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Biswas B, Lai KK, Bracey H, Datta SAK, Harvin D, Sowd GA, Aiken C, Rein A. Essential functions of inositol hexakisphosphate (IP6) in murine leukemia virus replication. mBio 2024; 15:e0115824. [PMID: 38912776 PMCID: PMC11253606 DOI: 10.1128/mbio.01158-24] [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: 04/18/2024] [Accepted: 05/14/2024] [Indexed: 06/25/2024] Open
Abstract
We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.IMPORTANCEInositol hexakisphosphate (IP6) is crucial for the assembly and replication of HIV-1. IP6 is packaged in HIV-1 particles and stabilizes the viral core enabling it to synthesize viral DNA early in viral infection. While its importance for HIV-1 is well established, its significance for other retroviruses is unknown. Here we report the role of IP6 in the gammaretrovirus, murine leukemia virus (MLV). We found that like HIV-1, MLV packages IP6, and as in HIV-1, IP6 stabilizes the MLV core thus promoting reverse transcription. Interestingly, we discovered a key difference in the role of IP6 in MLV versus HIV-1: while HIV-1 is not dependent upon IP6 levels in target cells, MLV replication is significantly reduced in IP6-deficient cell lines. We suggest that this difference in IP6 requirements reflects key differences between HIV-1 and MLV replication.
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Affiliation(s)
- Banhi Biswas
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Siddhartha A. K. Datta
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Demetria Harvin
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Gregory A. Sowd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
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2
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Arribas L, Menéndez-Arias L, Betancor G. May I Help You with Your Coat? HIV-1 Capsid Uncoating and Reverse Transcription. Int J Mol Sci 2024; 25:7167. [PMID: 39000271 PMCID: PMC11241228 DOI: 10.3390/ijms25137167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid is a protein core formed by multiple copies of the viral capsid (CA) protein. Inside the capsid, HIV-1 harbours all the viral components required for replication, including the genomic RNA and viral enzymes reverse transcriptase (RT) and integrase (IN). Upon infection, the RT transforms the genomic RNA into a double-stranded DNA molecule that is subsequently integrated into the host chromosome by IN. For this to happen, the viral capsid must open and release the viral DNA, in a process known as uncoating. Capsid plays a key role during the initial stages of HIV-1 replication; therefore, its stability is intimately related to infection efficiency, and untimely uncoating results in reverse transcription defects. How and where uncoating takes place and its relationship with reverse transcription is not fully understood, but the recent development of novel biochemical and cellular approaches has provided unprecedented detail on these processes. In this review, we present the latest findings on the intricate link between capsid stability, reverse transcription and uncoating, the different models proposed over the years for capsid uncoating, and the role played by other cellular factors on these processes.
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Affiliation(s)
- Laura Arribas
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain;
| | - Gilberto Betancor
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
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3
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Padron A, Dwivedi R, Chakraborty R, Prakash P, Kim K, Shi J, Ahn J, Pandhare J, Luban J, Aiken C, Balasubramaniam M, Dash C. Cyclophilin A Facilitates HIV-1 DNA Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599180. [PMID: 38948800 PMCID: PMC11212919 DOI: 10.1101/2024.06.15.599180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cyclophilin A (CypA) promotes HIV-1 infection by facilitating reverse transcription, nuclear entry and by countering the antiviral activity of TRIM5α. These multifunctional roles of CypA are driven by its binding to the viral capsid. Interestingly, recent studies suggest that the HIV-1 capsid lattice enters the nucleus of an infected cell and uncoats just before integration. Therefore, we tested whether CypA-capsid interaction regulates post-nuclear entry steps of infection, particularly integration. First, we challenged CypA-expressing (CypA +/+ ) and CypA-depleted (CypA -/- ) cells with HIV-1 particles and quantified the resulting levels of provirus. Surprisingly, CypA-depletion significantly reduced integration, an effect that was independent of CypA's effect on reverse transcription, nuclear entry, and the presence or absence of TRIM5α. Additionally, cyclosporin A, an inhibitor that disrupts CypA-capsid binding, inhibited HIV-1 integration in CypA +/+ cells but not in CypA -/- cells. Accordingly, HIV-1 capsid mutants (G89V and P90A) deficient in CypA binding were also blocked at integration in CypA +/+ cells but not in CypA -/- cells. Then, to understand the mechanism, we assessed the integration activity of HIV-1 preintegration complexes (PICs) extracted from infected cells. The PICs from CypA -/- cells had lower activity in vitro compared to those from CypA +/+ cells. PICs from cells depleted for CypA and TRIM5α also had lower activity, suggesting that CypA's effect on PIC activity is independent of TRIM5α. Finally, addition of CypA protein significantly stimulated the integration activity of PICs extracted from both CypA +/+ and CypA -/- cells. Collectively, these results suggest that CypA promotes HIV-1 integration, a previously unknown role of this host factor. Importance HIV-1 capsid interaction with host cellular factors is essential for establishing a productive infection. However, the molecular details of such virus-host interactions are not fully understood. Cyclophilin A (CypA) is the first host protein identified to specifically bind to the HIV-1 capsid. Now it is established that CypA promotes reverse transcription and nuclear entry steps of HIV-1 infection. In this report, we show that CypA promotes HIV-1 integration by binding to the viral capsid. Specifically, our results demonstrate that CypA promotes HIV-1 integration by stimulating the activity of the viral preintegration complex and identifies a novel role of CypA during HIV-1 infection. This new knowledge is important because recent reports suggest that an operationally intact HIV-1 capsid enters the nucleus of an infected cell.
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4
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Sumner RP, Blest H, Lin M, Maluquer de Motes C, Towers GJ. HIV-1 with gag processing defects activates cGAS sensing. Retrovirology 2024; 21:10. [PMID: 38778414 PMCID: PMC11112816 DOI: 10.1186/s12977-024-00643-0] [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: 04/08/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Detection of viruses by host pattern recognition receptors induces the expression of type I interferon (IFN) and IFN-stimulated genes (ISGs), which suppress viral replication. Numerous studies have described HIV-1 as a poor activator of innate immunity in vitro. The exact role that the viral capsid plays in this immune evasion is not fully understood. RESULTS To better understand the role of the HIV-1 capsid in sensing we tested the effect of making HIV-1 by co-expressing a truncated Gag that encodes the first 107 amino acids of capsid fused with luciferase or GFP, alongside wild type Gag-pol. We found that unlike wild type HIV-1, viral particles produced with a mixture of wild type and truncated Gag fused to luciferase or GFP induced a potent IFN response in THP-1 cells and macrophages. Innate immune activation by Gag-fusion HIV-1 was dependent on reverse transcription and DNA sensor cGAS, suggesting activation of an IFN response by viral DNA. Further investigation revealed incorporation of the Gag-luciferase/GFP fusion proteins into viral particles that correlated with subtle defects in wild type Gag cleavage and a diminished capacity to saturate restriction factor TRIM5α, likely due to aberrant particle formation. We propose that expression of the Gag fusion protein disturbs the correct cleavage and maturation of wild type Gag, yielding viral particles that are unable to effectively shield viral DNA from detection by innate sensors including cGAS. CONCLUSIONS These data highlight the crucial role of capsid in innate evasion and support growing literature that disruption of Gag cleavage and capsid formation induces a viral DNA- and cGAS-dependent innate immune response. Together these data demonstrate a protective role for capsid and suggest that antiviral activity of capsid-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.
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Affiliation(s)
- Rebecca P Sumner
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK.
