1
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Panei FP, Gkeka P, Bonomi M. Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN. Nat Commun 2024; 15:5725. [PMID: 38977675 PMCID: PMC11231146 DOI: 10.1038/s41467-024-49638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/05/2024] [Indexed: 07/10/2024] Open
Abstract
The rational targeting of RNA with small molecules is hampered by our still limited understanding of RNA structural and dynamic properties. Most in silico tools for binding site identification rely on static structures and therefore cannot face the challenges posed by the dynamic nature of RNA molecules. Here, we present SHAMAN, a computational technique to identify potential small-molecule binding sites in RNA structural ensembles. SHAMAN enables exploring the conformational landscape of RNA with atomistic molecular dynamics simulations and at the same time identifying RNA pockets in an efficient way with the aid of probes and enhanced-sampling techniques. In our benchmark composed of large, structured riboswitches as well as small, flexible viral RNAs, SHAMAN successfully identifies all the experimentally resolved pockets and ranks them among the most favorite probe hotspots. Overall, SHAMAN sets a solid foundation for future drug design efforts targeting RNA with small molecules, effectively addressing the long-standing challenges in the field.
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Affiliation(s)
- F P Panei
- Integrated Drug Discovery, Molecular Design Sciences, Sanofi, Vitry-sur-Seine, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France
- Sorbonne Université, Ecole Doctorale Complexité du Vivant, Paris, France
| | - P Gkeka
- Integrated Drug Discovery, Molecular Design Sciences, Sanofi, Vitry-sur-Seine, France.
| | - M Bonomi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
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2
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Ma Y, Mao G, Wu G, Zhang XE. Single-Particle Tracking Reveals the Interplay between HIV-1 Reverse Transcription and Uncoating. Anal Chem 2022; 94:2648-2654. [PMID: 35080851 DOI: 10.1021/acs.analchem.1c05199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reverse transcription uses the reverse transcriptase enzyme to synthesize deoxyribonucleic acid (DNA) from a ribonucleic acid (RNA) template. This plays an essential role in viral replication. There are still, however, many unknown facts regarding the timing and dynamic processes involved in this life stage. Here, three types of dual-fluorescence human immunodeficiency virus type-1 (HIV-1) particles were constructed with high infectivity, and the sequential process of reverse transcription was observed by real-time imaging of a single HIV-1 particle. Viral uncoating occurred at 60-120 min post infection. Subsequently, at 120-180 min post infection, the viral genome was separated into two parts and reverse-transcribed to generate a DNA product. Nevirapine (NVP), a reverse transcriptase inhibitor, can delay the dynamic process. This study revealed a delicate, sequential, and complex relationship between uncoating and reverse transcription, which may facilitate the development of antiviral drugs.
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Affiliation(s)
- Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guoqiang Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,National Key Laboratory of Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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3
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Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucleic Acids Res 2018; 46:6401-6415. [PMID: 29961805 PMCID: PMC6061845 DOI: 10.1093/nar/gky529] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Natural and lab-evolved proteins often recognize their RNA partners with exquisite affinity. Structural analysis of such complexes can offer valuable insight into sequence-selective recognition that can be exploited to alter biological function. Here, we describe the structure of a lab-evolved RNA recognition motif (RRM) bound to the HIV-1 trans-activation response (TAR) RNA element at 1.80 Å-resolution. The complex reveals a trio of arginines in an evolved β2-β3 loop penetrating deeply into the major groove to read conserved guanines while simultaneously forming cation-π and salt-bridge contacts. The observation that the evolved RRM engages TAR within a double-stranded stem is atypical compared to most RRMs. Mutagenesis, thermodynamic analysis and molecular dynamics validate the atypical binding mode and quantify molecular contributions that support the exceptionally tight binding of the TAR-protein complex (KD,App of 2.5 ± 0.1 nM). These findings led to the hypothesis that the β2-β3 loop can function as a standalone TAR-recognition module. Indeed, short constrained peptides comprising the β2-β3 loop still bind TAR (KD,App of 1.8 ± 0.5 μM) and significantly weaken TAR-dependent transcription. Our results provide a detailed understanding of TAR molecular recognition and reveal that a lab-evolved protein can be reduced to a minimal RNA-binding peptide.
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Affiliation(s)
- Ivan A Belashov
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - David W Crawford
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Chapin E Cavender
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick C Beardslee
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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4
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Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. J Med Chem 2016; 59:11148-11160. [PMID: 28002966 DOI: 10.1021/acs.jmedchem.6b01450] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Small molecules that bind to RNA potently and specifically are relatively rare. The study of molecules that bind to the HIV-1 transactivation response (TAR) hairpin, a cis-acting HIV genomic element, has long been an important model system for the chemistry of targeting RNA. Here we report the synthesis, biochemical, and structural evaluation of a series of molecules that bind to HIV-1 TAR RNA. A promising analogue, 15, retained the TAR binding affinity of the initial hit and displaced a Tat-derived peptide with an IC50 of 40 μM. NMR characterization of a soluble analogue, 2, revealed a noncanonical binding mode for this class of compounds. Finally, evaluation of 2 and 15 by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in binding to TAR within the context of an in vitro-synthesized 365-nt HIV-1 5'-untranslated region (UTR). Thus, these compounds exhibit a novel and specific mode of interaction with TAR, providing important suggestions for RNA ligand design.
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5
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Wadford DA, Kauffman RC, Deere JD, Aoki ST, Stanton RA, Higgins J, Van Rompay KKA, Villalobos A, Nettles JH, Schinazi RF, Pedersen NC, North TW. Variation of human immunodeficiency virus type-1 reverse transcriptase within the simian immunodeficiency virus genome of RT-SHIV. PLoS One 2014; 9:e86997. [PMID: 24498008 PMCID: PMC3909041 DOI: 10.1371/journal.pone.0086997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/17/2013] [Indexed: 11/25/2022] Open
Abstract
RT-SHIV is a chimera of simian immunodeficiency virus (SIV) containing the reverse transcriptase (RT)-encoding region of human immunodeficiency virus type 1 (HIV-1) within the backbone of SIVmac239. It has been used in a non-human primate model for studies of non-nucleoside RT inhibitors (NNRTI) and highly active antiretroviral therapy (HAART). We and others have identified several mutations that arise in the "foreign" HIV-1 RT of RT-SHIV during in vivo replication. In this study we catalogued amino acid substitutions in the HIV-1 RT and in regions of the SIV backbone with which RT interacts that emerged 30 weeks post-infection from seven RT-SHIV-infected rhesus macaques. The virus set points varied from relatively high virus load, moderate virus load, to undetectable virus load. The G196R substitution in RT was detected from 6 of 7 animals at week 4 post-infection and remained in virus from 4 of 6 animals at week 30. Virus from four high virus load animals showed several common mutations within RT, including L74V or V75L, G196R, L214F, and K275R. The foreign RT from high virus load isolates exhibited as much variation as that of the highly variable envelope surface glycoprotein, and 10-fold higher than that of the native RT of SIVmac239. Isolates from moderate virus load animals showed much less variation in the foreign RT than the high virus load isolates. No variation was found in SIVmac239 genes known to interact with RT. Our results demonstrate substantial adaptation of the foreign HIV-1 RT in RT-SHIV-infected macaques, which most likely reflects selective pressure upon the foreign RT to attain optimal activity within the context of the chimeric RT-SHIV and the rhesus macaque host.
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Affiliation(s)
- Debra A. Wadford
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Robert C. Kauffman
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Jesse D. Deere
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Scott T. Aoki
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Richard A. Stanton
- Children's Center for Drug Discovery (CDD), Departments of Pediatrics and Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Joanne Higgins
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Andradi Villalobos
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - James H. Nettles
- Children's Center for Drug Discovery (CDD), Departments of Pediatrics and Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Raymond F. Schinazi
- Emory University School of Medicine, Veterans Affairs Medical Center, Decatur, Georgia, United States of America
| | - Niels C. Pedersen
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Thomas W. North
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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6
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Lalonde MS, Lobritz MA, Ratcliff A, Chamanian M, Athanassiou Z, Tyagi M, Wong J, Robinson JA, Karn J, Varani G, Arts EJ. Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS Pathog 2011; 7:e1002038. [PMID: 21625572 PMCID: PMC3098202 DOI: 10.1371/journal.ppat.1002038] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
The RNA response element TAR plays a critical role in HIV replication by
providing a binding site for the recruitment of the viral transactivator protein
Tat. Using a structure-guided approach, we have developed a series of
conformationally-constrained cyclic peptides that act as structural mimics of
the Tat RNA binding region and block Tat-TAR interactions at nanomolar
concentrations in vitro. Here we show that these compounds
block Tat-dependent transcription in cell-free systems and in cell-based
reporter assays. The compounds are also cell permeable, have low toxicity, and
inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and
CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and
CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic
L50 exhibited an IC50 ∼250 nM. Surprisingly, inhibition of
LTR-driven HIV-1 transcription could not account for the full antiviral
activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic
inhibition curve with the first phase occurring after HIV-1 entry into the host
cell and during the initiation of HIV-1 reverse transcription. The second phase
coincides with inhibition of HIV-1 transcription. Reconstituted reverse
transcription assays confirm that HIV-1 (−) strand strong stop DNA
synthesis is blocked by L50-TAR RNA interactions in-vitro.
