1
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Mier NC, Roper DK. Effects of an indole derivative on cell proliferation, transfection, and alternative splicing in production of lentiviral vectors by transient co-transfection. PLoS One 2024; 19:e0297817. [PMID: 38833479 PMCID: PMC11149887 DOI: 10.1371/journal.pone.0297817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/12/2024] [Indexed: 06/06/2024] Open
Abstract
Lentiviral vectors derived from human immunodeficiency virus type I are widely used to deliver functional gene copies to mammalian cells for research and gene therapies. Post-transcriptional splicing of lentiviral vector transgene in transduced host and transfected producer cells presents barriers to widespread application of lentiviral vector-based therapies. The present study examined effects of indole derivative compound IDC16 on splicing of lentiviral vector transcripts in producer cells and corresponding yield of infectious lentiviral vectors. Indole IDC16 was shown previously to modify alternative splicing in human immunodeficiency virus type I. Human embryonic kidney 293T cells were transiently transfected by 3rd generation backbone and packaging plasmids using polyethyleneimine. Reverse transcription-quantitative polymerase chain reaction of the fraction of unspliced genomes in human embryonic kidney 293T cells increased up to 31% upon the indole's treatment at 2.5 uM. Corresponding yield of infectious lentiviral vectors decreased up to 4.5-fold in a cell transduction assay. Adjusting timing and duration of IDC16 treatment indicated that the indole's disruption of early stages of transfection and cell cycle had a greater effect on exponential time course of lentiviral vector production than its reduction of post-transcriptional splicing. Decrease in transfected human embryonic kidney 293T proliferation by IDC16 became significant at 10 uM. These findings indicated contributions by early-stage transfection, cell proliferation, and post-transcriptional splicing in transient transfection of human embryonic kidney 293T cells for lentiviral vector production.
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Affiliation(s)
- Nataly Carolina Mier
- Department of Biological Engineering, Utah State University, Logan, Utah, United States of America
| | - Donald Keith Roper
- Department of Biological Engineering, Utah State University, Logan, Utah, United States of America
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2
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Tsurutani N, Momose F, Ogawa K, Sano K, Morikawa Y. Intracellular trafficking of HIV-1 Gag via Syntaxin 6-positive compartments/vesicles: Involvement in tumor necrosis factor secretion. J Biol Chem 2024; 300:105687. [PMID: 38280430 PMCID: PMC10891346 DOI: 10.1016/j.jbc.2024.105687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/29/2024] Open
Abstract
HIV-1 Gag protein is synthesized in the cytosol and is transported to the plasma membrane, where viral particle assembly and budding occur. Endosomes are alternative sites of Gag accumulation. However, the intracellular transport pathways and carriers for Gag have not been clarified. We show here that Syntaxin6 (Syx6), a soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) involved in membrane fusion in post-Golgi networks, is a molecule responsible for Gag trafficking and also for tumor necrosis factor-α (TNFα) secretion and that Gag and TNFα are cotransported via Syx6-positive compartments/vesicles. Confocal and live-cell imaging revealed that Gag colocalized and cotrafficked with Syx6, a fraction of which localizes in early and recycling endosomes. Syx6 knockdown reduced HIV-1 particle production, with Gag distributed diffusely throughout the cytoplasm. Coimmunoprecipitation and pulldown show that Gag binds to Syx6, but not its SNARE partners or their assembly complexes, suggesting that Gag preferentially binds free Syx6. The Gag matrix domain and the Syx6 SNARE domain are responsible for the interaction and cotrafficking. In immune cells, Syx6 knockdown/knockout similarly impaired HIV-1 production. Interestingly, HIV-1 infection facilitated TNFα secretion, and this enhancement did not occur in Syx6-depleted cells. Confocal and live-cell imaging revealed that TNFα and Gag partially colocalized and were cotransported via Syx6-positive compartments/vesicles. Biochemical analyses indicate that TNFα directly binds the C-terminal domain of Syx6. Altogether, our data provide evidence that both Gag and TNFα make use of Syx6-mediated trafficking machinery and suggest that Gag expression does not inhibit but rather facilitates TNFα secretion in HIV-1 infection.
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Affiliation(s)
- Naomi Tsurutani
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Fumitaka Momose
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Keiji Ogawa
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kouichi Sano
- Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Yuko Morikawa
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.
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3
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Ying Y, Yang Y, Chen AK. Roles of RNA scaffolding in nanoscale Gag multimerization and selective protein sorting at HIV membranes. SCIENCE ADVANCES 2024; 10:eadk8297. [PMID: 38394201 PMCID: PMC10889351 DOI: 10.1126/sciadv.adk8297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
HIV-1 Gag proteins can multimerize upon the viral genomic RNA or multiple random cellular messenger RNAs to form a virus particle or a virus-like particle, respectively. To date, whether the two types of particles form via the same Gag multimerization process has remained unclarified. Using photoactivated localization microscopy to illuminate Gag organizations and dynamics at the nanoscale, here, we showed that genomic RNA mediates Gag multimerization in a more cluster-centric, cooperative, and spatiotemporally coordinated fashion, with the ability to drive dense Gag clustering dependent on its ability to act as a long-stranded scaffold not easily attainable by cellular messenger RNAs. These differences in Gag multimerization were further shown to affect downstream selective protein sorting into HIV membranes, indicating that the choice of RNA for packaging can modulate viral membrane compositions. These findings should advance the understanding of HIV assembly and further benefit the development of virus-like particle-based therapeutics.
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Affiliation(s)
- Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
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4
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Duchon A, Burdick RC, Pathak VK, Hu WS. Single-Virion Analysis: A Method to Visualize HIV-1 Particle Content Using Fluorescence Microscopy. Methods Mol Biol 2024; 2807:77-91. [PMID: 38743222 DOI: 10.1007/978-1-0716-3862-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
HIV-1 virions incorporate viral RNA, cellular RNAs, and proteins during the assembly process. Some of these components, such as the viral RNA genome and viral proteins, are essential for viral replication, whereas others, such as host innate immune proteins, can inhibit virus replication. Therefore, analyzing the virion content is an integral part of studying HIV-1 replication. Traditionally, virion contents have been examined using biochemical assays, which can provide information on the presence or absence of the molecule of interest but not its distribution in the virion population. Here, we describe a method, single-virion analysis, that directly examines the presence of molecules of interest in individual viral particles using fluorescence microscopy. Thus, this method can detect both the presence and the distribution of molecules of interest in the virion population. Single-virion analysis was first developed to study HIV-1 RNA genome packaging. In this assay, HIV-1 unspliced RNA is labeled with a fluorescently tagged RNA-binding protein (protein A) and some of the Gag proteins are labeled with a different fluorescent protein (protein B). Using fluorescence microscopy, HIV-1 particles can be identified by the fluorescent protein B signal and the presence of unspliced HIV-1 RNA can be identified by the fluorescent protein A signal. Therefore, the proportions of particles that contain unspliced RNA can be determined by the fraction of Gag particles that also have a colocalized RNA signal. By tagging the molecule of interest with fluorescent proteins, single-virion analysis can be easily adapted to study the incorporation of other viral or host cell molecules into particles. Indeed, this method has been adapted to examine the proportion of HIV-1 particles that contain APOBEC3 proteins and the fraction of particles that contain a modified Gag protein. Therefore, single-virion analysis is a flexible method to study the nucleic acid and protein content of HIV-1 particles.
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Affiliation(s)
- Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA.
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5
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Burdick RC, Duchon A, Hu WS, Pathak VK. Imaging HIV-1 Nuclear Import, Uncoating, and Proviral Transcription. Methods Mol Biol 2024; 2807:15-30. [PMID: 38743218 DOI: 10.1007/978-1-0716-3862-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Live-cell imaging has become a powerful tool for dissecting the behavior of viral complexes during HIV-1 infection with high temporal and spatial resolution. Very few HIV-1 particles in a viral population are infectious and successfully complete replication (~1/50). Single-particle live-cell imaging enables the study of these rare infectious viral particles, which cannot be accomplished in biochemical assays that measure the average property of the entire viral population, most of which are not infectious. The timing and location of many events in the early stage of the HIV-1 life cycle, including nuclear import, uncoating, and integration, have only recently been elucidated. Live-cell imaging also provides a valuable approach to study interactions of viral and host factors in distinct cellular compartments and at specific stages of viral replication. Successful live-cell imaging experiments require careful consideration of the fluorescent labeling method used and avoid or minimize its potential impact on normal viral replication and produce misleading results. Ideally, it is beneficial to utilize multiple virus labeling strategies and compare the results to ensure that the virion labeling did not adversely influence the viral replication step that is under investigation. Another potential benefit of using different labeling strategies is that they can provide information about the state of the viral complexes. Here, we describe our methods that utilize multiple fluorescent protein labeling approaches to visualize and quantify important events in the HIV-1 life cycle, including docking HIV-1 particles with the nuclear envelope (NE) and their nuclear import, uncoating, and proviral transcription.
