, -135 and -114 when compared to the original (wild-type) LTR sequence. Reporter gene assays indicated that LTRn promotes basal and Tat-mediated transactivation activity to levels significantly higher than those obtained with the wild-type LTR. Restoration experiments to the wild-type genotype indicated that both the -135 and -114 nucleic acid substitutions were responsible for the enhanced promoter activity of BIV LTRn.
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Affiliation(s)
- M Cojocariu
- Department of Biological Sciences, Université du Québec à Montréal, Succursale Centre-Ville, Canada
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3
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Mehta R, Sundaravaradan V, Ahmad N. Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression. Virology 2008; 375:170-81. [PMID: 18313715 DOI: 10.1016/j.virol.2008.01.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 12/15/2007] [Accepted: 01/31/2008] [Indexed: 11/24/2022]
Abstract
We determined the effect of mutations generated in HIV-1 LTR on viral gene expression in six mother-infant pairs following vertical transmission. We show that the functional domains critical for LTR function, the promoter (TATAA), enhancers (three SpI and two NFkappaB sites), the modulatory region (two AP-I sites, two NFAT, one NF-IL6 site, one Ets-1, and one USF-1) and the TAR region were generally conserved among mother-infant pairs, although we observed several patient and pair specific mutations in these important domains. We then determined the promoter activity of our mother-infant LTR sequences by measuring CAT gene expression, which was driven by these LTRs and found that most of these HIV-1 LTRs derived from 6 mother-infant pairs were functional. However, mutations in the important transcription factor binding sites, including TATAA, SpI, NFkappaB, AP-I, NFAT, NF-IL6, Ets-1, USF-1 and TAR resulted in reduced LTR driven CAT gene expression. Taken together, conservation of functional domains in the LTR during vertical transmission supports the notion that a functional LTR is critical in viral replication and pathogenesis and mutations generated during the course of infection correlated with HIV-1 gene expression.
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Affiliation(s)
- Roshni Mehta
- Department of Immunobiology, College of Medicine, The University of Arizona, 1501 N. Campbell Avenue, Tucson, Arizona 85724, USA
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4
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Estable MC. In search of a function for the most frequent naturally-occurring length polymorphism (MFNLP) of the HIV-1 LTR: retaining functional coupling, of Nef and RBF-2, at RBEIII? Int J Biol Sci 2007; 3:318-27. [PMID: 17589566 PMCID: PMC1893116 DOI: 10.7150/ijbs.3.318] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 06/07/2007] [Indexed: 11/05/2022] Open
Abstract
Although the prototypical HIV-1 LTR sequences were determined 22 years ago from the initial isolate, elucidating which transcription factors are critical to replication in vivo, has been difficult. One approach has been to examine HIV-1 LTRs that have gone through the gamut of in vivo mutation and selection, in search of absolutely conserved sequences. In this vein, RBEIII sequences are virtually 100% conserved in naturally occurring HIV-1 LTRs. This is because when they are mutated, the MFNLP recreates an RBEIII site. Here, I enumerate some retroviral mutation mechanisms, which could generate the MFNLP. I then review the literature corresponding to the MFNLP, highlighting the discovery in 1999, that RBEIII and MFNLP sequences, bind USF and TFII-I cooperatively, within the context of earlier and later work that suggests a role in HIV-1 activation, through T-cell receptor engagement and the MAPK cascade. One exception to the nearly absolute conservation of RBEIII, has been a group of long term non progressors (LTNP). These patients harbor deletions to the Nef gene. However, the Nef gene overlaps with the LTR, and the LTNP deletions abrogate RBEIII, in the absence of an MFNLP. I suggest that the MFNLP retains functional coupling between the MAPK-mediated effects of Nef and the HIV-1 LTR, through RBEIII. I propose that difficult-to-revert-mutations, to either Nef or RBEIII, result in the convergent LTNP Nef/LTR deletions recently observed. The potential exploitation of this highly conserved protein-binding site, for chimeric transcription factor repression (CTFR) of HIV-1, functionally striving to emulate the LTNP deletions, is further discussed.
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5
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St-Louis MC, Cojocariu M, Archambault D. The molecular biology of bovine immunodeficiency virus: a comparison with other lentiviruses. Anim Health Res Rev 2005; 5:125-43. [PMID: 15984320 DOI: 10.1079/ahr200496] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bovine immunodeficiency virus (BIV) was first isolated in 1969 from a cow, R-29, with a wasting syndrome. The virus isolated induced the formation of syncytia in cell cultures and was structurally similar to maedi-visna virus. Twenty years later, it was demonstrated that the bovine R-29 isolate was indeed a lentivirus with striking similarity to the human immunodeficiency virus. Like other lentiviruses, BIV has a complex genomic structure characterized by the presence of several regulatory/accessory genes that encode proteins, some of which are involved in the regulation of virus gene expression. This manuscript aims to review biological and, more particularly, molecular aspects of BIV, with emphasis on regulatory/accessory viral genes/proteins, in comparison with those of other lentiviruses.
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Affiliation(s)
- Marie-Claude St-Louis
- University of Québec at Montréal, Department of Biological Sciences, Montréal, Québec, Canada
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6
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Hogan TH, Stauff DL, Krebs FC, Gartner S, Quiterio SJ, Wigdahl B. Structural and functional evolution of human immunodeficiency virus type 1 long terminal repeat CCAAT/enhancer binding protein sites and their use as molecular markers for central nervous system disease progression. J Neurovirol 2003; 9:55-68. [PMID: 12587069 DOI: 10.1080/13550280390173292] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Revised: 09/30/2002] [Accepted: 10/11/2002] [Indexed: 10/20/2022]
Abstract
The appearance and progression of human immunodeficiency virus type 1 (HIV-1)-associated pathogenesis in the immune and central nervous systems is dependent on the ability of the virus to replicate in these compartments, which is, in turn, controlled by numerous factors, including viral binding and entry, receptor and coreceptor usage, and regulation of viral expression by the long terminal repeat (LTR). The LTR promotes viral expression in conjunction with viral and cellular regulatory proteins, including members of the CCAAT/enhancer binding protein (C/EBP) family, which modulate LTR activity through at least two cis-acting binding sites. Previous studies have shown that these sites are necessary for HIV-1 replication in cells of the monocyte/macrophage lineage, but dispensable in T lymphocytes. To establish potential links between this important family of transcription factors and HIV-1-associated pathogenesis, C/EBP site I and II sequence variation in peripheral blood mononuclear cell (PBMC)-derived LTRs from HIV-1-infected patients with varying degrees of disease severity was examined. A high prevalence of C/EBP site variants 3T (site I) and consensus B (site II) within PBMC-derived HIV-1 LTRs was shown to correlate with late stage disease in HIV-1-infected patients. These results suggest that the increased prevalence in the PBMCs of HIV-1 LTRs containing the 3T C/EBP site I variant and the consensus B site II variant may serve as a molecular marker for disease progression within the immune system. The relative low or high binding affinity of C/EBP beta to sites I and II in electrophoretic mobility shift (EMS) analyses correlated with low or high LTR activity, respectively, in transient expression analyses during both early and late disease stages. The 3T C/EBP site I was the only variant examined that was not found in LTRs derived from PBMCs of patients at early stages of HIV-1 disease, but was found at increasing frequencies in patients with late stage disease. Furthermore, the 3T C/EBP site I was not found in brain-derived LTRs of patients without HIV-1-associated dementia (HIVD), but was found in increasing numbers in brain-derived LTRs from patients diagnosed with HIVD. The C/EBP site I 3T variant appears to be exclusive to patients progressing to increasingly severe HIV-1-associated immunologic and neurologic disease.
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Affiliation(s)
- Tricia H Hogan
- Department of Microbiology and Immunology, The Pennsylvania State University, College of Medicine, Hershey 17033, USA
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7
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Simm M, Miller LS, Durkin HG, Allen M, Chao W, Lesner A, Potash MJ, Volsky DJ. Induction of secreted human immunodeficiency virus type 1 (HIV-1) resistance factors in CD4-positive T lymphocytes by attenuated HIV-1 infection. Virology 2002; 294:1-12. [PMID: 11886260 DOI: 10.1006/viro.2001.1300] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This report describes induction of HIV-1 resistance and synthesis of resistance factors in immortal CD4-positive T lymphocytes. SupT1 cells were infected by NL4-3 attenuated by a defect in the vif gene through coculture with infected primary lymphocytes. Cell lines from this infection, termed R1, expressed CD4 and CXCR4, carried low levels of HIV-1 DNA, but expressed no other detectable viral products and were resistant to infection by wild-type HIV-1. Investigation of challenge infection in resistant R1 lines demonstrated entry, reverse transcription, and integration by incoming HIV-1 but no synthesis of viral RNA. By assay of marker gene expression, we found that Tat was unable to activate LTR-driven transcription in R1 lines. HIV-1-resistant R1 lines secreted soluble factors that inhibited productive infection of primary lymphocytes by several strains of HIV-1 and blocked viral RNA synthesis in newly infected cells. Resistance factors also blocked the induction of HIV-1 transcription in ACH-2 cells as assayed by viral antigen expression and Northern blot of viral RNA. Soluble factors produced by HIV-1-resistant, immortal R1 cells may form the basis of new approaches to control HIV-1 infection.