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Henry Blest
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Meiyin Lin
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | | | - Greg J Towers
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
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Scott TM, Arnold LM, Powers JA, McCann DA, Christensen DE, Pereira MJ, Zhou W, Torrez RM, Iwasa JH, Kranzusch PJ, Sundquist WI, Johnson JS. Cell-free assays reveal the HIV-1 capsid protects reverse transcripts from cGAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590513. [PMID: 38712059 PMCID: PMC11071359 DOI: 10.1101/2024.04.22.590513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response. However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect their genomes from cGAS even after completion of reverse transcription. Viral DNA could be "deprotected" by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, capsid inhibitors also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
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Affiliation(s)
- Tiana M. Scott
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Lydia M. Arnold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jordan A. Powers
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Delaney A. McCann
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Devin E. Christensen
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Miguel J. Pereira
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology; Shenzhen, Guangdong 518055, China
| | - Rachel M. Torrez
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Janet H. Iwasa
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School; Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute; Boston, MA 02115, USA
| | - Wesley I. Sundquist
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jarrod S. Johnson
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
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6
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Eschbach JE, Puray-Chavez M, Mohammed S, Wang Q, Xia M, Huang LC, Shan L, Kutluay SB. HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products via the cGAS-STING pathway. mBio 2024; 15:e0034824. [PMID: 38530034 PMCID: PMC11077976 DOI: 10.1128/mbio.00348-24] [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: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune sensing of HIV-1, a direct link between core stability and sensing of HIV-1 nucleic acids has not been established. Herein, we assessed how manipulating the stability of the CA lattice through chemical and genetic approaches affects innate immune recognition of HIV-1. We found that destabilization of the CA lattice resulted in potent sensing of reverse transcription products when destabilization per se does not completely block reverse transcription. Surprisingly, due to the combined effects of enhanced reverse transcription and defects in nuclear entry, two separate CA mutants that form hyperstable cores induced innate immune sensing more potently than destabilizing CA mutations. At low concentrations that allowed the accumulation of reverse transcription products, CA-targeting compounds GS-CA1 and lenacapavir measurably impacted CA lattice stability in cells and modestly enhanced innate immune sensing of HIV. Interestingly, innate immune activation observed with viruses containing unstable cores was abolished by low doses of lenacapavir. Innate immune activation observed with both hyperstable and unstable CA mutants was dependent on the cGAS-STING DNA-sensing pathway and reverse transcription. Overall, our findings demonstrate that CA lattice stability and reverse transcription are finely balanced to support reverse transcription and minimize cGAS-STING-mediated sensing of the resulting viral DNA. IMPORTANCE In HIV-1 particles, the dimeric RNA genome and associated viral proteins and enzymes are encased in a proteinaceous lattice composed of the viral capsid protein. Herein, we assessed how altering the stability of this capsid lattice through orthogonal genetic and chemical approaches impacts the induction of innate immune responses. Specifically, we found that decreasing capsid lattice stability results in more potent sensing of viral reverse transcription products, but not the genomic RNA, in a cGAS-STING-dependent manner. The recently developed capsid inhibitors lenacapavir and GS-CA1 enhanced the innate immune sensing of HIV-1. Unexpectedly, due to increased levels of reverse transcription and cytosolic accumulation of the resulting viral cDNA, capsid mutants with hyperstable cores also resulted in the potent induction of type I interferon-mediated innate immunity. Our findings suggest that HIV-1 capsid lattice stability and reverse transcription are finely balanced to minimize exposure of reverse transcription products in the cytosol of host cells.
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Affiliation(s)
- Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ming Xia
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lin-Chen Huang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
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7
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Kizito F, Nguyen K, Mbonye U, Shukla M, Luttge B, Checkley MA, Agaponova A, Leskov K, Karn J. Structural rearrangements in the nucleus localize latent HIV proviruses to a perinucleolar compartment supportive of reactivation. Proc Natl Acad Sci U S A 2024; 121:e2202003121. [PMID: 38669184 PMCID: PMC11067448 DOI: 10.1073/pnas.2202003121] [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: 02/03/2022] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
Using an immunofluorescence assay based on CRISPR-dCas9-gRNA complexes that selectively bind to the HIV LTR (HIV Cas-FISH), we traced changes in HIV DNA localization in primary effector T cells from early infection until the cells become quiescent as they transition to memory cells. Unintegrated HIV DNA colocalized with CPSF6 and HIV capsid (CA, p24) was found in the cytoplasm and nuclear periphery at days 1 and 3 post infection. From days 3 to 7, most HIV DNA was distributed primarily in the nuclear intermediate euchromatic compartment and was transcribed. By day 21, the cells had entered quiescence, and HIV DNA accumulated in the perinucleolar compartment (PNC). The localization of proviruses to the PNC was blocked by integrase inhibitor Raltegravir, suggesting it was due to chromosomal rearrangements. During the reactivation of latently infected cells through the T cell receptor (TCR), nascent viral mRNA transcripts associated with HIV DNA in the PNC were detected. The viral trans-activator Tat and its regulatory partners, P-TEFb and 7SK snRNA, assembled in large interchromatin granule clusters near the provirus within 2 h of TCR activation. As T cell activation progressed, the HIV DNA shifted away from the PNC. HIV DNA in latently infected memory T cells from patients also accumulated in the PNC and showed identical patterns of nuclear rearrangements after cellular reactivation. Thus, in contrast to transformed cells where proviruses are found primarily at the nuclear periphery, in primary memory T cells, the nuclear architecture undergoes rearrangements that shape the transcriptional silencing and reactivation of proviral HIV.
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Affiliation(s)
- Fredrick Kizito
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Uri Mbonye
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Meenakshi Shukla
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Benjamin Luttge
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Mary Ann Checkley
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Anna Agaponova
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Konstantin Leskov
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH44106
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8
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Burdick RC, Morse M, Rouzina I, Williams MC, Hu WS, Pathak VK. HIV-1 uncoating requires long double-stranded reverse transcription products. SCIENCE ADVANCES 2024; 10:eadn7033. [PMID: 38657061 PMCID: PMC11042746 DOI: 10.1126/sciadv.adn7033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.
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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, 21702, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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9
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Guedán A, Burley M, Caroe ER, Bishop KN. HIV-1 Capsid Rapidly Induces Long-Lived CPSF6 Puncta in Non-Dividing Cells, but Similar Puncta Already Exist in Uninfected T-Cells. Viruses 2024; 16:670. [PMID: 38793552 PMCID: PMC11125723 DOI: 10.3390/v16050670] [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: 01/30/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
The HIV-1 capsid (CA) protein forms the outer shell of the viral core that is released into the cytoplasm upon infection. CA binds various cellular proteins, including CPSF6, that direct HIV-1 integration into speckle-associated domains in host chromatin. Upon HIV-1 infection, CPSF6 forms puncta in the nucleus. Here, we characterised these CPSF6 puncta further in HeLa cells, T-cells and macrophages and confirmed that integration and reverse transcription are not required for puncta formation. Indeed, we found that puncta formed very rapidly after infection, correlating with the time that CA entered the nucleus. In aphidicolin-treated HeLa cells and macrophages, puncta were detected for the length of the experiment, suggesting that puncta are only lost upon cell division. CA still co-localised with CPSF6 puncta at the latest time points, considerably after the peak of reverse transcription and integration. Intriguingly, the number of puncta induced in macrophages did not correlate with the MOI or the total number of nuclear speckles present in each cell, suggesting that CA/CPSF6 is only directed to a few nuclear speckles. Furthermore, we found that CPSF6 already co-localised with nuclear speckles in uninfected T-cells, suggesting that HIV-1 promotes a natural behaviour of CPSF6.
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Affiliation(s)
| | | | | | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK; (A.G.); (M.B.); (E.R.C.)