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Affiliation(s)
- Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
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6
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Dibsy R, Inamdar K, Favard C, Muriaux D. Visualizing HIV-1 Assembly at the T-Cell Plasma Membrane Using Single-Molecule Localization Microscopy. Methods Mol Biol 2024; 2807:61-76. [PMID: 38743221 DOI: 10.1007/978-1-0716-3862-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The 20-year revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and timely acquisition, allows the visualization of nanoscaled objects in cell biology. Currently, the use of a recent generation of super-resolution fluorescence microscope coupled with improved fluorescent probes gives the possibility to study the replicative cycle of viruses in living cells, at the single-virus particle or protein level. Here, we highlight the protocol for visualizing HIV-1 Gag assembly at the host T-cell plasma membrane using super-resolution light microscopy. Total internal reflection fluorescence microscopy (TIRF-M) coupled with single-molecule localization microscopy (SMLM) enables the detection and characterization of the assembly of viral proteins at the plasma membrane of infected host cells at the single protein level. Here, we describe the TIRF equipment, the T-cell culture for HIV-1, the sample preparation for single-molecule localization microscopies such as PALM and STORM, acquisition protocols, and Gag assembling cluster analysis.
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Affiliation(s)
- Rayane Dibsy
- CNRS, University of Montpellier, Institut de Recherche en Infectiologie de Montpellier - IRIM, UMR9004, Montpellier, France
| | - Kaushik Inamdar
- CNRS, University of Montpellier, Institut de Recherche en Infectiologie de Montpellier - IRIM, UMR9004, Montpellier, France
| | - Cyril Favard
- CNRS, University of Montpellier, Institut de Recherche en Infectiologie de Montpellier - IRIM, UMR9004, Montpellier, France
| | - Delphine Muriaux
- CNRS, University of Montpellier, Institut de Recherche en Infectiologie de Montpellier - IRIM, UMR9004, Montpellier, France.
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7
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Wang H, Gallet B, Moriscot C, Pezet M, Chatellard C, Kleman JP, Göttlinger H, Weissenhorn W, Boscheron C. An Inducible ESCRT-III Inhibition Tool to Control HIV-1 Budding. Viruses 2023; 15:2289. [PMID: 38140530 PMCID: PMC10748027 DOI: 10.3390/v15122289] [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: 10/18/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
HIV-1 budding as well as many other cellular processes require the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Understanding the architecture of the native ESCRT-III complex at HIV-1 budding sites is limited due to spatial resolution and transient ESCRT-III recruitment. Here, we developed a drug-inducible transient HIV-1 budding inhibitory tool to enhance the ESCRT-III lifetime at budding sites. We generated autocleavable CHMP2A, CHMP3, and CHMP4B fusion proteins with the hepatitis C virus NS3 protease. We characterized the CHMP-NS3 fusion proteins in the absence and presence of protease inhibitor Glecaprevir with regard to expression, stability, localization, and HIV-1 Gag VLP budding. Immunoblotting experiments revealed rapid and stable accumulation of CHMP-NS3 fusion proteins. Notably, upon drug administration, CHMP2A-NS3 and CHMP4B-NS3 fusion proteins substantially decrease VLP release while CHMP3-NS3 exerted no effect but synergized with CHMP2A-NS3. Localization studies demonstrated the relocalization of CHMP-NS3 fusion proteins to the plasma membrane, endosomes, and Gag VLP budding sites. Through the combined use of transmission electron microscopy and video-microscopy, we unveiled drug-dependent accumulation of CHMP2A-NS3 and CHMP4B-NS3, causing a delay in HIV-1 Gag-VLP release. Our findings provide novel insight into the functional consequences of inhibiting ESCRT-III during HIV-1 budding and establish new tools to decipher the role of ESCRT-III at HIV-1 budding sites and other ESCRT-catalyzed cellular processes.
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Affiliation(s)
- Haiyan Wang
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Benoit Gallet
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | | | - Mylène Pezet
- University Grenoble Alpes, INSERM, IAB, 38000 Grenoble, France;
| | - Christine Chatellard
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Jean-Philippe Kleman
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Winfried Weissenhorn
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Cécile Boscheron
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
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8
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Dibsy R, Bremaud E, Mak J, Favard C, Muriaux D. HIV-1 diverts cortical actin for particle assembly and release. Nat Commun 2023; 14:6945. [PMID: 37907528 PMCID: PMC10618566 DOI: 10.1038/s41467-023-41940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
Enveloped viruses assemble and bud from the host cell membranes. Any role of cortical actin in these processes have often been a source of debate. Here, we assessed if cortical actin was involved in HIV-1 assembly in infected CD4 T lymphocytes. Our results show that preventing actin branching not only increases HIV-1 particle release but also the number of individual HIV-1 Gag assembly clusters at the T cell plasma membrane. Indeed, in infected T lymphocytes and in in vitro quantitative model systems, we show that HIV-1 Gag protein prefers areas deficient in F-actin for assembling. Finally, we found that the host factor Arpin, an inhibitor of Arp2/3 branched actin, is recruited at the membrane of infected T cells and it can associate with the viral Gag protein. Altogether, our data show that, for virus assembly and particle release, HIV-1 prefers low density of cortical actin and may favor local actin debranching by subverting Arpin.
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Affiliation(s)
- Rayane Dibsy
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Erwan Bremaud
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Brisbane, Australia
| | - Cyril Favard
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Delphine Muriaux
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France.
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9
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Wang H, Gallet B, Moriscot C, Pezet M, Chatellard C, Kleman JP, Göttlinger H, Weissenhorn W, Boscheron C. An inducible ESCRT-III inhibition tool to control HIV-1 budding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562494. [PMID: 37905063 PMCID: PMC10614826 DOI: 10.1101/2023.10.16.562494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
HIV-1 budding as well as many other cellular processes require the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Understanding the architecture of the native ESCRT-III complex at HIV-1 budding sites is limited due to spatial resolution and transient ESCRT-III recruitment. Here, we developed a drug-inducible transient HIV-1 budding inhibitory tool to enhance the ESCRT-III lifetime at budding sites. We generated auto-cleavable CHMP2A, CHMP3, and CHMP4B fusion proteins with the hepatitis C virus NS3 protease. We characterized the CHMP-NS3 fusion proteins in the absence and presence of protease inhibitor Glecaprevir with regard to expression, stability, localization and HIV-1 Gag VLP budding. Immunoblotting experiments revealed rapid and stable accumulation of CHMP-NS3 fusion proteins with variable modification of Gag VLP budding upon drug administration. Notably, CHMP2A-NS3 and CHMP4B-NS3 fusion proteins substantially decrease VLP release while CHMP3-NS3 exerted a minor effect and synergized with CHMP2A-NS3. Localization studies demonstrated the re-localization of CHMP-NS3 fusion proteins to the plasma membrane, endosomes, and Gag VLP budding sites. Through the combined use of transmission electron microscopy and video-microscopy, we unveiled drug-dependent accumulation of CHMP2A-NS3 and CHMP4B-NS3, causing a delay in HIV-1 Gag-VLP release. Our findings provide novel insight into the functional consequences of inhibiting ESCRT-III during HIV-1 budding and establish new tools to decipher the role of ESCRT-III at HIV-1 budding sites and other ESCRT-catalyzed cellular processes.
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10
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. RESEARCH SQUARE 2023:rs.3.rs-3060076. [PMID: 37461524 PMCID: PMC10350206 DOI: 10.21203/rs.3.rs-3060076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
HIV-1 capsid assembly is an essential process in the virus infection cycle. Initiation of capsid assembly involves viral proteins, genomic RNA, and the inner leaflet of the plasma membrane, facilitated by a number of cellular factors1. The viral structural protein Gag plays a number of central roles in this process, including association with the membrane, selective binding of genomic RNA, and oligomerization and packaging to ultimately produce an immature budded pro-viral particle2. While there have been intensive studies regarding the early stages of Gag assembly, there is a lack of consensus on the mechanism for nucleation and growth of Gag complexes3-7. Here we show that myristoylated Gag forms a trimer nucleus in a model membrane that can selectively bind a dimeric RNA containing the packaging signal. Subsequent growth of myristoyl-Gag oligomers requires vRNA, and occurs by addition of 1 or 2 Gag monomers at a time from solution. These data support a model where the immature capsid lattice formation occurs by a gradual lattice edge expansion, following a trimeric nucleation event. The dynamic single molecule data that support this model were recorded using mass photometry, involving full length myristoylated protein, RNA, and lipid together. These data are the first to support a lattice edge expansion model of Gag during early stages of assembly in a biological-relevant setting, providing insights to the fundamental models of virus structural protein assembly process.
