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D’Souza AR, Jayaraman D, Long Z, Zeng J, Prestwood LJ, Chan C, Kappei D, Lever AML, Kenyon JC. HIV-1 Packaging Visualised by In-Gel SHAPE. Viruses 2021; 13:v13122389. [PMID: 34960658 PMCID: PMC8707378 DOI: 10.3390/v13122389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
HIV-1 packages two copies of its gRNA into virions via an interaction with the viral structural protein Gag. Both copies and their native RNA structure are essential for virion infectivity. The precise stepwise nature of the packaging process has not been resolved. This is largely due to a prior lack of structural techniques that follow RNA structural changes within an RNA-protein complex. Here, we apply the in-gel SHAPE (selective 2'OH acylation analysed by primer extension) technique to study the initiation of HIV-1 packaging, examining the interaction between the packaging signal RNA and the Gag polyprotein, and compare it with that of the NC domain of Gag alone. Our results imply interactions between Gag and monomeric packaging signal RNA in switching the RNA conformation into a dimerisation-competent structure, and show that the Gag-dimer complex then continues to stabilise. These data provide a novel insight into how HIV-1 regulates the translation and packaging of its genome.
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Affiliation(s)
- Aaron R. D’Souza
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
| | - Dhivya Jayaraman
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
| | - Ziqi Long
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Jingwei Zeng
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Liam J. Prestwood
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrew M. L. Lever
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (A.R.D.); (D.J.)
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)1-2237-47308 (J.C.K.)
| | - Julia C. Kenyon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (C.C.); (D.K.)
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital, Cambridge CB2 0QQ, UK; (Z.L.); (J.Z.); (L.J.P.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Homerton College, University of Cambridge, Cambridge CB2 8PH, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)1-2237-47308 (J.C.K.)
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RNA Helicase A Regulates the Replication of RNA Viruses. Viruses 2021; 13:v13030361. [PMID: 33668948 PMCID: PMC7996507 DOI: 10.3390/v13030361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 01/20/2023] Open
Abstract
The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.
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Ilina T, Slack RL, Guerrero M, Ishima R. Effect of Lysyl-tRNA Synthetase on the Maturation of HIV-1 Reverse Transcriptase. ACS OMEGA 2020; 5:16619-16627. [PMID: 32685828 PMCID: PMC7364630 DOI: 10.1021/acsomega.0c01449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
In human immunodeficiency virus-1 (HIV-1), reverse transcriptase (RT) is encoded as a 66 kDa protein, p66, in the Gag-Pol polyprotein. This protein is proteolytically cleaved by HIV-1 protease (PR) to finally generate a mature RT that is a heterodimer, composed of a p66 subunit and a p66-derived 51 kDa subunit, p51. In our prior work, we demonstrated that tRNALys3 binding to p66/p66 facilitates efficient cleavage of p66 to p51 by PR. However, tRNALys3 is known to be recruited to the virus by forming a complex with lysyl-tRNA synthetase (LysRS). Herein, we tested whether LysRS can have an effect on RT maturation in vitro. Importantly, our data show no significant differences in RT maturation in the presence of LysRS. Furthermore, no apparent p66/66 interaction with LysRS was observed. Although PR cleaved LysRS, it did not immediately release tRNALys3 from LysRS. Thus, we conclude that a free fraction of tRNALys3, which is in equilibrium with a LysRS-bound form, interacts with p66/p66 without any additional mechanism involving release of tRNALys3 from LysRS. Given that only transient tRNALys3-p66/p66 interaction is needed for efficient RT maturation, a small amount of free tRNA may be sufficient for this process. These studies reveal molecular level insights into RT maturation and will be useful for the design of cellular/viral experiments to better understand the role of tRNA in HIV-1 replication.
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Post K, Olson ED, Naufer MN, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K, Levin JG. Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition. Retrovirology 2016; 13:89. [PMID: 28034301 PMCID: PMC5198506 DOI: 10.1186/s12977-016-0322-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC. Non-human primates are frequently used as a platform to study retroviral infection in vivo; thus, it is important to understand underlying mechanistic differences between HIV-1 and SIV NC. RESULTS Here, we characterize SIV NC chaperone activity for the first time. Only modest differences are observed in the ability of SIV NC to facilitate reactions that mimic the minus-strand annealing and transfer steps of reverse transcription relative to HIV-1 NC, with the latter displaying slightly higher strand transfer and annealing rates. Quantitative single molecule DNA stretching studies and dynamic light scattering experiments reveal that these differences are due to significantly increased DNA compaction energy and higher aggregation capability of HIV-1 NC relative to the SIV protein. Using salt-titration binding assays, we find that both proteins are strikingly similar in their ability to specifically interact with HIV-1 Psi RNA. In contrast, they do not demonstrate specific binding to an RNA derived from the putative SIV packaging signal. CONCLUSIONS Based on these studies, we conclude that (1) HIV-1 NC is a slightly more efficient NA chaperone protein than SIV NC, (2) mechanistic differences between the NA interactions of highly similar retroviral NC proteins are revealed by quantitative single molecule DNA stretching, and (3) SIV NC demonstrates cross-species recognition of the HIV-1 Psi RNA packaging signal.
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Affiliation(s)
- Klara Post
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - M. Nabuan Naufer
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201 USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
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Seif E, Niu M, Kleiman L. In virio SHAPE analysis of tRNA(Lys3) annealing to HIV-1 genomic RNA in wild type and protease-deficient virus. Retrovirology 2015; 12:40. [PMID: 25981241 PMCID: PMC4445796 DOI: 10.1186/s12977-015-0171-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/06/2015] [Indexed: 11/29/2022] Open
Abstract
Background tRNALys3 annealing to the viral RNA of human immunodeficiency virus type-1 (HIV-1) is an essential step in the virus life cycle, because this tRNA serves as the primer for initiating reverse transcription. tRNALys3 annealing to viral RNA occurs in two steps. First, Gag promotes annealing of tRNALys3 to the viral RNA during cytoplasmic HIV-1 assembly. Second, mature nucleocapsid (NCp7), produced from the processing of Gag by viral protease during viral budding from the cell, remodels the annealed complex to form a more stable interaction between the viral RNA and tRNALys3, resulting in a more tightly bound and efficient primer for reverse transcription. Results In this report, we have used in virio SHAPE analysis of both the 5´-untranslated region in HIV-1 RNA and the annealed tRNALys3 to determine structural differences of the annealed complex that occur between protease-negative (Pr-) and wild type viruses. Our results indicate that the weaker binding of tRNALys3 annealed by Gag in Pr- virions reflects both missing interactions of tRNALys3 with viral RNA regions in the upper PBS stem, and a weaker interaction with the internal stem-loop found within the unannealed primer binding site in viral RNA. Conclusions We propose secondary structure models for the tRNALys3/viral RNA annealed complexes in PR- and wild type viruses that support the two-step annealing model by showing that Gag promotes a partial annealing of tRNALys3 to HIV-1 viral RNA, followed by a more complete annealing by NCp7. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elias Seif
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada. .,Department of Medicine, McGill University, Montreal, QC, H3A 1A1, Canada.
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Chamontin C, Rassam P, Ferrer M, Racine PJ, Neyret A, Lainé S, Milhiet PE, Mougel M. HIV-1 nucleocapsid and ESCRT-component Tsg101 interplay prevents HIV from turning into a DNA-containing virus. Nucleic Acids Res 2014; 43:336-47. [PMID: 25488808 PMCID: PMC4288153 DOI: 10.1093/nar/gku1232] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HIV-1, the agent of the AIDS pandemic, is an RNA virus that reverse transcribes its RNA genome (gRNA) into DNA, shortly after its entry into cells. Within cells, retroviral assembly requires thousands of structural Gag proteins and two copies of gRNA as well as cellular factors, which converge to the plasma membrane in a finely regulated timeline. In this process, the nucleocapsid domain of Gag (GagNC) ensures gRNA selection and packaging into virions. Subsequent budding and virus release require the recruitment of the cellular ESCRT machinery. Interestingly, mutating GagNC results into the release of DNA-containing viruses, by promo-ting reverse transcription (RTion) prior to virus release, through an unknown mechanism. Therefore, we explored the biogenesis of these DNA-containing particles, combining live-cell total internal-reflection fluorescent microscopy, electron microscopy, trans-complementation assays and biochemical characterization of viral particles. Our results reveal that DNA virus production is the consequence of budding defects associated with Gag aggregation at the plasma membrane and deficiency in the recruitment of Tsg101, a key ESCRT-I component. Indeed, targeting Tsg101 to virus assembly sites restores budding, restricts RTion and favors RNA packaging into viruses. Altogether, our results highlight the role of GagNC in the spatiotemporal control of RTion, via an ESCRT-I-dependent mechanism.
