1
|
Guo H, Yang W, Li H, Yang J, Huang Y, Tang Y, Wang S, Ni F, Yang W, Yu XF, Wei W. The SAMHD1-MX2 axis restricts HIV-1 infection at postviral DNA synthesis. mBio 2024:e0136324. [PMID: 38888311 DOI: 10.1128/mbio.01363-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
HIV-1 replication is tightly regulated in host cells, and various restriction factors have important roles in inhibiting viral replication. SAMHD1, a well-known restriction factor, suppresses HIV-1 replication by hydrolyzing intracellular dNTPs, thereby limiting the synthesis of viral cDNA in quiescent cells. In this study, we revealed an additional and distinct mechanism of SAMHD1 inhibition during the postviral cDNA synthesis stage. Using immunoprecipitation and mass spectrometry analysis, we demonstrated the interaction between SAMHD1 and MX2/MxB, an interferon-induced antiviral factor that inhibits HIV-1 cDNA nuclear import. The disruption of endogenous MX2 expression significantly weakened the ability of SAMHD1 to inhibit HIV-1. The crucial region within SAMHD1 that binds to MX2 has been identified. Notably, we found that SAMHD1 can act as a sensor that recognizes and binds to the incoming HIV-1 core, subsequently delivering it to the molecular trap formed by MX2, thereby blocking the nuclear entry of the HIV-1 core structure. SAMHD1 mutants unable to recognize the HIV-1 core showed a substantial decrease in antiviral activity. Certain mutations in HIV-1 capsids confer resistance to MX2 inhibition while maintaining susceptibility to suppression by the SAMHD1-MX2 axis. Overall, our study identifies an intriguing antiviral pattern wherein two distinct restriction factors, SAMHD1 and MX2, collaborate to establish an alternative mechanism deviating from their actions. These findings provide valuable insight into the complex immune defense networks against exogenous viral infections and have implications for the development of targeted anti-HIV therapeutics. IMPORTANCE In contrast to most restriction factors that directly bind to viral components to exert their antiviral effects, SAMHD1, the only known deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, indirectly inhibits viral replication in quiescent cells by reducing the pool of dNTP substrates available for viral cDNA synthesis. Our study provides a novel perspective on the antiviral functions of SAMHD1. In addition to its role in dNTP hydrolysis, SAMHD1 cooperates with MX2 to inhibit HIV-1 nuclear import. In this process, SAMHD1 acts as a sensor for incoming HIV-1 cores, detecting and binding to them, before subsequently delivering the complex to the molecular trap formed by MX2, thereby immobilizing the virus. This study not only reveals a new antiviral pathway for SAMHD1 but also identifies a unique collaboration and interaction between two distinct restriction factors, establishing a novel line of defense against HIV-1 infection, which challenges the traditional view of restriction factors acting independently. Overall, our findings further indicate the intricate complexity of the host immune defense network and provide potential targets for promoting host antiviral immune defense.
Collapse
Affiliation(s)
- Haoran Guo
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Wanying Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Huili Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Jiaxin Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Yuehan Huang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Yubin Tang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Shijin Wang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | - Fushun Ni
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
| | | | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wei
- Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin, China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin, China
| |
Collapse
|
2
|
Yi D, An N, Li Q, Liu Q, Shao H, Zhou R, Wang J, Zhang Y, Ma L, Guo F, Li X, Liu Z, Cen S. Interferon-induced MXB protein restricts vimentin-dependent viral infection. Acta Pharm Sin B 2024; 14:2520-2536. [PMID: 38828143 PMCID: PMC11143536 DOI: 10.1016/j.apsb.2024.03.029] [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] [Received: 12/07/2023] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 06/05/2024] Open
Abstract
Type I interferon (IFN) inhibits a wide spectrum of viruses through stimulating the expression of antiviral proteins. As an IFN-induced protein, myxovirus resistance B (MXB) protein was reported to inhibit multiple highly pathogenic human viruses. It remains to be determined whether MXB employs a common mechanism to restrict different viruses. Here, we find that IFN alters the subcellular localization of hundreds of host proteins, and this IFN effect is partially lost upon MXB depletion. The results of our mechanistic study reveal that MXB recognizes vimentin (VIM) and recruits protein kinase B (AKT) to phosphorylate VIM at amino acid S38, which leads to reorganization of the VIM network and impairment of intracellular trafficking of virus protein complexes, hence causing a restriction of virus infection. These results highlight a new function of MXB in modulating VIM-mediated trafficking, which may lead towards a novel broad-spectrum antiviral strategy to control a large group of viruses that depend on VIM for successful replication.