These findings are consistent with genetic evidence that TAR plays critical
roles both during reverse transcription and during HIV gene expression. Our
results suggest that antiviral drugs targeting TAR RNA might be highly effective
due to a dual inhibitory mechanism. The HIV-1 transactivator protein (Tat), together with the elongation factor
P-TEFb binds to an HIV-1 RNA secondary structure in the 5′-UTRs of nascent
viral mRNAs (TAR) and promotes transcription elongation. This process has been
an attractive target for drug development but previous inhibitors that bind
either Tat or TAR have been plagued by poor inhibition of virus replication,
limited cell penetration, and off-target effects. In this article, we describe a
series of rationally designed cyclic peptides that block Tat-TAR interactions.
L50, the most potent of these compounds, inhibits a wide range of HIV-1 strains
from around the world. Remarkably, L50 inhibits two distinct steps in the HIV-1
lifecycle. As expected, L50 inhibits Tat-dependent HIV-1 transcription, but the
majority of its anti-HIV activity is due to a block in reverse transcription,
i.e. synthesis of the proviral DNA from the RNA genome. L50 inhibition of
reverse transcription reveals an important role for TAR RNA during reverse
transcription as well as providing one of first examples of a drug with a dual
mechanism of action.
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Affiliation(s)
- Matthew S. Lalonde
- Department of Biochemistry, Case Western
Reserve University, Cleveland, Ohio, United States of America
| | - Michael A. Lobritz
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Annette Ratcliff
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Mastooreh Chamanian
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Zafiria Athanassiou
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Mudit Tyagi
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Julian Wong
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - John A. Robinson
- Department of Chemistry, University of Zurich,
Zurich, Switzerland
| | - Jonathan Karn
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Gabriele Varani
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Eric J. Arts
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
- Division of Infectious Diseases, Department of
Medicine, Case Western Reserve University, Cleveland, Ohio, United States of
America
- * E-mail:
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7
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Dutta S, Bhaduri N, Rastogi N, Chandel SG, Vandavasi JK, Upadhayaya RS, Chattopadhyaya J. Carba-LNA modified siRNAs targeting HIV-1 TAR region downregulate HIV-1 replication successfully with enhanced potency. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00225a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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Pandey VN, Upadhyay A, Chaubey B. Prospects for antisense peptide nucleic acid (PNA) therapies for HIV. Expert Opin Biol Ther 2009; 9:975-89. [PMID: 19534584 DOI: 10.1517/14712590903052877] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of gene expression by targeting translation or transcription processes. This review discusses the present and future therapeutic potential of this class of compound as anti-HIV-1 drugs.
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Affiliation(s)
- Virendra N Pandey
- University of Medicine and Dentistry, New Jersey-New Jersey Medical School, Department of Biochemistry and Molecular Biology, Newark, NJ 07103, USA.
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9
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Brandt S, Grunwald T, Lucke S, Stang A, Überla K. Functional replacement of the R region of simian immunodeficiency virus-based vectors by heterologous elements. J Gen Virol 2006; 87:2297-2307. [PMID: 16847126 DOI: 10.1099/vir.0.81883-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Substitution of lentiviral cis-acting elements by heterologous sequences might allow the safety of lentiviral vectors to be enhanced by reducing the risk of homologous recombination and vector mobilization. Therefore, a substitution and deletion analysis of the R region of simian immunodeficiency virus (SIV)-based vectors was performed and the effect of the modifications on packaging and transfer by SIV and human immunodeficiency virus type 1 (HIV-1) particles was analysed. Deletion of the first 7 nt of R reduced vector titres by 10- to 20-fold, whilst deletion of the entire R region led to vector titres that were 1500-fold lower. Replacement of the R region of SIV-based vectors by HIV-1 or Moloney murine sarcoma virus R regions partially restored vector titres. A non-retroviral cellular sequence was also functional, although to a lesser extent. In the absence of tat, modification of the R region had only minor effects on cytoplasmic RNA stability, steady-state levels of vector RNA and packaging, consistent with the known primary function of R during reverse transcription. Although the SIV R region of SIV-based vectors could be replaced functionally by heterologous sequences, the same modifications of R led to a severe replication defect in the context of a replication-competent SIV. As SIV-based vectors containing the HIV-1 R region were transferred less efficiently by HIV-1 particles than wild-type SIV vectors, a match between R and cis-acting elements of the vector construct seems to be more important than a match between R and the Gag or Pol proteins of the vector particle.
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Affiliation(s)
- Sabine Brandt
- Department of Molecular and Medical Virology, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Thomas Grunwald
- Department of Molecular and Medical Virology, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Susann Lucke
- Department of Molecular and Medical Virology, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Alexander Stang
- Department of Molecular and Medical Virology, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Klaus Überla
- Department of Molecular and Medical Virology, Ruhr University Bochum, D-44780 Bochum, Germany
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10
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Sierra S, Kupfer B, Kaiser R. Basics of the virology of HIV-1 and its replication. J Clin Virol 2005; 34:233-44. [PMID: 16198625 DOI: 10.1016/j.jcv.2005.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Accepted: 09/02/2005] [Indexed: 11/17/2022]
Abstract
Human immunodeficiency virus is undoubtedly the causative agent of AIDS. The understanding of HIV-1 pathogenesis is essential to develop and maintain antiretroviral treatment and vaccination. Since the first isolation of HIV-1 in cell culture, thousands of publications dealing with HIV and/or AIDS per year were released. In this review we give a basic overview of the virology of HIV-1 including the functions of the different HIV-1 proteins required for effective viral replication. Moreover, we summarize the interactive processes between HIV-1 and its target cells. Finally, the HIV-1 specific immune response and the current status of antiretroviral therapy are briefly described in this review.
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Affiliation(s)
- Saleta Sierra
- Institute of Virology, University of Cologne, Fürst-Pückler Str. 56, D-50935 Cologne, Germany
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11
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Kanevsky I, Chaminade F, Ficheux D, Moumen A, Gorelick R, Negroni M, Darlix JL, Fossé P. Specific Interactions Between HIV-1 Nucleocapsid Protein and the TAR Element. J Mol Biol 2005; 348:1059-77. [PMID: 15854644 DOI: 10.1016/j.jmb.2005.03.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Accepted: 03/16/2005] [Indexed: 11/24/2022]
Abstract
During retroviral reverse transcription, the minus-strand strong-stop DNA (ss-cDNA) is transferred to the 3' end of the genomic RNA and this requires the repeat (R) sequences present at both ends of the genome. In vitro, the human immunodeficiency virus type 1 (HIV-1) R sequence can promote DNA strand transfer when present in ectopic internal positions. Using HIV-1 model systems, the R sequences and nucleocapsid protein (NC) were found to be key determinants of ss-cDNA transfer. To gain insights into specific interactions between HIV-1 NC and RNA and the influence of NC on R folding, we investigated the secondary structures of R in two natural contexts, namely at the 5' or 3' end of RNAs representing the terminal regions of the genome, and in two ectopic internal positions that also support efficient minus-strand transfer. To investigate the roles of NC zinc fingers and flanking basic domains in the NC/RNA interactions, we used NC mutants. Analyses of the viral RNA/NC complexes by chemical and enzymatic probings, and gel retardation assays were performed under conditions allowing ss-cDNA transfer by reverse transcriptase. We report that NC binds the TAR apical loop specifically in the four genetic contexts without changing the folding of the TAR hairpin and R region significantly, and this requires the NC zinc fingers. In addition, we show that efficient annealing of cTAR DNA to the 3' R relies on sequence complementarities between TAR and cTAR terminal loops. These findings suggest that the TAR apical loop in the acceptor RNA is the initiation site for the annealing reaction that is chaperoned by NC during the minus-strand transfer.
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Affiliation(s)
- Igor Kanevsky
- CNRS UMR8113, LBPA-Alembert, Ecole Normale Supérieure de Cachan, 94235 Cachan cedex, France
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12
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Bradrick TD, Marino JP. Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA. RNA (NEW YORK, N.Y.) 2004; 10:1459-68. [PMID: 15273324 PMCID: PMC1370632 DOI: 10.1261/rna.7620304] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Accepted: 05/28/2004] [Indexed: 05/22/2023]
Abstract
Replication of human immunodeficiency virus type 1 (HIV-1) is regulated in part through an interaction between the virally encoded trans-activator protein Tat and the trans-activator responsive region (TAR) of the viral RNA genome. Because TAR is highly conserved and its interaction with Tat is required for efficient viral replication, it has received much attention as an antiviral drug target. Here, we report a 2-aminopurine (2-AP) fluorescence-based assay for evaluating potential TAR inhibitors. Through selective incorporation of 2-AP within the bulge (C23 or U24) of a truncated form of the TAR sequence (delta TAR-ap23 and delta TAR-ap24), binding of argininamide, a 24-residue arginine-rich peptide derived from Tat, and Neomycin has been characterized using steady-state fluorescence. Binding of argininamide to the 2-AP deltaTAR constructs results in a four- to 11-fold increase in fluorescence intensity, thus providing a sensitive reporter of that interaction (KD approximately 1 mM). Similarly, binding of the Tat peptide results in an initial 14-fold increase in fluorescence (KD approximately 25 nM), but is then followed by a slight decrease that is attributed to an additional, lower-affinity association(s). Using the deltaTAR-ap23 and TAR-ap24 constructs, two classes of Neomycin binding sites are detected; the first molecule of antibiotic binds as a noncompetitive inhibitor of Tat/argininamide (KD approximately 200 nM), whereas the second, more weakly bound molecule(s) becomes associated in a presumably nonspecific manner (KD approximately 4 microM). Taken together, the results demonstrate that the 2-AP fluorescence-detected binding assays provide accurate and general methods for quantitatively assessing TAR interactions.