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Affiliation(s)
- Malgorzata Simm
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center, Antenucci Researech Building, 432 West 58th Street, New York, NY 10019, USA
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8
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Hiebenthal-Millow K, Kirchhoff F. The most frequent naturally occurring length polymorphism in the HIV-1 LTR has little effect on proviral transcription and viral replication. Virology 2002; 292:169-75. [PMID: 11878920 DOI: 10.1006/viro.2001.1282] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
About 38% of primary HIV-1 long terminal repeats (LTRs) contain an insertion (consensus: 5prime prime or minute-ACYGCTGA-3prime prime or minute), termed the most frequent naturally occurring length polymorphism (MFNLP). The MFNLP binds several transcription factors and might affect HIV-1 replication and disease progression in infected individuals. However, its relevance for proviral transcription and for HIV-1 replication in primary cells is unclear. We utilized HIV-1 NL4-3 LTR variants to investigate the effect of the MFNLP on 5prime prime or minuteLTR transcriptional activity in various cell types. Notably, viral promoter activity was studied in primary cells in the context of the integrated provirus, using both single cycle assays with pseudotyped Luciferase reporter viruses and replication-competent HIV-1 mutants. Our results demonstrate that the presence, absence, or duplication of the 5prime prime or minute-ACYGCTGA-3prime prime or minute motif has little effect on viral promoter activity in T cell lines, peripheral blood mononuclear cells (PBMC), and monocyte-derived macrophages (MDM). Furthermore, all HIV-1 LTR variants showed efficient induction upon stimulation with TPA and/or ionomycin and replicated with comparable efficiency in a human T cell line and in PBMC. Thus, the MFNLP does not significantly affect HIV-1 5prime prime or minuteLTR transcriptional activity and viral replication in primary cells, suggesting that this common sequence variation has little impact on the clinical course of HIV-1 infection.
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Affiliation(s)
- Kirsten Hiebenthal-Millow
- Institute for Clinical and Molecular Virology, University of Erlangen-Nürnberg, Schlossgarten 4, Erlangen, 91054, Germany
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9
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Novelli P, Vella C, Oxford J, Daniels RS. Construction and characterization of a full-length HIV-1(92UG001) subtype D infectious molecular clone. AIDS Res Hum Retroviruses 2002; 18:85-8. [PMID: 11804560 DOI: 10.1089/088922202753394754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Here we report the construction, sequencing, and biological characterization of a molecular clone of HIV-1(92UG001), a virus representative of subtype D strains circulating in Uganda. The virus produced by the clone has an aggressive syncytium-inducing phenotype, which matches that of the parental virus. This phenotype may be related to duplication of a binding site for a transcription factor, T cell factor 1alpha (TCF-1alpha), in the long terminal repeat of the virus.
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Affiliation(s)
- P Novelli
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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10
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Blackard JT, Renjifo B, Fawzi W, Hertzmark E, Msamanga G, Mwakagile D, Hunter D, Spiegelman D, Sharghi N, Kagoma C, Essex M. HIV-1 LTR subtype and perinatal transmission. Virology 2001; 287:261-5. [PMID: 11531404 DOI: 10.1006/viro.2001.1059] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multiple subtypes of HIV-1 have been identified; however, there is little data on the relative transmissibility of viruses belonging to different subtypes. A matched case-control study addressed whether viruses with different long terminal repeat (LTR) subtypes were transmitted equally from mother to infant. The LTR subtype was determined for 45 matched cases and controls who participated in a clinical trial in Tanzania. HIV-1 subtypes A, C, and D and intersubtype recombinant sequences were identified. Exact matched logistic regression analysis showed that viruses containing subtype A or intersubtype recombinant LTRs were 3.2 and 4.8 times more likely to be transmitted from mother to infant than viruses with subtype D LTRs. Viruses containing subtype C LTRs were 6.1 times more likely to be transmitted than those with subtype D LTRs. These differences in transmission were independent of maternal CD4 at enrollment. Thus, it appears that HIV-1 subtype may be associated with differing rates of perinatal transmission in Tanzania.
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Affiliation(s)
- J T Blackard
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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11
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Krebs FC, Mehrens D, Pomeroy S, Goodenow MM, Wigdahl B. Human immunodeficiency virus type 1 long terminal repeat quasispecies differ in basal transcription and nuclear factor recruitment in human glial cells and lymphocytes. J Biomed Sci 2000; 5:31-44. [PMID: 9570512 DOI: 10.1007/bf02253354] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The generation of genomic diversity during the course of infection has the potential to affect all aspects of HIV-1 replication, including expression of the proviral genome. To gain a better understanding of the impact of long terminal repeat (LTR) sequence diversity on LTR-directed gene expression in cells of the central nervous system (CNS) and immune system, we amplified and cloned LTRs from proviral DNA in HIV-1-infected peripheral blood. Sequence analysis of nineteen LTRs cloned from 2 adult and 3 pediatric patients revealed an average of 33 nucleotide changes (with respect to the sequence of the LAI LTR) within the 455-bp U3 region. Transient expression analyses in cells of neuroglial and lymphocytic origin demonstrated that some of these LTRs had activities which varied significantly from the LAI LTR in U-373 MG cells (an astrocytoma cell line) as well as in Jurkat cells (a CD4-positive lymphocyte cell line). While LTRs which demonstrated the highest activities in U-373 MG cells also yielded high activities in Jurkat cells, the LTRs were generally more active in Jurkat cells when compared to the LAI LTR. Differences in LTR sequence also resulted in differences in transcription factor recruitment to cis-acting sites within the U3 region of the LTR, as demonstrated by electrophoretic mobility shift assays. In particular, naturally occurring sequence variation impacted transcription factor binding to an activating transcription factor/cAMP response element binding (ATF/CREB) binding site (located between the LEF-1 and distal NF-kappaB transcription factor binding sites) that we identified in previous studies of the HIV-1 LTR. These findings suggest that LTR sequence changes can significantly affect basal LTR function and transcription factor recruitment, which may, in turn, alter the course of viral replication in cells of CNS and immune system origin.
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Affiliation(s)
- F C Krebs
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey 17033, USA
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12
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Blackard JT, Renjifo B, Chaplin B, Msamanga G, Fawzi W, Essex M. Diversity of the HIV-1 long terminal repeat following mother-to-child transmission. Virology 2000; 274:402-11. [PMID: 10964782 DOI: 10.1006/viro.2000.0466] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A study of the human immunodeficiency virus Type 1 (HIV-1) 5' long terminal repeat (LTR) was performed to determine the extent of variation found within the LTR from 19 mother-infant pairs in Tanzania and to assess whether the LTR is useful in distinguishing maternal sequences that were transmitted to infants. HIV-1 subtypes A, C, and D as well as intersubtype recombinant LTR sequences were detected in mothers and infants. The LTR subtype was 100% concordant between mothers and their infants. Diversity calculations showed a significant reduction in LTR variation in infants compared to their mothers. However, the overall magnitude of LTR variation was less than that found in the env gene from the same individuals. These data suggest a selective constraint active upon the 5' long terminal repeat that is distinct from immune selective pressure(s) directed against HIV-1 structural genes. Detection of maternal LTR variants that were transmitted to infants may yield important information concerning nonstructural determinants of HIV-1 transmission from mother to infant.