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Affiliation(s)
- Anne X.-Z. Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John A. Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
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11
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Liu D, Pan L, Zhai H, Qiu HJ, Sun Y. Virus tracking technologies and their applications in viral life cycle: research advances and future perspectives. Front Immunol 2023; 14:1204730. [PMID: 37334362 PMCID: PMC10272434 DOI: 10.3389/fimmu.2023.1204730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Viruses are simple yet highly pathogenic microorganisms that parasitize within cells and pose serious threats to the health, economic development, and social stability of both humans and animals. Therefore, it is crucial to understand the dynamic mechanism of virus infection in hosts. One effective way to achieve this is through virus tracking technology, which utilizes fluorescence imaging to track the life processes of virus particles in living cells in real-time, providing a comprehensively and detailed spatiotemporal dynamic process and mechanism of virus infection. This paper provides a broad overview of virus tracking technology, including the selection of fluorescent labels and virus labeling components, the development of imaging microscopes, and its applications in various virus studies. Additionally, we discuss the possibilities and challenges of its future development, offering theoretical guidance and technical support for effective prevention and control of the viral disease outbreaks and epidemics.
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Affiliation(s)
| | | | | | - Hua-Ji Qiu
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
| | - Yuan Sun
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
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12
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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13
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525415. [PMID: 36747785 PMCID: PMC9901173 DOI: 10.1101/2023.01.27.525415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mass photometry (MP) was used to investigate the assembly of myristoylated full-length HIV-1 Gag (myr-Gag) and vRNA 5’ UTR fragment in a supported lipid bilayer (SLB) model system. The MP trajectories demonstrated that Gag trimerization on the membrane is a key step of early Gag assembly in the presence of vRNA. Growth of myr-Gag oligomers requires vRNA, occuring by addition of 1 or 2 monomers at a time from solution. These data support a model where formation of the Gag hexamers characteristic of the immature capsid lattice occurs by a gradual edge expansion, following a trimeric nucleation event. These dynamic single molecule data involving protein, RNA, and lipid components together, provide novel and fundamental insights into the initiation of virus capsid assembly.
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14
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Quantifying membrane binding and diffusion with fluorescence correlation spectroscopy diffusion laws. Biophys J 2023:S0006-3495(23)00006-1. [PMID: 36632034 DOI: 10.1016/j.bpj.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/05/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Many transient processes in cells arise from the binding of cytosolic proteins to membranes. Quantifying this membrane binding and its associated diffusion in the living cell is therefore of primary importance. Dynamic photonic microscopies, e.g., single/multiple particle tracking, fluorescence recovery after photobleaching, and fluorescence correlation spectroscopy (FCS), enable non-invasive measurement of molecular mobility in living cells and their plasma membranes. However, FCS with a single beam waist is of limited applicability with complex, non-Brownian, motions. Recently, the development of FCS diffusion laws methods has given access to the characterization of these complex motions, although none of them is applicable to the membrane binding case at the moment. In this study, we combined computer simulations and FCS experiments to propose an FCS diffusion law for membrane binding. First, we generated computer simulations of spot-variation FCS (svFCS) measurements for a membrane binding process combined to 2D and 3D diffusion at the membrane and in the bulk/cytosol, respectively. Then, using these simulations as a learning set, we derived an empirical diffusion law with three free parameters: the apparent binding constant KD, the diffusion coefficient on the membrane D2D, and the diffusion coefficient in the cytosol, D3D. Finally, we monitored, using svFCS, the dynamics of retroviral Gag proteins and associated mutants during their binding to supported lipid bilayers of different lipid composition or at plasma membranes of living cells, and we quantified KD and D2D in these conditions using our empirical diffusion law. Based on these experiments and numerical simulations, we conclude that this new approach enables correct estimation of membrane partitioning and membrane diffusion properties (KD and D2D) for peripheral membrane molecules.
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15
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Azad K, Guilligay D, Boscheron C, Maity S, De Franceschi N, Sulbaran G, Effantin G, Wang H, Kleman JP, Bassereau P, Schoehn G, Roos WH, Desfosses A, Weissenhorn W. Structural basis of CHMP2A-CHMP3 ESCRT-III polymer assembly and membrane cleavage. Nat Struct Mol Biol 2023; 30:81-90. [PMID: 36604498 DOI: 10.1038/s41594-022-00867-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
The endosomal sorting complex required for transport (ESCRT) is a highly conserved protein machinery that drives a divers set of physiological and pathological membrane remodeling processes. However, the structural basis of ESCRT-III polymers stabilizing, constricting and cleaving negatively curved membranes is yet unknown. Here we present cryo-EM structures of membrane-coated CHMP2A-CHMP3 filaments from Homo sapiens of two different diameters at 3.3 and 3.6 Å resolution. The structures reveal helical filaments assembled by CHMP2A-CHMP3 heterodimers in the open ESCRT-III conformation, which generates a partially positive charged membrane interaction surface, positions short N-terminal motifs for membrane interaction and the C-terminal VPS4 target sequence toward the tube interior. Inter-filament interactions are electrostatic, which may facilitate filament sliding upon VPS4-mediated polymer remodeling. Fluorescence microscopy as well as high-speed atomic force microscopy imaging corroborate that VPS4 can constrict and cleave CHMP2A-CHMP3 membrane tubes. We therefore conclude that CHMP2A-CHMP3-VPS4 act as a minimal membrane fission machinery.
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Affiliation(s)
- Kimi Azad
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Delphine Guilligay
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Cecile Boscheron
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Nicola De Franceschi
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.,Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guidenn Sulbaran
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Gregory Effantin
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Haiyan Wang
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Philippe Kleman
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Patricia Bassereau
- Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guy Schoehn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Ambroise Desfosses
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Winfried Weissenhorn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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16
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Roos WH. High-speed AFM reveals the dynamics of virus budding. Biophys J 2022; 121:4022-4023. [PMID: 36243010 PMCID: PMC9675024 DOI: 10.1016/j.bpj.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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17
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Harel S, Altaras Y, Nachmias D, Rotem-Dai N, Dvilansky I, Elia N, Rousso I. Analysis of individual HIV-1 budding event using fast AFM reveals a multiplexed role for VPS4. Biophys J 2022; 121:4229-4238. [PMID: 36042696 PMCID: PMC9674973 DOI: 10.1016/j.bpj.2022.08.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
The assembly and budding of newly formed human immunodeficiency virus-1 (HIV-1) particles occur at the plasma membrane of infected cells. Although the molecular basis for viral budding has been studied extensively, investigation of its spatiotemporal characteristics has been limited by the small dimensions (∼100 nm) of HIV particles and the fast kinetics of the process (a few minutes from bud formation to virion release). Here we applied ultra-fast atomic force microscopy to achieve real-time visualization of individual HIV-1 budding events from wild-type (WT) cell lines as well as from mutated lines lacking vacuolar protein sorting-4 (VPS4) or visceral adipose tissue-1 protein (VTA1). Using single-particle analysis, we show that HIV-1 bud formation follows two kinetic pathways (fast and slow) with each composed of three distinct phases (growth, stationary, decay). Notably, approximately 38% of events did not result in viral release and were characterized by the formation of short (rather than tall) particles that slowly decayed back into the cell membrane. These non-productive events became more abundant in VPS4 knockout cell lines. Strikingly, the absence of VPS4B, rather than VPS4A, increased the production of short viral particles, suggesting a role for VPS4B in earlier stages of HIV-1 budding than traditionally thought.