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Affiliation(s)
- Thomas D Bradrick
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland 20850, USA
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13
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Huigen MCDG, Kamp W, Nottet HSLM. Multiple effects of HIV-1 trans-activator protein on the pathogenesis of HIV-1 infection. Eur J Clin Invest 2004; 34:57-66. [PMID: 14984439 DOI: 10.1111/j.1365-2362.2004.01282.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The HIV-1 trans-activator (Tat) protein is proposed as an important factor in the complex HIV-induced pathogenesis of AIDS. In this paper, multiple effects of this viral protein are described. Originally discovered as an intracellular activator of HIV-1 transcription, Tat was found to regulate viral reverse transcription as well. Trans-activator was found to be secreted by HIV-infected cells and taken up by neighbouring cells. In this way, Tat is able to affect both infected and uninfected cells. Intracellularly, Tat can deregulate the expression of several heterologous cellular and viral genes. Extracellular Tat can contribute to the spreading of HIV-1 and immunosuppression of uninfected cells. Finally, there is evidence that exogenous Tat is involved in AIDS-associated pathologies such as Kaposi's sarcoma and HIV-associated dementia. These capacities together accelerate the progression towards AIDS and make Tat an interesting candidate as a constituent of an anti-AIDS vaccine.
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Affiliation(s)
- M C D G Huigen
- Eijkman-Winkler Center for Microbiology, Infectious Disease and Inflammation, Utrecht, The Netherlands
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14
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Beltz H, Azoulay J, Bernacchi S, Clamme JP, Ficheux D, Roques B, Darlix JL, Mély Y. Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7. J Mol Biol 2003; 328:95-108. [PMID: 12684000 DOI: 10.1016/s0022-2836(03)00244-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reverse transcription of HIV-1 genomic RNA to double-stranded DNA by reverse transcriptase (RT) is a critical step in HIV-1 replication. This process relies on two viral proteins, the RT enzyme and nucleocapsid protein NCp7 that has well documented nucleic acid chaperone properties. At the beginning of the linear DNA synthesis, the newly made minus-strand strong-stop DNA ((-)ssDNA) is transferred to the 3'end of the genomic RNA by means of an hybridization reaction between transactivation response element (TAR) RNA and cTAR DNA sequences. Since both TAR sequences exhibit stable hairpin structures, NCp7 needs to destabilize the TAR structures in order to chaperone their hybridization. To further characterize the relationships between TAR stability and NC-mediated destabilization, the role of the A(49) and G(52) bulged residues in cTAR DNA stability was investigated. The stability of cTAR and mutants where one or the two terminal bulges were replaced by base-pairs as well as the NCp7-mediated destabilization of these cTAR sequences were examined. Thermodynamic data indicate that the two bulges cooperatively destabilize cTAR by reducing the stacking interactions between the bases. This causes a free energy change of about 6.4 kcal/mol and seems to be critical for NC activity. Time-resolved fluorescence data of doubly labelled cTAR derivatives suggest that NC-mediated melting of cTAR ends propagates up to the 10C.A(44) mismatch or T(40) bulge. Fluorescence correlation spectroscopy using two-photon excitation was also used to monitor cTAR ends fraying by NC. Results show that NC causes a very significant increase of cTAR ends fraying, probably limited to the terminal base-pair in the case of cTAR mutants. Since the TAR RNA and cTAR DNA bulges or mismatches appear well conserved among all HIV-1 strains, the present data support the notion of a co-evolutionary relationship between TAR and NC activity.
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Affiliation(s)
- Hervé Beltz
- Laboratoire de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France
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15
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Guo X, Kameoka M, Wei X, Roques B, Gotte M, Liang C, Wainberg MA. Suppression of an intrinsic strand transfer activity of HIV-1 Tat protein by its second-exon sequences. Virology 2003; 307:154-63. [PMID: 12667823 DOI: 10.1016/s0042-6822(02)00068-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Tat protein of human immunodeficiency virus type 1 (HIV-1) has been shown to restrict premature reverse transcription at late stages of virus infection and to thus ensure the integrity of the viral RNA genome for packaging. To gain further insights into the roles of Tat in HIV-1 reverse transcription, we have assessed its effects on the first-strand transfer during the synthesis of minus-strand DNA through use of a reconstituted cell-free system. The results demonstrated that a form of Tat, containing only the first exon (Tat72), was able to enhance the first-strand transfer as efficiently as did the viral nucleocapsid protein. Coincidentally, this form of Tat was unable to inhibit the production of minus-strand strong-stop DNA. Further studies with various mutated forms of Tat showed that its Cys-rich region, rather than the core and Arg-rich domains, was essential for this strand transfer activity. Moreover, this activity of Tat is largely independent of the TAR RNA structure. Although full-length Tat protein (Tat86) was also able to promote strand transfer, this activity was limited by a strong overall inhibition of reverse transcription because of the presence of the second Tat exon. Other nucleic-acid-binding proteins (e.g., single-strand DNA-binding protein) were employed as negative controls and were unable to promote strand transfer in these assays. We propose that Tat possesses nucleic acid chaperone activity and can promote the first-strand transfer during HIV-1 reverse transcription; however, these activities are restricted by the second Tat exon, and the roles of these Tat activities in viral replication remain to be elucidated.
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Affiliation(s)
- Xiaofeng Guo
- McGill AIDS Centre, Lady Davis Institute/Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
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16
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Michienzi A, Li S, Zaia JA, Rossi JJ. A nucleolar TAR decoy inhibitor of HIV-1 replication. Proc Natl Acad Sci U S A 2002; 99:14047-52. [PMID: 12376617 PMCID: PMC137834 DOI: 10.1073/pnas.212229599] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tat is a critical regulatory factor in HIV-1 gene expression. It mediates the transactivation of transcription from the HIV-1 LTR by binding to the transactivation response (TAR) element in a complex with cyclin T1. Because of its critical and early role in HIV gene expression, Tat and its interaction with the TAR element constitute important therapeutic targets for the treatment of HIV-1 infection. Based on the known nucleolar localization properties of Tat, we constructed a chimeric small nucleolar RNA-TAR decoy that localizes to the nucleoli of human cells and colocalizes in the nucleolus with a Tat-enhanced GFP fusion protein. When the chimeric RNA was stably expressed in human T lymphoblastoid CEM cells it potently inhibited HIV-1 replication. These results demonstrate that the nucleolar trafficking of Tat is critical for HIV-1 replication and suggests a role for the nucleolus in HIV-1 viral replication.
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Affiliation(s)
- Alessandro Michienzi
- Divisions of Molecular Biology and Virology, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010-3011, USA
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17
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Weik M, Modrof J, Klenk HD, Becker S, Mühlberger E. Ebola virus VP30-mediated transcription is regulated by RNA secondary structure formation. J Virol 2002; 76:8532-9. [PMID: 12163572 PMCID: PMC136988 DOI: 10.1128/jvi.76.17.8532-8539.2002] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The nucleocapsid protein VP30 of Ebola virus (EBOV), a member of the Filovirus family, is known to act as a transcription activator. By using a reconstituted minigenome system, the role of VP30 during transcription was investigated. We could show that VP30-mediated transcription activation is dependent on formation of a stem-loop structure at the first gene start site. Destruction of this secondary structure led to VP30-independent transcription. Analysis of the transcription products of bicistronic minigenomes with and without the ability to form the secondary structure at the first transcription start signal revealed that transcription initiation at the first gene start site is a prerequisite for transcription of the second gene, independent of the presence of VP30. When the transcription start signal of the second gene was exchanged with the transcription start signal of the first gene, transcription of the second gene also was regulated by VP30, indicating that the stem-loop structure of the first transcription start site acts autonomously and independently of its localization on the RNA genome. Our results suggest that VP30 regulates a very early step of EBOV transcription, most likely by inhibiting pausing of the transcription complex at the RNA structure of the first transcription start site.
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Affiliation(s)
- Michael Weik
- Institut für Virologie der Philipps-Universität Marburg, 35037 Marburg, Germany
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18
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Paillart JC, Skripkin E, Ehresmann B, Ehresmann C, Marquet R. In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic RNA. J Biol Chem 2002; 277:5995-6004. [PMID: 11744696 DOI: 10.1074/jbc.m108972200] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5'-untranslated leader region of human immunodeficiency virus type 1 (HIV-1) RNA contains multiple signals that control distinct steps of the viral replication cycle such as transcription, reverse transcription, genomic RNA dimerization, splicing, and packaging. It is likely that fine tuned coordinated regulation of these functions is achieved through specific RNA-protein and RNA-RNA interactions. In a search for cis-acting elements important for the tertiary structure of the 5'-untranslated region of HIV-1 genomic RNA, we identified, by ladder selection experiments, a short stretch of nucleotides directly downstream of the poly(A) signal that interacts with a nucleotide sequence located in the matrix region. Confirmation of the sequence of the interacting sites was obtained by partial or complete inhibition of this interaction by antisense oligonucleotides and by nucleotide substitutions. In the wild type RNA, this long range interaction was intramolecular, since no intermolecular RNA association was detected by gel electrophoresis with an RNA mutated in the dimerization initiation site and containing both sequences involved in the tertiary interaction. Moreover, the functional importance of this interaction is supported by its conservation in all HIV-1 isolates as well as in HIV-2 and simian immunodeficiency virus. Our results raise the possibility that this long range RNA-RNA interaction might be involved in the full-length genomic RNA selection during packaging, repression of the 5' polyadenylation signal, and/or splicing regulation.