Collapse
Affiliation(s)
- Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Huihan Shao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Rui Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Fei Guo
- Institute of Pathogen Biology, Chinese Academy of Medical Science, Beijing 100730, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
| | | | | | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK; (A.G.); (M.B.); (E.R.C.)
| |
Collapse
|
4
|
Steiert B, Andersen SE, McCaslin PN, Elwell CA, Faris R, Tijerina X, Smith P, Eldridge Q, Imai BS, Arrington JV, Yau PM, Mirrashidi KM, Johnson JR, Verschueren E, Von Dollen J, Jang GM, Krogan NJ, Engel JN, Weber MM. Global mapping of the Chlamydia trachomatis conventional secreted effector - host interactome reveals CebN interacts with nucleoporins and Rae1 to impede STAT1 nuclear translocation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.587017. [PMID: 38712050 PMCID: PMC11071493 DOI: 10.1101/2024.04.25.587017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Chlamydia trachomatis ( C.t .), the leading cause of bacterial sexually transmitted infections, employs a type III secretion system (T3SS) to translocate two classes of effectors, inclusion membrane proteins and conventional T3SS (cT3SS) effectors, into the host cell to counter host defense mechanisms. Here we employed three assays to directly evaluate secretion during infection, validating secretion for 23 cT3SS effectors. As bioinformatic analyses have been largely unrevealing, we conducted affinity purification-mass spectrometry to identify host targets and gain insights into the functions of these effectors, identifying high confidence interacting partners for 21 cT3SS effectors. We demonstrate that CebN localizes to the nuclear envelope in infected and bystander cells where it interacts with multiple nucleoporins and Rae1, blocking STAT1 nuclear import following IFN-γ stimulation. By building a cT3SS effector-host interactome, we have identified novel pathways that are targeted during bacterial infection and have begun to address how C.t. effectors combat cell autonomous immunity.
Collapse
|
5
|
Twentyman J, Emerman M, Ohainle M. Capsid-dependent lentiviral restrictions. J Virol 2024; 98:e0030824. [PMID: 38497663 PMCID: PMC11019884 DOI: 10.1128/jvi.00308-24] [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] [Indexed: 03/19/2024] Open
Abstract
Host antiviral proteins inhibit primate lentiviruses and other retroviruses by targeting many features of the viral life cycle. The lentiviral capsid protein and the assembled viral core are known to be inhibited through multiple, directly acting antiviral proteins. Several phenotypes, including those known as Lv1 through Lv5, have been described as cell type-specific blocks to infection against some but not all primate lentiviruses. Here we review important features of known capsid-targeting blocks to infection together with several blocks to infection for which the genes responsible for the inhibition still remain to be identified. We outline the features of these blocks as well as how current methodologies are now well suited to find these antiviral genes and solve these long-standing mysteries in the HIV and retrovirology fields.
Collapse
Affiliation(s)
- Joy Twentyman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Molly Ohainle
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California Berkeley, Berkeley, California, USA
| |
Collapse
|
6
|
Schieweck R, Götz M. Pan-cellular organelles and suborganelles-from common functions to cellular diversity? Genes Dev 2024; 38:98-114. [PMID: 38485267 PMCID: PMC10982711 DOI: 10.1101/gad.351337.123] [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: 04/02/2024]
Abstract
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
Collapse
Affiliation(s)
- Rico Schieweck
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy;
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Magdalena Götz
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany;
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, 82152 Planegg-Martinsried, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
7
|
Chintala K, Yandrapally S, Faiz W, Kispotta CR, Sarkar S, Mishra K, Banerjee S. The nuclear pore protein NUP98 impedes LTR-driven basal gene expression of HIV-1, viral propagation, and infectivity. Front Immunol 2024; 15:1330738. [PMID: 38449868 PMCID: PMC10914986 DOI: 10.3389/fimmu.2024.1330738] [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: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024] Open
Abstract