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Affiliation(s)
- Shimon Harel
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yarin Altaras
- Department of Life Sciences and NIBN, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dikla Nachmias
- Department of Life Sciences and NIBN, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Noa Rotem-Dai
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Inbar Dvilansky
- Department of Life Sciences and NIBN, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Natalie Elia
- Department of Life Sciences and NIBN, Ben-Gurion University of the Negev, Beer Sheva, Israel.
| | - Itay Rousso
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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18
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Eid J, Socol M, Naillon A, Feuillard J, Ciandrini L, Margeat E, Charlot B, Mougel M. Viro-fluidics: Real-time analysis of virus production kinetics at the single-cell level. BIOPHYSICAL REPORTS 2022; 2:100068. [PMID: 36425325 PMCID: PMC9680794 DOI: 10.1016/j.bpr.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Real-time visualization and quantification of viruses released by a cell are crucial to further decipher infection processes. Kinetics studies at the single-cell level will circumvent the limitations of bulk assays with asynchronous virus replication. We have implemented a "viro-fluidic" method, which combines microfluidics and virology at single-cell and single-virus resolutions. As an experimental model, we used standard cell lines producing fluorescent HIV-like particles (VLPs). First, to scale the strategy to the single-cell level, we validated a sensitive flow virometry system to detect VLPs in low concentration samples (≥104 VLPs/mL). Then, this system was coupled to a single-cell trapping device to monitor in real-time the VLPs released, one at a time, from single cells under cell culture conditions. Our results revealed an average production rate of 50 VLPs/h/cell similar to the rate estimated for the same cells grown in population. Thus, the virus-producing capacities of the trapped cells were preserved and its real-time monitoring was accurate. Moreover, single-cell analysis revealed a release of VLPs with stochastic bursts with typical time intervals of few minutes, revealing the existence of limiting step(s) in the virus biogenesis process. Our tools can be applied to other pathogens or to extracellular vesicles to elucidate the dissemination mechanisms of these biological nanoparticles.
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Affiliation(s)
- Joëlle Eid
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Marius Socol
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Antoine Naillon
- Université Grenoble Alpes, CNRS, Grenoble INP, 3SR, Grenoble, France
| | - Jérôme Feuillard
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Luca Ciandrini
- CBS, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Emmanuel Margeat
- CBS, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Benoit Charlot
- IES, Université de Montpellier, CNRS, Montpellier, France
| | - Marylène Mougel
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
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19
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Evans EL, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses 2022; 14:903. [PMID: 35632645 PMCID: PMC9145009 DOI: 10.3390/v14050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell imaging has emerged as a powerful means to study viral replication dynamics and identify sites of virus−host interactions. Multivariate aspects of viral replication cycles yield challenges inherent to handling large, complex imaging datasets. Herein, we describe the design and implementation of an automated, imaging-based strategy, “Human Immunodeficiency Virus Red-Green-Blue” (HIV RGB), for deriving comprehensive single-cell measurements of HIV-1 unspliced (US) RNA nuclear export, translation, and bulk changes to viral RNA and protein (HIV-1 Rev and Gag) subcellular distribution over time. Differentially tagged fluorescent viral RNA and protein species are recorded using multicolor long-term (>24 h) time-lapse video microscopy, followed by image processing using a new open-source computational imaging workflow dubbed “Nuclear Ring Segmentation Analysis and Tracking” (NR-SAT) based on ImageJ plugins that have been integrated into the Konstanz Information Miner (KNIME) analytics platform. We describe a typical HIV RGB experimental setup, detail the image acquisition and NR-SAT workflow accompanied by a step-by-step tutorial, and demonstrate a use case wherein we test the effects of perturbing subcellular localization of the Rev protein, which is essential for viral US RNA nuclear export, on the kinetics of HIV-1 late-stage gene regulation. Collectively, HIV RGB represents a powerful platform for single-cell studies of HIV-1 post-transcriptional RNA regulation. Moreover, we discuss how similar NR-SAT-based design principles and open-source tools might be readily adapted to study a broad range of dynamic viral or cellular processes.
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Affiliation(s)
- Edward L. Evans
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ginger M. Pocock
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Gabriel Einsdorf
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
| | - Marcel Wiedenmann
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | | | - Paul Ahlquist
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Morgridge Institute for Research, Madison, WI 53715, USA
- John and Jeanne Rowe Center for Research in Virology, Madison, WI 53715, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
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20
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Deciphering the Assembly of Enveloped Viruses Using Model Lipid Membranes. MEMBRANES 2022; 12:membranes12050441. [PMID: 35629766 PMCID: PMC9142974 DOI: 10.3390/membranes12050441] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 01/09/2023]
Abstract
The cell plasma membrane is mainly composed of phospholipids, cholesterol and embedded proteins, presenting a complex interface with the environment. It maintains a barrier to control matter fluxes between the cell cytosol and its outer environment. Enveloped viruses are also surrounded by a lipidic membrane derived from the host-cell membrane and acquired while exiting the host cell during the assembly and budding steps of their viral cycle. Thus, model membranes composed of selected lipid mixtures mimicking plasma membrane properties are the tools of choice and were used to decipher the first step in the assembly of enveloped viruses. Amongst these viruses, we choose to report the three most frequently studied viruses responsible for lethal human diseases, i.e., Human Immunodeficiency Type 1 (HIV-1), Influenza A Virus (IAV) and Ebola Virus (EBOV), which assemble at the host-cell plasma membrane. Here, we review how model membranes such as Langmuir monolayers, bicelles, large and small unilamellar vesicles (LUVs and SUVs), supported lipid bilayers (SLBs), tethered-bilayer lipid membranes (tBLM) and giant unilamellar vesicles (GUVs) contribute to the understanding of viral assembly mechanisms and dynamics using biophysical approaches.
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21
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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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22
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Sumner C, Ono A. Relationship between HIV-1 Gag Multimerization and Membrane Binding. Viruses 2022; 14:v14030622. [PMID: 35337029 PMCID: PMC8949992 DOI: 10.3390/v14030622] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
HIV-1 viral particle assembly occurs specifically at the plasma membrane and is driven primarily by the viral polyprotein Gag. Selective association of Gag with the plasma membrane is a key step in the viral assembly pathway, which is traditionally attributed to the MA domain. MA regulates specific plasma membrane binding through two primary mechanisms including: (1) specific interaction of the MA highly basic region (HBR) with the plasma membrane phospholipid phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2], and (2) tRNA binding to the MA HBR, which prevents Gag association with non-PI(4,5)P2 containing membranes. Gag multimerization, driven by both CA–CA inter-protein interactions and NC-RNA binding, also plays an essential role in viral particle assembly, mediating the establishment and growth of the immature Gag lattice on the plasma membrane. In addition to these functions, the multimerization of HIV-1 Gag has also been demonstrated to enhance its membrane binding activity through the MA domain. This review provides an overview of the mechanisms regulating Gag membrane binding through the MA domain and multimerization through the CA and NC domains, and examines how these two functions are intertwined, allowing for multimerization mediated enhancement of Gag membrane binding.
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23
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Lerner G, Weaver N, Anokhin B, Spearman P. Advances in HIV-1 Assembly. Viruses 2022; 14:v14030478. [PMID: 35336885 PMCID: PMC8952333 DOI: 10.3390/v14030478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.
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24
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Dynamics of HIV-1 Gag Processing as Revealed by Fluorescence Lifetime Imaging Microscopy and Single Virus Tracking. Viruses 2022; 14:v14020340. [PMID: 35215933 PMCID: PMC8874525 DOI: 10.3390/v14020340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 12/04/2022] Open
Abstract
The viral polyprotein Gag plays a central role for HIV-1 assembly, release and maturation. Proteolytic processing of Gag by the viral protease is essential for the structural rearrangements that mark the transition from immature to mature, infectious viruses. The timing and kinetics of Gag processing are not fully understood. Here, fluorescence lifetime imaging microscopy and single virus tracking are used to follow Gag processing in nascent HIV-1 particles in situ. Using a Gag polyprotein labelled internally with eCFP, we show that proteolytic release of the fluorophore from Gag is accompanied by an increase in its fluorescence lifetime. By tracking nascent virus particles in situ and analyzing the intensity and fluorescence lifetime of individual traces, we detect proteolytic cleavage of eCFP from Gag in a subset (6.5%) of viral particles. This suggests that for the majority of VLPs, Gag processing occurs with a delay after particle assembly.