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Affiliation(s)
- Jean-Christophe Paillart
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, Strasbourg F-67084, France.
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19
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Kaushik N, Talele TT, Monel R, Palumbo P, Pandey VN. Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog. Nucleic Acids Res 2001; 29:5099-106. [PMID: 11812842 PMCID: PMC97570 DOI: 10.1093/nar/29.24.5099] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs by extension of the cellular tRNA3(Lys) which anneals to the primer-binding site (PBS) on the 5' non-translated region of the viral RNA genome. The A-rich sequence (A-loop) upstream of the PBS interacts with the anticodon loop of tRNA3(Lys) and has been proposed to be essential for conferring specificity to tRNA3(Lys) for priming the initiation of HIV-1 reverse transcription. We observed that polyamide nucleic acid targeted to the A-loop sequence (PNAAL) exhibits high binding specificity for its target sequence. The PNAAL pre-bound to the A-loop sequence prevents tRNA3(Lys) priming on the viral RNA consequently blocking in vitro initiation of reverse transcription. Further, PNAAL can efficiently disrupt the preformed [tRNA3(Lys)--viral RNA] complex thereby rendering it non-functional for reverse transcription. The endogenous reverse transcription in disrupted HIV-1 virions containing packaged tRNA3(Lys) and its replicating enzyme RT was significantly inhibited by PNAAL, thus providing direct evidence of the involvement of the A-loop region of viral RNA genome in tRNA3(Lys) priming process. These findings suggest the potential of the A-loop region as a critical target for blocking HIV-1 replication.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA, Antisense/chemistry
- DNA, Antisense/metabolism
- DNA, Antisense/pharmacology
- Dose-Response Relationship, Drug
- Genome, Viral
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nylons/chemistry
- Peptide Nucleic Acids/chemistry
- Peptide Nucleic Acids/metabolism
- Peptide Nucleic Acids/pharmacology
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/chemistry
- RNA, Viral/drug effects
- RNA, Viral/genetics
- Transcription, Genetic/drug effects
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Affiliation(s)
- N Kaushik
- Department of Biochemistry and Molecular Biology, Center for the Study of Emerging and Re-Emerging Pathogens UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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20
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Guan Y, Diallo K, Whitney JB, Liang C, Wainberg MA. An intact U5-leader stem is important for efficient replication of simian immunodeficiency virus. J Virol 2001; 75:11924-9. [PMID: 11689678 PMCID: PMC114783 DOI: 10.1128/jvi.75.23.11924-11929.2001] [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: 11/20/2022] Open
Abstract
Previous work has shown that four deletions in simian immunodeficiency virus (SIV), termed SD1a, SD1b, SD1c, and SD6, which eliminated sequences at nucleotide positions 322 to 362, 322 to 370, 322 to 379, and 371 to 379, respectively, located downstream of the primer binding site, impaired viral replication capacity to different extents. Long-term culturing of viruses containing the SD1a, SD1b, and SD6 deletions led to revertants that possessed wild-type replication kinetics. We now show that these revertants retained the original deletions in each case but that novel additional mutations were also present. These included a large deletion termed D1 (nt +216 to +237) within the U5 region that was shown to be biologically relevant to reversion of both the SD1a and SD1b constructs. In the case of SD6, two compensatory point mutations, i.e., A+369G, termed M1, located immediately upstream of the SD6 deletion, and C+201T, termed M2, within U5, were identified and could act either singly or in combination to restore viral replication. Secondary structure suggests that an intact U5-leader stem is important in SIV for infectiousness and that the additional mutants described played important roles in restoration of this motif.
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Affiliation(s)
- Y Guan
- McGill AIDS Center, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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21
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Smith SM, Khoroshev M, Marx PA, Orenstein J, Jeang KT. Constitutively dead, conditionally live HIV-1 genomes. Ex vivo implications for a live virus vaccine. J Biol Chem 2001; 276:32184-90. [PMID: 11397795 DOI: 10.1074/jbc.m101604200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An effective vaccine against AIDS is unlikely to be available for many years. As we approach two decades since the first identification of human immunodeficiency virus, type 1 (HIV-1), currently, only one subunit vaccine candidate has reached phase 3 of clinical trials. The subunit approach has been criticized for its inability to elicit effectively cytotoxic T-lymphocyte (CTL) response, which is felt by many to be needed for protection against HIV-1 infection. In subhuman primates, a live attenuated simian immunodeficiency virus (SIV) vaccine candidate, capable of inducing CTL, has been found to confer prophylactic immunity sufficient to prevent simian AIDS. Because replication competent (live) attenuated viruses could over time revert to virulence, such a live attenuated approach has largely been dismissed for HIV-1. Here, we describe the creation of constitutively dead conditionally live (CDCL) HIV-1 genomes. These genomes are constitutively defective for the Tat/TAR axis and are conditionally dependent on tetracycline for attenuated replication with robust expression of viral antigens. Our results suggest that CDCL genomes merit consideration as safer "live" attenuated HIV-1 vaccine candidates.
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Affiliation(s)
- S M Smith
- Saint Michael's Medical Center and the New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07102, USA
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22
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Berkhout B, Vastenhouw NL, Klasens BI, Huthoff H. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA (NEW YORK, N.Y.) 2001; 7:1097-1114. [PMID: 11497429 PMCID: PMC1370158 DOI: 10.1017/s1355838201002035] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There is accumulating evidence that retroviral R regions contain features other than sequence complementarity that stimulate this critical nucleic acid hybridization step. The R region of the human immunodeficiency virus type 1 (HIV-1) is relatively extended (97 nt) and encodes two well-conserved stem-loop structures, the TAR and poly(A) hairpins. The role of these motifs was studied in an in vitro strand-transfer assay with two separate templates, the 5'R donor and the 3'R acceptor, and mutants thereof. The results indicate that the upper part of the TAR hairpin structure in the 5'R donor is critical for efficient strand transfer. This seems to pose a paradox, as the 5'R template is degraded by RNase H before strand transfer occurs. We propose that it is not the RNA hairpin motif in the 5'R donor, but rather the antisense motif in the ssDNA copy, which can also fold a hairpin structure, that is critical for strand transfer. Mutation of the loop sequence in the TAR hairpin of the donor RNA, which is copied in the loop of the cDNA hairpin, reduces the transfer efficiency more than fivefold. It is proposed that the natural strand-transfer reaction is enhanced by interaction of the anti-TAR ssDNA hairpin with the TAR hairpin in the 3'R acceptor. Base pairing can occur between the complementary loops ("loop-loop kissing"), and strand transfer is completed by the subsequent formation of an extended RNA-cDNA duplex.
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Affiliation(s)
- B Berkhout
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands.
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23
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Berkhout B. Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 48:29-73. [PMID: 10987088 DOI: 10.1016/s1054-3589(00)48003-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- B Berkhout
- Department of Human Retrovirology, University of Amsterdam, The Netherlands
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24
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Mayhood T, Kaushik N, Pandey PK, Kashanchi F, Deng L, Pandey VN. Inhibition of Tat-mediated transactivation of HIV-1 LTR transcription by polyamide nucleic acid targeted to TAR hairpin element. Biochemistry 2000; 39:11532-9. [PMID: 10995220 DOI: 10.1021/bi000708q] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tat, an essential human immunodeficiency virus type 1 protein interacts with the transactivation response element (TAR) and stimulates transcription from the viral long-terminal repeat (LTR). Blockage of Tat-TAR interaction halts viral transcription and hence replication. We have found that polyamide nucleic acid (PNA), targeted to the TAR sequences of viral RNA genome is able to prevent Tat-TAR interaction by efficient sequestration of the TAR. Anti-TAR PNA competes for TAR and prevents Tat-mediated stimulation of HIV-1 LTR transcription in vitro but has no influence on the basal level of transcription in the absence of Tat. Using a reporter gene construct pHIV LTR-CAT and pCMV-Tat in cell culture, we have further shown that anti-TAR PNA is able to block Tat-mediated transactivation of HIV-1 LTR transcription in vivo as judged by the extent of LTR driven CAT gene expression in the absence and presence of anti-TAR PNA. Supplementation of 100 nM of anti-TAR PNA into the culture medium further enhances the suppression of transactivation. Nonspecific scrambled PNA had no influence on Tat-TAR interaction and LTR-driven CAT gene expression in cell culture. These results suggest that PNA targeted to the TAR sequence of the viral genome may be a potential inhibitor of HIV-1 gene expression.
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Affiliation(s)
- T Mayhood
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, USA
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25
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Ohi Y, Clever JL. Sequences in the 5' and 3' R elements of human immunodeficiency virus type 1 critical for efficient reverse transcription. J Virol 2000; 74:8324-34. [PMID: 10954531 PMCID: PMC116342 DOI: 10.1128/jvi.74.18.8324-8334.2000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of human immunodeficiency virus type 1 (HIV-1) contains two direct repeats (R) of 97 nucleotides at each end. These elements are of critical importance during the first-strand transfer of reverse transcription, during which the minus-strand strong-stop DNA (-sssDNA) is transferred from the 5' end to the 3' end of the genomic RNA. This transfer is critical for the synthesis of the full-length minus-strand cDNA. These repeats also contain a variety of other functional domains involved in many aspects of the viral life cycle. In this study, we have introduced a series of mutations into the 5', the 3', or both R sequences designed to avoid these other functional domains. Using a single-round infectivity assay, we determined the ability of these mutants to undergo the various steps of reverse transcription utilizing a semiquantitative PCR analysis. We find that mutations within the first 10 nucleotides of either the 5' or the 3' R sequence resulted in virions that were markedly defective for reverse transcription in infected cells. These mutations potentially introduce mismatches between the full-length -sssDNA and 3' acceptor R. Even mutations that would create relatively small mismatches, as little as 3 bp, resulted in inefficient reverse transcription. In contrast, virions containing identically mutated R elements were not defective for reverse transcription or infectivity. Using an endogenous reverse transcription assay with disrupted virus, we show that virions harboring the 5' or the 3' R mutations were not intrinsically defective for DNA synthesis. Similarly sized mismatches slightly further downstream in either the 5', the 3', or both R sequences were not detrimental to continued reverse transcription in infected cells. These data are consistent with the idea that certain mismatches within 10 nucleotides downstream of the U3-R junction in HIV-1 cause defects in the stability of the cDNA before or during the first-strand transfer of reverse transcription leading to the rapid disappearance of the -sssDNA in infected cells. These data also suggest that the great majority of first-strand transfers in HIV-1 occur after the copying of virtually the entire 5' R.