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10
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Ingram Z, Kline C, Hughson AK, Singh PK, Fischer HL, Sowd GA, Watkins SC, Kane M, Engelman AN, Ambrose Z. Spatiotemporal binding of cyclophilin A and CPSF6 to capsid regulates HIV-1 nuclear entry and integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588584. [PMID: 38645162 PMCID: PMC11030324 DOI: 10.1101/2024.04.08.588584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Human immunodeficiency virus type 1 (HIV-1) capsid, which is the target of the antiviral lenacapavir, protects the viral genome and binds multiple host proteins to influence intracellular trafficking, nuclear import, and integration. Previously, we showed that capsid binding to cleavage and polyadenylation specificity factor 6 (CPSF6) in the cytoplasm is competitively inhibited by cyclophilin A (CypA) binding and regulates capsid trafficking, nuclear import, and infection. Here we determined that a capsid mutant with increased CypA binding affinity had significantly reduced nuclear entry and mislocalized integration. However, disruption of CypA binding to the mutant capsid restored nuclear entry, integration, and infection in a CPSF6-dependent manner. Furthermore, relocalization of CypA expression from the cell cytoplasm to the nucleus failed to restore mutant HIV-1 infection. Our results clarify that sequential binding of CypA and CPSF6 to HIV-1 capsid is required for optimal nuclear entry and integration targeting, informing antiretroviral therapies that contain lenacapavir.
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Affiliation(s)
- Zachary Ingram
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Christopher Kline
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alexandra K. Hughson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - Parmit K. Singh
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Hannah L. Fischer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Gregory A. Sowd
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Simon C. Watkins
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Melissa Kane
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alan N. Engelman
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA
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11
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Ananth S, Ambiel I, Schifferdecker S, Müller TG, Wratil PR, Mejias-Perez E, Kräusslich HG, Müller B, Keppler OT, Fackler OT. Spatial resolution of HIV-1 post-entry steps in resting CD4 T cells. Cell Rep 2024; 43:113941. [PMID: 38478523 DOI: 10.1016/j.celrep.2024.113941] [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: 08/11/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Resting CD4 T cells resist productive HIV-1 infection. The HIV-2/simian immunodeficiency virus protein viral accessory protein X (Vpx) renders these cells permissive to infection, presumably by alleviating blocks at cytoplasmic reverse transcription and subsequent nuclear import of reverse-transcription/pre-integration complexes (RTC/PICs). Here, spatial analyses using quantitative virus imaging techniques reveal that HIV-1 capsids containing RTC/PICs are readily imported into the nucleus, recruit the host dependency factor CPSF6, and translocate to nuclear speckles in resting CD4 T cells. Reverse transcription, however, remains incomplete, impeding proviral integration and viral gene expression. Vpx or pharmacological inhibition of the deoxynucleotide triphosphohydrolase (dNTPase) activity of the restriction factor SAM domain and HD domain-containing protein 1 (SAMHD1) increases levels of nuclear reverse-transcribed cDNA and facilitates HIV-1 integration. Nuclear import and intranuclear transport of viral complexes therefore do not pose important blocks to HIV-1 in resting CD4 T cells, and the limitation to reverse transcription by SAMHD1's dNTPase activity constitutes the main pre-integration block to infection.
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Affiliation(s)
- Swetha Ananth
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Ina Ambiel
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Sandra Schifferdecker
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Thorsten G Müller
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Ernesto Mejias-Perez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Hans-Georg Kräusslich
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site München, Munich, Germany
| | - Oliver T Fackler
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Integrative Virology, Center of Integrative Infectious Disease Research (CIID), Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
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12
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Sever B, Otsuka M, Fujita M, Ciftci H. A Review of FDA-Approved Anti-HIV-1 Drugs, Anti-Gag Compounds, and Potential Strategies for HIV-1 Eradication. Int J Mol Sci 2024; 25:3659. [PMID: 38612471 PMCID: PMC11012182 DOI: 10.3390/ijms25073659] [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: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is an enormous global health threat stemming from human immunodeficiency virus (HIV-1) infection. Up to now, the tremendous advances in combination antiretroviral therapy (cART) have shifted HIV-1 infection from a fatal illness into a manageable chronic disorder. However, the presence of latent reservoirs, the multifaceted nature of HIV-1, drug resistance, severe off-target effects, poor adherence, and high cost restrict the efficacy of current cART targeting the distinct stages of the virus life cycle. Therefore, there is an unmet need for the discovery of new therapeutics that not only bypass the limitations of the current therapy but also protect the body's health at the same time. The main goal for complete HIV-1 eradication is purging latently infected cells from patients' bodies. A potential strategy called "lock-in and apoptosis" targets the budding phase of the life cycle of the virus and leads to susceptibility to apoptosis of HIV-1 infected cells for the elimination of HIV-1 reservoirs and, ultimately, for complete eradication. The current work intends to present the main advantages and disadvantages of United States Food and Drug Administration (FDA)-approved anti-HIV-1 drugs as well as plausible strategies for the design and development of more anti-HIV-1 compounds with better potency, favorable pharmacokinetic profiles, and improved safety issues.
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Affiliation(s)
- Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Türkiye;
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Halilibrahim Ciftci
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
- Department of Bioengineering Sciences, Izmir Katip Celebi University, Izmir 35620, Türkiye
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13
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Siew ZY, Asudas E, Khoo CT, Cho GH, Voon K, Fang CM. Fighting nature with nature: antiviral compounds that target retroviruses. Arch Microbiol 2024; 206:130. [PMID: 38416180 DOI: 10.1007/s00203-024-03846-3] [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: 11/16/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/29/2024]
Abstract
The human immunodeficiency virus (HIV) is a type of lentivirus that targets the human immune system and leads to acquired immunodeficiency syndrome (AIDS) at a later stage. Up to 2021, there are millions still living with HIV and many have lost their lives. To date, many anti-HIV compounds have been discovered in living organisms, especially plants and marine sponges. However, no treatment can offer a complete cure, but only suppressing it with a life-long medication, known as combined antiretroviral therapy (cART) or highly active antiretroviral therapy (HAART) which are often associated with various adverse effects. Also, it takes many years for a discovered compound to be approved for clinical use. Thus, by employing advanced technologies such as automation, conducting systematic screening and testing protocols may boost the discovery and development of potent and curative therapeutics for HIV infection/AIDS. In this review, we aim to summarize the antiretroviral therapies/compounds and their associated drawbacks since the discovery of azidothymidine. Additionally, we aim to provide an updated analysis of the most recent discoveries of promising antiretroviral candidates, along with an exploration of the current limitations within antiretroviral research. Finally, we intend to glean insightful perspectives and propose future research directions in this crucial area of study.
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Affiliation(s)
- Zhen Yun Siew
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
| | - Elishea Asudas
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chia Ting Khoo
- School of Biosciences, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Gang Hyeon Cho
- School of Pharmacy, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Kenny Voon
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chee-Mun Fang
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
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14
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Biswas B, Lai KK, Bracey H, Datta SA, Harvin D, Sowd GA, Aiken C, Rein A. Essential functions of Inositol hexakisphosphate (IP6) in Murine Leukemia Virus replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.581940. [PMID: 38464197 PMCID: PMC10925174 DOI: 10.1101/2024.02.27.581940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.
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Affiliation(s)
- Banhi Biswas
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Siddhartha A.K. Datta
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Demetria Harvin
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Gregory A. Sowd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
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15
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Faysal KMR, Walsh JC, Renner N, Márquez CL, Shah VB, Tuckwell AJ, Christie MP, Parker MW, Turville SG, Towers GJ, James LC, Jacques DA, Böcking T. Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure. eLife 2024; 13:e83605. [PMID: 38347802 PMCID: PMC10863983 DOI: 10.7554/elife.83605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
The HIV-1 capsid has emerged as a tractable target for antiretroviral therapy. Lenacapavir, developed by Gilead Sciences, is the first capsid-targeting drug approved for medical use. Here, we investigate the effect of lenacapavir on HIV capsid stability and uncoating. We employ a single particle approach that simultaneously measures capsid content release and lattice persistence. We demonstrate that lenacapavir's potent antiviral activity is predominantly due to lethal hyperstabilisation of the capsid lattice and resultant loss of compartmentalisation. This study highlights that disrupting capsid metastability is a powerful strategy for the development of novel antivirals.