Nucleoporins (NUPs) are cellular effectors of human immunodeficiency virus-1 (HIV-1) replication that support nucleocytoplasmic trafficking of viral components. However, these also non-canonically function as positive effectors, promoting proviral DNA integration into the host genome and viral gene transcription, or as negative effectors by associating with HIV-1 restriction factors, such as MX2, inhibiting the replication of HIV-1. Here, we investigated the regulatory role of NUP98 on HIV-1 as we observed a lowering of its endogenous levels upon HIV-1 infection in CD4+ T cells. Using complementary experiments in NUP98 overexpression and knockdown backgrounds, we deciphered that NUP98 negatively affected HIV-1 long terminal repeat (LTR) promoter activity and lowered released virus levels. The negative effect on promoter activity was independent of HIV-1 Tat, suggesting that NUP98 prevents the basal viral gene expression. ChIP-qPCR showed NUP98 to be associated with HIV-1 LTR, with the negative regulatory element (NRE) of HIV-1 LTR playing a dominant role in NUP98-mediated lowering of viral gene transcription. Truncated mutants of NUP98 showed that the attenuation of HIV-1 LTR-driven transcription is primarily contributed by its N-terminal region. Interestingly, the virus generated from the producer cells transiently expressing NUP98 showed lower infectivity, while the virus generated from NUP98 knockdown CD4+ T cells showed higher infectivity as assayed in TZM-bl cells, corroborating the anti-HIV-1 properties of NUP98. Collectively, we show a new non-canonical function of a nucleoporin adding to the list of moonlighting host factors regulating viral infections. Downregulation of NUP98 in a host cell upon HIV-1 infection supports the concept of evolutionary conflicts between viruses and host antiviral factors.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| |
Collapse
|
8
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
9
|
Fu L, Weiskopf EN, Akkermans O, Swanson NA, Cheng S, Schwartz TU, Görlich D. HIV-1 capsids enter the FG phase of nuclear pores like a transport receptor. Nature 2024; 626:843-851. [PMID: 38267583 PMCID: PMC10881386 DOI: 10.1038/s41586-023-06966-w] [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: 04/21/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024]
Abstract
HIV-1 infection requires nuclear entry of the viral genome. Previous evidence suggests that this entry proceeds through nuclear pore complexes (NPCs), with the 120 × 60 nm capsid squeezing through an approximately 60-nm-wide central channel1 and crossing the permeability barrier of the NPC. This barrier can be described as an FG phase2 that is assembled from cohesively interacting phenylalanine-glycine (FG) repeats3 and is selectively permeable to cargo captured by nuclear transport receptors (NTRs). Here we show that HIV-1 capsid assemblies can target NPCs efficiently in an NTR-independent manner and bind directly to several types of FG repeats, including barrier-forming cohesive repeats. Like NTRs, the capsid readily partitions into an in vitro assembled cohesive FG phase that can serve as an NPC mimic and excludes much smaller inert probes such as mCherry. Indeed, entry of the capsid protein into such an FG phase is greatly enhanced by capsid assembly, which also allows the encapsulated clients to enter. Thus, our data indicate that the HIV-1 capsid behaves like an NTR, with its interior serving as a cargo container. Because capsid-coating with trans-acting NTRs would increase the diameter by 10 nm or more, we suggest that such a 'self-translocating' capsid undermines the size restrictions imposed by the NPC scaffold, thereby bypassing an otherwise effective barrier to viral infection.
Collapse
Affiliation(s)
- Liran Fu
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Erika N Weiskopf
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Onno Akkermans
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas A Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shiya Cheng
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Albarnaz JD, Kite J, Oliveira M, Li H, Di Y, Christensen MH, Paulo JA, Antrobus R, Gygi SP, Schmidt FI, Huttlin EL, Smith GL, Weekes MP. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection. Nat Commun 2023; 14:8134. [PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8] [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: 12/21/2022] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Modified vaccinia Ankara (MVA) virus does not replicate in human cells and is the vaccine deployed to curb the current outbreak of mpox. Here, we conduct a multiplexed proteomic analysis to quantify >9000 cellular and ~80% of viral proteins throughout MVA infection of human fibroblasts and macrophages. >690 human proteins are down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets are not shared with replication-competent vaccinia. Viral intermediate/late gene expression is necessary for MVA antagonism of innate immunity, and suppression of interferon effectors such as ISG20 potentiates virus gene expression. Proteomic changes specific to infection of macrophages indicate modulation of the inflammatory response, including inflammasome activation. Our approach thus provides a global view of the impact of MVA on the human proteome and identifies mechanisms that may underpin its abortive infection. These discoveries will prove vital to design future generations of vaccines.