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Affiliation(s)
- Célia Chamontin
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Patrice Rassam
- Centre de Biochimie Structurale, UMR5048 CNRS, University of Montpellier, 34090 Montpellier, France
| | - Mireia Ferrer
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Pierre-Jean Racine
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Aymeric Neyret
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Sébastien Lainé
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale, UMR5048 CNRS, University of Montpellier, 34090 Montpellier, France U1054 INSERM, 30090 Montpellier, France
| | - Marylène Mougel
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
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Xing L, Zhao X, Guo F, Kleiman L. The role of A-kinase anchoring protein 95-like protein in annealing of tRNALys3 to HIV-1 RNA. Retrovirology 2014; 11:58. [PMID: 25034436 PMCID: PMC4223510 DOI: 10.1186/1742-4690-11-58] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/07/2014] [Indexed: 12/04/2022] Open
Abstract
Background RNA helicase A (RHA), a DExH box protein, promotes annealing of tRNALys3, a primer for reverse transcription, to HIV-1 RNA and assembles into virus particles. A-kinase anchoring protein 95-like protein (HAP95) is a binding partner of RHA. The role of HAP95 in the annealing of tRNALys3 was examined in this study. Results HAP95 associates with the reverse transcriptase region of Pol protein of HIV-1. Decreasing endogenous HAP95 in HIV-1-producing 293T cells by siRNA reduces the amount of tRNALys3 annealed on viral RNA. This defect was further deteriorated by knockdown of RHA in the same cells, suggesting a cooperative effect between these two proteins. Biochemical assay in vitro using purified GST-tagged HAP95 shows that HAP95 may inhibit the activity of RHA. Conclusion The results support a hypothesis that HAP95 may transiently block RHA’s activity to protect the annealed tRNALys3 on viral RNA in the cells from removing by RHA during the packaging of RHA into virus particles, thus facilitating the annealing of tRNALys3 to HIV-1 RNA.
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Affiliation(s)
- Li Xing
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, Canada.
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Wang W, Naiyer N, Mitra M, Li J, Williams MC, Rouzina I, Gorelick RJ, Wu Z, Musier-Forsyth K. Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity. Nucleic Acids Res 2014; 42:7145-59. [PMID: 24813443 PMCID: PMC4066767 DOI: 10.1093/nar/gku335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) maturation, three different forms of nucleocapsid (NC) protein—NCp15 (p9 + p6), NCp9 (p7 + SP2) and NCp7—appear successively. A mutant virus expressing NCp15 shows greatly reduced infectivity. Mature NCp7 is a chaperone protein that facilitates remodeling of nucleic acids (NAs) during reverse transcription. To understand the strict requirement for NCp15 processing, we compared the chaperone function of the three forms of NC. NCp15 anneals tRNA to the primer-binding site at a similar rate as NCp7, whereas NCp9 is the most efficient annealing protein. Assays to measure NA destabilization show a similar trend. Dynamic light scattering studies reveal that NCp15 forms much smaller aggregates relative to those formed by NCp7 and NCp9. Nuclear magnetic resonance studies suggest that the acidic p6 domain of HIV-1 NCp15 folds back and interacts with the basic zinc fingers. Neutralizing the acidic residues in p6 improves the annealing and aggregation activity of NCp15 to the level of NCp9 and increases the protein–NA aggregate size. Slower NCp15 dissociation kinetics is observed by single-molecule DNA stretching, consistent with the formation of electrostatic inter-protein contacts, which likely contribute to the distinct aggregate morphology, irregular HIV-1 core formation and non-infectious virus.
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Affiliation(s)
- Wei Wang
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Nada Naiyer
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mithun Mitra
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jialin Li
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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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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Godet J, Boudier C, Humbert N, Ivanyi-Nagy R, Darlix JL, Mély Y. Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1. Virus Res 2012; 169:349-60. [PMID: 22743066 PMCID: PMC7114403 DOI: 10.1016/j.virusres.2012.06.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
Abstract
RNA chaperones are proteins able to rearrange nucleic acid structures towards their most stable conformations. In retroviruses, the reverse transcription of the viral RNA requires multiple and complex nucleic acid rearrangements that need to be chaperoned. HIV-1 has evolved different viral-encoded proteins with chaperone activity, notably Tat and the well described nucleocapsid protein NCp7. We propose here an overview of the recent reports that examine and compare the nucleic acid chaperone properties of Tat and NCp7 during reverse transcription to illustrate the variety of mechanisms of action of the nucleic acid chaperone proteins.
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Affiliation(s)
- Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg, 67401 Illkirch, France
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11
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Sleiman D, Goldschmidt V, Barraud P, Marquet R, Paillart JC, Tisné C. Initiation of HIV-1 reverse transcription and functional role of nucleocapsid-mediated tRNA/viral genome interactions. Virus Res 2012; 169:324-39. [PMID: 22721779 DOI: 10.1016/j.virusres.2012.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 12/28/2022]
Abstract
HIV-1 reverse transcription is initiated from a tRNA(Lys)(3) molecule annealed to the viral RNA at the primer binding site (PBS). The annealing of tRNA(Lys)(3) requires the opening of its three-dimensional structure and RNA rearrangements to form an efficient initiation complex recognized by the reverse transcriptase. This annealing is mediated by the nucleocapsid protein (NC). In this paper, we first review the actual knowledge about HIV-1 viral RNA and tRNA(Lys)(3) structures. Then, we summarize the studies explaining how NC chaperones the formation of the tRNA(Lys)(3)/PBS binary complex. Additional NMR data that investigated the NC interaction with tRNA(Lys)(3) D-loop are presented. Lastly, we focused on the additional interactions occurring between tRNA(Lys)(3) and the viral RNA and showed that they are dependent on HIV-1 isolates, i.e. the sequence and the structure of the viral RNA.
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Affiliation(s)
- Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, Université Paris-Descartes, CNRS UMR 8015, 4 avenue de l'Observatoire, 75006 Paris, France
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12
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Didierlaurent L, Racine PJ, Houzet L, Chamontin C, Berkhout B, Mougel M. Role of HIV-1 RNA and protein determinants for the selective packaging of spliced and unspliced viral RNA and host U6 and 7SL RNA in virus particles. Nucleic Acids Res 2011; 39:8915-27. [PMID: 21791531 PMCID: PMC3203606 DOI: 10.1093/nar/gkr577] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 01/22/2023] Open
Abstract
HIV-1 particles contain RNA species other than the unspliced viral RNA genome. For instance, viral spliced RNAs and host 7SL and U6 RNAs are natural components that are non-randomly incorporated. To understand the mechanism of packaging selectivity, we analyzed the content of a large panel of HIV-1 variants mutated either in the 5'UTR structures of the viral RNA or in the Gag-nucleocapsid protein (GagNC). In parallel, we determined whether the selection of host 7SL and U6 RNAs is dependent or not on viral RNA and/or GagNC. Our results reveal that the polyA hairpin in the 5'UTR is a major packaging determinant for both spliced and unspliced viral RNAs. In contrast, 5'UTR RNA structures have little influence on the U6 and 7SL RNAs, indicating that packaging of these host RNAs is independent of viral RNA packaging. Experiments with GagNC mutants indicated that the two zinc-fingers and N-terminal basic residues restrict the incorporation of the spliced RNAs, while favoring unspliced RNA packaging. GagNC through the zinc-finger motifs also restricts the packaging of 7SL and U6 RNAs. Thus, GagNC is a major contributor to the packaging selectivity. Altogether our results provide new molecular insight on how HIV selects distinct RNA species for incorporation into particles.
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Affiliation(s)
- L. Didierlaurent
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - P. J. Racine
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - L. Houzet
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - C. Chamontin
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - B. Berkhout
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - M. Mougel
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
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13
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Coordinate roles of Gag and RNA helicase A in promoting the annealing of formula to HIV-1 RNA. J Virol 2010; 85:1847-60. [PMID: 21106734 DOI: 10.1128/jvi.02010-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
RNA helicase A (RHA) has been shown to promote HIV-1 replication at both the translation and reverse transcription stages. A prerequisite step for reverse transcription involves the annealing of tRNA(3)(Lys), the primer for reverse transcription, to HIV-1 RNA. tRNA(3)(Lys) annealing is a multistep process that is initially facilitated by Gag prior to viral protein processing. Herein, we report that RHA promotes this annealing through increasing both the quantity of tRNA(3)(Lys) annealed by Gag and the ability of tRNA(3)(Lys) to prime the initiation of reverse transcription. This improved annealing is the result of an altered viral RNA conformation produced by the coordinate action of Gag and RHA. Since RHA has been reported to promote the translation of unspliced viral RNA to Gag protein, our observations suggest that the conformational change in viral RNA induced by RHA and newly produced Gag may help facilitate the switch in viral RNA from a translational mode to one facilitating tRNA(3)(Lys) annealing.
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14
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Wu T, Datta SA, Mitra M, Gorelick RJ, Rein A, Levin JG. Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein and Gag or Gag-derived proteins: biological implications. Virology 2010; 405:556-67. [PMID: 20655566 PMCID: PMC2963451 DOI: 10.1016/j.virol.2010.06.042] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/16/2010] [Accepted: 06/23/2010] [Indexed: 01/31/2023]
Abstract
The HIV-1 Gag polyprotein precursor has multiple domains including nucleocapsid (NC). Although mature NC and NC embedded in Gag are nucleic acid chaperones (proteins that remodel nucleic acid structure), few studies include detailed analysis of the chaperone activity of partially processed Gag proteins and comparison with NC and Gag. Here we address this issue by using a reconstituted minus-strand transfer system. NC and NC-containing Gag proteins exhibited annealing and duplex destabilizing activities required for strand transfer. Surprisingly, unlike NC, with increasing concentrations, Gag proteins drastically inhibited the DNA elongation step. This result is consistent with "nucleic acid-driven multimerization" of Gag and the reported slow dissociation of Gag from bound nucleic acid, which prevent reverse transcriptase from traversing the template ("roadblock" mechanism). Our findings illustrate one reason why NC (and not Gag) has evolved as a critical cofactor in reverse transcription, a paradigm that might also extend to other retrovirus systems.