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Affiliation(s)
- KM Rifat Faysal
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Nadine Renner
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Chantal L Márquez
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Vaibhav B Shah
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Andrew J Tuckwell
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Michelle P Christie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
| | - Michael W Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
- Structural Biology Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | | | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Leo C James
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
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16
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Dickson CF, Hertel S, Tuckwell AJ, Li N, Ruan J, Al-Izzi SC, Ariotti N, Sierecki E, Gambin Y, Morris RG, Towers GJ, Böcking T, Jacques DA. The HIV capsid mimics karyopherin engagement of FG-nucleoporins. Nature 2024; 626:836-842. [PMID: 38267582 PMCID: PMC10881392 DOI: 10.1038/s41586-023-06969-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024]
Abstract
HIV can infect non-dividing cells because the viral capsid can overcome the selective barrier of the nuclear pore complex and deliver the genome directly into the nucleus1,2. Remarkably, the intact HIV capsid is more than 1,000 times larger than the size limit prescribed by the diffusion barrier of the nuclear pore3. This barrier in the central channel of the nuclear pore is composed of intrinsically disordered nucleoporin domains enriched in phenylalanine-glycine (FG) dipeptides. Through multivalent FG interactions, cellular karyopherins and their bound cargoes solubilize in this phase to drive nucleocytoplasmic transport4. By performing an in vitro dissection of the nuclear pore complex, we show that a pocket on the surface of the HIV capsid similarly interacts with FG motifs from multiple nucleoporins and that this interaction licences capsids to penetrate FG-nucleoporin condensates. This karyopherin mimicry model addresses a key conceptual challenge for the role of the HIV capsid in nuclear entry and offers an explanation as to how an exogenous entity much larger than any known cellular cargo may be able to non-destructively breach the nuclear envelope.
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Affiliation(s)
- C F Dickson
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - S Hertel
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - A J Tuckwell
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - N Li
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - J Ruan
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - S C Al-Izzi
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - N Ariotti
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - E Sierecki
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Y Gambin
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - R G Morris
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - G J Towers
- Infection and Immunity, University College London, London, UK
| | - T Böcking
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - D A Jacques
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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17
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Gifford LB, Melikyan GB. HIV-1 Capsid Uncoating Is a Multistep Process That Proceeds through Defect Formation Followed by Disassembly of the Capsid Lattice. ACS NANO 2024; 18:2928-2947. [PMID: 38241476 PMCID: PMC10832047 DOI: 10.1021/acsnano.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
The HIV-1 core consists of a cone-shaped capsid shell made of capsid protein (CA) hexamers and pentamers encapsulating the viral genome. HIV-1 capsid disassembly, referred to as uncoating, is important for productive infection; however, the location, timing, and regulation of uncoating remain controversial. Here, we employ amber codon suppression to directly label CA. In addition, a fluid phase fluorescent probe is incorporated into the viral core to detect small defects in the capsid lattice. This double-labeling strategy enables the visualization of uncoating of single cores in vitro and in living cells, which we found to always proceed through at least two distinct steps─the formation of a defect in the capsid lattice that initiates gradual loss of CA below a detectable level. Importantly, intact cores containing the fluid phase and CA fluorescent markers enter and uncoat in the nucleus, as evidenced by a sequential loss of both markers, prior to establishing productive infection. This two-step uncoating process is observed in different cells, including a macrophage line. Notably, the lag between the release of fluid phase marker and terminal loss of CA appears to be independent of the cell type or reverse transcription and is much longer (>5-fold) for nuclear capsids compared to cell-free cores or cores in the cytosol, suggesting that the capsid lattice is stabilized by capsid-binding nuclear factors. Our results imply that intact HIV-1 cores enter the cell nucleus and that uncoating is initiated through a localized defect in the capsid lattice prior to a global loss of CA.
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Affiliation(s)
- Levi B. Gifford
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Gregory B. Melikyan
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
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18
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Hudait A, Voth GA. HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex. Proc Natl Acad Sci U S A 2024; 121:e2313737121. [PMID: 38241438 PMCID: PMC10823262 DOI: 10.1073/pnas.2313737121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024] Open
Abstract
Nuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). Notably, the central channel of the NPC appears to often accommodate and allow passage of intact HIV-1 capsid, though mechanistic details of the process remain to be fully understood. Here, we investigate the molecular interactions that operate in concert between the HIV-1 capsid and the NPC that regulate capsid translocation through the central channel. To this end, we develop a "bottom-up" coarse-grained (CG) model of the human NPC from recently released cryo-electron tomography structure and then construct composite membrane-embedded CG NPC models. We find that successful translocation from the cytoplasmic side to the NPC central channel is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel from the cytoplasmic side. The translocation dynamics is driven by maximizing the contacts between phenylalanine-glycine nucleoporins at the central channel and the capsid. For the docked intact capsids, structural analysis reveals correlated striated patterns of lattice disorder likely related to the intrinsic capsid elasticity. Uncondensed genomic material inside the docked capsid augments the overall lattice disorder of the capsid. Our results suggest that the intrinsic "elasticity" can also aid the capsid to adapt to the stress and remain structurally intact during translocation.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
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19
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Dwivedi R, Prakash P, Kumbhar BV, Balasubramaniam M, Dash C. HIV-1 capsid and viral DNA integration. mBio 2024; 15:e0021222. [PMID: 38085100 PMCID: PMC10790781 DOI: 10.1128/mbio.00212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE HIV-1 capsid protein (CA)-independently or by recruiting host factors-mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA's known roles, as well as probing of CA's novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA's multifunctional role in HIV-1 replication-with a special emphasis on CA's newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.
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Affiliation(s)
- Richa Dwivedi
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
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20
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Köppke J, Keller LE, Stuck M, Arnow ND, Bannert N, Doellinger J, Cingöz O. Direct translation of incoming retroviral genomes. Nat Commun 2024; 15:299. [PMID: 38182622 PMCID: PMC10770327 DOI: 10.1038/s41467-023-44501-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
Viruses that carry a positive-sense, single-stranded (+ssRNA) RNA translate their genomes soon after entering the host cell to produce viral proteins, with the exception of retroviruses. A distinguishing feature of retroviruses is reverse transcription, where the +ssRNA genome serves as a template to synthesize a double-stranded DNA copy that subsequently integrates into the host genome. As retroviral RNAs are produced by the host cell transcriptional machinery and are largely indistinguishable from cellular mRNAs, we investigated the potential of incoming retroviral genomes to directly express proteins. Here we show through multiple, complementary methods that retroviral genomes are translated after entry. Our findings challenge the notion that retroviruses require reverse transcription to produce viral proteins. Synthesis of retroviral proteins in the absence of productive infection has significant implications for basic retrovirology, immune responses and gene therapy applications.
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Affiliation(s)
- Julia Köppke
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Luise-Elektra Keller
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
- Institute of Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
| | - Michelle Stuck
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
- Department of Chemistry, Heidelberg University, Heidelberg, Germany
| | - Nicolas D Arnow
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Norbert Bannert
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Joerg Doellinger
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Oya Cingöz
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany.
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21
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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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22
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Twarock R, Towers GJ, Stockley PG. Molecular frustration: a hypothesis for regulation of viral infections. Trends Microbiol 2024; 32:17-26. [PMID: 37507296 DOI: 10.1016/j.tim.2023.07.003] [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: 11/30/2022] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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23
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Salas-Briceno K, Zhao W, Ross SR. Murine leukemia virus infection of non-dividing dendritic cells is dependent on nucleoporins. PLoS Pathog 2024; 20:e1011640. [PMID: 38215165 PMCID: PMC10810426 DOI: 10.1371/journal.ppat.1011640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/25/2024] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
Retroviral reverse transcription starts within the capsid and uncoating and reverse transcription are mutually dependent. There is still debate regarding the timing and cellular location of HIV's uncoating and reverse transcription and whether it occurs solely in the cytoplasm, nucleus or both. HIV can infect non-dividing cells because there is active transport of the preintegration complex (PIC) across the nuclear membrane, but Murine Leukemia Virus (MLV) is thought to depend on cell division for replication and whether MLV uncoating and reverse transcription is solely cytoplasmic has not been studied. Here, we used NIH3T3 and primary mouse dendritic cells to determine where the different stages of reverse transcription occur and whether cell division is needed for nuclear entry. Our data strongly suggest that in both NIH3T3 cells and dendritic cells (DCs), the initial step of reverse transcription occurs in the cytoplasm. However, we detected MLV RNA/DNA hybrid intermediates in the nucleus of dividing NIH3T3 cells and non-dividing DCs, suggesting that reverse transcription can continue after nuclear entry. We also confirmed that the MLV PIC requires cell division to enter the nucleus of NIH3T3 cells. In contrast, we show that MLV can infect non-dividing primary DCs, although integration of MLV DNA in DCs still required the viral p12 protein. Knockdown of several nuclear pore proteins dramatically reduced the appearance of integrated MLV DNA in DCs but not NIH3T3 cells. Additionally, MLV capsid associated with the nuclear pore proteins NUP358 and NUP62 during infection. These findings suggest that simple retroviruses, like the complex retrovirus HIV, gain nuclear entry by traversing the nuclear pore complex in non-mitotic cells.