Collapse
Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
| | - Joanne Kite
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Marisa Oliveira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Hanqi Li
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ying Di
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, University of Bonn, 53127, Bonn, Germany
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Layish B, Goli R, Flick H, Huang SW, Zhang RZ, Kvaratskhelia M, Kane M. Virus specificity and nucleoporin requirements for MX2 activity are affected by GTPase function and capsid-CypA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567336. [PMID: 38014352 PMCID: PMC10680775 DOI: 10.1101/2023.11.16.567336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human myxovirus resistance 2 (MX2/MXB) is an interferon-induced GTPase that inhibits human immunodeficiency virus-1 (HIV-1) infection by preventing nuclear import of the viral preintegration complex. The HIV-1 capsid (CA) is the major viral determinant for sensitivity to MX2, and complex interactions between MX2, CA, nucleoporins (Nups), cyclophilin A (CypA), and other cellular proteins influence the outcome of viral infection. To explore the interactions between MX2, the viral CA, and CypA, we utilized a CRISPR-Cas9/AAV approach to generate CypA knock-out cell lines as well as cells that express CypA from its endogenous locus, but with specific point mutations that would abrogate CA binding but should not affect enzymatic activity or cellular function. We found that infection of CypA knock-out and point mutant cell lines with wild-type HIV-1 and CA mutants recapitulated the phenotypes observed upon cyclosporine A (CsA) addition, indicating that effects of CsA treatment are the direct result of blocking CA-CypA interactions and are therefore independent from potential interactions between CypA and MX2 or other cellular proteins. Notably, abrogation of GTP hydrolysis by MX2 conferred enhanced antiviral activity when CA-CypA interactions were abolished, and this effect was not mediated by the CA-binding residues in the GTPase domain, or by phosphorylation of MX2 at position T151. We additionally found that elimination of GTPase activity also altered the Nup requirements for MX2 activity. Our data demonstrate that the antiviral activity of MX2 is affected by CypA-CA interactions in a virus-specific and GTPase activity-dependent manner. These findings further highlight the importance of the GTPase domain of MX2 in regulation of substrate specificity and interaction with nucleocytoplasmic trafficking pathways.
Collapse
Affiliation(s)
- Bailey Layish
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Ram Goli
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Haley Flick
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Szu-Wei Huang
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Robert Z Zhang
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Melissa Kane
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| |
Collapse
|
14
|
Jühlen R, Fahrenkrog B. From the sideline: Tissue-specific nucleoporin function in health and disease, an update. FEBS Lett 2023; 597:2750-2768. [PMID: 37873737 DOI: 10.1002/1873-3468.14761] [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] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The subcellular compartmentalisation of eukaryotic cells requires selective exchange between the cytoplasm and the nucleus. Intact nucleocytoplasmic transport is vital for normal cell function and mutations in the executing machinery have been causally linked to human disease. Central players in nucleocytoplasmic exchange are nuclear pore complexes (NPCs), which are built from ~30 distinct proteins collectively termed nucleoporins. Aberrant nucleoporin expression was detected in human cancers and autoimmune diseases since quite some time, while it was through the increasing use of next generation sequencing that mutations in nucleoporin genes associated with mainly rare hereditary diseases were revealed. The number of newly identified mutations is steadily increasing, as is the number of diseases. Mutational hotspots have emerged: mutations in the scaffold nucleoporins seemingly affect primarily inner organs, such as heart, kidney, and ovaries, whereas genetic alterations in peripheral, cytoplasmic nucleoporins affect primarily the central nervous system and development. In this review, we summarise latest insights on altered nucleoporin function in the context of human hereditary disorders, with a focus on those where mechanistic insights are beginning to emerge.
Collapse
Affiliation(s)
- Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | | |
Collapse
|
15
|
Bayer A, Child SJ, Malik HS, Geballe AP. A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB. J Virol 2023; 97:e0083023. [PMID: 37796130 PMCID: PMC10617587 DOI: 10.1128/jvi.00830-23] [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] [Received: 06/01/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Herpesviruses present a major global disease burden. Understanding the host cell mechanisms that block viral infections, as well as how viruses can evolve to counteract these host defenses, is critically important for understanding viral disease pathogenesis. This study reveals that the major human variant of the antiviral protein myxovirus resistance protein B (MxB) inhibits the human pathogen herpes simplex virus (HSV-1), whereas a minor human variant and orthologous MxB genes from even closely related primates do not. Thus, in contrast to the many antagonistic virus-host interactions in which the virus is successful in thwarting the host's defense systems, here the human gene appears to be at least temporarily winning at this interface of the primate-herpesvirus evolutionary arms race. Our findings further show that a polymorphism at amino acid 83 in a small fraction of the human population is sufficient to abrogate MxB's ability to inhibit HSV-1, which could have important implications for human susceptibility to HSV-1 pathogenesis.