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25
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Tsg101/ESCRT-I recruitment regulated by the dual binding modes of K63-linked diubiquitin. Structure 2022; 30:289-299.e6. [PMID: 35120596 PMCID: PMC10015442 DOI: 10.1016/j.str.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/03/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022]
Abstract
The ESCRT-I protein Tsg101 plays a critical role in viral budding and endocytic sorting. Although Tsg101 is known to recognize monoubiquitin (Ub1), here we show that it can also bind several diubiquitins (K48-Ub2, N-Ub2, and K63-Ub2), with a preference for K63-linked Ub2. The NMR structure of the Tsg101:K63-Ub2 complex showed that while the Ub1-binding site accommodates the distal domain of Ub2, the proximal domain alternatively binds two different sites, the vestigial active site and an N-terminal helix. Mutation of each site results in distinct phenotypes regarding the recruitment of Tsg101 partners. Mutation in the vestigial active site abrogates interaction between Tsg101 and the HIV-1 protein Gag but not Hrs, a cellular protein. Mutation at the N-terminal helix alters Gag but not Hrs-Tsg101 localization. Given the broad involvement of Tsg101 in diverse cellular functions, this discovery advances our understanding of how the ESCRT protein recognizes binding partners and sorts endocytic cargo.
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26
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Dufloo J, Planchais C, Frémont S, Lorin V, Guivel-Benhassine F, Stefic K, Casartelli N, Echard A, Roingeard P, Mouquet H, Schwartz O, Bruel T. Broadly neutralizing anti-HIV-1 antibodies tether viral particles at the surface of infected cells. Nat Commun 2022; 13:630. [PMID: 35110562 PMCID: PMC8810770 DOI: 10.1038/s41467-022-28307-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023] Open
Abstract
Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) are promising molecules for therapeutic or prophylactic interventions. Beyond neutralization, bNAbs exert Fc-dependent functions including antibody-dependent cellular cytotoxicity and activation of the complement. Here, we show that a subset of bNAbs targeting the CD4 binding site and the V1/V2 or V3 loops inhibit viral release from infected cells. We combined immunofluorescence, scanning electron microscopy, transmission electron microscopy and immunogold staining to reveal that some bNAbs form large aggregates of virions at the surface of infected cells. This activity correlates with the capacity of bNAbs to bind to Env at the cell surface and to neutralize cell-free viral particles. We further show that antibody bivalency is required for viral retention, and that aggregated virions are neutralized. We have thus identified an additional antiviral activity of bNAbs, which block HIV-1 release by tethering viral particles at the surface of infected cells. Broadly neutralizing antibodies (bNAbs) neutralize HIV-1 and exert Fc-dependent activities against infected cells. Here, Dufloo et al. show that bNAbs also block HIV-1 release by trapping viral particles at the surface of infected cells.
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Affiliation(s)
- Jérémy Dufloo
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France.,Université de Paris, École doctorale BioSPC 562, 75013, Paris, France.,Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980, València, Spain
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Humoral Immunology Laboratory, 75015, Paris, France
| | - Stéphane Frémont
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 75015, Paris, France
| | - Valérie Lorin
- Institut Pasteur, Université de Paris, INSERM U1222, Humoral Immunology Laboratory, 75015, Paris, France
| | | | - Karl Stefic
- CHRU de Tours, Hôpital Bretonneau, Service de Bactériologie-Virologie, 37000, Tours, France
| | - Nicoletta Casartelli
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 75015, Paris, France
| | - Philippe Roingeard
- Université de Tours, CHRU de Tours, INSERM U1259 MAVIVH and Plateforme IBiSA de Microscopie Électronique, 37000, Tours, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Humoral Immunology Laboratory, 75015, Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France. .,Vaccine Research Institute, 94000, Créteil, France.
| | - Timothée Bruel
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, 75015, Paris, France. .,Vaccine Research Institute, 94000, Créteil, France.
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27
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Durand S, Seigneuret F, Burlaud-Gaillard J, Lemoine R, Tassi MF, Moreau A, Mougel M, Roingeard P, Tauber C, de Rocquigny H. Quantitative analysis of the formation of nucleoprotein complexes between HIV-1 Gag protein and genomic RNA using transmission electron microscopy. J Biol Chem 2022; 298:101500. [PMID: 34929171 PMCID: PMC8760521 DOI: 10.1016/j.jbc.2021.101500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/06/2023] Open
Abstract
In HIV, the polyprotein precursor Gag orchestrates the formation of the viral capsid. In the current view of this viral assembly, Gag forms low-order oligomers that bind to the viral genomic RNA triggering the formation of high-ordered ribonucleoprotein complexes. However, this assembly model was established using biochemical or imaging methods that do not describe the cellular location hosting Gag-gRNA complex nor distinguish gRNA packaging in single particles. Here, we studied the intracellular localization of these complexes by electron microscopy and monitored the distances between the two partners by morphometric analysis of gold beads specifically labeling Gag and gRNA. We found that formation of these viral clusters occurred shortly after the nuclear export of the gRNA. During their transport to the plasma membrane, the distance between Gag and gRNA decreases together with an increase of gRNA packaging. Point mutations in the zinc finger patterns of the nucleocapsid domain of Gag caused an increase in the distance between Gag and gRNA as well as a sharp decrease of gRNA packaged into virions. Finally, we show that removal of stem loop 1 of the 5'-untranslated region does not interfere with gRNA packaging, whereas combined with the removal of stem loop 3 is sufficient to decrease but not abolish Gag-gRNA cluster formation and gRNA packaging. In conclusion, this morphometric analysis of Gag-gRNA cluster formation sheds new light on HIV-1 assembly that can be used to describe at nanoscale resolution other viral assembly steps involving RNA or protein-protein interactions.
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Affiliation(s)
- Stéphanie Durand
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Florian Seigneuret
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Julien Burlaud-Gaillard
- Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Roxane Lemoine
- B Cell Ressources Platform, EA4245 "Transplantation, Immunology and Inflammation", University of Tours, Tours Cedex 1, France
| | - Marc-Florent Tassi
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Alain Moreau
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Marylène Mougel
- Équipe R2D2 Retroviral RNA Dynamics and Delivery, IRIM, CNRS UMR9004, University of Montpellier, Montpellier, France
| | - Philippe Roingeard
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France; Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Clovis Tauber
- UMR U1253 iBrain, Inserm, University of Tours, Tours Cedex 1, France
| | - Hugues de Rocquigny
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France.
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28
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Wang L, Sandmeyer A, Hübner W, Li H, Huser T, Chen BK. A Replication-Competent HIV Clone Carrying GFP-Env Reveals Rapid Env Recycling at the HIV-1 T Cell Virological Synapse. Viruses 2021; 14:v14010038. [PMID: 35062242 PMCID: PMC8781834 DOI: 10.3390/v14010038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/08/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 infection is enhanced by cell-cell adhesions between infected and uninfected T cells called virological synapses (VS). VS are initiated by the interactions of cell-surface HIV-1 envelope glycoprotein (Env) and CD4 on target cells and act as sites of viral assembly and viral transfer between cells. To study the process that recruits and retains HIV-1 Env at the VS, a replication-competent HIV-1 clone carrying an Env-sfGFP fusion protein was designed to enable live tracking of Env within infected cells. Combined use of surface pulse-labeling of Env and fluorescence recovery after photobleaching (FRAP) studies, enabled the visualization of the targeted accumulation and sustained recycling of Env between endocytic compartments (EC) and the VS. We observed dynamic exchange of Env at the VS, while the viral structural protein, Gag, was largely immobile at the VS. The disparate exchange rates of Gag and Env at the synapse support that the trafficking and/or retention of a majority of Env towards the VS is not maintained by entrapment by a Gag lattice or immobilization by binding to CD4 on the target cell. A FRAP study of an Env endocytosis mutant showed that recycling is not required for accumulation at the VS, but is required for the rapid exchange of Env at the VS. We conclude that the mechanism of Env accumulation at the VS and incorporation into nascent particles involves continuous internalization and targeted secretion rather than irreversible interactions with the budding virus, but that this recycling is largely dispensable for VS formation and viral transfer across the VS.
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Affiliation(s)
- Lili Wang
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
| | - Alice Sandmeyer
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Wolfgang Hübner
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Hongru Li
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany; (A.S.); (W.H.); (T.H.)
| | - Benjamin K. Chen
- Department of Medicine, Division of Infectious Disease, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (L.W.); (H.L.)
- Correspondence:
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29
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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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30
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McClelland RD, Culp TN, Marchant DJ. Imaging Flow Cytometry and Confocal Immunofluorescence Microscopy of Virus-Host Cell Interactions. Front Cell Infect Microbiol 2021; 11:749039. [PMID: 34712624 PMCID: PMC8546218 DOI: 10.3389/fcimb.2021.749039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Viruses are diverse pathogens that use host factors to enter cells and cause disease. Imaging the entry and replication phases of viruses and their interactions with host factors is key to fully understanding viral infections. This review will discuss how confocal microscopy and imaging flow cytometry are used to investigate virus entry and replication mechanisms in fixed and live cells. Quantification of viral images and the use of cryo-electron microscopy to gather structural information of viruses is also explored. Using imaging to understand how viruses replicate and interact with host factors, we gain insight into cellular processes and identify novel targets to develop antiviral therapeutics and vaccines.