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Affiliation(s)
- Tiyun Wu
- Laboratory of Molecular Genetics, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
| | - Siddhartha A.K. Datta
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Mithun Mitra
- Laboratory of Molecular Genetics, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Alan Rein
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Judith G. Levin
- Laboratory of Molecular Genetics, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 6B, Room 216, 6 Center Drive, Bethesda, MD 20892-2780, USA
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15
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Jalalirad M, Laughrea M. Formation of immature and mature genomic RNA dimers in wild-type and protease-inactive HIV-1: differential roles of the Gag polyprotein, nucleocapsid proteins NCp15, NCp9, NCp7, and the dimerization initiation site. Virology 2010; 407:225-36. [PMID: 20828778 DOI: 10.1016/j.virol.2010.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 08/06/2010] [Accepted: 08/13/2010] [Indexed: 12/22/2022]
Abstract
Formation of immature genomic RNA (gRNA) dimers is exquisitely nucleocapsid (NC)-dependent in protease-inactive (PR-in) HIV-1. This establishes that Pr55gag/Pr160gag-pol has NC-dependent chaperone activity within intact HIV-1. Mutations in the proximal zinc finger and the linker of the NC sequence of Pr55gag/Pr160gag-pol abolish gRNA dimerization in PR-in HIV-1. In wild type, where the NC of Pr55gag is processed into progressively smaller proteins termed NCp15 (NCp7-p1-p6), NCp9 (NCp7-p1) and NCp7, formation of immature dimers is much swifter than in PR-in HIV-1. NCp7 and NCp15 direct this rapid accumulation. NCp9 is sluggish in this process, but it stimulates the transition from immature to mature gRNA dimer as well as NCp7 and much better than NCp15. The amino-terminus, proximal zinc finger, linker, and distal zinc finger of NCp7 contribute to this maturation event in intact HIV-1. The DIS is a dimerization initiation site for all immature gRNA dimers, irrespective of their mechanism of formation.
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Affiliation(s)
- Mohammad Jalalirad
- McGill AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal QC, Canada H3T 1E2
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16
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Isel C, Ehresmann C, Marquet R. Initiation of HIV Reverse Transcription. Viruses 2010; 2:213-243. [PMID: 21994608 PMCID: PMC3185550 DOI: 10.3390/v2010213] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 01/08/2010] [Accepted: 01/13/2010] [Indexed: 12/01/2022] Open
Abstract
Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target.
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Affiliation(s)
- Catherine Isel
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
| | | | - Roland Marquet
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
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17
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Saadatmand J, Niu M, Kleiman L, Guo F. The contribution of the primer activation signal to differences between Gag- and NCp7-facilitated tRNA(Lys3) annealing in HIV-1. Virology 2009; 391:334-41. [PMID: 19616817 DOI: 10.1016/j.virol.2009.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 06/15/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
Abstract
During tRNA(Lys3) annealing in HIV-1, tRNA(Lys3) binds to both the primer binding site (PBS) and to an 8 nucleotide base-paired sequence upstream of the PBS known as the primer activation signal (PAS). In protease-negative (Pr(-)) HIV-1, the amount of tRNA(Lys3) annealed by Gag is 35% less than that annealed by mature nucleocapsid (NCp7) in protease-positive (Pr(+)) virions. Gag-annealed tRNA(Lys3) also has a reduced ability to initiate reverse transcription, and binds less tightly to viral RNA than NCp7-annealed tRNA(Lys3). Pr(-) virions containing a constitutively single-stranded PAS (2R mutant), show a significant increase in the ability to initiate reverse transcription with little change in the amount of tRNA(Lys3) annealed. However, the 2R mutant does not achieve levels of RT initiation achieved in Pr(+) virions, and tRNA(Lys3) binding to viral RNA remains weak. Wild type levels of initiation and tRNA(Lys3) binding to viral RNA can only be recovered by transient exposure of Pr(-) or Pr(-)2R viral RNA to NCp7. This suggests that in addition to facilitating annealing of tRNA(Lys3) to the PBS and possible denaturation of the PAS, other functions of NCp7 involved in annealing are required. The effect of an inactive protease and/or the 2R mutation upon tRNA(Lys3) annealing and initiation are also observed when the tRNA(Lys3) is annealed in vitro to wild type or mutant viral RNA using either NCp7 or GagDeltap6, indicating a direct effect of the 2R mutation upon tRNA(Lys3) annealing.
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Affiliation(s)
- Jenan Saadatmand
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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18
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Roles of Gag and NCp7 in facilitating tRNA(Lys)(3) Annealing to viral RNA in human immunodeficiency virus type 1. J Virol 2009; 83:8099-107. [PMID: 19494012 DOI: 10.1128/jvi.00488-09] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In protease-negative human immunodeficiency virus type 1 (HIV-1) [Pr(-)], the amount of tRNA(3)(Lys) annealed by Gag is modestly reduced ( approximately 25%) compared to that annealed by mature nucleocapsid (NCp7) in protease-positive HIV-1 [Pr(+)]. However, the tRNA(3)(Lys) annealed by Gag also has a strongly reduced ability to initiate reverse transcription and binds less tightly to viral RNA. Both in vivo and in vitro, APOBEC3G (A3G) inhibits tRNA(3)(Lys) annealing facilitated by NCp7 but not annealing facilitated by Gag. While transient exposure of Pr(-) viral RNA to NCp7 in vitro returns the quality and quantity of tRNA(3)(Lys) annealing to Pr(+) levels, the presence of A3G both prevents this rescue and creates a further reduction in tRNA(3)(Lys) annealing. Since A3G inhibition of NCp7-facilitated tRNA(3)(Lys) annealing in vitro requires the presence of A3G during the annealing process, these results suggest that in Pr(+) viruses NCp7 can displace Gag-annealed tRNA(3)(Lys) and re-anneal it to viral RNA, the re-annealing step being subject to A3G inhibition. This supports the possibility that the initial annealing of tRNA(3)(Lys) in wild-type, Pr(+) virus may be by Gag and not by NCp7, perhaps offering the advantage of Gag's preference for binding to RNA stem-loops in the 5' region of viral RNA near the tRNA(3)(Lys) annealing region.
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19
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Stephen AG, Fisher RJ. Methods for the analysis of HIV-1 nucleocapsid protein interactions with oligonucleotides. Methods Mol Biol 2009; 485:209-221. [PMID: 19020828 DOI: 10.1007/978-1-59745-170-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
HIV-1 Nucleocapsid protein (NC) is a small basic protein that contains two retroviral zinc fingers. It is a highly effective nucleic acid chaperone that plays a critical role in viral replication acting as a cofactor in reverse transcription as well as other aspects of the viral lifecycle. We have used a variety of biophysical techniques to characterize the high affinity binding of NC to a short deoxyoligonucleotide (d(TG)(4)). Here we outline in detail the use of fluorescence anisotropy and surface plasmon resonance spectroscopy to study the binding of NC to d(TG)(4).
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Affiliation(s)
- Andrew G Stephen
- Protein Chemistry Laboratory, Research Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick MD, USA
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20
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Cen S, Guo F, Kleiman L. Methods for analysis of incorporation and annealing methods for analysis of tRNA(Lys) in HIV-1. Methods Mol Biol 2009; 485:223-232. [PMID: 19020829 DOI: 10.1007/978-1-59745-170-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In HIV-1, tRNA(Lys3) serves as the primer for reverse transcription of minus strand strong stop cDNA. During viral assembly, the tRNA(Lys) isoacceptors, tRNA(Lys1,2) and tRNA(Lys3), are selectively packaged into the virion. The selectively packaging of tRNA(Lys3) facilitates the annealing of tRNA(Lys3) to the viral genome and the initiation of reverse transcription. We describe herein a set of experimental approaches for studying the mechanism by which tRNA(Lys) is selectively incorporated into HIV-1 and investigate how primer tRNA(Lys3) is annealed to viral genome. The methods described will also help in the analysis of cellular RNAs packaged in the virus particles.
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Affiliation(s)
- Shan Cen
- Department of Medicine, McGill University, Lady Davis Institute for Medical Research Jewish General Hospital, Montreal, QC, Canada
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21
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Yabar CA, Salvatierra J, Quijano E. Polymorphism, recombination, and mutations in HIV type 1 gag-infecting Peruvian male sex workers. AIDS Res Hum Retroviruses 2008; 24:1405-13. [PMID: 19000025 DOI: 10.1089/aid.2008.0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV genetic diversity in female sex workers (FSW) has been previously described in Peru; however this information is not yet available for male sex workers (MSW). Therefore, purified peripheral blood mononuclear cell DNA from 147 HIV-infected subjects identified as MSW and FSW was used to amplify a 460-bp fragment corresponding to the p24-p7 region of the gag gene. The PCR product was digested with restriction enzymes to identify genetic polymorphism. Later, a random group of samples (n = 19) was sequenced to perform phylogenetic analysis, intragenic recombination analysis, and deleterious mutations leading to a nonfunctional protein in conservative regions of the Gag protein. RFLP analysis revealed 11 genetic variants for AluI and five for MspI. A group of nonsex workers (NSW) used for comparison showed different RFLP genetic variant distributions. Of interest, nine cases of mixed genetic variants were observed for MSW, one case for FSW, and none for NSW. Phylogenetic analysis revealed that all HIV-1 species were subtype B. Intragenic recombination analysis showed a B/C recombination case from an FSW (boostrap = 1000; p value < 0.05). Of interest, deleterious mutations were observed in three cases of conservative D2 zinc domains for Gag 3/19 and one case of the high homology region (1/19). This study shows that gag of HIV circulating from MSW has high genetic polymorphism involving deleterious mutations in conserved domains from the p24-p7 gag region.
