1
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Faysal KMR, Walsh JC, Renner N, Márquez CL, Shah VB, Tuckwell AJ, Christie MP, Parker MW, Turville SG, Towers GJ, James LC, Jacques DA, Böcking T. Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure. eLife 2024; 13:e83605. [PMID: 38347802 PMCID: PMC10863983 DOI: 10.7554/elife.83605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
The HIV-1 capsid has emerged as a tractable target for antiretroviral therapy. Lenacapavir, developed by Gilead Sciences, is the first capsid-targeting drug approved for medical use. Here, we investigate the effect of lenacapavir on HIV capsid stability and uncoating. We employ a single particle approach that simultaneously measures capsid content release and lattice persistence. We demonstrate that lenacapavir's potent antiviral activity is predominantly due to lethal hyperstabilisation of the capsid lattice and resultant loss of compartmentalisation. This study highlights that disrupting capsid metastability is a powerful strategy for the development of novel antivirals.
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Affiliation(s)
- KM Rifat Faysal
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Nadine Renner
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Chantal L Márquez
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Vaibhav B Shah
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Andrew J Tuckwell
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Michelle P Christie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
| | - Michael W Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
- Structural Biology Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | | | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Leo C James
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
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2
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Gifford LB, Melikyan GB. HIV-1 Capsid Uncoating Is a Multistep Process That Proceeds through Defect Formation Followed by Disassembly of the Capsid Lattice. ACS NANO 2024; 18:2928-2947. [PMID: 38241476 PMCID: PMC10832047 DOI: 10.1021/acsnano.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
The HIV-1 core consists of a cone-shaped capsid shell made of capsid protein (CA) hexamers and pentamers encapsulating the viral genome. HIV-1 capsid disassembly, referred to as uncoating, is important for productive infection; however, the location, timing, and regulation of uncoating remain controversial. Here, we employ amber codon suppression to directly label CA. In addition, a fluid phase fluorescent probe is incorporated into the viral core to detect small defects in the capsid lattice. This double-labeling strategy enables the visualization of uncoating of single cores in vitro and in living cells, which we found to always proceed through at least two distinct steps─the formation of a defect in the capsid lattice that initiates gradual loss of CA below a detectable level. Importantly, intact cores containing the fluid phase and CA fluorescent markers enter and uncoat in the nucleus, as evidenced by a sequential loss of both markers, prior to establishing productive infection. This two-step uncoating process is observed in different cells, including a macrophage line. Notably, the lag between the release of fluid phase marker and terminal loss of CA appears to be independent of the cell type or reverse transcription and is much longer (>5-fold) for nuclear capsids compared to cell-free cores or cores in the cytosol, suggesting that the capsid lattice is stabilized by capsid-binding nuclear factors. Our results imply that intact HIV-1 cores enter the cell nucleus and that uncoating is initiated through a localized defect in the capsid lattice prior to a global loss of CA.
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Affiliation(s)
- Levi B. Gifford
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Gregory B. Melikyan
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
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3
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Jang S, Engelman AN. Capsid-host interactions for HIV-1 ingress. Microbiol Mol Biol Rev 2023; 87:e0004822. [PMID: 37750702 PMCID: PMC10732038 DOI: 10.1128/mmbr.00048-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.
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Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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4
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Badieyan S, Lichon D, Andreas MP, Gillies JP, Peng W, Shi J, DeSantis ME, Aiken CR, Böcking T, Giessen TW, Campbell EM, Cianfrocco MA. HIV-1 binds dynein directly to hijack microtubule transport machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555335. [PMID: 37693451 PMCID: PMC10491134 DOI: 10.1101/2023.08.29.555335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein's tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically 'hijacks' the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
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Affiliation(s)
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael P Andreas
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Christopher R Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tobias W Giessen
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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5
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Ten Eyck A, Chen YC, Gifford L, Torres-Rivera D, Dyer EL, Melikyan GB. Label-free imaging of nuclear membrane for analysis of nuclear import of viral complexes. J Virol Methods 2023; 322:114834. [PMID: 37875225 PMCID: PMC10841631 DOI: 10.1016/j.jviromet.2023.114834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
HIV-1 enters the nucleus of non-dividing cells through the nuclear pore complex where it integrates into the host genome. The mechanism of HIV-1 nuclear import remains poorly understood. A powerful means to investigate the docking of HIV-1 at the nuclear pore and nuclear import of viral complexes is through single virus tracking in live cells. This approach necessitates fluorescence labeling of HIV-1 particles and the nuclear envelope, which may be challenging, especially in the context of primary cells. Here, we leveraged a deep neural network model for label-free visualization of the nuclear envelope using transmitted light microscopy. A training image set of cells with fluorescently labeled nuclear Lamin B1 (ground truth), along with the corresponding transmitted light images, was acquired and used to train our model to predict the morphology of the nuclear envelope in fixed cells. This protocol yielded accurate predictions of the nuclear membrane and was used in conjunction with virus infection to examine the nuclear entry of fluorescently labeled HIV-1 complexes. Analyses of HIV-1 nuclear import as a function of virus input yielded identical numbers of fluorescent viral complexes per nucleus using the ground truth and predicted nuclear membrane images. We also demonstrate the utility of predicting the nuclear envelope based on transmitted light images for multicolor fluorescence microscopy of infected cells. Importantly, we show that our model can be adapted to predict the nuclear membrane of live cells imaged at 37 °C, making this approach compatible with single virus tracking. Collectively, these findings demonstrate the utility of deep learning approaches for label-free imaging of cellular structures during early stages of virus infection.