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Affiliation(s)
- Ryley D McClelland
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
| | - Tyce N Culp
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
| | - David J Marchant
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
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31
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Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC. RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. Cell 2021; 184:5419-5431.e16. [PMID: 34597582 PMCID: PMC8929533 DOI: 10.1016/j.cell.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/03/2021] [Accepted: 09/03/2021] [Indexed: 11/26/2022]
Abstract
Many enveloped viruses require the endosomal sorting complexes required for transport (ESCRT) pathway to exit infected cells. This highly conserved pathway mediates essential cellular membrane fission events, which restricts the acquisition of adaptive mutations to counteract viral co-option. Here, we describe duplicated and truncated copies of the ESCRT-III factor CHMP3 that block ESCRT-dependent virus budding and arose independently in New World monkeys and mice. When expressed in human cells, these retroCHMP3 proteins potently inhibit release of retroviruses, paramyxoviruses, and filoviruses. Remarkably, retroCHMP3 proteins have evolved to reduce interactions with other ESCRT-III factors and have little effect on cellular ESCRT processes, revealing routes for decoupling cellular ESCRT functions from viral exploitation. The repurposing of duplicated ESCRT-III proteins thus provides a mechanism to generate broad-spectrum viral budding inhibitors without blocking highly conserved essential cellular ESCRT functions.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kate Bredbenner
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA
| | - Gaelle Mercenne
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Phuong Tieu Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christina R Necessary
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John McCullough
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Anthony P Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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32
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Meng B, Vallejo Ramirez PP, Scherer KM, Bruggeman E, Kenyon JC, Kaminski CF, Lever AM. EAP45 association with budding HIV-1: Kinetics and domain requirements. Traffic 2021; 22:439-453. [PMID: 34580994 DOI: 10.1111/tra.12820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/25/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022]
Abstract
A number of viruses including HIV use the ESCRT system to bud from the infected cell. We have previously confirmed biochemically that ESCRT-II is involved in this process in HIV-1 and have defined the molecular domains that are important for this. Here, using SNAP-tag fluorescent labelling and both fixed and live cell imaging we show that the ESCRT-II component EAP45 colocalises with the HIV protein Gag at the plasma membrane in a temporal and quantitative manner, similar to that previously shown for ALIX and Gag. We show evidence that a proportion of EAP45 may be packaged within virions, and we confirm the importance of the N terminus of EAP45 and specifically the H0 domain in this process. By contrast, the Glue domain of EAP45 is more critical for recruitment during cytokinesis, emphasising that viruses have ways of recruiting cellular components that may be distinct from those used by some cellular processes. This raises the prospect of selective interference with the pathway to inhibit viral function while leaving cellular functions relatively unperturbed.
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Affiliation(s)
- Bo Meng
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Pedro P Vallejo Ramirez
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Katharina M Scherer
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Ezra Bruggeman
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Julia C Kenyon
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore.,Homerton College, University of Cambridge, Cambridge, UK
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Andrew M Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Department of Medicine, National University of Singapore, Singapore, Singapore
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33
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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34
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Saccon E, Mikaeloff F, Figueras Ivern P, Végvári Á, Sönnerborg A, Neogi U, van Domselaar R. Cytotoxic Lymphocytes Target HIV-1 Gag Through Granzyme M-Mediated Cleavage. Front Immunol 2021; 12:669347. [PMID: 33953729 PMCID: PMC8089382 DOI: 10.3389/fimmu.2021.669347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
Untreated HIV-1 infection leads to a slow decrease in CD4+ T cell lymphocytes over time resulting in increased susceptibility to opportunistic infections (acquired immunodeficiency syndrome, AIDS) and ultimately death of the infected individual. Initially, the host's immune response controls the infection, but cannot eliminate the HIV-1 from the host. Cytotoxic lymphocytes are the key effector cells in this response and can mediate crucial antiviral responses through the release of a set of proteases called granzymes towards HIV-1-infected cells. However, little is known about the immunological molecular mechanisms by which granzymes could control HIV-1. Since we noted that HIV-1 subtype C (HIV-1C) Gag with the tetrapeptide insertion PYKE contains a putative granzyme M (GrM) cleavage site (KEPL) that overlaps with the PYKE insertion, we analyzed the proteolytic activity of GrM towards Gag. Immunoblot analysis showed that GrM could cleave Gag proteins from HIV-1B and variants from HIV-1C of which the Gag-PYKE variant was cleaved with extremely high efficiency. The main cleavage site was directly after the insertion after leucine residue 483. GrM-mediated cleavage of Gag was also observed in co-cultures using cytotoxic lymphocytes as effector cells and this cleavage could be inhibited by a GrM inhibitor peptide. Altogether, our data indicate towards a noncytotoxic immunological mechanism by which GrM-positive cytotoxic lymphocytes target the HIV-1 Gag protein within infected cells to potentially control HIV-1 infection. This mechanism could be exploited in new therapeutic strategies to treat HIV-1-infected patients to improve immunological control of the infection.
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Affiliation(s)
- Elisa Saccon
- Division of Clinical Microbiology, ANA Futura Laboratory, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Flora Mikaeloff
- Division of Clinical Microbiology, ANA Futura Laboratory, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pol Figueras Ivern
- Division of Infectious Diseases, ANA Futura Laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, ANA Futura Laboratory, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, ANA Futura Laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Ujjwal Neogi
- Division of Clinical Microbiology, ANA Futura Laboratory, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Robert van Domselaar
- Division of Infectious Diseases, ANA Futura Laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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35
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Deng Y, Hammond JA, Pauszek R, Ozog S, Chai I, Rabuck-Gibbons J, Lamichhane R, Henderson SC, Millar DP, Torbett BE, Williamson JR. Discrimination between Functional and Non-functional Cellular Gag Complexes involved in HIV-1 Assembly. J Mol Biol 2021; 433:166842. [PMID: 33539875 DOI: 10.1016/j.jmb.2021.166842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023]
Abstract
HIV-1 Gag and Gag-Pol are responsible for viral assembly and maturation and represent a major paradigm for enveloped virus assembly. Numerous intracellular Gag-containing complexes (GCCs) have been identified in cellular lysates using sucrose gradient ultracentrifugation. While these complexes are universally present in Gag-expressing cells, their roles in virus assembly are not well understood. Here we demonstrate that most GCC species are predominantly comprised of monomeric or dimeric Gag molecules bound to ribosomal complexes, and as such, are not on-pathway intermediates in HIV assembly. Rather, these GCCs represent a population of Gag that is not yet functionally committed for incorporation into a viable virion precursor. We hypothesize that these complexes act as a reservoir of monomeric Gag that can incorporate into assembling viruses, and serve to mitigate non-specific intracellular Gag oligomerization. We have identified a subset of large GCC complexes, comprising more than 20 Gag molecules, that may be equivalent to membrane-associated puncta previously shown to be bona fide assembling-virus intermediates. This work provides a clear rationale for the existence of diverse GCCs, and serves as the foundation for characterizing on-pathway intermediates early in virus assembly.