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Affiliation(s)
- J T Blackard
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, Massachusetts 02115-6017, USA
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13
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Chen P, Flory E, Avots A, Jordan BW, Kirchhoff F, Ludwig S, Rapp UR. Transactivation of naturally occurring HIV-1 long terminal repeats by the JNK signaling pathway. The most frequent naturally occurring length polymorphism sequence introduces a novel binding site for AP-1 factors. J Biol Chem 2000; 275:20382-90. [PMID: 10764760 DOI: 10.1074/jbc.m001149200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To study the role of MAPK cascades in the regulation of naturally occurring human immunodeficiency virus type 1 long terminal repeats (HIV-1 LTRs), we analyzed several HIV-1 LTRs from patients at different stages of disease progression. One of these naturally occurring HIV-1 LTRs contains an insertion termed the most frequent naturally occurring length polymorphism (MFNLP) and exhibited high inducibility upon T cell activation. We found that the protein kinase mixed lineage kinase 3/src-homology 3 domain-containing proline-rich kinase, a specific activator of the stress-activated protein kinase (SAPK)/JNK signaling pathway in T lymphocytes, induces high transcriptional activation of this promoter. Promoter inducibility is inhibited by the SAPK/JNK inhibitor, the JNK binding domain of the JNK interacting protein 1, and Tam-67 (N-terminal deletion mutant of c-Jun). In electrophoretic mobility shift assay, several protein complexes were found to bind to the MFNLP sequence in T cells. We identified AP-1 factors c-Fos and JunB as MFNLP-binding proteins, whose binding is abolished by introducing point mutations in the 3'-half of the MFNLP sequence. Introduction of these point mutations into the MFNLP containing HIV-1 LTR reduced src-homology 3 domain-containing proline-rich kinase -mediated transactivation. These data indicate that the AP-1-like binding site in the MFNLP sequence gives rise to a higher inducibility of natural HIV-LTRs by the SAPK/JNK signaling pathway.
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Affiliation(s)
- P Chen
- Institut für Medizinische Strahlenkunde und Zellforschung, Universität Würzburg, Versbacher Strasse 5, D-97078 Würzburg, Germany
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14
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Gómez-Román VR, Vázquez JA, del Carmen Basualdo M, Estrada FJ, Ramos-Kuri M, Soler C. nef/long terminal repeat quasispecies from HIV type 1-infected Mexican patients with different progression patterns and their pathogenesis in hu-PBL-SCID mice. AIDS Res Hum Retroviruses 2000; 16:441-52. [PMID: 10772530 DOI: 10.1089/088922200309106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To examine the genetic features of the long terminal repeat (LTR) derived from six HIV-1-infected individuals enrolled in the Mexico City Cohort, we cloned and sequenced a 505-bp fragment of the proviral LTR from their peripheral blood mononuclear cells (PBMCs). All patients harbored HIV-1 LTR quasispecies corresponding to the B subtype. Three patients with high CD4+ T cell counts (>500/mm3) presented LTR sequences with point mutations in the TAR bulge. The LTR sequence from a patient classified as a long-term nonprogressor (LTNP) presented the most frequent naturally occurring length polymorphism (MFNLP) and two substitutions in the TAR region that were predicted to result in two alternative secondary RNA structures. A novel 18-bp deletion, which eliminates part of the putative binding site for the nuclear factor of activated T cells (NFAT-1), was identified in the overlapping nef/LTR sequence derived from a patient progressing to AIDS. This deletion coincides with the ability of this virus to consistently replicate at low levels in vivo (viral load <500 RNA copies/ml) and in vitro (unsuccessful virus isolation). On one occasion, when virus isolation was successful, the 18-bp deletion was no longer evident and LTR sequences with intact NFAT-1-binding sites were observed. Inoculation of hu-PBL-SCID mice with viruses from several Mexican patients resulted in differential CD4+ T cell depletion patterns 15 days postinfection, which agree with the in vivo CD4+ T cell count data from each patient.
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Affiliation(s)
- V R Gómez-Román
- Unidad de Investigación en Retrovirus Humanos, Instituto de Investigaciones Biomédicas, Universidad Nacional Autonoma de México, DF Mexico
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15
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Kar-Roy A, Dong W, Michael N, Li Y. Green fluorescence protein as a transcriptional reporter for the long terminal repeats of the human immunodeficiency virus type 1. J Virol Methods 2000; 84:127-38. [PMID: 10680962 DOI: 10.1016/s0166-0934(99)00122-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Using the enhanced green fluorescence protein (EGFP), a transient reporter expression system was established to assess the transcriptional activity of the long terminal repeats (LTR) of primary isolates of the human immunodeficiency virus type 1 (HIV-1). Consistent with the conventional chloramphenicol acetyl transferase (CAT) reporter, EGFP expression, under the direction of HIV-1 LTR, was readily detected in the transient transfection and was elevated by co-transfection of HIV-1 tat-expression vector. Comparing to CAT, however, EGFP expression system has two advantages: (i) Using a fluorescence activated cell sorter (FACS), it was possible to simultaneously measure transfection efficiency and fluorescence intensity of the transfected live cells without the necessity of co-transfection of a reference plasmid for comparing the transcriptional activity of two promoters; and (ii) EGFP expression was readily detected at a DNA concentration where CAT activity was not detectable possibly because the transfectants could be 'gated'. On the other hand, at a higher concentration of DNA, CAT signal became more prominent than that of EGFP, possibly because the enzymatic activity of CAT 'amplified' the signal. EGFP fluorescence detected by FACS was a direct measurement of the expressed chromophore. It is concluded that the system is rapid, reproducible, convenient and useful for quantitative analysis of transcription.
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Affiliation(s)
- A Kar-Roy
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore 21201, USA
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16
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Visco-Comandini U, Yun Z, Vahlne A, Sönnerborg A. No association of HIV type 1 long terminal repeat sequence pattern with long-term nonprogression and in vivo viral replication levels in European subjects. AIDS Res Hum Retroviruses 1999; 15:609-17. [PMID: 10331439 DOI: 10.1089/088922299310908] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 long terminal repeat (LTR) promotes and modulates proviral transcription in the infected cell. It has been suggested that truncations and even point mutations in functional sites of the LTR are associated with low viral replication and attenuated pathogenesis in HIV-1-infected long-term nonprogressors (LTNPs). We performed a detailed analysis of LTR sequences from proviral DNA of 21 Italian and Swedish, well-characterized LTNPs and of 15 progressor patients. No truncation was found and no correlation was identified between specific LTR mutations and disease progression. We also failed to find a significant correlation between phylogenetic distance and clinical status. Although HIV-1 LTR interpatient heterogeneity among LTNPs and subjects with HIV-1 RNA levels <500 copies/ml tended to be lower, no sequence mutation was correlated with in vivo viral loads. Our results suggest that HIV-1 LTR defects are rare among Italian and Swedish LTNPs.
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Affiliation(s)
- U Visco-Comandini
- Department of Immunology, Microbiology, Pathology and Infectious Diseases, Karolinska Institutet, Huddinge, Sweden.
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17
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Oelrichs RB, Workman C, Laukkanen T, McCutchan FE, Deacon NJ. A novel subtype A/G/J recombinant full-length HIV type 1 genome from Burkina Faso. AIDS Res Hum Retroviruses 1998; 14:1495-500. [PMID: 9824329 DOI: 10.1089/aid.1998.14.1495] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- R B Oelrichs
- AIDS Molecular Biology Laboratory, Macfarlane Burnet Centre for Medical Research, Fairfield, Australia
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18
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Estable MC, Bell B, Hirst M, Sadowski I. Naturally occurring human immunodeficiency virus type 1 long terminal repeats have a frequently observed duplication that binds RBF-2 and represses transcription. J Virol 1998; 72:6465-74. [PMID: 9658089 PMCID: PMC109809 DOI: 10.1128/jvi.72.8.6465-6474.1998] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/1997] [Accepted: 04/15/1998] [Indexed: 02/08/2023] Open
Abstract
Approximately 38% of human immunodeficiency virus type 1 (HIV-1)-infected patients within the Vancouver Lymphadenopathy-AIDS Study have proviruses bearing partial 15- to 34-nucleotide duplications upstream of the NF-kappaB binding sites within the 5' long terminal repeat (LTR). This most frequent naturally occurring length polymorphism (MFNLP) of the HIV-1 5' LTR encompasses potential binding sites for several candidate transcription factors, including TCF-1alpha/hLEF, c-Ets, AP-4, and Ras-responsive binding factor 2 (RBF-2) (M. C. Estable et al., J. Virol. 70:4053-4062, 1996). RBF-2 and an apparently related factor, RBF-1, bind to at least four cis elements within the LTR which are required for full transcriptional responsiveness to protein-tyrosine kinases and v-Ras (B. Bell and I. Sadowski, Oncogene 13:2687-2697, 1996). Here we demonstrate that representative MFNLPs from two patients specifically bind RBF-2. In both cases, deletion of the MFNLP caused elevated LTR-directed transcription in cells expressing RBF-2 but not in cells with undetectable RBF-2. RBF-1, but not RBF-2, appears to contain the Ets transcription factor family member GABPalpha/GABPbeta1. Taken together with the fact that every MFNLP from a comparative study of over 500 LTR sequences from 42 patients contains a predicted binding site for RBF-2, our data suggest that the MFNLP is selected in vivo because it provides a duplicated RBF-2 cis element, which may limit transcription in monocytes and activated T cells.