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Affiliation(s)
- Andrew Ten Eyck
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA
| | - Yen-Cheng Chen
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Levi Gifford
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Graduate Division of Biological and Biomedical Sciences, Biochemistry, Cell and Developmental Biology Program, Emory University, Atlanta, GA, USA
| | - Dariana Torres-Rivera
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Graduate Division of Biological and Biomedical Sciences, Biochemistry, Cell and Developmental Biology Program, Emory University, Atlanta, GA, USA
| | - Eva L Dyer
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA; Department of Electrical & Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gregory B Melikyan
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA; Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Children's Healthcare of Atlanta, GA, USA.
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6
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Horns F, Martinez JA, Fan C, Haque M, Linton JM, Tobin V, Santat L, Maggiolo AO, Bjorkman PJ, Lois C, Elowitz MB. Engineering RNA export for measurement and manipulation of living cells. Cell 2023; 186:3642-3658.e32. [PMID: 37437570 PMCID: PMC10528933 DOI: 10.1016/j.cell.2023.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently package and secrete cargo RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. Further, by incorporating fusogens into the nanoparticles, we demonstrated the delivery, expression, and functional activity of exported mRNA in recipient cells. We term these systems COURIER (controlled output and uptake of RNA for interrogation, expression, and regulation). COURIER enables measurement of cell dynamics and establishes a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA.
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Affiliation(s)
- Felix Horns
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Joe A Martinez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mehernaz Haque
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victoria Tobin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leah Santat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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7
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Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.548988. [PMID: 37546793 PMCID: PMC10402013 DOI: 10.1101/2023.07.24.548988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembled in vitro, as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mathias Percipalle
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Darya Chernikova
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Gergely Pinke
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Dario Porley
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Florian KM Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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8
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Highland CM, Tan A, Ricaña CL, Briggs JAG, Dick RA. Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2220545120. [PMID: 37094124 PMCID: PMC10160977 DOI: 10.1073/pnas.2220545120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/12/2023] [Indexed: 04/26/2023] Open
Abstract
The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly ("lattice templating") that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.
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Affiliation(s)
- Carolyn M. Highland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - Aaron Tan
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
| | - Clifton L. Ricaña
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - John A. G. Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Munich82512, Germany
| | - Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
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9
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Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, Feng Q, Lusk CP, Aiken C, Engelman AN, Perilla JR, Pathak VK, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proc Natl Acad Sci U S A 2023; 120:e2202815120. [PMID: 36943880 PMCID: PMC10068764 DOI: 10.1073/pnas.2202815120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
Increasing evidence has suggested that the HIV-1 capsid enters the nucleus in a largely assembled, intact form. However, not much is known about how the cone-shaped capsid interacts with the nucleoporins (NUPs) in the nuclear pore for crossing the nuclear pore complex. Here, we elucidate how NUP153 binds HIV-1 capsid by engaging the assembled capsid protein (CA) lattice. A bipartite motif containing both canonical and noncanonical interaction modules was identified at the C-terminal tail region of NUP153. The canonical cargo-targeting phenylalanine-glycine (FG) motif engaged the CA hexamer. By contrast, a previously unidentified triple-arginine (RRR) motif in NUP153 targeted HIV-1 capsid at the CA tri-hexamer interface in the capsid. HIV-1 infection studies indicated that both FG- and RRR-motifs were important for the nuclear import of HIV-1 cores. Moreover, the presence of NUP153 stabilized tubular CA assemblies in vitro. Our results provide molecular-level mechanistic evidence that NUP153 contributes to the entry of the intact capsid into the nucleus.