Collapse
Affiliation(s)
- Avraham Bayer
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephanie J. Child
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Harmit S. Malik
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Adam P. Geballe
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| |
Collapse
|
16
|
Jackson-Jones KA, McKnight Á, Sloan RD. The innate immune factor RPRD2/REAF and its role in the Lv2 restriction of HIV. mBio 2023; 14:e0257221. [PMID: 37882563 PMCID: PMC10746242 DOI: 10.1128/mbio.02572-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
Intracellular innate immunity involves co-evolved antiviral restriction factors that specifically inhibit infecting viruses. Studying these restrictions has increased our understanding of viral replication, host-pathogen interactions, and pathogenesis, and represent potential targets for novel antiviral therapies. Lentiviral restriction 2 (Lv2) was identified as an unmapped early-phase restriction of HIV-2 and later shown to also restrict HIV-1 and simian immunodeficiency virus. The viral determinants of Lv2 susceptibility have been mapped to the envelope and capsid proteins in both HIV-1 and HIV-2, and also viral protein R (Vpr) in HIV-1, and appears dependent on cellular entry mechanism. A genome-wide screen identified several likely contributing host factors including members of the polymerase-associated factor 1 (PAF1) and human silencing hub (HUSH) complexes, and the newly characterized regulation of nuclear pre-mRNA domain containing 2 (RPRD2). Subsequently, RPRD2 (or RNA-associated early-stage antiviral factor) has been shown to be upregulated upon T cell activation, is highly expressed in myeloid cells, binds viral reverse transcripts, and potently restricts HIV-1 infection. RPRD2 is also bound by HIV-1 Vpr and targeted for degradation by the proteasome upon reverse transcription, suggesting RPRD2 impedes reverse transcription and Vpr targeting overcomes this block. RPRD2 is mainly localized to the nucleus and binds RNA, DNA, and DNA:RNA hybrids. More recently, RPRD2 has been shown to negatively regulate genome-wide transcription and interact with the HUSH and PAF1 complexes which repress HIV transcription and are implicated in maintenance of HIV latency. In this review, we examine Lv2 restriction and the antiviral role of RPRD2 and consider potential mechanism(s) of action.
Collapse
Affiliation(s)
- Kathryn A. Jackson-Jones
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- Division of Infectious Diseases & Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Áine McKnight
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Richard D. Sloan
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- ZJU-UoE Institute, Zhejiang University, Haining, China
| |
Collapse
|
17
|
Döhner K, Serrero MC, Sodeik B. The role of nuclear pores and importins for herpes simplex virus infection. Curr Opin Virol 2023; 62:101361. [PMID: 37672874 DOI: 10.1016/j.coviro.2023.101361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023]
Abstract
Microtubule transport and nuclear import are functionally connected, and the nuclear pore complex (NPC) can interact with microtubule motors. For several alphaherpesvirus proteins, nuclear localization signals (NLSs) and their interactions with specific importin-α proteins have been characterized. Here, we review recent insights on the roles of microtubule motors, capsid-associated NLSs, and importin-α proteins for capsid transport, capsid docking to NPCs, and genome release into the nucleoplasm, as well as the role of importins for nuclear viral transcription, replication, capsid assembly, genome packaging, and nuclear capsid egress. Moreover, importin-α proteins exert antiviral effects by promoting the nuclear import of transcription factors inducing the expression of interferons (IFN), cytokines, and IFN-stimulated genes, and the IFN-inducible MxB restricts capsid docking to NPCs.
Collapse
Affiliation(s)
- Katinka Döhner
- Institute of Virology, Hannover Medical School, Hannover, Germany; Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence, Hannover Medical School, Hannover, Germany.
| | - Manutea C Serrero
- Institute of Virology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence, Hannover Medical School, Hannover, Germany; DZIF - German Centre for Infection Research, Braunschweig, Hannover, Germany.