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Affiliation(s)
- M C Estable
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, UBC Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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19
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Rousseau C, Abrams E, Lee M, Urbano R, King MC. Long terminal repeat and nef gene variants of human immunodeficiency virus type 1 in perinatally infected long-term survivors and rapid progressors. AIDS Res Hum Retroviruses 1997; 13:1611-23. [PMID: 9430253 DOI: 10.1089/aid.1997.13.1611] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
HIV-1 sequences from perinatally infected children were analyzed in the long terminal repeat (LTR) region and nef in order to investigate associations of viral variation and disease progression. Four long-term survivors who reached 10 years of age or older, and four rapid progressors who survived less than 2 years, participated in this study. LTR sequences of multiple independent viral variants from each individual were compared. No sequence pattern within the LTR consistently distinguished long-term survivors from rapid progressors or vice versa. Deletions and insertions within transcription factor binding sites of the LTR and nef ranging from 8 to 341 bp were found in viral variants from the eldest long-term survivor (LTS047). These deletions and duplications may be associated with the survival of LTS047 via an unknown mechanism. Among all children in this study, the sites in the untranslated region (NF-kappaB, SP1, and TATA box) were more conserved than the sites in the nef/LTR overlap region (NFAT, purine-rich region, USF, TCF1alpha), reflecting the importance of the sites in the untranslated region for viral replication. A mutation in the E box motif within the USF site among the sequences from a long-term survivor (LTS113) is predicted to disrupt protein binding and may be associated with slow disease progression. Mutations of the SP1-III site in a rapid progressor (RP056) indicate that this site is not necessary for rapid disease progression.
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Affiliation(s)
- C Rousseau
- Division of Medical Genetics, University of Washington, Seattle 98195-7720, USA.
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20
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Kirchhoff F, Greenough TC, Hamacher M, Sullivan JL, Desrosiers RC. Activity of human immunodeficiency virus type 1 promoter/TAR regions and tat1 genes derived from individuals with different rates of disease progression. Virology 1997; 232:319-31. [PMID: 9191845 DOI: 10.1006/viro.1997.8586] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Different rates of disease progression may be associated with different human immunodeficiency virus type 1 (HIV-1) promoter and/or transactivator activities. We therefore analyzed the sequences and activities of the first exon of Tat, tat1, and the promoter/trans-acting responsive (TAR) regions amplified directly from peripheral blood mononuclear cells obtained from five long-term nonprogressors and eight progressing HIV-1-infected individuals. The majority of tat1 alleles and promoter/TAR regions from all patients were intact and showed comparable activities in transient reporter assays. A substantial number of point mutations and some length variations were observed in the promoter/TAR region. In a single nonprogressor, the Sp1 binding site 3 was consistently altered and the transcriptional activity in the presence of Tat was diminished. Some LTR clones from a rapid progressor contained a fourth Sp1 binding site, which was associated with an elevated basal promoter activity. These data suggest that defects in the promoter/TAR region or tat1 are rare and that different promoter/transactivator activities are not commonly associated with different progression rates.
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Affiliation(s)
- F Kirchhoff
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University, Erlangen, Germany.
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21
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Zhang L, Huang Y, Yuan H, Chen BK, Ip J, Ho DD. Identification of a replication-competent pathogenic human immunodeficiency virus type 1 with a duplication in the TCF-1alpha region but lacking NF-kappaB binding sites. J Virol 1997; 71:1651-6. [PMID: 8995694 PMCID: PMC191225 DOI: 10.1128/jvi.71.2.1651-1656.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Multiple human immunodeficiency virus type 1 (HIV-1) sequences with deletions of NF-kappaB binding sites at both the 5' and 3' long terminal repeats (LTRs) were identified in serial samples collected from an infected individual. The effect of this deletion on the level of transcription was studied by transient transfection of an LTR-driven luciferase reporter gene and by infection with a full-length recombinant HIV-1 containing a luciferase reporter (HIVHXBluc). Detectable levels of gene expression were found in both systems, in the presence or absence of the viral transactivator Tat. Interestingly, a duplication of a putative TCF-1alpha motif was found in place of the NF-kappaB elements in these viruses. Higher transcriptional activity was observed with HXBLTR (NF-kappaB intact) than with the patient's LTR (NF-kappaB deleted), suggesting that the NF-kappaB binding sites may promote optimal levels of viral gene transcription. The ability of these viruses with NF-kappaB deleted to replicate and cause substantial decline in CD4 cell counts demonstrates that the NF-kappaB binding sites are not absolutely required for viral replication or pathogenicity in vivo. These results are consistent with the notion that the HIV-1 LTR possesses functional redundancy which allows it to interact with multiple transcription factors, thereby ensuring viral replication in a variety of cell types.
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Affiliation(s)
- L Zhang
- The Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10016, USA
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22
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Shahabuddin M, Bentsman G, Volsky B, Rodriguez I, Volsky DJ. A mechanism of restricted human immunodeficiency virus type 1 expression in human glial cells. J Virol 1996; 70:7992-8002. [PMID: 8892923 PMCID: PMC190872 DOI: 10.1128/jvi.70.11.7992-8002.1996] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We characterized in detail the life cycle of human immunodeficiency virus type 1 (HIV-1) in human glioma H4/CD4 cells which stably express transfected CD4 DNA (B. Volsky, K. Sakai, M. Reddy, and D. J. Volsky, Virology 186:303-308, 1992). Infection of cloned H4/CD4 cells with the N1T strain of cell-free HIV-1 (HIV-1/N1T) was rapid and highly productive as measured by the initial expression of viral DNA, RNA, and protein, but all viral products declined to low levels by 14 days after infection. Chronically infected, virus-producing H4/CD4 cells could be obtained by cell cloning, indicating that HIV-1 DNA can integrate and remain expressed in these cells. The HIV-1 produced in H4/CD4 cells was noninfectious to glial cells, but it could be transmitted with low efficiency to CEM cells. Examination of viral protein composition by immunoprecipitation with AIDS serum or anti-gp120 antibody revealed that HIV-1/N1T-infected H4/CD4 cells produced all major viral proteins including gp160, but not gp120. Deglycosylation experiments with three different glycosidases determined that the absence of gp120 was not due to aberrant glycosylation of gp160, indicating a defect in gp160 proteolytic processing. Similar results were obtained in acutely and chronically infected H4/CD4 cells. To determine the generality of this HIV-1 replication phenotype in H4/CD4 cells, nine different viral clones were tested for replication in H4/CD4 cells by transfection. Eight were transiently productive like N1T, but one clone, NL4-3, established a long-lived productive infection in H4/CD4 cells, produced infectious progeny virus, and produced both gp160 and gp120. We conclude that for most HIV-1 strains tested, HIV-1 infection of H4/CD4 is restricted to a single cycle because of the defective processing of gp160, resulting in the absence of gp120 on progeny virus.
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Affiliation(s)
- M Shahabuddin
- Molecular Virology Laboratory, St. Luke's-Roosevelt Hospital Center, New York, New York 10019, USA
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23
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Simm M, Chao W, Pekarskaya O, Sova P, Gupta P, Balachandran R, Volsky DJ. Genetic variability and function of the long terminal repeat from syncytium-inducing and non-syncytium-inducing human immunodeficiency virus type 1. AIDS Res Hum Retroviruses 1996; 12:801-9. [PMID: 8738432 DOI: 10.1089/aid.1996.12.801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We analyzed sequence variability and function of the long terminal repeat (LTR) from syncytium-inducing (SI) and non-syncytium-inducing (NSI) HIV-1. Twenty LTR DNA clones were obtained by polymerase chain reaction amplification and molecular cloning from short-term cultures of SI and NSI viruses from an AIDS patient and two asymptomatic individuals, respectively. All the LTR clones tested contained multiple nucleotide changes (mostly G-to-A transitions), compared to the subtype B consensus sequence, which were clustered within the negative regulatory element, including NF-AT, USF, and TCF-1 alpha binding sites. The core promoter/TAR region sequences were highly conserved. The basal and Tat-mediated transcriptional activities of selected LTR clones tested were 0.1 to 1 and 0.2 to 0.5 times that of the control, respectively, regardless of the SI or NSI origin of the clones. Phylogenetic analysis revealed interi-solate sequence divergence in the LTR that was similar but not identical to previously analyzed vif sequences from the same samples. In particular, the inter-isolate distances from reference sequences differed for the LTR and vif. This raises the possibility that recombination occurred between corresponding LTR and vif loci of the quasi-species present in the isolates described here.