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Affiliation(s)
- Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Sushila Kumari
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Ryan C. Burdick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Swapnil C. Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Taoran Tian
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Therese N. Tripler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Vinay K. Pathak
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
- Department of Biomedical Engineering, Yale University, New Haven, CT06511
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
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10
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Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nat Struct Mol Biol 2023; 30:425-435. [PMID: 36807645 PMCID: PMC10121901 DOI: 10.1038/s41594-023-00925-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Delivering the virus genome into the host nucleus through the nuclear pore complex (NPC) is pivotal in human immunodeficiency virus 1 (HIV-1) infection. The mechanism of this process remains mysterious owing to the NPC complexity and the labyrinth of molecular interactions involved. Here we built a suite of NPC mimics-DNA-origami-corralled nucleoporins with programmable arrangements-to model HIV-1 nuclear entry. Using this system, we determined that multiple cytoplasm-facing Nup358 molecules provide avid binding for capsid docking to the NPC. The nucleoplasm-facing Nup153 preferentially attaches to high-curvature regions of the capsid, positioning it for tip-leading NPC insertion. Differential capsid binding strengths of Nup358 and Nup153 constitute an affinity gradient that drives capsid penetration. Nup62 in the NPC central channel forms a barrier that viruses must overcome during nuclear import. Our study thus provides a wealth of mechanistic insight and a transformative toolset for elucidating how viruses like HIV-1 enter the nucleus.
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11
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Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays Biochem 2022; 66:EBC20220047. [PMID: 36504386 DOI: 10.1042/ebc20220047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2024]
Abstract
Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein-protein interactions are mediated through the recognition of host globular domains by short linear motifs (SLiMs), or longer intrinsically disordered domains (IDD), in the disordered regions of viral proteins. However, viruses also employ their own globular domains for binding to SLiMs and IDDs present in host proteins or virus proteins. In this review, we focus on the different strategies adopted by viruses to utilize proteins or protein domains for binding to the disordered regions of human or/and viral ligands. With a set of examples, we describe viral domains that bind human SLiMs. We also provide examples of viral proteins that bind to SLiMs, or IDDs, of viral proteins as a part of complex assembly and regulation of protein functions. The protein-protein interactions are often crucial for viral replication, and may thus offer possibilities for innovative inhibitor design.
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Affiliation(s)
- Priyanka Madhu
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, U.K
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
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12
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Morizako N, Butlertanaka EP, Tanaka YL, Shibata H, Okabayashi T, Mekata H, Saito A. Generation of a bovine cell line for gene engineering using an HIV-1-based lentiviral vector. Sci Rep 2022; 12:16952. [PMID: 36258028 PMCID: PMC9579131 DOI: 10.1038/s41598-022-20970-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors are indispensable tools for gene engineering in mammalian cells. Conversely, lentiviral vector transduction is severely inhibited in bovine cells. Previous studies demonstrated that this inhibition is caused by the anti-lentiviral host factor tripartite motif containing 5 (TRIM5), which targets incoming HIV-1 virions by interacting with the viral capsid. In this study, we investigated several methods for overcoming the limited applicability of lentiviral vectors in bovine cells. First, we demonstrated that the SPRY domain of bovine TRIM5 is the major determinant of anti-viral activity. Second, we found that mutations that allow the capsid to evade rhesus macaque TRIM5α minimally rescued HIV-1 infectivity in bovine-derived MDBK cells. Third, we found that cyclosporine A, which relieves the inhibition of HIV-1 infection in monkey cells, significantly rescued the impaired HIV-1 infectivity in MDBK cells. Lastly, we successfully generated a bovine cell line lacking intact TRIM5 using the CRISPR/Cas9 technique. This TRIM5 knockout cell line displayed significantly higher susceptibility to an HIV-1-based lentiviral vector. In conclusion, our findings provide a promising gene engineering strategy for bovine cells, thereby contributing to innovations in agriculture and improvements in animal health.