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Affiliation(s)
- Yisong Deng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - John A Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Raymond Pauszek
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Stosh Ozog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Ilean Chai
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Jessica Rabuck-Gibbons
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Rajan Lamichhane
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Scott C Henderson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - David P Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Bruce E Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States; The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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36
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Sarca AD, Sardo L, Fukuda H, Matsui H, Shirakawa K, Horikawa K, Takaori-Kondo A, Izumi T. FRET-Based Detection and Quantification of HIV-1 Virion Maturation. Front Microbiol 2021; 12:647452. [PMID: 33767685 PMCID: PMC7985248 DOI: 10.3389/fmicb.2021.647452] [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: 12/29/2020] [Accepted: 01/18/2021] [Indexed: 01/27/2023] Open
Abstract
HIV-1 infectivity is achieved through virion maturation. Virus particles undergo structural changes via cleavage of the Gag polyprotein mediated by the viral protease, causing the transition from an uninfectious to an infectious status. The majority of proviruses in people living with HIV-1 treated with combination antiretroviral therapy are defective with large internal deletions. Defective proviral DNA frequently preserves intact sequences capable of expressing viral structural proteins to form virus-like particles whose maturation status is an important factor for chronic antigen-mediated immune stimulation and inflammation. Thus, novel methods to study the maturation capability of defective virus particles are needed to characterize their immunogenicity. To build a quantitative tool to study virion maturation in vitro, we developed a novel single virion visualization technique based on fluorescence resonance energy transfer (FRET). We inserted an optimized intramolecular CFP-YPF FRET donor-acceptor pair bridged with an HIV-1 protease cleavage sequence between the Gag MA-CA domains. This system allowed us to microscopically distinguish mature and immature virions via their FRET signal when the FRET donor and acceptor proteins were separated by the viral protease during maturation. We found that approximately 80% of the FRET labeled virus particles were mature with equivalent infectivity to wild type. The proportion of immature virions was increased by treatment of virus producer cells with a protease inhibitor in a dose-dependent manner, which corresponded to a relative decrease in infectivity. Potential areas of application for this tool are assessing maturation efficiency in different cell type settings of intact or deficient proviral DNA integrated cells. We believe that this FRET-based single-virion imaging platform will facilitate estimating the impact on the immune system of both extracellular intact and defective viruses by quantifying the Gag maturation status.
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Affiliation(s)
- Anamaria D Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Luca Sardo
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Hirofumi Fukuda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuki Horikawa
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, Tokushima, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Taisuke Izumi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses 2021; 13:v13030451. [PMID: 33802145 PMCID: PMC8001593 DOI: 10.3390/v13030451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
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38
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Knoener R, Evans E, Becker JT, Scalf M, Benner B, Sherer NM, Smith LM. Identification of host proteins differentially associated with HIV-1 RNA splice variants. eLife 2021; 10:e62470. [PMID: 33629952 PMCID: PMC7906601 DOI: 10.7554/elife.62470] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs, each playing distinct roles in viral replication. Elucidating their host protein 'interactomes' is crucial to understanding virus-host interplay. Here, we present HyPR-MSSV for isolation of US, PS, and CS transcripts from a single population of infected CD4+ T-cells and mass spectrometric identification of their in vivo protein interactomes. Analysis revealed 212 proteins differentially associated with the unique RNA classes, including preferential association of regulators of RNA stability with US and PS transcripts and, unexpectedly, mitochondria-linked proteins with US transcripts. Remarkably, >80 of these factors screened by siRNA knockdown impacted HIV-1 gene expression. Fluorescence microscopy confirmed several to co-localize with HIV-1 US RNA and exhibit changes in abundance and/or localization over the course of infection. This study validates HyPR-MSSV for discovery of viral splice variant protein interactomes and provides an unprecedented resource of factors and pathways likely important to HIV-1 replication.
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Affiliation(s)
- Rachel Knoener
- Department of Chemistry, University of WisconsinMadisonUnited States
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Edward Evans
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Jordan T Becker
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of WisconsinMadisonUnited States
| | - Bayleigh Benner
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of WisconsinMadisonUnited States
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Application of Advanced Light Microscopy to the Study of HIV and Its Interactions with the Host. Viruses 2021; 13:v13020223. [PMID: 33535486 PMCID: PMC7912744 DOI: 10.3390/v13020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022] Open
Abstract
This review highlights the significant observations of human immunodeficiency virus (HIV) assembly, release and maturation made possible with advanced light microscopy techniques. The advances in technology which now enables these light microscopy measurements are discussed with special emphasis on live imaging approaches including Total Internal Reflection Fluorescence (TIRF), high-resolution light microscopy techniques including PALM and STORM and single molecule measurements, including Fluorescence Resonance Energy Transfer (FRET). The review concludes with a discussion on what new insights and understanding can be expected from these measurements.
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Optical technologies for the detection of viruses like COVID-19: Progress and prospects. Biosens Bioelectron 2021; 178:113004. [PMID: 33497877 PMCID: PMC7832448 DOI: 10.1016/j.bios.2021.113004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.
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Groves NS, Bruns MM, van Engelenburg SB. A Quantitative Live-Cell Superresolution Imaging Framework for Measuring the Mobility of Single Molecules at Sites of Virus Assembly. Pathogens 2020; 9:pathogens9110972. [PMID: 33233482 PMCID: PMC7700196 DOI: 10.3390/pathogens9110972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
The insurgence of superresolution microscopy into the fields of virology and microbiology has begun to enable the mapping of molecular assemblies critical for host–pathogen interfaces that organize on a scale below the resolution limit of the light microscope. It is, however, challenging to completely understand the molecular interactions between host and pathogen from strictly time-invariant observations. Herein, we describe a method using simultaneous dual-color superresolution microscopy to gain both structural and dynamic information about HIV-1 assembly. Specifically, we demonstrate the reconstruction of single virus assembly sites using live-cell photo-activated localization microscopy (PALM) while concurrently assessing the sub-viral mobility of the HIV-1 envelope glycoprotein during interaction with the viral lattice. We propose that our method is broadly applicable to elucidating pathogen and host protein–protein interactions through quantification of the dynamics of these proteins at the nanoscale.
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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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Gupta S, Bendjennat M, Saffarian S. Abrogating ALIX Interactions Results in Stuttering of the ESCRT Machinery. Viruses 2020; 12:v12091032. [PMID: 32948012 PMCID: PMC7551432 DOI: 10.3390/v12091032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT) proteins assemble on budding cellular membranes and catalyze their fission. Using live imaging of HIV virions budding from cells, we followed recruitment of ESCRT proteins ALIX, CHMP4B and VPS4. We report that the ESCRT proteins transiently co-localize with virions after completion of virion assembly for durations of 45 ± 30 s. We show that mutagenizing the YP domain of Gag which is the primary ALIX binding site or depleting ALIX from cells results in multiple recruitments of the full ESCRT machinery on the same virion (referred to as stuttering where the number of recruitments to the same virion >3). The stuttering recruitments are approximately 4 ± 3 min apart and have the same stoichiometry of ESCRTs and same residence time (45 ± 30 s) as the single recruitments in wild type interactions. Our observations suggest a role for ALIX during fission and question the linear model of ESCRT recruitment, suggesting instead a more complex co-assembly model.
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Affiliation(s)
- Shilpa Gupta
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA; (S.G.); (M.B.)
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mourad Bendjennat
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA; (S.G.); (M.B.)
- Radiation Oncology Department, University of Miami, Miami, FL 33136, USA
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Saveez Saffarian
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA; (S.G.); (M.B.)
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- Correspondence:
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Gupta S, Bromley J, Saffarian S. High-speed imaging of ESCRT recruitment and dynamics during HIV virus like particle budding. PLoS One 2020; 15:e0237268. [PMID: 32886660 PMCID: PMC7473513 DOI: 10.1371/journal.pone.0237268] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022] Open
Abstract
Endosomal sorting complexes required for transport proteins (ESCRT) catalyze the fission of cellular membranes during budding of membrane away from the cytosol. Here we have used Total Internal Reflection Fluorescence (TIRF) microscopy to visualize the recruitment of ESCRTs specifically, ALIX, CHMP4b and VPS4 onto the budding HIV Gag virus-like particles (VLPs). We imaged the budding VLPs with 200 millisecond time resolution for 300 frames. Our data shows three phases for ESCRT dynamics: 1) recruitment in which subunits of ALIX, CHMP4b and VPS4 are recruited with constant proportions on the budding sites of HIV Gag virus like particles for nearly 10 seconds, followed by 2) disassembly of ALIX and CHMP4b while VPS4 signal remains constant for nearly 20 seconds followed by 3) disassembly of VPS4. We hypothesized that the disassembly observed in step 2 was catalyzed by VPS4 and powered by ATP hydrolysis. To test this hypothesis, we performed ATP depletion using (-) glucose medium, deoxyglucose and oligomycin. Imaging ATP depleted cells, we show that the disassembly of CHMP4b and ALIX observed in step 2 is ATP dependent. ATP depletion resulted in the recruitment of approximately 2-fold as many subunits of all ESCRTs. Resuming ATP production in cells, resulted in disassembly of the full ESCRT machinery which had been locked in place during ATP depletion. With some caveats, our experiments provide insight into the formation of the ESCRT machinery at the budding site of HIV during budding.