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Affiliation(s)
- Y Ohi
- Department of Microbiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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26
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Harrich D, Hooker CW, Parry E. The human immunodeficiency virus type 1 TAR RNA upper stem-loop plays distinct roles in reverse transcription and RNA packaging. J Virol 2000; 74:5639-46. [PMID: 10823871 PMCID: PMC112051 DOI: 10.1128/jvi.74.12.5639-5646.2000] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) RNA genome is flanked by a repeated sequence (R) that is required for HIV-1 replication. The first 57 nucleotides of R form a stable stem-loop structure called the transactivation response element (TAR) that can interact with the virally encoded transcription activator protein, Tat, to promote high levels of gene expression. Recently, we demonstrated that TAR is also important for efficient HIV-1 reverse transcription, since HIV-1 mutated in the upper stem-loop of TAR showed a reduced ability both to initiate and to complete reverse transcription. We have analyzed a series of HIV-1 mutant viruses to better defined the structural or sequence elements required for natural endogenous reverse transcription and packaging of virion RNA. Our results indicate that the requirement for TAR in reverse transcription is conformation dependent, since mutants with mutations that alter the upper stem-loop orientation are defective for reverse transcription initiation and have minor defects in RNA packaging. In contrast, TAR mutations that allowed the formation of alternative upper stem-loop structure greatly reduced RNA packaging but did not affect reverse transcription efficiency. These results are consistent with direct involvement of the upper stem-loop structure in packaging of genomic RNA and suggest that the TAR RNA stem-loop from nucleotide +18 to +42 interacts with other components of the reverse transcription initiation complex to promote efficient reverse transcription.
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Affiliation(s)
- D Harrich
- HIV Research Unit, National Centre for HIV Virology Research, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston, Queensland, Australia 4029.
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27
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Chen H, He J, Fong S, Wilcox G, Wood C. Jembrana disease virus Tat can regulate human immunodeficiency virus (HIV) long terminal repeat-directed gene expression and can substitute for HIV Tat in viral replication. J Virol 2000; 74:2703-13. [PMID: 10684286 PMCID: PMC111760 DOI: 10.1128/jvi.74.6.2703-2713.2000] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Jembrana disease virus (JDV) is a bovine lentivirus genetically similar to bovine immunodeficiency virus; it causes an acute and sometimes fatal disease in infected animals. This virus carries a very potent Tat that can strongly activate not only its own long terminal repeat (LTR) but also the human immunodeficiency virus (HIV) LTR. In contrast, HIV Tat cannot reciprocally activate the JDV LTR (H. Chen, G. E. Wilcox, G. Kertayadnya, and C. Wood, J. Virol. 73:658-666, 1999). This indicates that in transactivation JDV Tat may utilize a mechanism similar to but not the same as that of the HIV Tat. To further study the similarity of JDV and HIV tat in transactivation, we first tested the responses of a series of HIV LTR mutants to the JDV Tat. Cross-transactivation of HIV LTR by JDV Tat was impaired by mutations that disrupted the HIV type 1 transactivation response element (TAR) RNA stem-loop structure. Our results demonstrated that JDV Tat, like HIV Tat, transactivated the HIV LTR at least partially in a TAR-dependent manner. However, the sequence in the loop region of TAR was not as critical for the function of JDV Tat as it was for HIV Tat. The competitive inhibition of Tat-induced transactivation by the truncated JDV or HIV Tat, which consisted only of the activation domain, suggested that similar cellular factors were involved in both JDV and HIV Tat-induced transactivation. Based on the one-round transfection assay with HIV tat mutant proviruses, the cotransfected JDV tat plasmid can functionally complement the HIV tat defect. To further characterize the effect of JDV Tat on HIV, a stable chimeric HIV carrying the JDV tat gene was generated. This chimeric HIV replicated in a T-cell line, C8166, and in peripheral blood mononuclear cells, which suggested that JDV Tat can functionally substitute for HIV Tat. Further characterization of this chimeric virus will help to elucidate how JDV Tat functions and to explain the differences between HIV and JDV Tat transactivation.
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MESH Headings
- Animals
- Base Sequence
- Binding Sites
- Binding, Competitive
- Cattle
- Cells, Cultured
- Gene Expression
- Gene Expression Regulation, Viral
- Gene Products, tat/classification
- Gene Products, tat/genetics
- Gene Products, tat/metabolism
- Genetic Complementation Test
- HIV Long Terminal Repeat
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Lentiviruses, Bovine/genetics
- Leukocytes, Mononuclear/cytology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Proviruses/genetics
- RNA, Viral
- Transcriptional Activation
- Virus Replication/physiology
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- H Chen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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28
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Helga-Maria C, Hammarskjöld ML, Rekosh D. An intact TAR element and cytoplasmic localization are necessary for efficient packaging of human immunodeficiency virus type 1 genomic RNA. J Virol 1999; 73:4127-35. [PMID: 10196309 PMCID: PMC104192 DOI: 10.1128/jvi.73.5.4127-4135.1999] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/1998] [Accepted: 02/01/1999] [Indexed: 12/13/2022] Open
Abstract
Although most reports defining the human immunodeficiency virus type 1 (HIV-1) genomic RNA packaging signal have focused on the region downstream of the major 5' splice site, others have suggested that sequences upstream of the splice site may also play an important role. In this study we have directly examined the role played by the HIV-1 TAR region in RNA packaging. For these experiments we used a proviral expression system that is largely independent of Tat for transcriptional activation. This allowed us to create constructs that efficiently expressed RNAs carrying mutations in TAR and to determine the ability of these RNAs to be packaged. Our results indicate that loss of sequences in TAR significantly reduce the ability of a viral RNA to be packaged. The requirement for TAR sequences in RNA packaging was further examined by using a series of missense mutations positioned throughout the entire TAR structure. TAR mutations previously shown to influence Tat transactivation, such as G31U in the upper loop region or UCU to AAG in the bulge (nucleotides [nt] 22 to 24), failed to have any effect on RNA packaging. Mutations which disrupted the portion of the TAR stem immediately below the bulge also had little effect. In contrast, dramatic effects on RNA packaging were observed with constructs containing mutations in the lower portion of the TAR stem. Point mutations which altered nt 5 to 9, 10 to 15, 44 to 49, or 50 to 54 all reduced RNA packaging 11- to 25-fold. However, compensatory double mutations which restored the stem structure were able to restore packaging. These results indicate that an intact lower stem structure, rather than a specific sequence, is required for RNA packaging. Our results also showed that RNA molecules retained within the nucleus cannot be packaged, unless they are transported to the cytoplasm by either Rev/Rev response element or the Mason-Pfizer monkey virus constitutive transport element.
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Affiliation(s)
- C Helga-Maria
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
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Kang SM, Zhang Z, Morrow CD. Identification of a human immunodeficiency virus type 1 that stably uses tRNALys1,2 rather than tRNALys,3 for initiation of reverse transcription. Virology 1999; 257:95-105. [PMID: 10208924 DOI: 10.1006/viro.1999.9615] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HIV-1 virions contain approximately equal amounts of tRNALys,3 and tRNALys1,2, yet tRNALys,3 has been found to be exclusively used for initiation of reverse transcription. Since previous studies have shown that even if the primer binding site (PBS) was mutated to be complementary to tRNALys1,2, the virus did not stably use tRNALys1,2 to initiate reverse transcription, the virus must have evolved a mechanism for the exclusive use of tRNALys,3 to initiate reverse transcription. To investigate how HIV-1 discriminates tRNALys1,2 from tRNALys,3 for initiation of reverse transcription, two proviral genomes that contain nucleotide changes in U5 and a PBS to be complementary to regions of tRNALys1,2 were constructed. One genome contains 5 [HXB2(L12-AC)] nucleotides while another contains 15 [HXB2(L12-ACgg)] nucleotides in U5 complementary to the anticodon region of tRNALys1,2. Viruses derived from the transfection of the proviral genomes were infectious in SupT1 cells. Analysis of the endogenous reverse transcription reactions from viruses derived from HXB2 (L12-AC) and HXB2 (L12-ACgg) obtained from transfection revealed that both exclusively used tRNALys1,2 to initiate reverse transcription. Following extensive in vitro culture, though, sequence analysis of proviral genomes revealed that while the virus derived from HXB2(L12-AC) stably maintained a PBS complementary to tRNALys1,2, the virus derived from HXB2 (L12-ACgg) had reverted back to contain a PBS complementary to tRNALys,3. RNA modeling of the U5-PBS of the genome from HXB2(L12-AC) supports the conclusion that the fine specificity for discrimination between tRNALys,3 and tRNALys1,2 for use as a primer for HIV-1 reverse transcription resides in the structure of the U5-PBS region of the viral genome.