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Affiliation(s)
- Karen Salas-Briceno
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, United States of America
| | - Wenming Zhao
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, United States of America
| | - Susan R. Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, United States of America
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24
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Jang S, Engelman AN. Capsid-host interactions for HIV-1 ingress. Microbiol Mol Biol Rev 2023; 87:e0004822. [PMID: 37750702 PMCID: PMC10732038 DOI: 10.1128/mmbr.00048-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.
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Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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25
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Badieyan S, Lichon D, Andreas MP, Gillies JP, Peng W, Shi J, DeSantis ME, Aiken CR, Böcking T, Giessen TW, Campbell EM, Cianfrocco MA. HIV-1 binds dynein directly to hijack microtubule transport machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555335. [PMID: 37693451 PMCID: PMC10491134 DOI: 10.1101/2023.08.29.555335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein's tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically 'hijacks' the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
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Affiliation(s)
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael P Andreas
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Christopher R Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tobias W Giessen
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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26
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Ten Eyck A, Chen YC, Gifford L, Torres-Rivera D, Dyer EL, Melikyan GB. Label-free imaging of nuclear membrane for analysis of nuclear import of viral complexes. J Virol Methods 2023; 322:114834. [PMID: 37875225 PMCID: PMC10841631 DOI: 10.1016/j.jviromet.2023.114834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
HIV-1 enters the nucleus of non-dividing cells through the nuclear pore complex where it integrates into the host genome. The mechanism of HIV-1 nuclear import remains poorly understood. A powerful means to investigate the docking of HIV-1 at the nuclear pore and nuclear import of viral complexes is through single virus tracking in live cells. This approach necessitates fluorescence labeling of HIV-1 particles and the nuclear envelope, which may be challenging, especially in the context of primary cells. Here, we leveraged a deep neural network model for label-free visualization of the nuclear envelope using transmitted light microscopy. A training image set of cells with fluorescently labeled nuclear Lamin B1 (ground truth), along with the corresponding transmitted light images, was acquired and used to train our model to predict the morphology of the nuclear envelope in fixed cells. This protocol yielded accurate predictions of the nuclear membrane and was used in conjunction with virus infection to examine the nuclear entry of fluorescently labeled HIV-1 complexes. Analyses of HIV-1 nuclear import as a function of virus input yielded identical numbers of fluorescent viral complexes per nucleus using the ground truth and predicted nuclear membrane images. We also demonstrate the utility of predicting the nuclear envelope based on transmitted light images for multicolor fluorescence microscopy of infected cells. Importantly, we show that our model can be adapted to predict the nuclear membrane of live cells imaged at 37 °C, making this approach compatible with single virus tracking. Collectively, these findings demonstrate the utility of deep learning approaches for label-free imaging of cellular structures during early stages of virus infection.
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Affiliation(s)
- Andrew Ten Eyck
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA
| | - Yen-Cheng Chen
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Levi Gifford
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Graduate Division of Biological and Biomedical Sciences, Biochemistry, Cell and Developmental Biology Program, Emory University, Atlanta, GA, USA
| | - Dariana Torres-Rivera
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Graduate Division of Biological and Biomedical Sciences, Biochemistry, Cell and Developmental Biology Program, Emory University, Atlanta, GA, USA
| | - Eva L Dyer
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA; Department of Electrical & Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gregory B Melikyan
- Department of Biomedical Engineering, Georgia Institute of Technology-Emory School of Medicine, Atlanta, GA, USA; Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, GA, USA; Children's Healthcare of Atlanta, GA, USA.
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27
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Padron A, Prakash P, Pandhare J, Luban J, Aiken C, Balasubramaniam M, Dash C. Emerging role of cyclophilin A in HIV-1 infection: from producer cell to the target cell nucleus. J Virol 2023; 97:e0073223. [PMID: 37843371 PMCID: PMC10688351 DOI: 10.1128/jvi.00732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The HIV-1 genome encodes a small number of proteins with structural, enzymatic, regulatory, and accessory functions. These viral proteins interact with a number of host factors to promote the early and late stages of HIV-1 infection. During the early stages of infection, interactions between the viral proteins and host factors enable HIV-1 to enter the target cell, traverse the cytosol, dock at the nuclear pore, gain access to the nucleus, and integrate into the host genome. Similarly, the viral proteins recruit another set of host factors during the late stages of infection to orchestrate HIV-1 transcription, translation, assembly, and release of progeny virions. Among the host factors implicated in HIV-1 infection, Cyclophilin A (CypA) was identified as the first host factor to be packaged within HIV-1 particles. It is now well established that CypA promotes HIV-1 infection by directly binding to the viral capsid. Mechanistic models to pinpoint CypA's role have spanned from an effect in the producer cell to the early steps of infection in the target cell. In this review, we will describe our understanding of the role(s) of CypA in HIV-1 infection, highlight the current knowledge gaps, and discuss the potential role of this host factor in the post-nuclear entry steps of HIV-1 infection.
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Affiliation(s)
- Adrian Padron
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Jeremy Luban
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chris Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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28
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Deshpande A, Bryer AJ, Andino J, Shi J, Hong J, Torres C, Harel S, Francis AC, Perilla JR, Aiken C, Rousso I. Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560083. [PMID: 37808653 PMCID: PMC10557754 DOI: 10.1101/2023.09.29.560083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
HIV-1 infection requires passage of the viral core through the nuclear pore of the cell, a process that depends on functions of the viral capsid 1,2 . Recent studies have shown that HIV- 1 cores enter the nucleus prior to capsid disassembly 3-5 . Interactions with the nuclear pore complex are necessary but not sufficient for nuclear entry, and the mechanism by which the viral core traverses the comparably sized nuclear pore is unknown. Here we show that the HIV-1 core is highly elastic and that this property is linked to nuclear entry and infectivity. Using atomic force microscopy-based approaches, we found that purified wild type cores rapidly returned to their normal conical morphology following a severe compression. Results from independently performed molecular dynamic simulations of the mature HIV-1 capsid also revealed its elastic property. Analysis of four HIV-1 capsid mutants that exhibit impaired nuclear entry revealed that the mutant viral cores are brittle. Suppressors of the mutants restored elasticity and rescued infectivity and nuclear entry. Elasticity was also reduced by treatment of cores with the capsid-targeting compound PF74 and the antiviral drug lenacapavir. Our results indicate that capsid elasticity is a fundamental property of the HIV-1 core that enables its passage through the nuclear pore complex, thereby facilitating infection. These results provide new insights into the mechanisms of HIV-1 nuclear entry and the antiviral mechanisms of HIV-1 capsid inhibitors.