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Affiliation(s)
- Carlos Augusto Yabar
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Javier Salvatierra
- Centro Especializado en Enfermedades de Transmisión Sexual “Alberto Barton,” Callao, Peru
| | - Eberth Quijano
- Centro Especializado en Enfermedades de Transmisión Sexual “Alberto Barton,” Callao, Peru
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22
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Didierlaurent L, Houzet L, Morichaud Z, Darlix JL, Mougel M. The conserved N-terminal basic residues and zinc-finger motifs of HIV-1 nucleocapsid restrict the viral cDNA synthesis during virus formation and maturation. Nucleic Acids Res 2008; 36:4745-53. [PMID: 18641038 PMCID: PMC2504319 DOI: 10.1093/nar/gkn474] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reverse transcription of the genomic RNA by reverse transcriptase occurs soon after HIV-1 infection of target cells. The viral nucleocapsid (NC) protein chaperones this process via its nucleic acid annealing activities and its interactions with the reverse transcriptase enzyme. To function, NC needs its two conserved zinc fingers and flanking basic residues. We recently reported a new role for NC, whereby it negatively controls reverse transcription in the course of virus formation. Indeed, deleting its zinc fingers causes reverse transcription activation in virus producer cells. To investigate this new NC function, we used viruses with subtle mutations in the conserved zinc fingers and its flanking domains. We monitored by quantitative PCR the HIV-1 DNA content in producer cells and in produced virions. Results showed that the two intact zinc-finger structures are required for the temporal control of reverse transcription by NC throughout the virus replication cycle. The N-terminal basic residues also contributed to this new role of NC, while Pro-31 residue between the zinc fingers and Lys-59 in the C-terminal region did not. These findings further highlight the importance of NC as a major target for anti-HIV-1 drugs.
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23
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Jacob DT, DeStefano JJ. A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming. Virology 2008; 378:385-96. [PMID: 18632127 DOI: 10.1016/j.virol.2008.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 05/26/2008] [Accepted: 06/05/2008] [Indexed: 11/28/2022]
Abstract
The current study indicates a new role for HIV nucleocapsid protein (NC) in modulating the specificity of plus strand priming. RNase H cleavage by reverse transcriptase (RT) during minus strand synthesis gives rise to RNA fragments that could potentially be used as primers for synthesis of the plus strand, leading to the initiation of priming from multiple points as has been observed for other retroviruses. For HIV, the central and 3' polypurine tracts (PPTs) are the major sites of plus strand initiation. Using reconstituted in vitro assays, results showed that NC greatly reduced the efficiency of extension of non-PPT RNA primers, but not PPT. Experiments mimicking HIV replication showed that RT generated and used both PPT and non-PPT RNAs to initiate "plus strand" synthesis, but non-PPT usage was strongly inhibited by NC. The results support a role for NC in specifying primer usage during plus strand synthesis.
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Affiliation(s)
- Deena T Jacob
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
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24
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Kafaie J, Song R, Abrahamyan L, Mouland AJ, Laughrea M. Mapping of nucleocapsid residues important for HIV-1 genomic RNA dimerization and packaging. Virology 2008; 375:592-610. [PMID: 18343475 DOI: 10.1016/j.virol.2008.02.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 01/14/2008] [Accepted: 02/01/2008] [Indexed: 11/26/2022]
Abstract
Retroviral genomic RNA (gRNA) dimerization appears essential for viral infectivity, and the nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) facilitates HIV-1 gRNA dimerization. To identify the relevant and dispensable positions of NC, 34 of its 55 residues were mutated, individually or in small groups, in a panel of 40 HIV-1 mutants prepared by site-directed mutagenesis. It was found that the amino-terminus, the proximal zinc finger, the linker, and the distal zinc finger of NC each contributed roughly equally to efficient HIV-1 gRNA dimerization. The N-terminal and linker segments appeared to play predominantly electrostatic and steric roles, respectively. Mutating the hydrophobic patch of either zinc finger, or substituting alanines for their glycine doublet, was as disabling as deleting the corresponding finger. Replacing the CysX(2)CysX(4)HisX(4)Cys motif of either finger by CysX(2)CysX(4)CysX(4)Cys or CysX(2)CysX(4)HisX(4)His, interchanging the zinc fingers or, replacing one zinc finger by a copy of the other one, had generally intermediate effects; among these mutations, the His23-->Cys substitution in the N-terminal zinc finger had the mildest effect. The charge of NC could be increased or decreased by up to 18%, that of the linker could be reduced by 75% or increased by 50%, and one or two electric charges could be added or subtracted from either zinc finger, without affecting gRNA dimerization. Shortening, lengthening, or making hydrophobic the linker was as disabling as deleting the N-terminal or the C-terminal zinc finger, but a neutral and polar linker was innocuous. The present work multiplies by 4 and by 33 the number of retroviral and lentiviral NC mutations known to inhibit gRNA dimerization, respectively. It shows the first evidence that gRNA dimerization can be inhibited by: 1) mutations in the N-terminus or the linker of retroviral NC; 2) mutations in the proximal zinc finger of lentiviral NC; 3) mutations in the hydrophobic patch or the conserved glycines of the proximal or the distal retroviral zinc finger. Some NC mutations impaired gRNA dimerization more than mutations inactivating the viral protease, indicating that gRNA dimerization may be stimulated by the NC component of the Gag polyprotein. Most, but not all, mutations inhibited gRNA packaging; some had a strong effect on virus assembly or stability.
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Affiliation(s)
- Jafar Kafaie
- McGill AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
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25
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Nucleocapsid protein function in early infection processes. Virus Res 2008; 134:39-63. [PMID: 18279991 DOI: 10.1016/j.virusres.2007.12.006] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/13/2007] [Accepted: 12/13/2007] [Indexed: 01/15/2023]
Abstract
The role of nucleocapsid protein (NC) in the early steps of retroviral replication appears largely that of a facilitator for reverse transcription and integration. Using a wide variety of cell-free assay systems, the properties of mature NC proteins (e.g. HIV-1 p7(NC) or MLV p10(NC)) as nucleic acid chaperones have been extensively investigated. The effect of NC on tRNA annealing, reverse transcription initiation, minus-strand-transfer, processivity of reverse transcription, plus-strand-transfer, strand-displacement synthesis, 3' processing of viral DNA by integrase, and integrase-mediated strand-transfer has been determined by a large number of laboratories. Interestingly, these reactions can all be accomplished to varying degrees in the absence of NC; some are facilitated by both viral and non-viral proteins and peptides that may or may not be involved in vivo. What is one to conclude from the observation that NC is not strictly required for these necessary reactions to occur? NC likely enhances the efficiency of each of these steps, thereby vastly improving the productivity of infection. In other words, one of the major roles of NC is to enhance the effectiveness of early infection, thereby increasing the probability of productive replication and ultimately of retrovirus survival.
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26
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Guo F, Cen S, Niu M, Yang Y, Gorelick RJ, Kleiman L. The interaction of APOBEC3G with human immunodeficiency virus type 1 nucleocapsid inhibits tRNA3Lys annealing to viral RNA. J Virol 2007; 81:11322-31. [PMID: 17670826 PMCID: PMC2045548 DOI: 10.1128/jvi.00162-07] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) containing human APOBEC3G (hA3G) has a reduced ability to produce viral DNA in newly infected cells. At least part of this hA3G-facilitated inhibition is due to a cytidine deamination-independent reduction in the ability to initiate reverse transcription. HIV-1 nucleocapsid (NCp7) is required both for the incorporation of hA3G into virions and for the annealing between viral RNA and tRNA(3)(Lys), the primer tRNA for reverse transcription. Herein we present evidence that the interaction of hA3G with nucleocapsid is required for the inhibition of reverse transcription initiation. A tRNA(3)(Lys) priming complex was produced in vitro by the NCp7-facilitated annealing of tRNA(3)(Lys) to synthetic viral RNA in the absence or presence of hA3G. The effect of hA3G on the annealing of tRNA(3)(Lys) to viral RNA and the ability of tRNA(3)(Lys) to initiate reverse transcription was measured. Our results show the following. (i) Electrophoretic band shift and primer binding site assays show that hA3G reduces the annealing of tRNA(3)(Lys) 44 and 60%, respectively, but does not disrupt the annealed complex once formed. (ii) hA3G inhibits tRNA(3)(Lys) priming 70 to 80%. (iii) Inhibition of tRNA(3)(Lys) priming by hA3G requires an interaction between hA3G and NCp7 during annealing. Thus, annealing of tRNA(3)(Lys) is insensitive to hA3G inhibition when facilitated by a zinc finger mutant of NCp7 unable to interact with hA3G. NCp7-independent annealing of DNA to viral RNA also is insensitive to hA3G inhibition. These results indicate that hA3G does not sterically block tRNA(3)(Lys) annealing by binding to viral RNA. Annealing and priming are not affected by another RNA binding protein, QKI-6.
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Affiliation(s)
- Fei Guo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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Thomas JA, Shulenin S, Coren LV, Bosche WJ, Gagliardi TD, Gorelick RJ, Oroszlan S. Characterization of human immunodeficiency virus type 1 (HIV-1) containing mutations in the nucleocapsid protein at a putative HIV-1 protease cleavage site. Virology 2006; 354:261-70. [PMID: 16904152 DOI: 10.1016/j.virol.2006.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 03/24/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
The HIV-1 nucleocapsid protein (NC) has been hypothesized to be cleaved by the viral protease (PR) during early infection. Characterization of viruses, with amino-acid substitutions that modulate PR cleavage of NC in vitro, was performed in cell culture. Two of the NC mutants, NCN17F and NCN17G, had decreased infectivity and exhibited severe H9 replication defects. Examination of viral DNA after infections revealed defects in reverse transcription and integration, although integration defects were cell-type dependent. However, while the defects in reverse transcription and integration correlate with lowered infectivity in a single-round of infection, they did not approach the magnitude of the replication defect measured in H9 cells over multiple rounds. Importantly, we fail to see evidence that H9 cells are re-infected with the NCN17G and NCN17F viruses 24 h after the initial infection, which suggests that the principal defect caused by these NC mutations occurs during late events of viral replication.