| |
Collapse
|
18
|
Santos MF, Rappa G, Karbanová J, Diana P, Cirrincione G, Carbone D, Manna D, Aalam F, Wang D, Vanier C, Corbeil D, Lorico A. HIV-1-induced nuclear invaginations mediated by VAP-A, ORP3, and Rab7 complex explain infection of activated T cells. Nat Commun 2023; 14:4588. [PMID: 37563144 PMCID: PMC10415338 DOI: 10.1038/s41467-023-40227-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
The mechanism of human immunodeficiency virus 1 (HIV-1) nuclear entry, required for productive infection, is not fully understood. Here, we report that in HeLa cells and activated CD4+ T cells infected with HIV-1 pseudotyped with VSV-G and native Env protein, respectively, Rab7+ late endosomes containing endocytosed HIV-1 promote the formation of nuclear envelope invaginations (NEIs) by a molecular mechanism involving the VOR complex, composed of the outer nuclear membrane protein VAP-A, hyperphosphorylated ORP3 and Rab7. Silencing VAP-A or ORP3 and drug-mediated impairment of Rab7 binding to ORP3-VAP-A inhibited the nuclear transfer of the HIV-1 components and productive infection. In HIV-1-resistant quiescent CD4+ T cells, ORP3 was not hyperphosphorylated and neither VOR complex nor NEIs were formed. This new cellular pathway and its molecular players are potential therapeutic targets, perhaps shared by other viruses that require nuclear entry to complete their life cycle.
Collapse
Affiliation(s)
- Mark F Santos
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA
| | - Germana Rappa
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA
| | - Jana Karbanová
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Patrizia Diana
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Girolamo Cirrincione
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Daniela Carbone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - David Manna
- Touro College of Osteopathic Medicine, Middletown, New York, NY, USA
| | - Feryal Aalam
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA
| | - David Wang
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA
| | - Cheryl Vanier
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA
- Imgen Research, LLC, 5495 South Rainbow #201, Las Vegas, NV, USA
| | - Denis Corbeil
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany.
| | - Aurelio Lorico
- Touro University Nevada College of Osteopathic Medicine, Henderson, NV, USA.
| |
Collapse
|
19
|
Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
Collapse
Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
Collapse
Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| |
Collapse
|
22
|
Bayer A, Child SJ, Malik HS, Geballe AP. A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542951. [PMID: 37398298 PMCID: PMC10312577 DOI: 10.1101/2023.05.30.542951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Myxovirus resistance proteins (MxA and MxB) are interferon-induced proteins that exert antiviral activity against a diverse range of RNA and DNA viruses. In primates, MxA has been shown to inhibit myxoviruses, bunyaviruses, and hepatitis B virus, whereas MxB restricts retroviruses and herpesviruses. As a result of their conflicts with viruses, both genes have been undergoing diversifying selection during primate evolution. Here, we investigate how MxB evolution in primates has affected its restriction of herpesviruses. In contrast to human MxB, we find that most primate orthologs, including the closely related chimpanzee MxB, do not inhibit HSV-1 replication. However, all primate MxB orthologs tested restrict human cytomegalovirus. Through the generation of human and chimpanzee MxB chimeras we show that a single residue, M83, is the key determinant of restriction of HSV-1 replication. Humans are the only primate species known to encode a methionine at this position, whereas most other primate species encode a lysine. Residue 83 is also the most polymorphic residue in MxB in human populations, with M83 being the most common variant. However, ∼2.5% of human MxB alleles encode a threonine at this position, which does not restrict HSV-1. Thus, a single amino acid variant in MxB, which has recently risen to high frequency in humans, has endowed humans with HSV-1 antiviral activity. Importance Herpesviruses present a major global disease burden. Understanding the host cell mechanisms that block viral infections as well as how viruses can evolve to counteract these host defenses is critically important for understanding viral disease pathogenesis, and for developing therapeutic tools aimed at treating or preventing viral infections. Additionally, understanding how these host and viral mechanisms adapt to counter one another can aid in identifying the risks of, and barriers to, cross-species transmission events. As highlighted by the recent SARS-CoV-2 pandemic, episodic transmission events can have severe consequences for human health. This study reveals that the major human variant of the antiviral protein MxB inhibits the human pathogen HSV-1, whereas human minor variants and orthologous MxB genes from even closely related primates do not. Thus, in contrast to the many antagonistic virus-host interactions in which the virus is successful in thwarting the defense systems of their native hosts, in this case the human gene appears to be at least temporarily winning at this interface of the primate-herpesviral evolutionary arms race. Our findings further show that a polymorphism at amino acid 83 in a small fraction of the human population is sufficient to abrogate MxB's ability to inhibit HSV-1, which could have important implications for human susceptibility to HSV-1 pathogenesis.