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Affiliation(s)
- M Simm
- Molecular Virology Laboratory, St. Luke's-Roosevelt Hospital Center, Columbia University, New York, New York 10019, USA
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24
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Estable MC, Bell B, Merzouki A, Montaner JS, O'Shaughnessy MV, Sadowski IJ. Human immunodeficiency virus type 1 long terminal repeat variants from 42 patients representing all stages of infection display a wide range of sequence polymorphism and transcription activity. J Virol 1996; 70:4053-62. [PMID: 8648743 PMCID: PMC190286 DOI: 10.1128/jvi.70.6.4053-4062.1996] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Despite extensive in vitro studies identifying a myriad of cellular transcription factors that bind the human immunodeficiency virus type 1 5' long terminal repeat (LTR), the relative contribution of these factors to human immunodeficiency virus type 1 replication in infected individuals remains obscure. To address this question, we investigated 478 proviral quasispecies derived from uncultured peripheral blood mononuclear cells of 42 patients representing all stages of infection. In addition to highly conserved TATA box, SP-1, and NF-kappaB sites, the Ets core and an adjacent 5'-ACYGCTGA-3' motif were extremely conserved. Importantly, the most frequent naturally occurring length polymorphism (MFNLP) duplicated 5'-ACYGCTGA-3' motifs in LTRs in which this same motif was disrupted or in LTRs in which a single point mutation to the Ets core ablated binding of c-Ets 1 and another factor distinct from both c-Ets 1 and Elf 1. The MFNLP's location was precise (position -121) and surprisingly frequent (38% of patients) and demarcated LTR Nef-coding sequences from LTR noncoding sequences that appear to be evolving independently. Aside from these features, we found no definitive clinical or transcription phenotype common to all MFNLP LTRs. We also found previously described and novel point polymorphisms, including some conferring TAR-dependent and TAR- independent Tat unresponsiveness, and showed that differential binding of nuclear factor(s) to a TCTAA TATA box variant may be the mechanism for the latter.
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Affiliation(s)
- M C Estable
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Canada, Vancouver
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25
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Volsky DJ, Simm M, Shahabuddin M, Li G, Chao W, Potash MJ. Interference to human immunodeficiency virus type 1 infection in the absence of downmodulation of the principal virus receptor, CD4. J Virol 1996; 70:3823-33. [PMID: 8648718 PMCID: PMC190259 DOI: 10.1128/jvi.70.6.3823-3833.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
It is thought that interference during human immunodeficiency virus type 1 (HIV-1) infection is established by downmodulation of the principal virus receptor, CD4. Here we present evidence to the contrary. At various times after primary infection, we superinfected T cells in vitro by exposure to a genetically distinct viral clone or to a virus carrying the chloramphenicol acetyltransferase gene. Replication of each virus strain was determined by restriction enzyme analysis of total cellular DNA, by PCR amplification of viral DNA, or by assay of cell extracts for chloramphenicol acetyltransferase activity. We found that efficient viral interference is established within 24 h of infection at a multiplicity of infection of 1. At that time, expression of viral structural proteins was low and infected cells displayed undiminished levels of surface CD4 and were fully susceptible to virus binding and fusion. Superinfection by either cell-free HIV-1 or cocultivation was blocked. Cells resistant to superinfection by HIV-1 remained susceptible to Moloney murine leukemia and vaccinia viruses. No interference was observed 4 h after primary infection or in cells infected with either UV-inactivated HIV-1 or a mutant virus defective in virus-cell fusion activity, indicating that binding of primary virus to CD4 is insufficient to prevent superinfection. The minimum viral requirements for this interference are that HIV-1 must be able to enter cells and synthesize viral DNA; Tat-mediated transcription is dispensable. Our results support the existence of a novel pathway to interference to HIV-1 infection, which we term postentry interference, which blocks superinfection during intracellular phases of the virus life cycle.
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Affiliation(s)
- D J Volsky
- Molecular Virology Laboratory, St. Luke's-Roosevelt Hospital Center, New York 10019, USA.
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26
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Volsky DJ, Potash MJ, Simm M, Sova P, Ma XY, Chao W, Shahabuddin M. The human immunodeficiency virus type 1 vif gene: the road from an accessory to an essential role in human immunodeficiency virus type 1 replication. Curr Top Microbiol Immunol 1995; 193:157-68. [PMID: 7648874 DOI: 10.1007/978-3-642-78929-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- D J Volsky
- Molecular Virology Laboratory, St. Luke's-Roosevelt Hospital Center, New York, NY, USA
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27
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Knuchel M, Bednarik DP, Chikkala N, Villinger F, Folks TM, Ansari AA. Development of a novel quantitative assay for the measurement of chloramphenicol acetyl transferase (CAT) mRNA. J Virol Methods 1994; 48:325-38. [PMID: 7989447 DOI: 10.1016/0166-0934(94)90131-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most host cells transfected with chloramphenicol acetyl transferase (CAT) expressing plasmids display relatively low levels of constitutive CAT activity. While this is ideal to study factors that enhance gene transcription, decreases in CAT levels are difficult to quantitate, using conventional CAT assays. Thus, investigators have used cell activating agents or co-transfection of the cell lines with a second enhancer plasmid to yield higher levels of CAT activity. However, such measures can interfere with the cellular pathways studied and eventually alter the results. To avoid this problem, our laboratory has designed an RT-PCR assay to quantitate CAT mRNA. The ability of this assay to detect CAT mRNA but not CAT DNA demonstrates its specificity and is achieved using a tailed oligoprimer for the reverse transcription step. This assay is able to measure the equivalent of as few as eight copies of CAT mRNA, is reproducible and relatively easy to perform. The quantitative capability of the assay relies on a constant production of CAT mRNA, which is achieved using permanently transfected and cloned cell lines bearing a defined number of CAT DNA copies per cell. This assay provides a tool for monitoring events at the transcriptional level and thereby complements the currently used CAT ELISA and thin-layer chromatography assays.
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Affiliation(s)
- M Knuchel
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322
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28
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Michael NL, D'Arcy L, Ehrenberg PK, Redfield RR. Naturally occurring genotypes of the human immunodeficiency virus type 1 long terminal repeat display a wide range of basal and Tat-induced transcriptional activities. J Virol 1994; 68:3163-74. [PMID: 7908701 PMCID: PMC236807 DOI: 10.1128/jvi.68.5.3163-3174.1994] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The primary body of information on the structure of human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR)/gag leader genotypes has been determined from the analysis of cocultivated isolates. Functional studies of this regulatory portion of the provirus have been derived from the study of in vitro-generated mutations of laboratory-adapted molecular clones of HIV-1. We have performed a longitudinal analysis of molecular clones from the LTR/gag leader region amplified directly from the peripheral blood of four patients over three years. We have found a remarkable number of point mutations and length polymorphisms in cis- and trans-acting regulatory elements within this cohort. Most of the length polymorphisms were associated with duplications of Sp1 and TCF-1 alpha sequences. These mutations were associated with a wide range of transcriptional activities for these genotypes in a reporter gene assay. Mutations in conserved Sp1 sequences correlated with a diminished capacity of such genotypes to bind purified Sp1 protein. Although no generalized trend in transcriptional activity was seen, a single patient accumulated mutations in NF-kappa B, Sp1, and TAR elements over this period. The analysis of naturally occurring mutations of LTR genotypes provides a means to study the molecular genetic consequences of virus-host interactions and to assess the functional impact of HIV therapeutics.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA-Binding Proteins/metabolism
- Gene Products, tat/pharmacology
- Genes, Reporter
- Genes, gag/genetics
- Genotype
- HIV Infections/blood
- HIV Long Terminal Repeat/genetics
- HIV-1/genetics
- Humans
- Leukocytes, Mononuclear/microbiology
- Lymphoid Enhancer-Binding Factor 1
- Molecular Sequence Data
- Point Mutation
- Polymorphism, Restriction Fragment Length
- Protein Binding
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Homology, Nucleic Acid
- Sp1 Transcription Factor/metabolism
- T Cell Transcription Factor 1
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- N L Michael
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland
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29
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Tillmann M, Krebs FC, Wessner R, Pomeroy SM, Goodenow MM, Wigdahl B. Neuroglial-specific factors and the regulation of retrovirus transcription. ADVANCES IN NEUROIMMUNOLOGY 1994; 4:305-18. [PMID: 7874399 DOI: 10.1016/s0960-5428(06)80271-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Retroviruses have been implicated as causative agents of a variety of human diseases including malignancy, immune system dysfunction, and neurologic disorders. Despite the isolation of various retroviral agents from patients suffering from malignant neoplasias and neurologic disorders, only the human T-cell lymphotropic virus type I (HTLV-I) and the human immunodeficiency virus (HIV) have been definitively accepted as etiologic agents of human disease (Hjelle, 1991; Gessain and Gout, 1992; Rosenblatt, 1993). Because of their increasingly defined roles in disease progression, the replication of HTLV-I and HIV is an important focus for understanding the pathogenic processes resulting from viral infection. Of particular interest are the molecular mechanisms by which expression of retroviral genomes is regulated by their regulatory units, the long terminal repeats (LTR), in a manner specific to the cellular targets which they infect.