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Affiliation(s)
- James A Thomas
- AIDS Vaccine Program, SAIC-Frederick, Inc NCI-Frederick, Bldg 535, Room 410, PO Box B, Frederick, MD 21702-1201, USA.
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28
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Barnor JS, Miyano-Kurosaki N, Takaku H, Yamaguchi K, Sakamoto A, Ishikawa K, Yamamoto N, Osei-Kwasi M, Ofori-Adjei D. The middle to 3' end of the HIV-1 vif gene sequence is important for vif biological activity and could be used for antisense oligonucleotide targets. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:1745-61. [PMID: 16438045 DOI: 10.1080/10810730500265823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1)-encoded vif protein is essential for viral replication, virion production, and pathogenicity. HIV-1 Vif interacts with the endogenous human APOBEC3G protein (an mRNA editor) in target cells to prevent its encapsidation into virions. Some studies have established targets within the HIV-1 vif gene that are important for its biologic function; however, it is important to determine effective therapeutic targets in vif because of its critical role in HIV-1 infectivity and pathogenicity. The present study demonstrates that virions generated in transfected HeLa-CD4+ cells, especially from HIV-1 vif frame-shift mutant (3' delta vif; 5561-5849), were affected in splicing and had low infectivity in MT-4 cells. In addition, HIV-1 vif antisense RNA fragments constructed within the same region, notably the region spanning nucleic acid positions 5561-5705 (M-3'-AS), which corresponds to amino acid residues 96-144, significantly inhibited HIV-1 replication in MT-4 and reduced the HIV-1 vif mRNA transcripts and reporter gene (EGFP) expression. The generated virions showed low secondary infection in H9 cells. These data therefore suggest that the middle to the 3' end of vif is important for its biological activity in the target cells.
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Affiliation(s)
- Jacob Samson Barnor
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, Japan
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29
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Cruceanu M, Urbaneja MA, Hixson CV, Johnson DG, Datta SA, Fivash MJ, Stephen AG, Fisher RJ, Gorelick RJ, Casas-Finet JR, Rein A, Rouzina I, Williams MC. Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins. Nucleic Acids Res 2006; 34:593-605. [PMID: 16449201 PMCID: PMC1356529 DOI: 10.1093/nar/gkj458] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Gag polyprotein of HIV-1 is essential for retroviral replication and packaging. The nucleocapsid (NC) protein is the primary region for the interaction of Gag with nucleic acids. In this study, we examine the interactions of Gag and its NC cleavage products (NCp15, NCp9 and NCp7) with nucleic acids using solution and single molecule experiments. The NC cleavage products bound DNA with comparable affinity and strongly destabilized the DNA duplex. In contrast, the binding constant of Gag to DNA was found to be approximately 10-fold higher than that of the NC proteins, and its destabilizing effect on dsDNA was negligible. These findings are consistent with the primary function of Gag as a nucleic acid binding and packaging protein and the primary function of the NC proteins as nucleic acid chaperones. Also, our results suggest that NCp7's capability for fast sequence-nonspecific nucleic acid duplex destabilization, as well as its ability to facilitate nucleic acid strand annealing by inducing electrostatic attraction between strands, likely optimize the fully processed NC protein to facilitate complex nucleic acid secondary structure rearrangements. In contrast, Gag's stronger DNA binding and aggregation capabilities likely make it an effective chaperone for processes that do not require significant duplex destabilization.
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Affiliation(s)
- Margareta Cruceanu
- Department of Physics, Northeastern University111 Dana Research Center, 110 Forsyth Street, Boston, MA 02115, USA
| | - Maria A. Urbaneja
- AIDS Vaccine Program, SAIC-Frederick, Inc.NCI at Frederick, Frederick, MD 21702, USA
| | - Catherine V. Hixson
- AIDS Vaccine Program, SAIC-Frederick, Inc.NCI at Frederick, Frederick, MD 21702, USA
| | - Donald G. Johnson
- AIDS Vaccine Program, SAIC-Frederick, Inc.NCI at Frederick, Frederick, MD 21702, USA
| | | | - Matthew J. Fivash
- Data Management Services, Inc.NCI-Frederick, Frederick, MD 2170, USA
| | - Andrew G. Stephen
- Protein Chemistry Laboratory, SAIC Frederick, Inc.NCI at Frederick, Frederick, MD 2170, USA
| | - Robert J. Fisher
- Protein Chemistry Laboratory, SAIC Frederick, Inc.NCI at Frederick, Frederick, MD 2170, USA
| | - Robert J. Gorelick
- AIDS Vaccine Program, SAIC-Frederick, Inc.NCI at Frederick, Frederick, MD 21702, USA
| | | | - Alan Rein
- HIV Drug Resistance Program, NCI-FrederickFrederick, MD 21702-1201, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University111 Dana Research Center, 110 Forsyth Street, Boston, MA 02115, USA
- Center for Interdisciplinary Research on Complex Systems, Northeastern University111 Dana Research Center, 110 Forsyth Street, Boston, MA 02115, USA
- To whom correspondence should be addressed. Tel: 1 617 373 7323; Fax: 1 617 373 2943;
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30
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Fisher RJ, Fivash MJ, Stephen AG, Hagan NA, Shenoy SR, Medaglia MV, Smith LR, Worthy KM, Simpson JT, Shoemaker R, McNitt KL, Johnson DG, Hixson CV, Gorelick RJ, Fabris D, Henderson LE, Rein A. Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res 2006; 34:472-84. [PMID: 16434700 PMCID: PMC1351370 DOI: 10.1093/nar/gkj442] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 12/23/2005] [Accepted: 12/23/2005] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replication cycle as well. We previously reported that NC binds with high-affinity to the repeating sequence d(TG)n. We have now analyzed the interaction between NC and d(TG)4 in considerable detail, using surface plasmon resonance (SPR), tryptophan fluorescence quenching (TFQ), fluorescence anisotropy (FA), isothermal titration calorimetry (ITC) and electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). Our results show that the interactions between these two molecules are surprisngly complex: while the K(d) for binding of a single d(TG)4 molecule to NC is only approximately 5 nM in 150 mM NaCl, a single NC molecule is capable of interacting with more than one d(TG)4 molecule, and conversely, more than one NC molecule can bind to a single d(TG)4 molecule. The strengths of these additional binding reactions are quantitated. The implications of this multivalency for the functions of NC in virus replication are discussed.
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Affiliation(s)
- Robert J Fisher
- Protein Chemistry Laboratory, SAIC-Frederick, Inc. NCI Frederick, Frederick, MD 21702, USA.
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31
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Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. ACTA ACUST UNITED AC 2006; 80:217-86. [PMID: 16164976 DOI: 10.1016/s0079-6603(05)80006-6] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Judith G Levin
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Wei M, Cen S, Niu M, Guo F, Kleiman L. Defective replication in human immunodeficiency virus type 1 when non-primers are used for reverse transcription. J Virol 2005; 79:9081-7. [PMID: 15994802 PMCID: PMC1168737 DOI: 10.1128/jvi.79.14.9081-9087.2005] [Citation(s) in RCA: 11] [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
tRNA(3Lys), the primer for reverse transcriptase in human immunodeficiency virus type 1 (HIV-1), anneals to the primer binding site (PBS) in HIV-1 RNA. It has been shown that altering the PBS and U5 regions upstream of the PBS in HIV-1 so as to be complementary to sequences in tRNA(Met) or tRNA(His) will allow these tRNA species to be stably used as primers for reverse transcription. We have examined the replication of these mutant viruses in Sup-T1 cells. When Sup-T1 cells are infected by cocultivation with HIV-1-transfected 293T cells, viruses using tRNA(His) or tRNA(Met) are produced at rates that are approximately 1/10 or 1/100, respectively, of rates for wild-type virions that use tRNA(3Lys). When Sup-T1 cells are directly infected with equal amounts of these different viruses isolated from the culture supernatant of transfected 293T cells, virions using tRNA(Met) are produced at 1/100 the rate of wild-type viruses, and production of virions using tRNA(His) is not detected. Both wild-type and mutant virions selectively package tRNA(Lys) only, and examination of the ability of total viral RNA to prime reverse transcription in vitro indicates a >80% reduction in the annealing of tRNA(His) or tRNA(Met) to the mutant viral RNAs. PCR analysis of which of the three primer tRNAs is used indicates that only tRNA(3Lys) is detected as primer in wild-type virions and only tRNA(His) is detected as primer in virions containing a PBS complementary to tRNA(His), while the mutant viruses containing a PBS complementary to tRNA(Met) use both tRNA(Met) and tRNA(1,2Lys) as primer tRNAs.