Collapse
Affiliation(s)
- Avraham Bayer
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephanie J. Child
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Harmit S. Malik
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Adam P. Geballe
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Medicine and Microbiology, University of Washington, Seattle WA, USA
| |
Collapse
|
23
|
Masenga SK, Mweene BC, Luwaya E, Muchaili L, Chona M, Kirabo A. HIV-Host Cell Interactions. Cells 2023; 12:1351. [PMID: 37408185 DOI: 10.3390/cells12101351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 07/07/2023] Open
Abstract
The development of antiretroviral drugs (ARVs) was a great milestone in the management of HIV infection. ARVs suppress viral activity in the host cell, thus minimizing injury to the cells and prolonging life. However, an effective treatment has remained elusive for four decades due to the successful immune evasion mechanisms of the virus. A thorough understanding of the molecular interaction of HIV with the host cell is essential in the development of both preventive and curative therapies for HIV infection. This review highlights several inherent mechanisms of HIV that promote its survival and propagation, such as the targeting of CD4+ lymphocytes, the downregulation of MHC class I and II, antigenic variation and an envelope complex that minimizes antibody access, and how they collaboratively render the immune system unable to mount an effective response.
Collapse
Affiliation(s)
- Sepiso K Masenga
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
- Vanderbilt University Medical Center, Department of Medicine, Division of Clinical Pharmacology, Room 536 Robinson Research Building, Nashville, TN 37232-6602, USA
| | - Bislom C Mweene
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Emmanuel Luwaya
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Lweendo Muchaili
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Makondo Chona
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Annet Kirabo
- Vanderbilt University Medical Center, Department of Medicine, Division of Clinical Pharmacology, Room 536 Robinson Research Building, Nashville, TN 37232-6602, USA
| |
Collapse
|
24
|
Betancor G. You Shall Not Pass: MX2 Proteins Are Versatile Viral Inhibitors. Vaccines (Basel) 2023; 11:vaccines11050930. [PMID: 37243034 DOI: 10.3390/vaccines11050930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Myxovirus resistance (MX) proteins are pivotal players in the innate immune response to viral infections. Less than 10 years ago, three independent groups simultaneously showed that human MX2 is an interferon (IFN)-stimulated gene (ISG) with potent anti-human immunodeficiency virus 1 (HIV-1) activity. Thenceforth, multiple research works have been published highlighting the ability of MX2 to inhibit RNA and DNA viruses. These growing bodies of evidence have identified some of the key determinants regulating its antiviral activity. Therefore, the importance of the protein amino-terminal domain, the oligomerization state, or the ability to interact with viral components is now well recognized. Nonetheless, there are still several unknown aspects of MX2 antiviral activity asking for further research, such as the role of cellular localization or the effect of post-translational modifications. This work aims to provide a comprehensive review of our current knowledge on the molecular determinants governing the antiviral activity of this versatile ISG, using human MX2 and HIV-1 inhibition as a reference, but drawing parallelisms and noting divergent mechanisms with other proteins and viruses when necessary.
Collapse
Affiliation(s)
- Gilberto Betancor
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Canary Islands, Spain
| |
Collapse
|
25
|
Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, Feng Q, Lusk CP, Aiken C, Engelman AN, Perilla JR, Pathak VK, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proc Natl Acad Sci U S A 2023; 120:e2202815120. [PMID: 36943880 PMCID: PMC10068764 DOI: 10.1073/pnas.2202815120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
Increasing evidence has suggested that the HIV-1 capsid enters the nucleus in a largely assembled, intact form. However, not much is known about how the cone-shaped capsid interacts with the nucleoporins (NUPs) in the nuclear pore for crossing the nuclear pore complex. Here, we elucidate how NUP153 binds HIV-1 capsid by engaging the assembled capsid protein (CA) lattice. A bipartite motif containing both canonical and noncanonical interaction modules was identified at the C-terminal tail region of NUP153. The canonical cargo-targeting phenylalanine-glycine (FG) motif engaged the CA hexamer. By contrast, a previously unidentified triple-arginine (RRR) motif in NUP153 targeted HIV-1 capsid at the CA tri-hexamer interface in the capsid. HIV-1 infection studies indicated that both FG- and RRR-motifs were important for the nuclear import of HIV-1 cores. Moreover, the presence of NUP153 stabilized tubular CA assemblies in vitro. Our results provide molecular-level mechanistic evidence that NUP153 contributes to the entry of the intact capsid into the nucleus.