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Affiliation(s)
- Shilpa Gupta
- Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Josh Bromley
- Department of Physics and Astronomy, University of Utah, Salt Lake City, Utah, United States of America
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Department of Physics and Astronomy, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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45
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Bednarska J, Pelchen-Matthews A, Novak P, Burden JJ, Summers PA, Kuimova MK, Korchev Y, Marsh M, Shevchuk A. Rapid formation of human immunodeficiency virus-like particles. Proc Natl Acad Sci U S A 2020; 117:21637-21646. [PMID: 32817566 PMCID: PMC7474690 DOI: 10.1073/pnas.2008156117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular mechanisms involved in the assembly of viruses is essential for discerning how viruses transmit from cell to cell and host to host. Although molecular aspects of assembly have been studied for many viruses, we still have little information about these events in real time. Enveloped viruses such as HIV that assemble at, and bud from, the plasma membrane have been studied in some detail using live cell fluorescence imaging techniques; however, these approaches provide little information about the real-time morphological changes that take place as viral components come together to form individual virus particles. Here we used correlative scanning ion conductance microscopy and fluorescence confocal microscopy to measure the topological changes, together with the recruitment of fluorescently labeled viral proteins such as Gag and Vpr, during the assembly and release of individual HIV virus-like particles (VLPs) from the top, nonadherent surfaces of living cells. We show that 1) labeling of viral proteins with green fluorescent protein affects particle formation, 2) the kinetics of particle assembly on different plasma membrane domains can vary, possibly as a consequence of differences in membrane biophysical properties, and 3) VLPs budding from the top, unimpeded surface of cells can reach full size in 20 s and disappear from the budding site in 0.5 to 3 min from the moment curvature is initially detected, significantly faster than has been previously reported.
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Affiliation(s)
- Joanna Bednarska
- Department of Medicine, Imperial College London, W12 0NN London, United Kingdom
| | - Annegret Pelchen-Matthews
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom
| | - Pavel Novak
- Department of Medicine, Imperial College London, W12 0NN London, United Kingdom
- Functional Low-Dimensional Structures Laboratory, National University of Science and Technology "MISIS", 119991 Moscow, Russian Federation
| | - Jemima J Burden
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom
| | - Peter A Summers
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Marina K Kuimova
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Yuri Korchev
- Department of Medicine, Imperial College London, W12 0NN London, United Kingdom
- Nano Life Science Institute, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom;
| | - Andrew Shevchuk
- Department of Medicine, Imperial College London, W12 0NN London, United Kingdom;
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46
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Boutant E, Bonzi J, Anton H, Nasim MB, Cathagne R, Réal E, Dujardin D, Carl P, Didier P, Paillart JC, Marquet R, Mély Y, de Rocquigny H, Bernacchi S. Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane. Biophys J 2020; 119:419-433. [PMID: 32574557 PMCID: PMC7376094 DOI: 10.1016/j.bpj.2020.05.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 01/16/2023] Open
Abstract
The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol.
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Affiliation(s)
- Emmanuel Boutant
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
| | - Jeremy Bonzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Halina Anton
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Maaz Bin Nasim
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Raphael Cathagne
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Eléonore Réal
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Denis Dujardin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Philippe Carl
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Hugues de Rocquigny
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm - U1259 MAVIVH, Tours, France.
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France.
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Jiang X, Jia X, Sun J, Qi C, Lu L, Wang Y, Zhang L, Wei M. Overexpressed coiled-coil domain containing protein 8 (CCDC8) mediates newly synthesized HIV-1 Gag lysosomal degradation. Sci Rep 2020; 10:11416. [PMID: 32651437 PMCID: PMC7351720 DOI: 10.1038/s41598-020-68341-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/16/2020] [Indexed: 11/09/2022] Open
Abstract
Normally, HIV-1 enters into CD4+ cells through membrane fusion, and newly synthesized HIV-1 viral proteins assemble on the plasma membrane to form viral particles and bud out. In the previous study, we found host factor coiled-coil domain containing protein 8 (CCDC8) can strongly inhibit HIV-1 production, but the underline mechanism is not clear. Here we show that overexpression of CCDC8 reverses the normal HIV-1 production process, and causes newly assembled HIV-1 Gag particles to be endocytosed on the plasma membrane, rather than budding out. Live-cell imaging system captured the moment of CCDC8-mediated Gag internalization on the plasma membrane, and the speed of Gag turnover is up to 1.53 μm/s, much faster than Gag assembly on the plasma membrane. After Gag internalization, it accumulates in the cellular organelle-lysosome for degradation, but not proteasome, autophagosome, endoplasmic reticulum, clathrin or recycling endosome. In addition, CCDC8 is a membrane-associated protein, and N-terminal of CCDC8 is very important for membrane binding, and also important for inhibition of Gag assembly. C-terminal deletion of CCDC8 has a little effect on anti-HIV-1 effect. Moreover, CCDC8 is phosphorylated at amino acid threonine T87 and serine S261, and mono-methylated at lysine K491. Alanine mutations of T87A, S261A and K491A singly or in combination do not affect CCDC8 anti-HIV activity. In conclusion, overexpression of CCDC8 can cause newly assembled HIV-1 Gag particles on the plasma membrane to be endocytosed and degraded in lysosome.
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Affiliation(s)
| | - Xiaopeng Jia
- School of Medicine, Nankai University, Tianjin, China
| | - Jinhuan Sun
- School of Medicine, Nankai University, Tianjin, China
| | - Chunxia Qi
- School of Medicine, Nankai University, Tianjin, China
| | - Lingling Lu
- School of Medicine, Nankai University, Tianjin, China
| | - Yanfeng Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Lei Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Min Wei
- School of Medicine, Nankai University, Tianjin, China. .,Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China.
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48
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Sengupta P, Lippincott-Schwartz J. Revisiting Membrane Microdomains and Phase Separation: A Viral Perspective. Viruses 2020; 12:v12070745. [PMID: 32664429 PMCID: PMC7412473 DOI: 10.3390/v12070745] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Retroviruses selectively incorporate a specific subset of host cell proteins and lipids into their outer membrane when they bud out from the host plasma membrane. This specialized viral membrane composition is critical for both viral survivability and infectivity. Here, we review recent findings from live cell imaging of single virus assembly demonstrating that proteins and lipids sort into the HIV retroviral membrane by a mechanism of lipid-based phase partitioning. The findings showed that multimerizing HIV Gag at the assembly site creates a liquid-ordered lipid phase enriched in cholesterol and sphingolipids. Proteins with affinity for this specialized lipid environment partition into it, resulting in the selective incorporation of proteins into the nascent viral membrane. Building on this and other work in the field, we propose a model describing how HIV Gag induces phase separation of the viral assembly site through a mechanism involving transbilayer coupling of lipid acyl chains and membrane curvature changes. Similar phase-partitioning pathways in response to multimerizing structural proteins likely help sort proteins into the membranes of other budding structures within cells.
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Monette A, Niu M, Chen L, Rao S, Gorelick RJ, Mouland AJ. Pan-retroviral Nucleocapsid-Mediated Phase Separation Regulates Genomic RNA Positioning and Trafficking. Cell Rep 2020; 31:107520. [PMID: 32320662 PMCID: PMC8965748 DOI: 10.1016/j.celrep.2020.03.084] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023] Open
Abstract
The duality of liquid-liquid phase separation (LLPS) of cellular components into membraneless organelles defines the nucleation of both normal and disease processes including stress granule (SG) assembly. From mounting evidence of LLPS utility by viruses, we discover that HIV-1 nucleocapsid (NC) protein condenses into zinc-finger (ZnF)-dependent LLPSs that are dynamically influenced by cytosolic factors. ZnF-dependent and Zinc (Zn2+)-chelation-sensitive NC-LLPS are formed in live cells. NC-Zn2+ ejection reverses the HIV-1 blockade on SG assembly, inhibits NC-SG assembly, disrupts NC/Gag-genomic RNA (vRNA) ribonucleoprotein complexes, and causes nuclear sequestration of NC and the vRNA, inhibiting Gag expression and virus release. NC ZnF mutagenesis eliminates the HIV-1 blockade of SG assembly and repositions vRNA to SGs. We find that NC-mediated, Zn2+-coordinated phase separation is conserved among diverse retrovirus subfamilies, illustrating that this exquisitely evolved Zn2+-dependent feature of virus replication represents a critical target for pan-antiretroviral therapies.
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Affiliation(s)
- Anne Monette
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada.
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Lois Chen
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Biochemistry, Erasmus University Medical Center, Ee634, PO Box 2040, 3000CA Rotterdam, the Netherlands
| | - Robert James Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Andrew John Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montréal, QC H3G 2M1, Canada.
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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