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Affiliation(s)
- Min Wei
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Cote Ste-Catherine Road, Montreal, Quebec, Canada H3T 1E2
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33
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Renda MJ, Bradel-Tretheway B, Planelles V, Bambara RA, Dewhurst S. Inhibition of HIV type 1 replication using lentiviral-mediated delivery of mutant tRNA(Lys3)A58U. AIDS Res Hum Retroviruses 2004; 20:1324-34. [PMID: 15650425 DOI: 10.1089/aid.2004.20.1324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In previous studies, we showed that residue A58 of cellular tRNALys3 is necessary for appropriate termination of viral plus-strand strong-stop DNA (+SS DNA), and therefore plays a critical role in the life cycle of HIV-1. We also performed proof-of-principle studies that established that a mutant form of this tRNA primer (tRNA(Lys3)A58U, which lacks the M1A58 residue necessary for +SS DNA termination) could inhibit HIV-1 replication. In the present work, we examined whether a third generation lentiviral vector (SIN) could be used to deliver tRNA(Lys3)A58U to CEM cells. Using both viral kinetic studies and limiting dilution assays (LDA), we observed significant impairment of HIV-1 replication, up to 3 logs in the LDA, in CEM sublines expressing mutant tRNA(Lys3)A58U. No inhibition occurred in cells that either expressed wild-type tRNA(Lys3) or were transduced with empty SIN vector. Further, we observed impairment of viral replication using primary isolates of both HIV-1 and HIV-2 in sublines containing tRNA(Lys3)A58U. We also detected "breakthrough" HIV-1 replication in some tRNA(Lys3)A58U-expressing cultures. Interestingly, analyzed breakthrough viruses appeared to be both genetically and phenotypically wild type. One possible explanation for virological breakthrough is that it reflects the gradual accumulation of HIV-1 within the infected cell culture, to a level that ultimately exceeds the containment "threshold" conferred by tRNA(Lys3)A58U. The fact that HIV-1 does not appear to acquire heritable resistance to tRNA(Lys3)A58U-mediated blockade differentiates this antiviral modality from other therapeutic interventions. It also suggests that tRNA-mediated inhibition of viral replication might be a valuable adjunct to other antiviral approaches.
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Affiliation(s)
- Matthew J Renda
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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34
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Muriaux D, Costes S, Nagashima K, Mirro J, Cho E, Lockett S, Rein A. Role of murine leukemia virus nucleocapsid protein in virus assembly. J Virol 2004; 78:12378-85. [PMID: 15507624 PMCID: PMC525092 DOI: 10.1128/jvi.78.22.12378-12385.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The retroviral nucleocapsid protein (NC) originates by cleavage of the Gag polyprotein. It is highly basic and contains one or two zinc fingers. Mutations in either the basic residues or the zinc fingers can affect several events of the virus life cycle. They frequently prevent the specific packaging of the viral RNA, affect reverse transcription, and impair virion assembly. In this work, we explore the role of NC in murine leukemia virus (MLV) particle assembly and release. A panel of NC mutants, including mutants of the zinc finger and of a basic region, as well as truncations of the NC domain of Gag, were studied. Several of these mutations dramatically reduce the release of virus particles. A mutant completely lacking the NC domain is apparently incapable of assembling into particles, although its Gag protein is still targeted to the plasma membrane. By electron microscopy on thin sections of virus-producing cells, we observed that some NC mutants exhibit various stages of budding defects at the plasma membrane and have aberrant particle morphology; electron micrographs of cells expressing some of these mutants are strikingly similar to those of cells expressing "late-domain" mutants. However, the defects of NC mutants with respect to virus release and infectivity could be complemented by an MLV lacking the p12 domain. Therefore, the functions of NC in virus budding and infectivity are completely distinct from viral late-domain function.
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Affiliation(s)
- Delphine Muriaux
- HIV Drug Resistance Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
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35
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Cen S, Niu M, Kleiman L. The connection domain in reverse transcriptase facilitates the in vivo annealing of tRNALys3 to HIV-1 genomic RNA. Retrovirology 2004; 1:33. [PMID: 15494076 PMCID: PMC524520 DOI: 10.1186/1742-4690-1-33] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 10/19/2004] [Indexed: 11/19/2022] Open
Abstract
The primer tRNA for reverse transcription in HIV-1, tRNALys3, is selectively packaged into the virus during its assembly, and annealed to the viral genomic RNA. The ribonucleoprotein complex that is involved in the packaging and annealing of tRNALys into HIV-1 consists of Gag, GagPol, tRNALys, lysyl-tRNA synthetase (LysRS), and viral genomic RNA. Gag targets tRNALys for viral packaging through Gag's interaction with LysRS, a tRNALys-binding protein, while reverse transcriptase (RT) sequences within GagPol (the thumb domain) bind to tRNALys. The further annealing of tRNALys3 to viral RNA requires nucleocapsid (NC) sequences in Gag, but not the NC sequences GagPol. In this report, we further show that while the RT connection domain in GagPol is not required for tRNALys3 packaging into the virus, it is required for tRNALys3 annealing to the viral RNA genome.
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Affiliation(s)
- Shan Cen
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3T 1E2
| | - Meijuan Niu
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3T 1E2
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3T 1E2
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada H3T 1E2
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36
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Cen S, Guo F, Niu M, Saadatmand J, Deflassieux J, Kleiman L. The Interaction between HIV-1 Gag and APOBEC3G. J Biol Chem 2004; 279:33177-84. [PMID: 15159405 DOI: 10.1074/jbc.m402062200] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
APOBEC3G, a member of an RNA/DNA cytidine deaminase superfamily, has been identified as a cellular inhibitor of HIV-1 infectivity, possibly through the dC to dU deamination of the first minus strand cDNA synthesized during reverse transcription. Virions incorporate APOBEC3G during viral assembly in non-permissive cells, and this incorporation is inhibited by the viral protein Vif. The mechanism of APOBEC3G incorporation into HIV-1 is examined in this report. In the absence of Vif, cytoplasmic APOBEC3G becomes membrane-bound in cells expressing HIV-1 Gag, and its incorporation into Gag viral-like particles (VLPs) is proportional to the amount of APOBEC3G expressed in the cell. The expression of Vif, or mutant Gag unable to bind to membrane, prevents the APOBEC3G association with membrane. HIV-1 Gag alone among viral proteins is sufficient for packaging of APOBEC3G into Gag VLPs, and this incorporation requires the presence of Gag nucleocapsid. The presence of amino acids 104-156 in APOBEC3G, located in the linker region between two zinc coordination motifs, is also required for its incorporation into Gag VLPs. Evidence against an RNA bridge facilitating the Gag/APOBEC3G interaction includes data indicating that 1) the incorporation of APOBEC3G occurs independently of viral genomic RNA, 2) a Gag/APOBEC3G complex is immunoprecipitated from cell lysate after RNase treatment, and 3) the zinc coordination motif, rather than the regions flanking this motif, have been implicated in RNA binding in another family member, APOBEC1.
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Affiliation(s)
- Shan Cen
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Department of Medicine, McGill University, Montreal, Quebec H3T 1E2, Canada
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37
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Heilman-Miller SL, Wu T, Levin JG. Alteration of nucleic acid structure and stability modulates the efficiency of minus-strand transfer mediated by the HIV-1 nucleocapsid protein. J Biol Chem 2004; 279:44154-65. [PMID: 15271979 DOI: 10.1074/jbc.m401646200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During human immunodeficiency virus type 1 minus-strand transfer, the nucleocapsid protein (NC) facilitates annealing of the complementary repeat regions at the 3'-ends of acceptor RNA and minus-strand strong-stop DNA ((-) SSDNA). In addition, NC destabilizes the highly structured complementary trans-activation response element (TAR) stem-loop (TAR DNA) at the 3'-end of (-) SSDNA and inhibits TAR-induced self-priming, a dead-end reaction that competes with minus-strand transfer. To investigate the relationship between nucleic acid secondary structure and NC function, a series of truncated (-) SSDNA and acceptor RNA constructs were used to assay minus-strand transfer and self-priming in vitro. The results were correlated with extensive enzymatic probing and mFold analysis. As the length of (-) SSDNA was decreased, self-priming increased and was highest when the DNA contained little more than TAR DNA, even if NC and acceptor were both present; in contrast, truncations within TAR DNA led to a striking reduction or elimination of self-priming. However, destabilization of TAR DNA was not sufficient for successful strand transfer: the stability of acceptor RNA was also crucial, and little or no strand transfer occurred if the RNA was highly stable. Significantly, NC may not be required for in vitro strand transfer if (-) SSDNA and acceptor RNA are small, relatively unstructured molecules with low thermodynamic stabilities. Collectively, these findings demonstrate that for efficient NC-mediated minus-strand transfer, a delicate thermodynamic balance between the RNA and DNA reactants must be maintained.
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Affiliation(s)
- Susan L Heilman-Miller
- Laboratory of Molecular Genetics, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2780, USA
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38
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Paillart JC, Shehu-Xhilaga M, Marquet R, Mak J. Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol 2004; 2:461-72. [PMID: 15152202 DOI: 10.1038/nrmicro903] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jean-Christophe Paillart
- UPR 9002 du CNRS affiliée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
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Cen S, Javanbakht H, Niu M, Kleiman L. Ability of wild-type and mutant lysyl-tRNA synthetase to facilitate tRNA(Lys) incorporation into human immunodeficiency virus type 1. J Virol 2004; 78:1595-601. [PMID: 14722314 PMCID: PMC321381 DOI: 10.1128/jvi.78.3.1595-1601.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The major human tRNA(Lys) isoacceptors, tRNA1,2Lys and tRNA3Lys, are selectively packaged into human immunodeficiency virus type 1 (HIV-1) during assembly, where tRNA3Lys acts as a primer for reverse transcription. Lysyl-tRNA synthetase (LysRS) is also incorporated into HIV-1, independently of tRNA(Lys), via its interaction with Gag, and it is a strong candidate for being the signal that specifically targets tRNA(Lys) for viral incorporation. Expression of exogenous wild-type LysRS in cells results in an approximately twofold increase in the viral packaging of both LysRS and tRNA(Lys). Herein, we show that this increase in tRNA(Lys) incorporation into virions is dependent upon the ability of LysRS to bind to tRNA(Lys) but not upon its ability to aminoacylate the tRNA(Lys). COS7 cells were cotransfected with plasmids coding for both HIV-1 and either wild-type or mutant human LysRS, all of which are incorporated into virions with similar efficiency. However, N-terminally truncated LysRS, which binds poorly to tRNA(Lys), does not increase tRNA(Lys) packaging into viruses, while C-terminally truncated LysRS, which binds to but does not aminoacylate tRNA(Lys), still facilitates an increase in tRNA(Lys) packaging into virions.