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Affiliation(s)
- M Tillmann
- Department of Microbiology and Immunology, Pennsylvania State University, College of Medicine, Hershey 17033
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30
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Antoni BA, Stein SB, Rabson AB. Regulation of human immunodeficiency virus infection: implications for pathogenesis. Adv Virus Res 1994; 43:53-145. [PMID: 8191958 DOI: 10.1016/s0065-3527(08)60047-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- B A Antoni
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854
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31
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Golub EI, Radding CM, Ward DC. Inhibition of RNA polymerase II transcription by oligonucleotide-RecA protein filaments targeted to promoter sequences. Proc Natl Acad Sci U S A 1993; 90:7186-90. [PMID: 8346234 PMCID: PMC47101 DOI: 10.1073/pnas.90.15.7186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In the presence of RecA protein, which plays a major role in genetic recombination in Escherichia coli, an oligodeoxyribonucleotide can find its homologous counterpart in double-stranded DNA and form triple-stranded structures. A triple-stranded structure formed by an oligonucleotide with a sequence overlapping essential regulatory elements of a viral promoter, such as TATA or GC boxes, inhibited in vitro transcription driven by RNA polymerase II. An oligonucleotide with eight nucleotides homologous to its target suppressed RNA polymerase II activity in HeLa cell extracts. This procedure offers a potential alternative to the usual mutational analysis of transcriptional promoters.
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Affiliation(s)
- E I Golub
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
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32
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Schuitemaker H, Groenink M, Meyaard L, Kootstra NA, Fouchier RA, Gruters RA, Huisman HG, Tersmette M, Miedema F. Early replication steps but not cell type-specific signalling of the viral long terminal repeat determine HIV-1 monocytotropism. AIDS Res Hum Retroviruses 1993; 9:669-75. [PMID: 8369171 DOI: 10.1089/aid.1993.9.669] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The expression of human immunodeficiency virus type 1 (HIV-1) is enhanced after cell activation because of the interaction of cell-encoded nuclear factors that interact with binding sites in the long terminal repeats (LTRs). Here we studied the contribution of cell type-specific activation signals to differences in cytotropism of HIV-1 variants. Four closely related molecular HIV-1 clones with distinct biological phenotypes and different capacities to replicate in primary monocyte-derived macrophages (MDMs) or T cell lines were used. Sequence analysis of these LTRs revealed variation in functionally important regions. Adaptation of virus variants to particular host cells by differences in LTR responsiveness was analyzed. LTR-CAT constructs were transiently transfected in T cells that were stimulated with T cell-specific activation signals such as combinations of anti-CD3 or anti-CD28 MoAB or in primary monocytes that were stimulated with IL-3, IL-4, or GM-CSF. No differences in responsiveness to cell type-specific signals were demonstrated. To further elucidate the level of restriction in cell tropism, transfection of four full-length infectious molecular HIV-1 clones into 5-day cultured MDMs was performed. From all clones, competent virus could be rescued from MDMs by coculture with PHA-stimulated PBLs. However, following cell-free inoculation, proviral DNA could be detected by PCR analysis only in monocytes exposed to HIV-1 clones that previously were shown to establish productive infection.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- H Schuitemaker
- Central Laboratory of The Netherlands Red Cross Blood Transfusion Service, Amsterdam
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33
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Li G, Simm M, Potash MJ, Volsky DJ. Human immunodeficiency virus type 1 DNA synthesis, integration, and efficient viral replication in growth-arrested T cells. J Virol 1993; 67:3969-77. [PMID: 8099628 PMCID: PMC237764 DOI: 10.1128/jvi.67.7.3969-3977.1993] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) replicates efficiently in nonproliferating monocytes and macrophages but not in resting primary T lymphocytes. To determine the contribution of cell division to the HIV-1 replicative cycle in T cells, we evaluated HIV-1 expression, integration of proviral DNA, and production of infectious progeny virus in C8166 T-lymphoid cells blocked in cell division by treatment with either mitomycin, a DNA cross-linker, or aphidicolin, a DNA polymerase alpha inhibitor. The arrest of cell division was confirmed by assay of [3H]thymidine uptake; the nondividing cells remained viable for at least 3 days after treatment. HIV-1 was expressed and replicated equally well in nondividing and dividing C8166 cells, as judged by the comparison of the levels of p24 core antigens in culture supernatants, the proportion of cells expressing HIV-1 specific antigens, the pattern and quantity of HIV-1 DNA present in the extrachromosomal and total cellular DNA fractions, and the biological activity of progeny viruses. A polymerase chain reaction-based viral DNA integration assay indicated that HIV-1 provirus was integrated in C8166 cells treated with either of the two inhibitors of cell division. Similar results were obtained by using growth-arrested Jurkat T-lymphoid cells. We conclude that cell division and cellular DNA synthesis are not required for efficient HIV-1 expression in T cells.
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Affiliation(s)
- G Li
- Molecular Virology Laboratory, St. Luke's/Roosevelt Hospital Center, New York, New York
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34
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Tan W, Fredriksson R, Björndal A, Balfe P, Fenyö EM. Cotransfection of HIV-1 molecular clones with restricted cell tropism may yield progeny virus with altered phenotype. AIDS Res Hum Retroviruses 1993; 9:321-9. [PMID: 8512747 DOI: 10.1089/aid.1993.9.321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Seven infectious molecular clones were obtained from a human immunodeficiency virus type 1 isolate with rapid/high replicative capacity. Biological characterization of progeny viruses obtained after transfection of clones into peripheral blood mononuclear cells showed that six clones yielded virus with restricted cell tropism, whereas one clone yielded virus able to replicate in cell lines. Although transfection of each of the clones 12, 13, and 82 individually gave rise to viruses with restricted tropism, viruses recovered from cotransfection of the mixtures of these clones exhibited altered phenotype, inasmuch as they were able to replicate in cell lines. To test whether recombination and/or complementation has taken place in the mixture of clones 12 + 13 + 82, the progeny virus was diluted to end point in 15 parallel series. Viruses with diverse biological phenotypes were recovered. With the help of distinctive restriction enzyme markers in regions comprising the vpu/env junction and variable regions 4 and 5 (V4/V5) of the env gene, recombinant genotypes could be identified with high frequency. No particular biological phenotype could be linked to a certain genotype in this study. The results show that different coexisting variants may interact and thereby influence the biological phenotype of a viral population.
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Affiliation(s)
- W Tan
- Department of Virology, School of Medicine, Karolinska Institute, Stockholm, Sweden
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35
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Delassus S, Meyerhans A, Cheynier R, Wain-Hobson S. Absence of selection of HIV-1 variants in vivo based on transcription/transactivation during progression to AIDS. Virology 1992; 188:811-8. [PMID: 1350126 DOI: 10.1016/0042-6822(92)90536-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The activity of the human immunodeficiency virus type 1 (HIV-1) transactivation protagonists tat and TAR has been analyzed from sequential primary material. The sequences were amplified from uncultured peripheral blood mononuclear cells. Despite fluctuations within the tat and TAR quasispecies there was no obvious selection for a variant encoding more powerful transactivation components either in vivo or ex vivo, indicating that this system is not exploited during disease progression. The basal levels of the natural promoters were, depending on the cell line, two- to fourfold higher than that of the reference promoter, itself derived from ex vivo adapted HIV-1 Lai.
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Affiliation(s)
- S Delassus
- Laboratoire de Rétrovirologie Moléculaire, Institut Pasteur, Paris
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36
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Velpandi A, Nagashunmugam T, Otsuka T, Cartas M, Srinivasan A. Structure–Function Studies of HIV-1: Influence of Long Terminal Repeat U3 Region Sequences on Virus Production. DNA Cell Biol 1992; 11:369-76. [PMID: 1351391 DOI: 10.1089/dna.1992.11.369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
DNA sequence analyses of several human immunodeficiency virus (HIV) isolates revealed extensive genetic diversity in the env gene and, to a lesser extent, in other regions of the viral genome, including the long terminal repeat (LTR) sequences. Since the LTRs contain elements responsible for the control of transcription, the difference in the LTR region may play a crucial role in the overall replication rate of HIV. To evaluate the role of the LTR, we have constructed a number of infectious hybrid HIV molecular clones containing LTRs from different proviral DNAs linked to the body of the viral genome, and analyzed them in a transient expression system. Both parental and hybrid proviral DNAs were transfected into human rhabdomyosarcoma cells for monitoring virus production. Proviral DNA designate pZ6 (HIVZr6) showed a high level of virus in the medium of the transfected culture in comparison to the pHXB2 (HIVHTLV-III) and pARV (HIVSF-2) DNAs. Hybrid proviral DNAs containing viral genes from pZ6, linked to LTR U3 sequences of pHXB2 and pARV at the 5' end, showed virus production similar to the levels observed with pZ6. These results indicate that the extent of virus production does not correlate with the LTR U3 sequences, and may involve other regions of the viral genome.