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Affiliation(s)
- S M Kang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
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30
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Ulich C, Dunne A, Parry E, Hooker CW, Gaynor RB, Harrich D. Functional domains of Tat required for efficient human immunodeficiency virus type 1 reverse transcription. J Virol 1999; 73:2499-508. [PMID: 9971835 PMCID: PMC104497 DOI: 10.1128/jvi.73.3.2499-2508.1999] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tat expression is required for efficient human immunodeficiency virus type 1 (HIV-1) reverse transcription. In the present study, we generated a series of 293 cell lines that contained a provirus with a tat gene deletion (Deltatat). Cell lines that contained Deltatat and stably transfected vectors containing either wild-type tat or a number of tat mutants were obtained so that the abilities of these tat genes to stimulate HIV-1 gene expression and reverse transcription could be compared. tat genes with mutations in the amino terminus did not stimulate either viral gene expression or HIV-1 reverse transcription. In contrast, tat mutants in the activation, core, and basic domains of Tat did not stimulate HIV-1 gene expression but markedly stimulated HIV-1 reverse transcription. No differences in the levels of virion genomic RNA or tRNA3Lys were seen in the HIV-1 Deltatat viruses complemented with either mutant or wild-type tat. Finally, overexpression of the Tat-associated kinases CDK7 and CDK9, which are involved in Tat activation of HIV-1 transcription, was not able to complement the reverse transcription defects associated with the lack of a functional tat gene. These results indicate that the mechanism by which tat modulates HIV-1 reverse transcription is distinct from its ability to activate HIV-1 gene expression.
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Affiliation(s)
- C Ulich
- Division of Hematology and Oncology, Departments of Internal Medicine and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235-8594, USA
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31
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Clever JL, Eckstein DA, Parslow TG. Genetic dissociation of the encapsidation and reverse transcription functions in the 5' R region of human immunodeficiency virus type 1. J Virol 1999; 73:101-9. [PMID: 9847312 PMCID: PMC103813 DOI: 10.1128/jvi.73.1.101-109.1999] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The efficient packaging of genomic RNA into virions of human immunodeficiency virus type 1 (HIV-1) is directed by cis-acting encapsidation signals, which have been mapped to particular RNA stem-loop structures near the 5' end of the genome. Earlier studies have shown that three such stem-loops, located adjacent to the major 5' splice donor, are required for optimal packaging; more recent reports further suggest a requirement for the TAR and poly(A) hairpins of the 5' R region. In the present study, we have compared the phenotypes that result from mutating these latter elements in the HIV-1 provirus. Using a single-round infectivity assay, we find that mutations which disrupt base pairing in either the TAR or poly(A) stems cause profound defects in both packaging and viral replication. Decreased genomic packaging in a given mutant was always accompanied by increased packaging of spliced viral RNAs. Compensatory mutations that restored base pairing also restored encapsidation, indicating that the secondary structures of the TAR and poly(A) stems, rather than their primary sequences, are important for packaging activity. Despite having normal RNA contents, however, viruses with compensatory mutations at the base of the TAR stem were severely replication defective, owing to a defect in proviral DNA synthesis. Our findings thus confirm that the HIV-1 TAR stem-loop is required for at least three essential viral functions (transcriptional activation, RNA packaging, and reverse transcription) and reveal that its packaging and reverse transcription activities can be dissociated genetically by mutations at the base of the TAR stem.
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Affiliation(s)
- J L Clever
- Departments of Pathology and of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
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32
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Boulmé F, Freund F, Moreau S, Nielsen PE, Gryaznov S, Toulmé JJ, Litvak S. Modified (PNA, 2'-O-methyl and phosphoramidate) anti-TAR antisense oligonucleotides as strong and specific inhibitors of in vitro HIV-1 reverse transcription. Nucleic Acids Res 1998; 26:5492-500. [PMID: 9826777 PMCID: PMC148009 DOI: 10.1093/nar/26.23.5492] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Natural beta-phosphodiester 16mer and 15mer antisense oligonucleotides targeted against the HIV-1 and HIV-2 TAR RNAs respectively were previously described as sequence-specific inhibitors of in vitro retroviral reverse transcription. In this work, we tested chemically modified oligonucleotide analogues: alpha-phosphodiester, phosphorothioate, methylphosphonate, peptide nucleic acid or PNA, 2'- o -methyl and (N3'-P5') phosphoramidate versions of the 16mer anti-TAR oligonucleotide. PNA, 2'- O -methyl and (N3'-P5') phosphoramidate oligomers showed a strong inhibitory effect compared with the unmodified 16mer, with reverse transcription inhibition (IC50) values in the nanomolar range. The inhibition was sequence-specific, as scrambled and mismatched control oligonucleotides were not able to inhibit cDNA synthesis. No direct binding of the 2'- O -methyl, PNA or (N3'-P5') phosphoramidate anti-TAR oligonucleotides to the HIV-1 reverse transcriptase was observed. The higher T m obtained with 2'- O -methyl, (N3'-P5') phosphoramidate and PNA molecules concerning the annealing with the stem-loop structure of the TAR RNA, in comparison with the beta-phosphodiester oligonucleotides, is correlated with their high inhibitory effect on reverse transcription.
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Affiliation(s)
- F Boulmé
- EP-630, CNRS-Université Victor Segalen Bordeaux 2, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
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33
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Das AT, Klaver B, Berkhout B. The 5' and 3' TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle. J Virol 1998; 72:9217-23. [PMID: 9765469 PMCID: PMC110341 DOI: 10.1128/jvi.72.11.9217-9223.1998] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 RNA genome contains a terminal repeat (R) sequence that encodes the TAR hairpin motif, which has been implicated in Tat-mediated activation of transcription. More recently, a variety of other functions have been proposed for this structured RNA element. To determine the replicative roles of the 5' and 3' TAR hairpins, we analyzed multiple steps in the life cycle of wild-type and mutant viruses. A structure-destabilizing mutation was introduced in either the 5', the 3', or both TAR motifs of the proviral genome. As expected, opening of the 5' TAR hairpin caused a transcription defect. Because the level of protein expression was not similarly reduced, the translation of this mRNA was improved. No effect of the 3' hairpin on transcription and translation was measured. Mutations of the 5' and 3' hairpin structures reduced the efficiency of RNA packaging to similar extents, and RNA packaging was further reduced in the 5' and 3' TAR double mutant. Upon infection of cells with these virions, a reduced amount of reverse transcription products was synthesized by the TAR mutant. However, no net reverse transcription defect was observed after correction for the reduced level of virion RNA. This result was confirmed in in vitro reverse transcription assays. These data indicate that the 5' and 3' TAR motifs play important roles in several steps of the replication cycle, but these structures have no significant effect on the mechanism of reverse transcription.
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Affiliation(s)
- A T Das
- Department of Human Retrovirology, University of Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
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34
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Li X, Liang C, Quan Y, Chandok R, Laughrea M, Parniak MA, Kleiman L, Wainberg MA. Identification of sequences downstream of the primer binding site that are important for efficient replication of human immunodeficiency virus type 1. J Virol 1997; 71:6003-10. [PMID: 9223491 PMCID: PMC191857 DOI: 10.1128/jvi.71.8.6003-6010.1997] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Reverse transcription of retroviruses is initiated from an 18-nucleotide (nt) primer binding site (PBS), located within the 5' region of viral genomic RNA, to which the host cell-derived tRNA primer is annealed and also involves viral genomic sequences outside the PBS. We constructed proviral DNA clones of human immunodeficiency virus (HIV) that had selective deletions of either a 7-nt segment found immediately downstream of the PBS or an extended nontranslated 54-nt stretch located immediately downstream of the PBS and containing the aforementioned 7-nt segment. Synthesis of minus-strand strong-stop DNA was assessed with MT-4 cells infected with viruses derived from COS-7 cells that had been transfected with these various constructs. We found that similar levels of minus-strand strong-stop DNA as well as DNA produced after template switching were expressed in MT-4 cells infected with COS-7-derived wild-type viruses or with viruses that had the 7-nt segment deleted. In contrast, significantly lower levels of viral DNA were detected in MT-4 cells after infection with viruses that had deletions of the 54-nt stretch. Furthermore, the molecular clone containing the 7-nt deletion was able to replicate with wild-type kinetics, while that containing the 54-nt deletion displayed a significantly diminished capacity in this regard. Further deletion analysis showed that a 16-nt segment at the 3' end of this 54-nt segment was largely responsible for these effects. We also conducted studies to determine levels of viral mRNA in COS-7 cells that had been transfected with equivalent amounts of DNA derived from either a wild-type HIV construct or our various deletion mutants. In the case of transfections performed with the 7-nt deletion mutant and wild-type HIV DNA, high levels of viral mRNA transcripts were detected, which was not the case for the 54 nt-deletion mutant. However, these various mRNAs possessed similar stabilities, as shown through studies in which transcript formation was arrested by treatment of cells with actinomycin D. Thus, the 54-nt segment of 5' nontranslated RNA, located downstream of the PBS, is involved in efficient expression of each of viral DNA, mRNA, and infectious virus.