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Affiliation(s)
- Shan Cen
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital. Departments of Medicine. Microbiology and Immunology, McGill University, Montreal, Quebec, Canada H3T 1E2
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40
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Guo F, Cen S, Niu M, Javanbakht H, Kleiman L. Specific inhibition of the synthesis of human lysyl-tRNA synthetase results in decreases in tRNA(Lys) incorporation, tRNA(3)(Lys) annealing to viral RNA, and viral infectivity in human immunodeficiency virus type 1. J Virol 2003; 77:9817-22. [PMID: 12941890 PMCID: PMC224598 DOI: 10.1128/jvi.77.18.9817-9822.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major human tRNA(Lys) isoacceptors, and, are selectively packaged into human immunodeficiency virus type 1 (HIV-1) during assembly, where acts as a primer for reverse transcription. Lysyl-tRNA synthetase (LysRS) is also incorporated into HIV-1, independently of tRNA(Lys), via its interaction with Gag, and is a strong candidate for being the signal that specifically targets tRNA(Lys) for viral incorporation. We have transfected 293T cells with HIV-1 proviral DNA and short interfering RNA (siRNA) specific for LysRS to study the effect of diminished cellular LysRS upon tRNA(Lys) packaging, annealing to viral genomic RNA, and viral production and infectivity. At early time points after siRNA transfection, an 80% inhibition of LysRS incorporation into viruses reflects an 80% reduction of newly synthesized LysRS, rather than a more limited 20 to 25% decrease in the concentration of total cell LysRS, indicating that newly synthesized LysRS in the cell may be the main source of viral LysRS. Viruses produced from cells transfected with siRNA show reduced tRNA(Lys) packaging, reduced annealing to viral RNA, and reduced viral infectivity.
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Affiliation(s)
- Fei Guo
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospita1, 3755 Côte St. Catherine Road, Montreal, Quebec, Canada H3T 1E2
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41
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Iwatani Y, Rosen AE, Guo J, Musier-Forsyth K, Levin JG. Efficient initiation of HIV-1 reverse transcription in vitro. Requirement for RNA sequences downstream of the primer binding site abrogated by nucleocapsid protein-dependent primer-template interactions. J Biol Chem 2003; 278:14185-95. [PMID: 12560327 DOI: 10.1074/jbc.m211618200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthesis of HIV-1 (-) strong-stop DNA is initiated following annealing of the 3' 18 nucleotides (nt) of tRNA(3)(Lys) to the primer binding site (PBS) near the 5' terminus of viral RNA. Here, we have investigated whether sequences downstream of the PBS play a role in promoting efficient (-) strong-stop DNA synthesis. Our findings demonstrate a template requirement for at least 24 bases downstream of the PBS when tRNA(3)(Lys) or an 18-nt RNA complementary to the PBS (R18), but not an 18-nt DNA primer, are used. Additional assays using 18-nt DNA-RNA chimeric primers, as well as melting studies and circular dichroism spectra of 18-nt primer:PBS duplexes, suggest that priming efficiency is correlated with duplex conformation and stability. Interestingly, in the presence of nucleocapsid protein (NC), the 24 downstream bases are dispensable for synthesis primed by tRNA(3)(Lys) but not by R18. We present data supporting the conclusion that NC promotes extended interactions between the anticodon stem and variable loop of tRNA(3)(Lys) and a sequence upstream of the A-rich loop in the template. Taken together, this study leads to new insights into the initiation of HIV-1 reverse transcription and the functional role of NC-facilitated tRNA-template interactions in this process.
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Affiliation(s)
- Yasumasa Iwatani
- Laboratory of Molecular Genetics, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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42
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Halwani R, Khorchid A, Cen S, Kleiman L. Rapid localization of Gag/GagPol complexes to detergent-resistant membrane during the assembly of human immunodeficiency virus type 1. J Virol 2003; 77:3973-84. [PMID: 12634357 PMCID: PMC150626 DOI: 10.1128/jvi.77.7.3973-3984.2003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) assembly in HIV-1-transfected COS7 cells, almost all steady-state Gag/Gag and Gag/GagPol complexes are membrane bound. However, exposure to 1% Triton X-100 gives results indicating that while all Gag/GagPol complexes remain associated with the detergent-resistant membrane (DRM), only 30% of Gag/Gag complexes are associated with the DRM. Analysis of the localization of newly synthesized Gag/Gag and Gag/GagPol to the membrane indicates that after a 10-min pulse with radioactive [(35)S]Cys-[(35)S]Met, all newly synthesized Gag/GagPol is found at the DRM. Only 30% of newly synthesized Gag/Gag moves to the membrane, and at 0 min of chase, only 38% of this membrane-bound Gag/Gag is associated with the DRM. During the first 30 min of chase, most membrane-bound Gag/Gag moves to the DRM, while between 30 and 60 min of chase, there is a significant decrease in membrane-bound Gag/Gag and Gag/GagPol. Since the localization of newly synthesized Gag/Gag to the DRM and the interaction of GagPol with Gag both depend upon Gag multimerization, the rapid localization of GagPol to the DRM probably reflects the interaction of all newly synthesized GagPol with the first newly synthesized polymeric Gag to associate with the DRM.
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Affiliation(s)
- Rabih Halwani
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Department of Medicine, McGill University, Montreal, Quebec, Canada H3T 1E2
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43
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Stephen AG, Worthy KM, Towler E, Mikovits JA, Sei S, Roberts P, Yang QE, Akee RK, Klausmeyer P, McCloud TG, Henderson L, Rein A, Covell DG, Currens M, Shoemaker RH, Fisher RJ. Identification of HIV-1 nucleocapsid protein: nucleic acid antagonists with cellular anti-HIV activity. Biochem Biophys Res Commun 2002; 296:1228-37. [PMID: 12207905 DOI: 10.1016/s0006-291x(02)02063-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The crucial functions of HIV-1 nucleocapsid-p7 protein (NC-p7) at different stages of HIV replication are dependent on its nucleic acid binding properties. In this study, a search has been made to identify antagonists of the interaction between NC-p7 and d(TG)(4). A chemical library of approximately 2000 small molecules (the NCI Diversity Set) was screened, of the 26 active inhibitors that were identified, five contained a xanthenyl ring structure. Further analysis of 63 structurally related compounds led to the identification of 2,3,4,5-tetrachloro-6-(4('),5('),6(')-trihydroxy-3(')-oxo-3H-xanthen-9(')-yl)benzoic acid, which binds to NC-p7 stoichiometrically. This compound exerted a significant anti-HIV activity in vitro with an IC(50) of 16.6+/-4.3 microM (means+/-SD). Synthetic variants lacking the two hydroxyls at positions 4(') and 5(') in the xanthenyl ring system failed to bind NC-p7 and showed significantly less protection against HIV infection. Molecular modeling predicts that these hydroxyl groups would bind to the amide nitrogen of Gly(35) with other contacts at the carbonyl oxygens of Gly(40) and Lys(33).
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Affiliation(s)
- Andrew G Stephen
- Protein Chemistry Laboratory, SAIC-Frederick, Inc., NCI Frederick, 21702, Frederick, MD, USA
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44
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Zhang WH, Hwang CK, Hu WS, Gorelick RJ, Pathak VK. Zinc finger domain of murine leukemia virus nucleocapsid protein enhances the rate of viral DNA synthesis in vivo. J Virol 2002; 76:7473-84. [PMID: 12097560 PMCID: PMC136396 DOI: 10.1128/jvi.76.15.7473-7484.2002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In vitro studies have indicated that retroviral nucleocapsid (NC) protein facilitates both DNA synthesis by reverse transcriptase (RT) and annealing of the nascent DNA with acceptor template. Increasing the rate of DNA synthesis is expected to reduce the frequency of RT template switching, whereas annealing the nascent DNA with acceptor template promotes template switching. We performed a mutational analysis of the murine leukemia virus (MLV) NC zinc finger domain to study its effect on RT template switching in vivo and to explore the role of NC during reverse transcription. The effects of NC mutations on RT template switching were determined by using a previously described in vivo direct-repeat deletion assay. A trans-complementation assay was also developed in which replication-defective NC mutants were rescued by coexpression of replication-defective RT mutants that provided wild-type NC in trans. We found that mutations in the MLV NC zinc finger domain increased the frequency of template switching approximately twofold. When a predicted stem-loop RNA secondary structure was introduced into the template RNA, the template-switching frequency increased 5-fold for wild-type NC and further increased up to an additional 6-fold for NC zinc finger domain mutants, resulting in an overall increase of as much as 30-fold. Thus, wild-type NC increased the efficiency with which RT was able to reverse transcribe through regions of RNA secondary structure that might serve as RT pause sites. These results provide the first in vivo evidence that NC enhances the rate of DNA synthesis by RT in regions of the template possessing stable RNA secondary structure.