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Affiliation(s)
- A Velpandi
- Wistar Institute of Anatomy and Biology, Philadelphia, PA 19104
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37
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Boris-Lawrie KA, Brady JN, Kumar A. Sequences within the R region of the long terminal repeat activate basal transcription from the HIV-1 promoter. Gene Expr 1992; 2:215-30. [PMID: 1450662 PMCID: PMC6057376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/1991] [Accepted: 03/11/1992] [Indexed: 12/27/2022]
Abstract
The importance of the R region in basal human immunodeficiency virus type 1 (HIV-1) transcription was addressed by comparing a panel of HIV-1 R region mutants using in vitro and in vivo assays. Using deletion, base substitution mutants, and compensatory mutants, the precise R region sequences essential for basal HIV-1 promoter activity in vitro were mapped to sequences between +17 to +21. Within this regulatory domain, nucleotides +19 and +21 appear to be critical. The effect of these mutations on steady state RNA levels in transfected cells has been analyzed by S1 nuclease protection assay using uniformly labeled probes. Two main conclusions may be drawn from these studies. First, HIV-1 basal transcription is abundant, with the majority of correctly initiated transcripts truncated between sequences +57 to +70. Second, analysis of the compensatory mutants indicates the secondary structure of the nascent R region RNA is not an obligate requirement for the production of the truncated transcripts. Mutations in R region primary sequence that selectively abolish the production of the truncated transcripts in vivo also exhibit reduced promoter activity in vitro. The appearance of high levels of truncated transcripts raise the interesting possibility that-similar to c-myc, c-myb, and c-fos--basal HIV-1 expression is regulated by transcription elongation.
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Affiliation(s)
- K A Boris-Lawrie
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, D.C. 20037
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38
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Wain-Hobson S. Human immunodeficiency virus type 1 quasispecies in vivo and ex vivo. Curr Top Microbiol Immunol 1992; 176:181-93. [PMID: 1600752 DOI: 10.1007/978-3-642-77011-1_12] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S Wain-Hobson
- Laboratoire de Rétrovirologie Moléculaire, Institut Pasteur, Paris, France
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Cann AJ, Churcher MJ, Boyd M, O'Brien W, Zhao JQ, Zack J, Chen IS. The region of the envelope gene of human immunodeficiency virus type 1 responsible for determination of cell tropism. J Virol 1992; 66:305-9. [PMID: 1727490 PMCID: PMC238288 DOI: 10.1128/jvi.66.1.305-309.1992] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Different isolates of human immunodeficiency virus type 1 (HIV-1) vary in the cell tropisms they display, i.e., the range of cell types in which they are able to establish a productive infection. Here, we report on the phenotypes of recombinants between two molecularly cloned strains of HIV-1. Our results prove that the envelope glycoprotein gp120 is solely responsible for the difference in cell tropism between the two parental isolates and that no other genes or sequences are involved in determining the cell tropism of these strains. The region of the envelope involved in the determination of cell tropism includes sequences which encode the V3 loop of gp120. Control of cell tropism by this region of the virus env gene is a general phenomenon which applies to many different HIV-1 isolates.
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Affiliation(s)
- A J Cann
- Department of Microbiology, University of Leicester, United Kingdom
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40
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Abstract
Animal cells differ in susceptibility to HIV-1 infection. To identify rodent cells which are permissive to HIV-1 replication, we transfected murine and rat cells with an infectious clone of HIV-1 and a vector containing the chloramphenicol acetyl transferase gene under the control of HIV-1 LTR. Three groups of transfectants were distinguished: (i) Cells which permit neither HIV-1 LTR activation nor viral protein expression; (ii) Cells which permit activation of the HIV-1 LTR but not HIV-1 protein expression; and (iii) Cells which are fully permissive to both HIV-1 LTR activation and virus production. The latter included rat embryonal fibroblastoid (Rat2) cells, which, in short-term transfection assays, produced titers of HIV-1 proteins similar to transfected T lymphoid cells. To establish persistently infected cells, Rat2 cells were stably transfected with a plasmid containing an infectious clone of HIV-1/N1T-A and a neo gene, yielding several G-418-resistant, HIV-1-producing cell cultures. Of these, Rat2/A1 and Rat2/A2 cell cultures expressed up to 60 ng HIV-1 p24 core antigen per 1 x 10(6) cells 3 days after cell subculture over a period of 3 months. Southern blot hybridization revealed that Rat2/A1 and Rat2/A2 carried one to two HIV-1 DNA copies per cell; no rearrangements or deletions in viral DNA were present. Restriction endonuclease analysis of HIV-1 DNA in Rat2/A2 cells suggested clonal expansion of cells containing integrated HIV-1 genome. Virus produced by the Rat2/A1 cells was infectious in human T cells. These data demonstrate that some rodent cells have no inherent restriction to persistent and efficient production of infectious HIV-1.
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Affiliation(s)
- Y Mizrachi
- Molecular Virology Laboratory, St. Luke's/Roosevelt Hospital Center, Columbia University, New York, New York 10019
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41
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Sakai K, Ma XY, Gordienko I, Volsky DJ. Recombinational analysis of a natural noncytopathic human immunodeficiency virus type 1 (HIV-1) isolate: role of the vif gene in HIV-1 infection kinetics and cytopathicity. J Virol 1991; 65:5765-73. [PMID: 1920615 PMCID: PMC250237 DOI: 10.1128/jvi.65.11.5765-5773.1991] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Two molecularly cloned coisolates of human immunodeficiency virus type 1 (HIV-1) have been found to exhibit different phenotypes of viral expression, either rapid and cytopathic (N1T-A virus) or delayed and noncytopathic (N1T-E virus [X. Ma, K. Sakai, F. Sinangil, E. Golub, and D. J. Volsky, Virology 176:184-194, 1990]). To identify the viral genetic elements responsible for these phenotypes, we prepared reciprocal recombinants in different regions of N1T-A and N1T-E viral genomes. Infectivity experiments with the recombinant viruses revealed that the rapid/cytopathic (N1T-A-like) phenotype assorted cleanly with the V1f-coding region and Vif expression. The smallest HIV-1 DNA region that conferred the complete phenotypic switch was a 284-bp NdeI-StuI fragment within the vif open reading frame. Nucleotide sequence analysis revealed a 35-bp deletion starting at nucleotide 218 in the N1T-E vif gene. A 23-kDa Vif protein was detected by immunoblotting using Vif-specific antiserum in extracts of cells infected with N1T-A but not N1T-E virus. No detectable vif protein was found in association with sedimented particles of either virus. Cotransfection of a eucaryotic vif expression plasmid with N1T-E DNA complemented the N1T-E defect; rapid/cytopathic infection similar to that in N1T-A-transfected cells was observed. We conclude that Vif controls the rate, and consequently the cytopathic outcome, of HIV-1 infection.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Southern
- Blotting, Western
- Cell Line
- Cloning, Molecular
- DNA, Viral/genetics
- Gene Expression
- Gene Products, vif/analysis
- Gene Products, vif/genetics
- Genes, vif
- Genetic Complementation Test
- HIV-1/genetics
- HIV-1/isolation & purification
- HIV-1/physiology
- Humans
- Kinetics
- Molecular Sequence Data
- Phenotype
- Proviruses/genetics
- Recombination, Genetic
- Restriction Mapping
- Sequence Homology, Nucleic Acid
- Transfection
- vif Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- K Sakai
- Molecular Virology Laboratory, St. Luke's Roosevelt Hospital Center, New York, New York
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42
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Nakanishi Y, Masamune Y, Kobayashi N. A novel cis-acting element that controls transcription of human immunodeficiency virus type 1 DNA, depending on cell type. J Virol 1991; 65:6334-8. [PMID: 1920636 PMCID: PMC250349 DOI: 10.1128/jvi.65.11.6334-6338.1991] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
cis-acting elements for the transcription of human immunodeficiency virus type 1 DNA were analyzed in cell-free transcription and DNA transfection assays. Besides previously identified cis elements, a region adjacent to the enhancer element was found to regulate transcription in both assays. Loss of this region caused 4.3- and 1.6-fold transcription inhibition in a transfection assay with a T-cell line, MOLT-4, and a monocyte line, U937, respectively, whereas the same region appeared to function negatively with other T-cell lines, MT-4 and Jurkat. These results suggest that this novel cis element regulates the transcription of proviral DNA in a cell-type-specific manner.