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Affiliation(s)
- X Li
- McGill University AIDS Centre, Jewish General Hospital, and Department of Medicine, McGill University, Montreal, Quebec, Canada
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35
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Van Lint C, Amella CA, Emiliani S, John M, Jie T, Verdin E. Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity. J Virol 1997; 71:6113-27. [PMID: 9223506 PMCID: PMC191872 DOI: 10.1128/jvi.71.8.6113-6127.1997] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
When transcriptionally active, the human immunodeficiency virus (HIV) promoter contains a nucleosome-free region encompassing both the promoter/enhancer region and a large region (255 nucleotides [nt]) downstream of the transcription start site. We have previously identified new binding sites for transcription factors downstream of the transcription start site (nt 465 to 720): three AP-1 sites (I, II, and III), an AP3-like motif (AP3-L), a downstream binding factor (DBF) site, and juxtaposed Sp1 sites. Here, we show that the DBF site is an interferon-responsive factor (IRF) binding site and that the AP3-L motif binds the T-cell-specific factor NF-AT. Mutations that abolish the binding of each factor to its cognate site are introduced in an infectious HIV-1 molecular clone to study their effect on HIV-1 transcription and replication. Individual mutation of the DBF or AP3-L site as well as the double mutation AP-1(III)/AP3-L did not affect HIV-1 replication compared to that of the wild-type virus. In contrast, proviruses carrying mutations in the Sp1 sites were totally defective in terms of replication. Virus production occurred with slightly delayed kinetics for viruses containing combined mutations in the AP-1(III), AP3-L, and DBF sites and in the AP3-L and DBF-sites, whereas viruses mutated in the AP-1(I,II,III) and AP3-L sites and in the AP-1(I,II,III), AP3-L, and DBF sites exhibited a severely defective replicative phenotype. No RNA-packaging defect could be measured for any of the mutant viruses as determined by quantification of their HIV genomic RNA. Measurement of the transcriptional activity of the HIV-1 promoter after transient transfection of the HIV-1 provirus DNA or of long terminal repeat-luciferase constructs showed a positive correlation between the transcriptional and the replication defects for most mutants.
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Affiliation(s)
- C Van Lint
- The Picower Institute for Medical Research, Manhasset, New York 11030, USA
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36
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Guo J, Henderson LE, Bess J, Kane B, Levin JG. Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J Virol 1997; 71:5178-88. [PMID: 9188585 PMCID: PMC191753 DOI: 10.1128/jvi.71.7.5178-5188.1997] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
During the first strand transfer in reverse transcription, minus-strand strong-stop DNA [(-) SSDNA] is annealed to the 3' end of the acceptor RNA in a reaction mediated by base-pairing between terminal repeat sequences in the RNA and their complement in the DNA. The large stem-loop structure in the repeat region known as TAR could interfere with this annealing reaction. We have developed an in vitro human immunodeficiency virus type 1 (HIV-1) system to investigate the effect of TAR on strand transfer. Mutational analysis demonstrates that the presence of TAR in the donor and acceptor templates inhibits strand transfer and is correlated with extensive synthesis of heterogeneous DNAs formed by self-priming from (-) SSDNA. These DNAs are not precursors to the transfer product. Interestingly, products of self-priming are not detected in HIV-1 endogenous reactions; this suggests that virions contain a component which prevents self-priming. Our results show that the viral nucleocapsid protein (NC), which can destabilize secondary structures, drastically reduces self-priming and dramatically increases the efficiency of strand transfer. In addition, the data suggest that the ability to eliminate self-priming is a general property of NC which is manifested during reverse transcriptase pausing at sites of secondary structure in the template. We conclude that this activity of NC is critical for achieving highly efficient and specific viral DNA synthesis. Our findings raise the possibility that inactivation of NC could provide a new approach for targeting reverse transcription in anti-HIV therapy.
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Affiliation(s)
- J Guo
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
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37
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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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38
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Lu Y, Planelles V, Li X, Palaniappan C, Day B, Challita-Eid P, Amado R, Stephens D, Kohn DB, Bakker A, Fay P, Bambara RA, Rosenblatt JD. Inhibition of HIV-1 replication using a mutated tRNALys-3 primer. J Biol Chem 1997; 272:14523-31. [PMID: 9169409 DOI: 10.1074/jbc.272.23.14523] [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: 02/04/2023] Open
Abstract
Cellular tRNALys-3 serves as the primer for reverse transcription of human immunodeficiency virus, type 1 (HIV-1). tRNALys-3 interacts directly with HIV-1 reverse transcriptase, is packaged into viral particles and anneals to the primer-binding site (PBS) of the HIV-1 genome to initiate reverse transcription. Therefore, the priming step of reverse transcription is a potential target for antiviral strategies. We have developed a mutant tRNALys-3 derivative with mutations in the PBS-binding region such that priming specificity was re-directed to the highly conserved TAR stem-loop region. This mutant tRNA retains high-affinity binding to HIV-1 reverse transcriptase, viral encapsidation, and is able to prime at both the targeted TAR sequence and at the viral PBS. Constitutive expression of mutant tRNA in T-cells results in marked inhibition of HIV-1 replication, as determined by measurements of viral infectivity, syncytium formation, and p24 production. Inhibition of retroviral replication through interference with the normal process of priming constitutes a new anti-retroviral approach and also provides a novel tool for dissecting molecular aspects of priming.
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Affiliation(s)
- Y Lu
- UCLA Department of Medicine, Division of Hematology-Oncology, UCLA AIDS Institute, Los Angeles, California 90095, USA
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McBride MS, Schwartz MD, Panganiban AT. Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation. J Virol 1997; 71:4544-54. [PMID: 9151848 PMCID: PMC191676 DOI: 10.1128/jvi.71.6.4544-4554.1997] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
To determine whether there is a cis-acting effect of translational expression of gag on RNA encapsidation, we compared the encapsidation of wild-type RNA with that of a mutant in which the translation of gag was ablated. This comparison indicated that there is not such a cis effect. To determine what is necessary and sufficient for encapsidation, we measured the relative encapsidation efficiencies of human immunodeficiency virus type 1 vector RNAs containing mutations in domains proximal to the canonical encapsidation signal or containing large deletions in the remainder of the genome. These data indicate that TAR and two additional regions are required for encapsidation and that the 5' end of the genome is sufficient for encapsidation. The Rev-responsive element is required mainly for efficient RNA transport from the nucleus to the cytoplasm. A foreign sequence was found to have a negative effect on encapsidation upon placement within the parental vector. Interestingly, this negative effect was compounded by multiple copies of the sequence.
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Affiliation(s)
- M S McBride
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison 53706, USA
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40
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Boulme F, Perälä-Heape M, Sarih-Cottin L, Litvak S. Specific inhibition of in vitro reverse transcription using antisense oligonucleotides targeted to the TAR regions of HIV-1 and HIV-2. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1351:249-55. [PMID: 9130587 DOI: 10.1016/s0167-4781(97)00026-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antisense oligonucleotides (ODNs) overlapping the stem-loop structure of the trans-activating responsive (TAR) element at the 5' end of HIV-1 and HIV-2 viral RNAs were tested for their inhibitory effect on cDNA synthesis by HIV-1 and HIV-2 reverse transcriptases (RT). Inhibition of reverse transcription is sequence-specific and enhanced by the presence of the RT-associated RNase H activity. The degree of inhibition obtained with the anti-TAR antisense is significantly higher than with other HIV-1 targeted antisense ODNs used before [1]. Gel retardation showed a stable specific complex between the 16- and 25-mer anti-TAR HIV-1 selected ODNs and the target region. No complex was observed with a non-inhibitor 22-mer anti-TAR ODN and with the corresponding control sequences. Targeting of the first stem-loop in the 5' region of HIV-2 RNA by anti-TAR ODNs inhibited very strongly reverse transcription by HIV-2 RT. The structure of the antisense and the target sequence affect annealing efficiency and hence the degree of inhibition of reverse transcription.
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Affiliation(s)
- F Boulme
- Laboratoire Reger, Institut de Biochimie et Génétique Cellulaires du CNRS, IBGC-CNRS, Bordeaux, France
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41
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Harrich D, Ulich C, García-Martínez LF, Gaynor RB. Tat is required for efficient HIV-1 reverse transcription. EMBO J 1997; 16:1224-35. [PMID: 9135139 PMCID: PMC1169721 DOI: 10.1093/emboj/16.6.1224] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The ability of human immunodeficiency virus-1 (HIV-1) to undergo efficient reverse transcription is dependent on a number of parameters. These include the binding of the tRNA(3)(Lys) to the HIV-1 primer binding site and the subsequent interaction with the heterodimeric reverse transcriptase. Recently, we demonstrated that TAR RNA was also necessary for efficient HIV-1 reverse transcription. Given the fact that the Tat protein is involved in the activation of HIV-1 gene expression in conjunction with TAR, we wished to determine whether Tat might also be involved in the control of HIV-1 reverse transcription. HIV-1 virions deleted in the tat gene were unable to initiate reverse transcription efficiently upon infection of peripheral blood mononuclear cells (PBMCs). This defect was not due to decreased amounts of genomic RNA, reverse transcriptase or other HIV-1 proteins which were incorporated into the virion. Following transfection of wild-type but not mutant tat genes into cell lines producing HIV-1 lacking tat, the virions produced could be complemented for defects in reverse transcription upon subsequent infection of PBMCs. In contrast, the defect in reverse transcription seen with HIV-1 lacking the tat gene could not be complemented when the target cells rather than the producer cells contained tat. Viruses lacking tat were also defective in endogenous assays of reverse transcription, although these viruses contained similar levels of reverse transcriptase. These results indicate that the Tat protein, in addition to regulating the level of gene expression, is also important for efficient HIV-1 reverse transcription.