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29
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Cabrera-Rodríguez R, Pérez-Yanes S, Lorenzo-Sánchez I, Trujillo-González R, Estévez-Herrera J, García-Luis J, Valenzuela-Fernández A. HIV Infection: Shaping the Complex, Dynamic, and Interconnected Network of the Cytoskeleton. Int J Mol Sci 2023; 24:13104. [PMID: 37685911 PMCID: PMC10487602 DOI: 10.3390/ijms241713104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
HIV-1 has evolved a plethora of strategies to overcome the cytoskeletal barrier (i.e., actin and intermediate filaments (AFs and IFs) and microtubules (MTs)) to achieve the viral cycle. HIV-1 modifies cytoskeletal organization and dynamics by acting on associated adaptors and molecular motors to productively fuse, enter, and infect cells and then traffic to the cell surface, where virions assemble and are released to spread infection. The HIV-1 envelope (Env) initiates the cycle by binding to and signaling through its main cell surface receptors (CD4/CCR5/CXCR4) to shape the cytoskeleton for fusion pore formation, which permits viral core entry. Then, the HIV-1 capsid is transported to the nucleus associated with cytoskeleton tracks under the control of specific adaptors/molecular motors, as well as HIV-1 accessory proteins. Furthermore, HIV-1 drives the late stages of the viral cycle by regulating cytoskeleton dynamics to assure viral Pr55Gag expression and transport to the cell surface, where it assembles and buds to mature infectious virions. In this review, we therefore analyze how HIV-1 generates a cell-permissive state to infection by regulating the cytoskeleton and associated factors. Likewise, we discuss the relevance of this knowledge to understand HIV-1 infection and pathogenesis in patients and to develop therapeutic strategies to battle HIV-1.
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Affiliation(s)
- Romina Cabrera-Rodríguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Silvia Pérez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Iria Lorenzo-Sánchez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
- Analysis Department, Faculty of Mathematics, Universidad de La Laguna (ULL), 38200 La Laguna, Spain
| | - Judith Estévez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Jonay García-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), 38200 La Laguna, Spain; (R.C.-R.); (S.P.-Y.); (I.L.-S.); (R.T.-G.); (J.E.-H.); (J.G.-L.)
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30
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Ay S, Di Nunzio F. HIV-Induced CPSF6 Condensates. J Mol Biol 2023; 435:168094. [PMID: 37061085 DOI: 10.1016/j.jmb.2023.168094] [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: 11/15/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/17/2023]
Abstract
Viruses are obligate parasites that rely on their host's cellular machinery for replication. To facilitate their replication cycle, many viruses have been shown to remodel the cellular architecture by inducing the formation of membraneless organelles (MLOs). Eukaryotic cells have evolved MLOs that are highly dynamic, self-organizing microenvironments that segregate biological processes and increase the efficiency of reactions by concentrating enzymes and substrates. In the context of viral infections, MLOs can be utilized by viruses to complete their replication cycle. This review focuses on the pathway used by the HIV-1 virus to remodel the nuclear landscape of its host, creating viral/host niches that enable efficient viral replication. Specifically, we discuss how the interaction between the HIV-1 capsid and the cellular factor CPSF6 triggers the formation of nuclear MLOs that support nuclear reverse transcription and viral integration in favored regions of the host chromatin. This review compiles current knowledge on the origin of nuclear HIV-MLOs and their role in early post-nuclear entry steps of the HIV-1 replication cycle.
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Affiliation(s)
- Selen Ay
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015 Paris, France.
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31
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Xue G, Yu HJ, Buffone C, Huang SW, Lee K, Goh SL, Gres AT, Guney MH, Sarafianos SG, Luban J, Diaz-Griffero F, KewalRamani VN. The HIV-1 capsid core is an opportunistic nuclear import receptor. Nat Commun 2023; 14:3782. [PMID: 37355754 PMCID: PMC10290713 DOI: 10.1038/s41467-023-39146-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/01/2023] [Indexed: 06/26/2023] Open
Abstract
The movement of viruses and other large macromolecular cargo through nuclear pore complexes (NPCs) is poorly understood. The human immunodeficiency virus type 1 (HIV-1) provides an attractive model to interrogate this process. HIV-1 capsid (CA), the chief structural component of the viral core, is a critical determinant in nuclear transport of the virus. HIV-1 interactions with NPCs are dependent on CA, which makes direct contact with nucleoporins (Nups). Here we identify Nup35, Nup153, and POM121 to coordinately support HIV-1 nuclear entry. For Nup35 and POM121, this dependence was dependent cyclophilin A (CypA) interaction with CA. Mutation of CA or removal of soluble host factors changed the interaction with the NPC. Nup35 and POM121 make direct interactions with HIV-1 CA via regions containing phenylalanine glycine motifs (FG-motifs). Collectively, these findings provide additional evidence that the HIV-1 CA core functions as a macromolecular nuclear transport receptor (NTR) that exploits soluble host factors to modulate NPC requirements during nuclear invasion.
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Affiliation(s)
- Guangai Xue
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Szu-Wei Huang
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - KyeongEun Lee
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shih Lin Goh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anna T Gres
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
| | - Mehmet Hakan Guney
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Stefan G Sarafianos
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
- Bond Life Sciences Center, MMI, Biochemistry, University of Missouri, Columbia, MO, 65201, USA
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vineet N KewalRamani
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023; 80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
Abstract
The spatiotemporal control of gene expression in complex multicellular organisms relies on noncoding regulatory sequences such as enhancers, which activate transcription of target genes often over large genomic distances. Despite the advances in the identification and characterization of enhancers, the principles and mechanisms by which enhancers select and control their target genes remain largely unknown. Here, we review recent interdisciplinary and quantitative approaches based on emerging techniques that aim to address open questions in the field, notably how regulatory information is encoded in the DNA sequence, how this information is transferred from enhancers to promoters, and how these processes are regulated in time.
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Affiliation(s)
- Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland. https://twitter.com/@MachPia
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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33
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Papa G, Albecka A, Mallery D, Vaysburd M, Renner N, James LC. IP6-stabilised HIV capsids evade cGAS/STING-mediated host immune sensing. EMBO Rep 2023; 24:e56275. [PMID: 36970882 PMCID: PMC10157305 DOI: 10.15252/embr.202256275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
HIV-1 uses inositol hexakisphosphate (IP6) to build a metastable capsid capable of delivering its genome into the host nucleus. Here, we show that viruses that are unable to package IP6 lack capsid protection and are detected by innate immunity, resulting in the activation of an antiviral state that inhibits infection. Disrupting IP6 enrichment results in defective capsids that trigger cytokine and chemokine responses during infection of both primary macrophages and T-cell lines. Restoring IP6 enrichment with a single mutation rescues the ability of HIV-1 to infect cells without being detected. Using a combination of capsid mutants and CRISPR-derived knockout cell lines for RNA and DNA sensors, we show that immune sensing is dependent upon the cGAS-STING axis and independent of capsid detection. Sensing requires the synthesis of viral DNA and is prevented by reverse transcriptase inhibitors or reverse transcriptase active-site mutation. These results demonstrate that IP6 is required to build capsids that can successfully transit the cell and avoid host innate immune sensing.
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Affiliation(s)
- Guido Papa
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Donna Mallery
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Marina Vaysburd
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Nadine Renner
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
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Mazurov D, Ramadan L, Kruglova N. Packaging and Uncoating of CRISPR/Cas Ribonucleoproteins for Efficient Gene Editing with Viral and Non-Viral Extracellular Nanoparticles. Viruses 2023; 15:v15030690. [PMID: 36992399 PMCID: PMC10056905 DOI: 10.3390/v15030690] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Rapid progress in gene editing based on clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) has revolutionized functional genomic studies and genetic disease correction. While numerous gene editing applications have been easily adapted by experimental science, the clinical utility of CRISPR/Cas remains very limited due to difficulty in delivery to primary cells and possible off-target effects. The use of CRISPR in the form of a ribonucleoprotein (RNP) complex substantially reduces the time of DNA exposure to the effector nuclease and minimizes its off-target activity. The traditional electroporation and lipofection methods lack the cell-type specificity of RNP delivery, can be toxic for cells, and are less efficient when compared to nanoparticle transporters. This review focuses on CRISPR/Cas RNP packaging and delivery using retro/lentiviral particles and exosomes. First, we briefly describe the natural stages of viral and exosomal particle formation, release and entry into the target cells. This helps us understand the mechanisms of CRISPR/Cas RNP packaging and uncoating utilized by the current delivery systems, which we discuss afterward. Much attention is given to the exosomes released during viral particle production that can be passively loaded with RNPs as well as the mechanisms necessary for particle fusion, RNP release, and transportation inside the target cells. Collectively, together with specific packaging mechanisms, all these factors can substantially influence the editing efficiency of the system. Finally, we discuss ways to improve CRISPR/Cas RNP delivery using extracellular nanoparticles.
