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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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Aydin H, Taylor MW, Lee JE. Structure-guided analysis of the human APOBEC3-HIV restrictome. Structure 2014; 22:668-84. [PMID: 24657093 DOI: 10.1016/j.str.2014.02.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/11/2014] [Accepted: 02/20/2014] [Indexed: 01/03/2023]
Abstract
Human APOBEC3 (A3) proteins are host-encoded intrinsic restriction factors that inhibit the replication of many retroviral pathogens. Restriction is believed to occur as a result of the DNA cytosine deaminase activity of the A3 proteins; this activity converts cytosines into uracils in single-stranded DNA retroviral replication intermediates. A3 proteins are also equipped with deamination-independent means to restrict retroviruses that work cooperatively with deamination-dependent restriction pathways. A3 proteins substantially bolster the intrinsic immune system by providing a powerful block to the transmission of retroviral pathogens; however, most retroviruses are able to subvert this replicative restriction in their natural host. HIV-1, for instance, evades A3 proteins through the activity of its accessory protein Vif. Here, we summarize data from recent A3 structural and functional studies to provide perspectives into the interactions between cellular A3 proteins and HIV-1 macromolecules throughout the viral replication cycle.
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Affiliation(s)
- Halil Aydin
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew W Taylor
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Sleiman D, Barraud P, Brachet F, Tisne C. The Interaction between tRNA(Lys) 3 and the primer activation signal deciphered by NMR spectroscopy. PLoS One 2013; 8:e64700. [PMID: 23762248 PMCID: PMC3675109 DOI: 10.1371/journal.pone.0064700] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/17/2013] [Indexed: 11/23/2022] Open
Abstract
The initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) requires the opening of the three-dimensional structure of the primer tRNALys3 for its annealing to the viral RNA at the primer binding site (PBS). Despite the fact that the result of this rearrangement is thermodynamically more stable, there is a high-energy barrier that requires the chaperoning activity of the viral nucleocapsid protein. In addition to the nucleotide complementarity to the PBS, several regions of tRNALys3 have been described as interacting with the viral genomic RNA. Among these sequences, a sequence of the viral genome called PAS for “primer activation signal” was proposed to interact with the T-arm of tRNALys3, this interaction stimulating the initiation of reverse transcription. In this report, we investigate the formation of this additional interaction with NMR spectroscopy, using a simple system composed of the primer tRNALys3, the 18 nucleotides of the PBS, the PAS (8 nucleotides) encompassed or not in a hairpin structure, and the nucleocapsid protein. Our NMR study provides molecular evidence of the existence of this interaction and highlights the role of the nucleocapsid protein in promoting this additional RNA-RNA annealing. This study presents the first direct observation at a single base-pair resolution of the PAS/anti-PAS association, which has been proposed to be involved in the chronological regulation of the reverse transcription.
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Affiliation(s)
- Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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4
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DМ. Structural model of the complete poly(A) region of HIV-1 pre-mRNA. J Biomol Struct Dyn 2012; 31:1044-56. [PMID: 22963228 DOI: 10.1080/07391102.2012.718530] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the HIV-1 retrovirus, identical sequences encompassing the AAUAAA hexamer and the U/GU-rich downstream sequence element (DSE) that compose the core poly(A) site are present at both the 5' and 3' ends of the HIV-1 pre-mRNA. The AAUAAA hexamer is partly occluded by base pairing in the upper part of a semi-stable polyA hairpin. This sets the stage for regulation of HIV-1 polyadenylation, which involves reaction suppression at the 5' end and its stimulation at the 3' end. Efficient utilization of the 3' core poly(A) site is promoted by major and minor upstream sequence elements (USEs) which are uniquely present at the 3' end of the HIV-1 transcript. The structures of the HIV-1 5' and 3' poly(A) sites are defined by overall architecture of complete 5' and 3' untranslated terminal regions (UTRs). To our knowledge, there is still no structural model of a complete 3' UTR of the HIV-1 pre-mRNA and complete 3' poly(A) region including the USEs except the fact that the polyA and transactivation response (TAR) hairpins are present at both ends of the HIV-1 pre-mRNA. In this work, we predicted a secondary structure of the 3' UTR of HIV-1 pre-mRNA based on our observation that the minor USEs are located in a region with a high potential to form G-quadruplex structures. We first present structural models for the major USE, complete 3' poly(A) region, and almost entire 3' UTR of HIV-1 pre-mRNA. Our models are built based on the mfold and UNAFold secondary structure prediction of these regions for about 1500 HIV-1 isolates of different subtypes and recombinant forms. We have demonstrated that these models are valid for most of the HIV-1 isolates studied. The proposed models include the known TAR and polyA hairpins and new structural elements containing the U-rich tract of the major USE and U/GU-rich DSE which are fully exposed and accessible to the polyadenylation machinery, which confirms the functional competence of our models.