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Affiliation(s)
- D Harrich
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas 75235-8594, USA
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42
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Das AT, Klaver B, Klasens BI, van Wamel JL, Berkhout B. A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication. J Virol 1997; 71:2346-56. [PMID: 9032371 PMCID: PMC191344 DOI: 10.1128/jvi.71.3.2346-2356.1997] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The untranslated leader region of the human immunodeficiency virus (HIV) RNA genome contains multiple hairpin motifs. The repeat region of the leader, which is reiterated at the 3' end of the RNA molecule, encodes the well-known TAR hairpin and a second hairpin structure with the polyadenylation signal AAUAAA in the single-stranded loop [the poly(A) hairpin]. The fact that this poly(A) stem-loop structure and its thermodynamic stability are well conserved among HIV and simian immunodeficiency virus isolates, despite considerable divergence in sequence, suggests a biological function for this RNA motif in viral replication. Consistent with this idea, we demonstrate that mutations that alter the stability of the stem region or delete the upper part of the hairpin do severely inhibit replication of HIV type 1. Whereas destabilizing mutations in either the left- or right-hand side of the base-paired stem interfere with virus replication, the double mutant, which allows the formation of new base pairs, replicates more rapidly than the two individual virus mutants. Upon prolonged culturing of viruses with an altered hairpin stability, revertant viruses were obtained with additional mutations that restore the thermodynamic stability of the poly(A) hairpin. Transient transfection experiments demonstrated that transcription of the proviral genomes, translation of the viral mRNAs, and reverse transcription of the genomic RNAs are not affected by mutation of the 5' poly(A) hairpin. We show that the genomic RNA content of the virions is reduced by destabilization of this poly(A) hairpin but not by stabilization or truncation of this structure. These results suggest that the formation of the poly(A) hairpin structure at the 5' end of the genomic RNA molecule is necessary for packaging of viral genomes into virions and/or stability of the virion RNA.
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Affiliation(s)
- A T Das
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
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Verhoef K, Tijms M, Berkhout B. Optimal Tat-mediated activation of the HIV-1 LTR promoter requires a full-length TAR RNA hairpin. Nucleic Acids Res 1997; 25:496-502. [PMID: 9016587 PMCID: PMC146473 DOI: 10.1093/nar/25.3.496] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
HIV-1 transcription from the LTR promoter is activated by the viral Tat protein through interaction with the nascent TAR RNA hairpin structure. The mechanism of Tat-mediated transcriptional activation has been extensively investigated with LTR-CAT reporter genes in transient transfections and, more recently, in infection experiments with mutant HIV-1 variants. Several discrepancies between these two assay systems have been reported. For instance, whereas opening of the lower part of the TAR RNA stem does not affect the promoter activity of an LTR-CAT plasmid in transient assays, the corresponding virus mutant is fully replication-impaired. With the aim to resolve this controversy, we have examined the activity of a set of TAR RNA mutants in transient transfection experiments with a variety of cell types. We now demonstrate that truncated TAR motifs exhibit a severe, but cell-type dependent transcription defect. Whereas full LTR activity is measured in COS cells that have been used regularly in previous transfection assays, a severe defect is apparent in a variety of human cell lines, including T cell lines that are typically used in HIV-1 replication studies. These results suggest the presence of a human protein that participates in Tat-mediated transcriptional activation through binding to the lower part of the TAR stem. Several candidate co-factors have been reported in literature. This study resolves the discrepancy between transfection and infection studies on the requirements of the lower TAR stem structure. The evidence also implies that LTR transcription studies should be performed preferentially in human cell types.
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Affiliation(s)
- K Verhoef
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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Kang SM, Zhang Z, Morrow CD. Identification of a sequence within U5 required for human immunodeficiency virus type 1 to stably maintain a primer binding site complementary to tRNA(Met). J Virol 1997; 71:207-17. [PMID: 8985340 PMCID: PMC191041 DOI: 10.1128/jvi.71.1.207-217.1997] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Initiation of reverse transcription of human immunodeficiency virus type 1 (HIV-1) occurs by extension from the 3' end of a cellular tRNA complexed to the primer binding site (PBS) located near the 5' end of the viral RNA genome. Although the PBSs for all naturally occurring HIV-1 viruses are complementary to the 3'-terminal 18 nucleotides of tRNA(Lys)3, we identified an HIV-1 virus which contained a PBS complementary to the 3' nucleotides of tRNA(Met); the PBS of this virus was not stable upon extended culture and reverted back to the wild type (S.-M. Kang, J. K. Wakefield, and C. D. Morrow, Virology 222:401-414, 1996). To further characterize the virus with a PBS complementary to tRNA(Met), a DNA fragment encompassing the PBS and U5 region from this proviral genome was substituted for the same region in the infectious HIV-1 proviral clone [named pHXB2(AC-Met)]. Three additional proviral genomes were also created: pHXB2(Met), which is isogenic with pHXB2 except for the PBS complementary to tRNA(Met); pHXB2(Met-AC-Met), which contains the PBS sequence complementary to the 3'-terminal nucleotides and the sequence upstream of this PBS in U5 complementary to the anticodon region of tRNA(Met); and pHXB2(Met-C-Met), which contains two G-to-C changes predicted to disrupt complementarity within the tRNA(Met) anticodon region. Viruses derived from the transfection of these proviral genomes were infectious, although the appearance of the viruses was delayed compared to that of the wild-type virus. PCR amplification and DNA sequence analysis of the PBS regions from proviral genomes revealed that the PBSs from viruses derived from pHXB2(Met) and pHXB2(AC-Met) reverted back to the wild type by days 16 and 44 postcoculture, respectively. Two new, novel mutant viruses were identified among viruses derived from pHXB2(Met-C-Met) at day 35 postcoculture: one contained a PBS complementary to tRNA(Lys)1,2, while the second maintained a PBS complementary to tRNA(Met) but contained a 26-nucleotide deletion in U5 upstream of the anticodon-complementary region. By day 125 postcoculture, the PBS in the virus from this culture had reverted back to the wild type, complementary to tRNA(Lys)3. In contrast, the viruses derived from pHXB2(Met-AC-Met) stably maintained a PBS complementary to tRNA(Met) during the 125-day culture period examined. The results of these studies support the idea that HIV-1 can maintain a PBS complementary to alternative tRNAs provided that the appropriate complementarity exists between the U5-PBS region of the viral RNA genome and the tRNA molecule used to initiate reverse transcription.
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Affiliation(s)
- S M Kang
- Department of Microbiology, University of Alabama at Birmingham, 35294, USA
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Abstract
Analysis of sequence information from RNA-based replication systems continues to challenge the computational molecular biology community. Recent sequence data from the study of primate lentiviruses indicate that extreme sequence heterogeneity, recombination, and cross-species transmissions are all observed in HIV evolution. These types of events will continue to make the development of effective anti-retroviral therapies difficult.
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Affiliation(s)
- M A McClure
- Department of Biological Sciences, University of Nevada, Las Vegas 89154-4004, USA.
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Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz PN, Girard M, Shaw GM, Hahn BH, Sharp PM. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J Virol 1996; 70:7013-29. [PMID: 8794346 PMCID: PMC190752 DOI: 10.1128/jvi.70.10.7013-7029.1996] [Citation(s) in RCA: 273] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Since 1989, human immunodeficiency virus type 1 (HIV-1) has spread explosively through the heterosexual population in Thailand. This epidemic is caused primarily by viruses classified as "subtype E", which, on the basis of limited sequence comparisons, appear to represent hybrids of subtypes A (gag) and E (env). However, the true evolutionary origins of "subtype E" viruses are still obscure since no complete genomes have been analyzed, and only one full-length subtype A sequence has been available for phylogenetic comparison. In this study, we determined full-length proviral sequences for "subtype E" viruses from Thailand (93TH253) and the Central African Republic (90CR402) and for a subtype A virus from Uganda (92UG037). We also sequenced the long terminal repeat (LTR) regions from 16 virus strains representing clades A, C, E, F, and G. Detailed phylogenetic analyses of these sequences indicated that "subtype E" viruses do indeed represent A/E recombinants with multiple points of crossover along their genomes. The extracellular portion of env, parts of vif and vpr, as well as most of the LTR are of subtype E origin, whereas the remainder of the genome is of subtype A origin. The possibility that the discordant phylogenetic positions of "subtype E" viruses in gag- and env-derived trees are the result of unusual rates or patterns of evolution was also considered but was ruled out on the basis of two lines of evidence: (i) phylogenetic trees constructed for synonymous and nonsynonymous substitutions yielded the same discordant branching orders for "subtype E" gag and env gene sequences, thus excluding selection-driven evolution, and (ii) multiple crossovers in the viral genome are most consistent with the copy choice model of recombination and have been observed in other documented examples of HIV-1 intersubtype recombination. Thai and CAR "subtype E" viruses exhibited the same pattern of A/E mosaicism, indicating that the recombination event occurred in Africa prior to the spread of virus to Asia. Finally, all "subtype E" viruses were found to contain a distinctive two-nucleotide bulge in their transactivation response (TAR) elements. This feature was present only in viruses which also contained a subtype A 5' pol region (i.e., subtype A viruses or A/D and A/E recombinants), raising the possibility of a functional linkage between the TAR region and the polymerase. The implications of epidemic spread of a recombinant HIV-1 strain to viral natural history and vaccine development are discussed.
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Affiliation(s)
- F Gao
- Department of Medicine, University of Alabama at Birmingham 35294, USA
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