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Affiliation(s)
- Dmitriy Mazurov
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Correspondence: or
| | - Lama Ramadan
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Natalia Kruglova
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia
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35
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Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nat Struct Mol Biol 2023; 30:425-435. [PMID: 36807645 PMCID: PMC10121901 DOI: 10.1038/s41594-023-00925-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Delivering the virus genome into the host nucleus through the nuclear pore complex (NPC) is pivotal in human immunodeficiency virus 1 (HIV-1) infection. The mechanism of this process remains mysterious owing to the NPC complexity and the labyrinth of molecular interactions involved. Here we built a suite of NPC mimics-DNA-origami-corralled nucleoporins with programmable arrangements-to model HIV-1 nuclear entry. Using this system, we determined that multiple cytoplasm-facing Nup358 molecules provide avid binding for capsid docking to the NPC. The nucleoplasm-facing Nup153 preferentially attaches to high-curvature regions of the capsid, positioning it for tip-leading NPC insertion. Differential capsid binding strengths of Nup358 and Nup153 constitute an affinity gradient that drives capsid penetration. Nup62 in the NPC central channel forms a barrier that viruses must overcome during nuclear import. Our study thus provides a wealth of mechanistic insight and a transformative toolset for elucidating how viruses like HIV-1 enter the nucleus.
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36
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Du Y, Hu Z, Luo Y, Wang HY, Yu X, Wang RF. Function and regulation of cGAS-STING signaling in infectious diseases. Front Immunol 2023; 14:1130423. [PMID: 36825026 PMCID: PMC9941744 DOI: 10.3389/fimmu.2023.1130423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
The efficacious detection of pathogens and prompt induction of innate immune signaling serve as a crucial component of immune defense against infectious pathogens. Over the past decade, DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) and its downstream signaling adaptor stimulator of interferon genes (STING) have emerged as key mediators of type I interferon (IFN) and nuclear factor-κB (NF-κB) responses in health and infection diseases. Moreover, both cGAS-STING pathway and pathogens have developed delicate strategies to resist each other for their survival. The mechanistic and functional comprehension of the interplay between cGAS-STING pathway and pathogens is opening the way for the development and application of pharmacological agonists and antagonists in the treatment of infectious diseases. Here, we briefly review the current knowledge of DNA sensing through the cGAS-STING pathway, and emphatically highlight the potent undertaking of cGAS-STING signaling pathway in the host against infectious pathogenic organisms.
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Affiliation(s)
- Yang Du
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiqiang Hu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Yien Luo
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Helen Y. Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiao Yu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
| | - Rong-Fu Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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37
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Pereira M, Vale N. Evolution of Antiretroviral Drug Rilpivirine and Approach to Oncology. Int J Mol Sci 2023; 24:ijms24032890. [PMID: 36769210 PMCID: PMC9917964 DOI: 10.3390/ijms24032890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Rilpivirine is an antiretroviral drug used to treat AIDS worldwide. The drug is a non-nucleoside reverse transcriptase inhibitor that halts the cDNA elongation process and, thus, the capacity of the HIV-1 virus to replicate. With the new wave of drug repurposing in recent years, rilpivirine has been studied in this regard. This drug is useful in Zika virus treatment, with in vivo results indicating regression in neuronal effects often associated with this infection. Several cancer types have also been researched, from breast to leukemia and pancreatic cancer, and rilpivirine has proved to have inhibitory effects in various cell lines with low concentrations, causing cellular death, apoptosis, and cell cycle arrest. The pathways are not yet established, but some works have hypothesized and demonstrated that rilpivirine causes inhibition of Aurora A kinase and has effects on the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway and the vascular endothelial growth factors-receptors (VEGFs-VEGFRs) pathway, which are known to be altered in cancer and tumors and can be targeted for cancer treatment. Further testing and clinical trials are needed, but this review demonstrates the potential of rilpivirine's repurposing for cancer treatment.
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Affiliation(s)
- Mariana Pereira
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), 4200-450 Porto, Portugal
- CINTESIS@RISE, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), Universidade do Porto (UP), 4050-313 Porto, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), 4200-450 Porto, Portugal
- CINTESIS@RISE, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Community Medicine, Health Information and Decision (MEDCIDS), Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
- Correspondence: ; Tel.: +351-220-426-537
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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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Abstract
The biggest challenge to immune control of HIV infection is the rapid within-host viral evolution, which allows selection of viral variants that escape from T cell and antibody recognition. Thus, it is impossible to clear HIV infection without targeting "immutable" components of the virus. Unlike the adaptive immune system that recognizes cognate epitopes, the CARD8 inflammasome senses the essential enzymatic activity of the HIV-1 protease, which is immutable for the virus. Hence, all subtypes of HIV clinical isolates can be recognized by CARD8. In HIV-infected cells, the viral protease is expressed as a subunit of the viral Gag-Pol polyprotein and remains functionally inactive prior to viral budding. A class of anti-HIV drugs, the non-nucleoside reverse transcriptase inhibitors (NNRTIs), can promote Gag-pol dimerization and subsequent premature intracellular activation of the viral protease. NNRTI treatment triggers CARD8 inflammasome activation, which leads to pyroptosis of HIV-infected CD4+ T cells and macrophages. Targeting the CARD8 inflammasome can be a potent and broadly effective strategy for HIV eradication.
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Affiliation(s)
- Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Priya Pal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Josh G Kim
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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40
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Viushkov VS, Lomov NA, Rubtsov MA, Vassetzky YS. Visualizing the Genome: Experimental Approaches for Live-Cell Chromatin Imaging. Cells 2022; 11:cells11244086. [PMID: 36552850 PMCID: PMC9776900 DOI: 10.3390/cells11244086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming "four-dimensional": our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, "programmed" proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods.
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Affiliation(s)
- Vladimir S. Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikolai A. Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Yegor S. Vassetzky
- CNRS UMR9018, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Correspondence:
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Abstract
Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
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42
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Genetic Code Expansion and Bio-Orthogonal Labeling Reveal Intact HIV-1 Capsids inside the Nucleus. mBio 2022; 13:e0234622. [PMID: 36098403 PMCID: PMC9600262 DOI: 10.1128/mbio.02346-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microscopy is one of the few techniques that can directly observe the HIV-1 capsid as it traverses the cell. However, an extrinsic or intrinsic label is needed to facilitate detection and this can perturb capsid behavior. Now, S. Schifferdecker, V. Zila, T. G. Muller, V. Sakin, et al. (mBio:e0195922, 2022, https://journals.asm.org/doi/10.1128/mbio.01959-22) have developed an ingenious direct labeling technology that uses genetic code expansion and click chemistry to produce infectious viruses whose capsids are labeled with only a single modified amino acid. Using this new system, together with electron tomography, the authors demonstrate that the capsid remains intact during its transport into the nucleus of T cells, supporting a late model of uncoating immediately before integration. Combining direct-labeled capsids with fluorescent nonstructural viral proteins or host cofactors promises to be hugely enabling for future studies. Moreover, the potential to install a bio-orthogonal label site specifically in the capsid is likely to have exciting applications beyond imaging.