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Affiliation(s)
- Wen-Hui Zhang
- HIV Drug Resistance Program, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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45
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Javanbakht H, Cen S, Musier-Forsyth K, Kleiman L. Correlation between tRNALys3 aminoacylation and its incorporation into HIV-1. J Biol Chem 2002; 277:17389-96. [PMID: 11884398 DOI: 10.1074/jbc.m112479200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) assembly, tRNA(Lys) is selectively packaged into the virus, where tRNA(Lys3) serves as the primer for reverse transcription. Lysyl-tRNA synthetase is also selectively incorporated into HIV-1 and is therefore a strong candidate for being the signal by which viral proteins interact with tRNA(Lys) isoacceptors. Previously, mutations in the tRNA(Lys3) anticodon have been shown to strongly inhibit the charging of tRNA(Lys3) by lysyl-tRNA synthetase in vitro, and we show here that in vivo aminoacylation is also inhibited by anticodon changes. The order of decreasing in vivo aminoacylation for tRNA(Lys3) anticodon mutants is: wild-type SUU (where S = mcm(5)S(2)U) 100%) --> SGU (49%) --> CGU (40%) --> SGA (0%) and CGA (0%). We found that the ability of these tRNA(Lys3) anticodon variants to be aminoacylated in vivo is directly correlated with their ability to be packaged into HIV-1. These data showed that the anticodon is a major determinant for tRNA(Lys3) packaging and support the conclusion that its productive interaction with lysyl-tRNA synthetase is important for tRNA(Lys3) incorporation into HIV-1.
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Affiliation(s)
- Hassan Javanbakht
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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46
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Abstract
We have examined the influence of RNA upon the interaction of Gag-Pol with Gag during human immunodeficiency virus type 1 (HIV-1) assembly. COS7 cells were transfected with protease-negative HIV-1 proviral DNA, and Gag/Gag-Pol complexes were detected by coimmunoprecipitation with anti-integrase. In COS7 cells, Gag/Gag-Pol is found almost entirely in pelletable, membrane-bound complexes. Exposure of cells to 1% Triton X-100 releases Gag/Gag-Pol from bulk membrane, but the complexes remain pelletable. The role of RNA in facilitating the interaction between Gag and Gag-Pol was examined in these bulk membrane-free, pelletable complexes. The specific presence of viral genomic RNA is not required to maintain the Gag/Gag-Pol interaction, but some type of RNA is, since exposure to RNase destabilized the Gag/Gag-Pol complex. When present only in Gag, the nucleocapsid mutation R7R10K11S, which inhibits Gag binding to RNA, inhibits the formation of both Gag and Gag/Gag-Pol complexes. When present only in Gag-Pol, this mutation has no effect upon complex formation. This result indicates that Gag-Pol may not interact directly with RNA but rather requires RNA-facilitated Gag multimerization for its interaction with Gag.
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Affiliation(s)
- Ahmad Khorchid
- Lady Davis Institute for Medical Research and McGill AIDS Center Jewish General Hospital, McGill University, Montreal, Quebec, Canada H3T 1E2
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47
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Kameoka M, Morgan M, Binette M, Russell RS, Rong L, Guo X, Mouland A, Kleiman L, Liang C, Wainberg MA. The Tat protein of human immunodeficiency virus type 1 (HIV-1) can promote placement of tRNA primer onto viral RNA and suppress later DNA polymerization in HIV-1 reverse transcription. J Virol 2002; 76:3637-45. [PMID: 11907203 PMCID: PMC136076 DOI: 10.1128/jvi.76.8.3637-3645.2002] [Citation(s) in RCA: 34] [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
Human immunodeficiency virus type-1 Tat has been proposed to play a role in the regulation of reverse transcription. We previously demonstrated that wild-type Tat can augment viral infectivity by suppressing the reverse transcriptase (RT) reaction at late stages of the viral life cycle in order to prevent the premature synthesis of potentially deleterious viral DNA products. Here we have performed a detailed analysis of the cell-free reverse transcription reaction to elucidate the mechanism(s) whereby Tat can affect this process. Our results show that Tat can suppress nonspecific DNA elongation while moderately affecting the specific initiation stage of reverse transcription. In addition, Tat has an RNA-annealing activity and can promote the placement of tRNA onto viral RNA. This points to a functional homology between Tat and the viral nucleocapsid (NC) protein that is known to be directly involved in this process. Experiments using a series of mutant Tat proteins revealed that the cysteine-rich and core domains of Tat are responsible for suppression of DNA elongation, while each of the cysteine-rich, core, and basic domains, as well as a glutamine-rich region in the C-terminal domain, are important for the placement of tRNA onto the viral RNA genome. These results suggest that Tat can play at least two different roles in the RT reaction, i.e., suppression of DNA polymerization and placement of tRNA onto viral RNA. We believe that the first of these activities of Tat may contribute to the overall efficiency of reverse transcription of the viral genome during a new round of infection as well as to enhanced production of infectious viral particles. We hypothesize that the second activity, illustrating functional homology between Tat and NC, suggests a potential role for NC in the displacement of Tat during viral maturation.
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Affiliation(s)
- Masanori Kameoka
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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48
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Cen S, Khorchid A, Javanbakht H, Gabor J, Stello T, Shiba K, Musier-Forsyth K, Kleiman L. Incorporation of lysyl-tRNA synthetase into human immunodeficiency virus type 1. J Virol 2001; 75:5043-8. [PMID: 11333884 PMCID: PMC114908 DOI: 10.1128/jvi.75.11.5043-5048.2001] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2000] [Accepted: 03/03/2001] [Indexed: 11/20/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) assembly, tRNA(Lys) isoacceptors are selectively incorporated into virions and tRNA(Lys)3 is used as the primer for reverse transcription. We show herein that the tRNA(Lys)-binding protein, lysyl-tRNA synthetase (LysRS), is also selectively packaged into HIV-1. The viral precursor protein Pr55gag alone will package LysRS into Pr55gag particles, independently of tRNA(Lys). With the additional presence of the viral precursor protein Pr160gag-pol, tRNA(Lys) and LysRS are both packaged into the particle. While the predominant cytoplasmic LysRS has an apparent M(r) of 70,000, viral LysRS associated with tRNA(Lys) packaging is shorter, with an apparent M(r) of 63,000. The truncation occurs independently of viral protease and might be required to facilitate interactions involved in the selective packaging and genomic placement of primer tRNA.
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Affiliation(s)
- S Cen
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, McGill University, Montreal, Quebec, Canada H3T 1E2
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49
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Hansen AC, Grunwald T, Lund AH, Schmitz A, Duch M, Uberla K, Pedersen FS. Transfer of primer binding site-mutated simian immunodeficiency virus vectors by genetically engineered artificial and hybrid tRNA-like primers. J Virol 2001; 75:4922-8. [PMID: 11312366 PMCID: PMC114249 DOI: 10.1128/jvi.75.10.4922-4928.2001] [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: 01/01/2023] Open
Abstract
Simian immunodeficiency viruses (SIV) harbor primer binding sites (PBS) matching tRNA or tRNA. To study determinants of primer usage in SIV, a SIVmac239-based vector was impaired by mutating the PBS to a sequence (PBS-X2) with no match to any tRNA. By cotransfection of a synthetic gene encoding a tRNA(Pro)-like RNA with a match to PBS-X2, the activity of this vector could be restored to a transduction efficiency slightly lower than that of the wild-type vector. A vector with a PBS matching tRNA(Pro) was functional at a level slightly below that of the wild-type vector, but higher transduction efficiency could be obtained by cotransfection of a gene for an engineered tRNA(Pro)-tRNA hybrid with a match to PBS-Pro. The importance of tRNA backbone identity was further analyzed by complementing the PBS-X2 vector with a gene for a matching x2 primer with a tRNA backbone, which led to three- to fourfold-higher titers than those observed for the x2 primer with the tRNA(Pro) backbone. In summary, our results demonstrate flexibility in PBS and primer usage for SIVmac239, with PBS-primer complementarity being the major determinant, in analogy with previous findings for murine leukemia viruses and human immunodeficiency virus type 1.
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Affiliation(s)
- A C Hansen
- Department of Molecular and Structural Biology, Aarhus University, DK-8000 Aarhus, Denmark
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50
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Muriaux D, Mirro J, Harvin D, Rein A. RNA is a structural element in retrovirus particles. Proc Natl Acad Sci U S A 2001; 98:5246-51. [PMID: 11320254 PMCID: PMC33195 DOI: 10.1073/pnas.091000398] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A single retroviral protein, Gag, is sufficient for virus particle assembly. While Gag is capable of specifically packaging the genomic RNA into the particle, this RNA species is unnecessary for particle assembly in vivo. In vitro, nucleic acids profoundly enhance the efficiency of assembly by recombinant Gag proteins, apparently by acting as "scaffolding" in the particle. To address the participation of RNA in retrovirus assembly in vivo, we analyzed murine leukemia virus particles that lack genomic RNA because of a deletion in the packaging signal of the viral RNA. We found that these particles contain cellular mRNA in place of genomic RNA. This result was particularly evident when Gag was expressed by using a Semliki Forest virus-derived vector: under these conditions, the Semliki Forest virus vector-directed mRNA became very abundant in the cells and was readily identified in the retroviral virus-like particles. Furthermore, we found that the retroviral cores were disrupted by treatment with RNase. Taken together, the data strongly suggest that RNA is a structural element in retrovirus particles.
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MESH Headings
- Animals
- Cell Line
- Cricetinae
- Gene Products, gag/genetics
- Gene Products, gag/metabolism
- Genetic Vectors/genetics
- Genome, Viral
- Humans
- Leukemia Virus, Murine/chemistry
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/analysis
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonuclease, Pancreatic/metabolism
- Semliki forest virus/genetics
- Sequence Deletion/genetics
- Virion/chemistry
- Virion/genetics
- Virion/metabolism
- Virus Assembly
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Affiliation(s)
- D Muriaux
- HIV Drug Resistance Program, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21702-1201, USA
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