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Affiliation(s)
- Y Nakanishi
- Faculty of Pharmaceutical Sciences, Kanazawa University, Japan
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43
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Velpandi A, Nagashunmugam T, Murthy S, Cartas M, Monken C, Srinivasan A. Generation of hybrid human immunodeficiency virus utilizing the cotransfection method and analysis of cellular tropism. J Virol 1991; 65:4847-52. [PMID: 1678438 PMCID: PMC248943 DOI: 10.1128/jvi.65.9.4847-4852.1991] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human immunodeficiency viruses (HIV) isolated from infected individuals show tremendous genetic and biologic diversity. To delineate the genetic determinants underlying specific biologic characteristics, such as rate of replication, cytopathic effects, and ability to infect macrophages and T4 lymphoid cells, generation of hybrid HIV using viruses which exhibit distinct biologic features is essential. To develop methods for generating hybrid HIV, we constructed truncated HIV proviral DNA plasmids. Upon digestion with restriction enzymes, these plasmid DNAs were cotransfected into human rhabdomyosarcoma cells to generate hybrid HIV. The hybrid HIVs derived by this method were infectious upon transmission to both phytohemagglutinin-stimulated peripheral blood lymphocytes and established human leukemic T-cell lines. The virus derived from molecular clone pHXB2 (HIVHTLV-III) productively infected CEMx174 cells. On the other hand, molecular clone pARV (HIVSF2)-derived virus did not show productive infection of CEMx174 cells when used as a cell-free virus. The hybrid HIV containing the 3' end of the genome from pARV and the 5' end of the genome from pHXB2 was effective in infecting CEMx174 cells, but the converse hybrid containing 5' pARV and 3' pHXB2 was not effective in infecting CEMx174 cells. These results suggest that differences in the genes outside of env and nef play a role in the ability of the virus to infect a certain cell type. The intracellular ligation method should be useful in the analysis of related and unrelated HIV-1 isolates with common restriction enzyme cleavage sites.
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Affiliation(s)
- A Velpandi
- Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania 19104-4268
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44
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Alexandersen S, Carpenter S. Characterization of variable regions in the envelope and S3 open reading frame of equine infectious anemia virus. J Virol 1991; 65:4255-62. [PMID: 1649329 PMCID: PMC248863 DOI: 10.1128/jvi.65.8.4255-4262.1991] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The polymerase chain reaction was used to amplify and clone parts of the envelope gene and overlapping S3 open reading frame, thought to encode rev, of the virulent in vivo-derived Th-1 isolate of equine infectious anemia virus (EIAV). The results indicated that EIAV consists of a heterogeneous mixture of genotypes present at the first febrile cycle after initial infection. We showed that the Th-1 isolate apparently contains nondefective genotypes as well as types which have transmembrane protein truncations or are rev deficient. Furthermore, we could confirm the presence of a hypervariable region in the gp90 envelope glycoprotein. Taken together with earlier data on the heterogeneity of the regulatory motifs present in the long terminal repeat sequences of viruses from the same in vivo isolate (S. Carpenter, S. Alexandersen, M. J. Long, S. Perryman, and B. Chesebro, J. Virol. 65:1605-1610, 1991), our findings indicate that EIAV uses a complex system of diversity in biological phenotypes together with variation in regulatory and antigenic makeup to evade host response and to cause persistent infection and recurrent chronic disease.
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Affiliation(s)
- S Alexandersen
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames 50011
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45
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1991; 19:4025-42. [PMID: 1862010 PMCID: PMC328534 DOI: 10.1093/nar/19.14.4025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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46
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Cooney AJ, Tsai SY, O'Malley BW, Tsai MJ. Chicken ovalbumin upstream promoter transcription factor binds to a negative regulatory region in the human immunodeficiency virus type 1 long terminal repeat. J Virol 1991; 65:2853-60. [PMID: 2033658 PMCID: PMC240909 DOI: 10.1128/jvi.65.6.2853-2860.1991] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) contains a negative regulatory element (NRE) which downregulates the rate of LTR-directed transcription and HIV-1 replication. Within the NRE is a GGTCA palindrome, which binds a possible member of the steroid/thyroid hormone receptor superfamily. Mutation of this site leads to an increase in LTR-directed transcriptional activity compared with the wild type, consistent with the element's being a functional part of the NRE. The palindrome contains significant identity to the chicken ovalbumin upstream promoter (COUP) element to which COUP transcription factors (COUP-TFs), members of the steroid/thyroid hormone receptor superfamily, bind. We demonstrate here that human COUP-TFs can bind specifically to this HIV-1 COUP-like element in a manner identical to binding to ovalbumin COUP. We show that the predominant COUP-TF family member synthesized in T cells is the 68-kDa form, which is likely to be responsible for any in vivo function of the HIV-1 COUP-like element in these cells. Finally, we have identified three HIV-1 variant strains that contain mutations in the HIV-1 COUP-like element which affect the binding affinity of COUP-TF for these variant COUP elements.
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Affiliation(s)
- A J Cooney
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
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47
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Wain-Hobson S, Vartanian JP, Henry M, Chenciner N, Cheynier R, Delassus S, Martins LP, Sala M, Nugeyre MT, Guétard D. LAV revisited: origins of the early HIV-1 isolates from Institut Pasteur. Science 1991; 252:961-5. [PMID: 2035026 DOI: 10.1126/science.2035026] [Citation(s) in RCA: 175] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two of the first human immunodeficiency virus type-1 (HIV-1) strains isolated were authenticated by reanalyzing original cultured samples stored at the Collection Nationale de Culture des Microorganismes as well as uncultured primary material. Cloned polymerase chain reaction products were used to analyze coding sequences of the V3 loop in the gp120 glycoprotein. The original isolate HIV-1 Bru, formerly called LAV, was derived from patient BRU. HIV-1 Lai was derived from patient LAI and contaminated a HIV-1 Bru culture between 20 July and 3 August 1983. The culture became, in effect, HIV-1 Lai, identifiable by a unique motif in the V3 loop. Because of this contamination two, rather than one, HIV-1 isolates were sent to the Laboratory of Tumor Cell Biology at the National Cancer Institute on 23 September 1983. Original HIV-1 Bru was indeed present in the sample marked JBB/LAV. However the M2T-/B sample harbored HIV-1 Lai, a strain capable of growing on established cell lines. The striking similarity between HIV-1 Lai (formerly LAV-Bru) and HTLV-3B sequences remains.
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Affiliation(s)
- S Wain-Hobson
- Laboratoire de Rétrovirologie Moléculaire, Institut Pasteur, Paris
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48
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Carpenter S, Alexandersen S, Long MJ, Perryman S, Chesebro B. Identification of a hypervariable region in the long terminal repeat of equine infectious anemia virus. J Virol 1991; 65:1605-10. [PMID: 1847479 PMCID: PMC239946 DOI: 10.1128/jvi.65.3.1605-1610.1991] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An avirulent, field-derived isolate of equine infectious anemia virus (EIAV), designated MA-1, was molecularly cloned, and the complete nucleotide sequence was determined for the 3' half of the viral genome. Comparisons between MA-1 and the prototype Wyoming strain of EIAV identified a 66-nucleotide stretch between CAAT (-91) and TATAA (-25) in the U3 region of the long terminal repeat, where sequence divergence was as high as 39.3%. The polymerase chain reaction was used to amplify and clone long terminal repeat sequences from Th-1, the in vivo parental stock of MA-1. Results indicated that the nucleotide sequences of MA-1 and Th-1 clones were less variable than was observed between MA-1 and Wyoming. However, MA-1 and Th-1 markedly differed in the types of enhancer sequences located in the hypervariable region. These results suggest that variation in lentivirus regulatory sequences may be important in EIAV host cell tropism and pathogenesis.
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Affiliation(s)
- S Carpenter
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames 50011
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49
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The long terminal repeat is not a major determinant of the cellular tropism of human immunodeficiency virus type 1. J Virol 1991; 65:1041-5. [PMID: 1987367 PMCID: PMC239855 DOI: 10.1128/jvi.65.2.1041-1045.1991] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The long terminal repeats (LTRs) of human immunodeficiency virus type 1 (HIV-1) strains from the central nervous systems of four patients with AIDS and of an HIV-1 isolate which is highly macrophage-tropic were isolated by using the polymerase chain reaction. In transient transfection assays, these LTRs demonstrated no significant difference in basal or stimulated levels of transcription in any of a variety of cell lines tested, compared with expression directed from the LTR of a T-lymphocyte-tropic strain of HIV-1. Chimeric viruses were created with the LTRs of the macrophage-tropic and brain-derived viruses ligated to the viral backbone from a T-lymphocyte-tropic strain. No change in cellular tropism was demonstrated with these chimeric viruses. Thus, unlike the LTRs of some murine retroviruses, the LTR of HIV-1 does not appear to play a major role in determining cellular tropism.
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50
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