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43
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Complex Relationships between HIV-1 Integrase and Its Cellular Partners. Int J Mol Sci 2022; 23:ijms232012341. [PMID: 36293197 PMCID: PMC9603942 DOI: 10.3390/ijms232012341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
RNA viruses, in pursuit of genome miniaturization, tend to employ cellular proteins to facilitate their replication. HIV-1, one of the most well-studied retroviruses, is not an exception. There is numerous evidence that the exploitation of cellular machinery relies on nucleic acid-protein and protein-protein interactions. Apart from Vpr, Vif, and Nef proteins that are known to regulate cellular functioning via interaction with cell components, another viral protein, integrase, appears to be crucial for proper virus-cell dialog at different stages of the viral life cycle. The goal of this review is to summarize and systematize existing data on known cellular partners of HIV-1 integrase and their role in the HIV-1 life cycle.
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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45
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Localization and functions of native and eGFP-tagged capsid proteins in HIV-1 particles. PLoS Pathog 2022; 18:e1010754. [PMID: 35951676 PMCID: PMC9426931 DOI: 10.1371/journal.ppat.1010754] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/30/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
In infectious HIV-1 particles, the capsid protein (CA) forms a cone-shaped shell called the capsid, which encases the viral ribonucleoprotein complex (vRNP). Following cellular entry, the capsid is disassembled through a poorly understood process referred to as uncoating, which is required to release the reverse transcribed HIV-1 genome for integration into host chromatin. Whereas single virus imaging using indirect CA labeling techniques suggested uncoating to occur in the cytoplasm or at the nuclear pore, a recent study using eGFP-tagged CA reported uncoating in the nucleus. To delineate the HIV-1 uncoating site, we investigated the mechanism of eGFP-tagged CA incorporation into capsids and the utility of this fluorescent marker for visualizing HIV-1 uncoating. We find that virion incorporated eGFP-tagged CA is effectively excluded from the capsid shell, and that a subset of the tagged CA is vRNP associated. These results thus imply that eGFP-tagged CA is not a direct marker for capsid uncoating. We further show that native CA co-immunoprecipitates with vRNP components, providing a basis for retention of eGFP-tagged and untagged CA by sub-viral complexes in the nucleus. Moreover, we find that functional viral replication complexes become accessible to integrase-interacting host factors at the nuclear pore, leading to inhibition of infection and demonstrating capsid permeabilization prior to nuclear import. Finally, we find that HIV-1 cores containing a mixture of wild-type and mutant CA interact differently with cytoplasmic versus nuclear pools of the CA-binding host cofactor CPSF6. Our results suggest that capsid remodeling (including a loss of capsid integrity) is the predominant pathway for HIV-1 nuclear entry and provide new insights into the mechanism of CA retention in the nucleus via interaction with vRNP components. The timing, location and mechanisms of HIV-1 capsid disassembly which is referred to as uncoating remains unclear. Direct labeling of HIV-1 capsids, by incorporating a few green fluorescent proteins (GFP) tagged capsid protein (CA) into virions allows to image the spatio-temporal loss of HIV-1 CA during virus infection. However, the localization and functions of a few virion incorporated eGFP-tagged CA proteins remain unclear, since <50% of virus packaged CA proteins participate to form the conical capsid shell that protects the HIV-1 genome. Here we developed several approaches to test the localization and function of eGFP-tagged CA proteins in virions. We found that eGFP-tagged CA proteins are excluded from the conical capsid shell and that a subset of these proteins is associated with the viral ribonucleoprotein complex (vRNPs), through direct interactions between CA and vRNP components. eGFP-tagged CA is retained in the nucleus by virtue of vRNP association and is unlikely to report on HIV-1 capsid disassembly. We also found that HIV-1 capsids become permeabilized and are remodeled during their transport into the nucleus. Our study provides new insights into the ability of CA to interact with vRNPs for its retention in the nucleus and highlights capsid remodeling as a preferred pathway for HIV-1 entry into the nucleus.
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46
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Müller TG, Zila V, Müller B, Kräusslich HG. Nuclear Capsid Uncoating and Reverse Transcription of HIV-1. Annu Rev Virol 2022; 9:261-284. [PMID: 35704745 DOI: 10.1146/annurev-virology-020922-110929] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After cell entry, human immunodeficiency virus type 1 (HIV-1) replication involves reverse transcription of the RNA genome, nuclear import of the subviral complex without nuclear envelope breakdown, and integration of the viral complementary DNA into the host genome. Here, we discuss recent evidence indicating that completion of reverse transcription and viral genome uncoating occur in the nucleus rather than in the cytoplasm, as previously thought, and suggest a testable model for nuclear import and uncoating. Multiple recent studies indicated that the cone-shaped capsid, which encases the genome and replication proteins, not only serves as a reaction container for reverse transcription and as a shield from innate immune sensors but also may constitute the elusive HIV-1 nuclear import factor. Rupture of the capsid may be triggered in the nucleus by completion of reverse transcription, by yet-unknown nuclear factors, or by physical damage, and it appears to occur in close temporal and spatial association with the integration process. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany; .,German Center for Infection Research, Heidelberg, Germany
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Tonello F, Massimino ML, Peggion C. Nucleolin: a cell portal for viruses, bacteria, and toxins. Cell Mol Life Sci 2022; 79:271. [PMID: 35503380 PMCID: PMC9064852 DOI: 10.1007/s00018-022-04300-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/18/2022]
Abstract
The main localization of nucleolin is the nucleolus, but this protein is present in multiple subcellular sites, and it is unconventionally secreted. On the cell surface, nucleolin acts as a receptor for various viruses, some bacteria, and some toxins. Aim of this review is to discuss the characteristics that make nucleolin able to act as receptor or co-receptor of so many and different pathogens. The important features that emerge are its multivalence, and its role as a bridge between the cell surface and the nucleus. Multiple domains, short linear motifs and post-translational modifications confer and modulate nucleolin ability to interact with nucleic acids, with proteins, but also with carbohydrates and lipids. This modular multivalence allows nucleolin to participate in different types of biomolecular condensates and to move to various subcellular locations, where it can act as a kind of molecular glue. It moves from the nucleus to the cell surface and can accompany particles in the reverse direction, from the cell surface into the nucleus, which is the destination of several pathogens to manipulate the cell in their favour.
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Affiliation(s)
- Fiorella Tonello
- CNR of Italy, Neuroscience Institute, viale G. Colombo 3, 35131, Padua, Italy.
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi, 58/B, 35131, Padua, Italy
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Nishiyama T, Takada T, Takeuchi H, Iwami S. Maternal embryonic leucine zipper kinase (MELK) optimally regulates the HIV-1 uncoating process. J Theor Biol 2022; 545:111152. [DOI: 10.1016/j.jtbi.2022.111152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/13/2022] [Accepted: 04/29/2022] [Indexed: 11/25/2022]
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Engelman AN, Kvaratskhelia M. Multimodal Functionalities of HIV-1 Integrase. Viruses 2022; 14:926. [PMID: 35632668 PMCID: PMC9144474 DOI: 10.3390/v14050926] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 01/11/2023] Open
Abstract
Integrase is the retroviral protein responsible for integrating reverse transcripts into cellular genomes. Co-packaged with viral RNA and reverse transcriptase into capsid-encased viral cores, human immunodeficiency virus 1 (HIV-1) integrase has long been implicated in reverse transcription and virion maturation. However, the underlying mechanisms of integrase in these non-catalytic-related viral replication steps have remained elusive. Recent results have shown that integrase binds genomic RNA in virions, and that mutational or pharmacological disruption of integrase-RNA binding yields eccentric virion particles with ribonucleoprotein complexes situated outside of the capsid shell. Such viruses are defective for reverse transcription due to preferential loss of integrase and viral RNA from infected target cells. Parallel research has revealed defective integrase-RNA binding and eccentric particle formation as common features of class II integrase mutant viruses, a phenotypic grouping of viruses that display defects at steps beyond integration. In light of these new findings, we propose three new subclasses of class II mutant viruses (a, b, and c), all of which are defective for integrase-RNA binding and particle morphogenesis, but differ based on distinct underlying mechanisms exhibited by the associated integrase mutant proteins. We also assess how these findings inform the role of integrase in HIV-1 particle maturation.
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Affiliation(s)
- Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
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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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