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Affiliation(s)
- Margarita I Zarudnaya
- a Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Zabolotnogo Str. , Kyiv , 03680 , Ukraine
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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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6
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Levin JG, Mitra M, Mascarenhas A, Musier-Forsyth K. Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription. RNA Biol 2010; 7:754-74. [PMID: 21160280 DOI: 10.4161/rna.7.6.14115] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which remodels nucleic acid structures so that the most thermodynamically stable conformations are formed. This activity is essential for virus replication and has a critical role in mediating highly specific and efficient reverse transcription. NC's function in this process depends upon three properties: (1) ability to aggregate nucleic acids; (2) moderate duplex destabilization activity; and (3) rapid on-off binding kinetics. Here, we present a detailed molecular analysis of the individual events that occur during viral DNA synthesis and show how NC's properties are important for almost every step in the pathway. Finally, we also review biological aspects of reverse transcription during infection and the interplay between NC, reverse transcriptase, and human APOBEC3G, an HIV-1 restriction factor that inhibits reverse transcription and virus replication in the absence of the HIV-1 Vif protein.
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Affiliation(s)
- Judith G Levin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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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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Qualley DF, Stewart-Maynard KM, Wang F, Mitra M, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K. C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 nucleocapsid protein via an electrostatic mechanism. J Biol Chem 2010; 285:295-307. [PMID: 19887455 PMCID: PMC2804176 DOI: 10.1074/jbc.m109.051334] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/30/2009] [Indexed: 12/14/2022] Open
Abstract
Retroviral nucleocapsid (NC) proteins are molecular chaperones that facilitate nucleic acid (NA) remodeling events critical in viral replication processes such as reverse transcription. Surprisingly, the NC protein from human T-cell leukemia virus type 1 (HTLV-1) is an extremely poor NA chaperone. Using bulk and single molecule methods, we find that removal of the anionic C-terminal domain (CTD) of HTLV-1 NC results in a protein with chaperone properties comparable with that of other retroviral NCs. Increasing the ionic strength of the solution also improves the chaperone activity of full-length HTLV-1 NC. To determine how the CTD negatively modulates the chaperone activity of HTLV-1 NC, we quantified the thermodynamics and kinetics of wild-type and mutant HTLV-1 NC/NA interactions. The wild-type protein exhibits very slow dissociation kinetics, and removal of the CTD or mutations that eliminate acidic residues dramatically increase the protein/DNA interaction kinetics. Taken together, these results suggest that the anionic CTD interacts with the cationic N-terminal domain intramolecularly when HTLV-1 NC is not bound to nucleic acids, and similar interactions occur between neighboring molecules when NC is NA-bound. The intramolecular N-terminal domain-CTD attraction slows down the association of the HTLV-1 NC with NA, whereas the intermolecular interaction leads to multimerization of HTLV-1 NC on the NA. The latter inhibits both NA/NC aggregation and rapid protein dissociation from single-stranded DNA. These features make HTLV-1 NC a poor NA chaperone, despite its robust duplex destabilizing capability.
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Affiliation(s)
- Dominic F. Qualley
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | | | - Fei Wang
- the Department of Physics, Northeastern University, Boston, Massachusetts 02115, and
| | - Mithun Mitra
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Robert J. Gorelick
- the AIDS and Cancer Virus Program, Science Applications International Corporation-Frederick, Inc., NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Ioulia Rouzina
- the Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark C. Williams
- the Department of Physics, Northeastern University, Boston, Massachusetts 02115, and
| | - Karin Musier-Forsyth
- From the Departments of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
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