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Affiliation(s)
- Nanami Morizako
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Erika P. Butlertanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Yuri L. Tanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Honoka Shibata
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Tamaki Okabayashi
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Miyazaki 8891692 Japan
| | - Hirohisa Mekata
- grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Akatsuki Saito
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Miyazaki 8891692 Japan
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13
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Troyano-Hernáez P, Reinosa R, Holguín Á. HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir. Front Microbiol 2022; 13:854974. [PMID: 35495642 PMCID: PMC9039614 DOI: 10.3389/fmicb.2022.854974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
The HIV p24 capsid protein has an essential, structural, and functional role in the viral replication cycle, being an interesting target for vaccine design, diagnostic tests, and new antiretroviral drugs (ARVs). The HIV-1 variability poses a challenge for the accuracy and efficiency of diagnostic and treatment tools. This study analyzes p24 diversity among HIV-1 variants and within its secondary structure in HIV-1 M, O, P, and N groups. All available HIV-1 p24 nucleotide sequences were downloaded from the Los Alamos HIV Sequence Database, selecting 23,671 sequences belonging to groups O, N, P, and M (9 subtypes, 7 sub-sub types, and 109 circulating recombinant forms or CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio program), we analyzed the amino acid conservation compared to the HXB2 subtype B reference sequence and the V-markers, or amino acid changes that were specific for each variant with at least 10 available sequences. We inferred the p24 consensus sequence for HIV-1 and for each group to analyze the overall conservation in p24 main structural regions, reporting the percentage of substitutions per variant affecting the capsid assembly and molecule-binding, including those associated with resistance to the new capsid-inhibitor lenacapavir, and the key residues involved in lenacapavir-p24 interaction, according to the bibliography. Although the overall structure of p24 was highly conserved, the conservation in the secondary structure varied between HIV-1 variants and the type of secondary structure. All HIV-1 variants presented >80% amino acid conservation vs. HXB2 reference sequence, except for group M sub-subtype F1 (69.27%). Mutants affecting the capsid assembly or lenacapavir capsid-binding were found in <1% of the p24 consensus sequence. Our study reports the HIV-1 variants carrying 14 unique single V-markers in 9/38 group M variants and the level of p24 conservation in each secondary structure region among the 4 HIV-1 groups and group M variants, revealing no natural resistance to lenacapavir in any HIV-1 variant. We present a thorough analysis of p24 variability among all HIV-1 variants circulating to date. Since p24 genetic variability can impact the viral replication cycle and the efficacy of new p24-based diagnostic, therapeutic, and vaccine strategies, conservation studies must consider all HIV-1 variants circulating worldwide.
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Affiliation(s)
- Paloma Troyano-Hernáez
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - Roberto Reinosa
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
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14
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Serrero MC, Girault V, Weigang S, Greco TM, Ramos-Nascimento A, Anderson F, Piras A, Hickford Martinez A, Hertzog J, Binz A, Pohlmann A, Prank U, Rehwinkel J, Bauerfeind R, Cristea IM, Pichlmair A, Kochs G, Sodeik B. The interferon-inducible GTPase MxB promotes capsid disassembly and genome release of herpesviruses. eLife 2022; 11:e76804. [PMID: 35475759 PMCID: PMC9150894 DOI: 10.7554/elife.76804] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
Host proteins sense viral products and induce defence mechanisms, particularly in immune cells. Using cell-free assays and quantitative mass spectrometry, we determined the interactome of capsid-host protein complexes of herpes simplex virus and identified the large dynamin-like GTPase myxovirus resistance protein B (MxB) as an interferon-inducible protein interacting with capsids. Electron microscopy analyses showed that cytosols containing MxB had the remarkable capability to disassemble the icosahedral capsids of herpes simplex viruses and varicella zoster virus into flat sheets of connected triangular faces. In contrast, capsids remained intact in cytosols with MxB mutants unable to hydrolyse GTP or to dimerize. Our data suggest that MxB senses herpesviral capsids, mediates their disassembly, and thereby restricts the efficiency of nuclear targeting of incoming capsids and/or the assembly of progeny capsids. The resulting premature release of viral genomes from capsids may enhance the activation of DNA sensors, and thereby amplify the innate immune responses.
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Affiliation(s)
- Manutea C Serrero
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
| | | | - Sebastian Weigang
- Institute of Virology, Freiburg University Medical Center, University of FreiburgFreiburgGermany
| | - Todd M Greco
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | | | - Fenja Anderson
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Antonio Piras
- Institute of Virology, Technical University MunichMunichGermany
| | | | - Jonny Hertzog
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Anne Binz
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
| | - Anja Pohlmann
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
| | - Ute Prank
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Jan Rehwinkel
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Rudolf Bauerfeind
- Research Core Unit Laser Microscopy, Hannover Medical SchoolHannoverGermany
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Andreas Pichlmair
- Institute of Virology, Technical University MunichMunichGermany
- German Center for Infection Research (DZIF), Munich Partner siteMunichGermany
| | - Georg Kochs
- Institute of Virology, Freiburg University Medical Center, University of FreiburgFreiburgGermany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
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15
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Rousso I, Deshpande A. Applications of Atomic Force Microscopy in HIV-1 Research. Viruses 2022; 14:v14030648. [PMID: 35337055 PMCID: PMC8955997 DOI: 10.3390/v14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/10/2022] Open
Abstract
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is a relatively new technique with unique capabilities, has been utilized to study HIV-1 biology. Atomic force microscopy can generate high-resolution images at the nanometer-scale and analyze the mechanical properties of individual HIV-1 virions, virus components (e.g., capsids), and infected live cells under near-physiological environments. This review describes the working principles and various imaging and analysis modes of atomic force microscopy, and elaborates on its distinctive contributions to HIV-1 research in areas such as mechanobiology and the physics of infection.
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16
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Balakrishnan K, Jaguva Vasudevan AA, Mohareer K, Luedde T, Münk C, Banerjee S. Encapsidation of Staufen-2 Enhances Infectivity of HIV-1. Viruses 2021; 13:v13122459. [PMID: 34960728 PMCID: PMC8703407 DOI: 10.3390/v13122459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
Staufen, the RNA-binding family of proteins, affects various steps in the Human Immuno-Deficiency Virus (HIV-1) replication cycle. While our previous study established Staufen-2–HIV-1 Rev interaction and its role in augmenting nucleocytoplasmic export of RRE-containing viral RNA, viral incorporation of Staufen-2 and its effect on viral propagation were unknown. Here, we report that Staufen-2 interacts with HIV-1 Gag and is incorporated into virions and that encapsidated Staufen-2 boosted viral infectivity. Further, Staufen-2 gets co-packaged into virions, possibly by interacting with host factors Staufen-1 or antiviral protein APOBEC3G, which resulted in different outcomes on the infectivity of Staufen-2-encapsidated virions. These observations suggest that encapsidated host factors influence viral population dynamics and infectivity. With the explicit identification of the incorporation of Staufen proteins into HIV-1 and other retroviruses, such as Simian Immunodeficiency Virus (SIV), we propose that packaging of RNA binding proteins, such as Staufen, in budding virions of retroviruses is probably a general phenomenon that can drive or impact the viral population dynamics, infectivity, and evolution.
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Affiliation(s)
- Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Krishnaveni Mohareer
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (A.A.J.V.); (T.L.)
- Correspondence: (C.M.); (S.B.); Tel.: +49-021-1811-0887 (C.M.); +91-40-2313-4573 (S.B.)
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India; (K.B.); (K.M.)
- Correspondence: (C.M.); (S.B.); Tel.: +49-021-1811-0887 (C.M.); +91-40-2313-4573 (S.B.)
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17
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Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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18
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Zhuang S, Torbett BE. Interactions of HIV-1 Capsid with Host Factors and Their Implications for Developing Novel Therapeutics. Viruses 2021; 13:417. [PMID: 33807824 PMCID: PMC8001122 DOI: 10.3390/v13030417] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) virion contains a conical shell, termed capsid, encasing the viral RNA genome. After cellular entry of the virion, the capsid is released and ensures the protection and delivery of the HIV-1 genome to the host nucleus for integration. The capsid relies on many virus-host factor interactions which are regulated spatiotemporally throughout the course of infection. In this paper, we will review the current understanding of the highly dynamic HIV-1 capsid-host interplay during the early stages of viral replication, namely intracellular capsid trafficking after viral fusion, nuclear import, uncoating, and integration of the viral genome into host chromatin. Conventional anti-retroviral therapies primarily target HIV-1 enzymes. Insights of capsid structure have resulted in a first-in-class, long-acting capsid-targeting inhibitor, GS-6207 (Lenacapavir). This inhibitor binds at the interface between capsid protein subunits, a site known to bind host factors, interferes with capsid nuclear import, HIV particle assembly, and ordered assembly. Our review will highlight capsid structure, the host factors that interact with capsid, and high-throughput screening techniques, specifically genomic and proteomic approaches, that have been and can be used to identify host factors that interact with capsid. Better structural and mechanistic insights into the capsid-host factor interactions will significantly inform the understanding of HIV-1 pathogenesis and the development of capsid-centric antiretroviral therapeutics.
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Affiliation(s)
- Shentian Zhuang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Bruce E. Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
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