Collapse
Affiliation(s)
- Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Sushila Kumari
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Ryan C. Burdick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Swapnil C. Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Taoran Tian
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Therese N. Tripler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Vinay K. Pathak
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
- Department of Biomedical Engineering, Yale University, New Haven, CT06511
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| |
Collapse
|
26
|
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.
Collapse
|
27
|
Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
Collapse
Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| |
Collapse
|
28
|
Tough Way In, Tough Way Out: The Complex Interplay of Host and Viral Factors in Nucleocytoplasmic Trafficking during HIV-1 Infection. Viruses 2022; 14:v14112503. [PMID: 36423112 PMCID: PMC9696704 DOI: 10.3390/v14112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is a retrovirus that integrates its reverse-transcribed genome as proviral DNA into the host genome to establish a successful infection. The viral genome integration requires safeguarding the subviral complexes, reverse transcription complex (RTC) and preintegration complex (PIC), in the cytosol from degradation, presumably effectively secured by the capsid surrounding these complexes. An intact capsid, however, is a large structure, which raises concerns about its translocation from cytoplasm to nucleus crossing the nuclear membrane, guarded by complex nuclear pore structures, which do not allow non-specific transport of large molecules. In addition, the generation of new virions requires the export of incompletely processed viral RNA from the nucleus to the cytoplasm, an event conventionally not permitted through mammalian nuclear membranes. HIV-1 has evolved multiple mechanisms involving redundant host pathways by liaison with the cell's nucleocytoplasmic trafficking system, failure of which would lead to the collapse of the infection cycle. This review aims to assemble the current developments in temporal and spatial events governing nucleocytoplasmic transport of HIV-1 factors. Discoveries are anticipated to serve as the foundation for devising host-directed therapies involving selective abolishment of the critical interactomes between viral proteins and their host equivalents.
Collapse
|
29
|
Defining the HIV Capsid Binding Site of Nucleoporin 153. mSphere 2022; 7:e0031022. [PMID: 36040047 PMCID: PMC9599535 DOI: 10.1128/msphere.00310-22] [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
The interaction between the HIV-1 capsid and human nucleoporin 153 (NUP153) is vital for delivering the HIV-1 preintegration complex into the nucleus via the nuclear pore complex. The interaction with the capsid requires a phenylalanine/glycine-containing motif in the C-terminus of NUP153 (NUP153C). This study used molecular modeling and biochemical assays to comprehensively determine the amino acids in NUP153 that are important for capsid interaction. Molecular dynamics, FoldX, and PyRosetta simulations delineated the minimal capsid binding motif of NUP153 based on the known structure of NUP153 bound to the HIV-1 capsid hexamer. Computational predictions were experimentally validated by testing the interaction of NUP153 with capsid using an in vitro binding assay and a cell-based TRIM-NUP153C restriction assay. This work identified eight amino acids from P1411 to G1418 that stably engage with capsid, with significant correlations between the interactions predicted by molecular models and empirical experiments. This validated the usefulness of this multidisciplinary approach to rapidly characterize the interaction between human proteins and the HIV-1 capsid. IMPORTANCE The human immunodeficiency virus (HIV) can infect nondividing cells by interacting with the host nuclear pore complex. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry. This study used a multidisciplinary approach combining computational and experimental techniques to comprehensively map the effect of mutating the amino acids of NUP153 on HIV capsid interaction. This work showed a significant correlation between computational and empirical data sets, revealing that the HIV capsid interacted specifically with only six amino acids of NUP153. The simplicity of the interaction motif suggested other FG-containing motifs could also interact with the HIV-1 capsid. Furthermore, it was predicted that naturally occurring polymorphisms in human and nonhuman primates would disrupt NUP153 interaction with capsid, potentially protecting certain populations from HIV-1 infection.
Collapse
|
30
|
Wang W, Li Y, Zhang Z, Wei W. Human immunodeficiency virus-1 core: The Trojan horse in virus–host interaction. Front Microbiol 2022; 13:1002476. [PMID: 36106078 PMCID: PMC9465167 DOI: 10.3389/fmicb.2022.1002476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is the major cause of acquired immunodeficiency syndrome (AIDs) worldwide. In HIV-1 infection, innate immunity is the first defensive line for immune recognition and viral clearance to ensure the normal biological function of the host cell and body health. Under the strong selected pressure generated by the human body over thousands of years, HIV has evolved strategies to counteract and deceive the innate immune system into completing its lifecycle. Recently, several studies have demonstrated that HIV capsid core which is thought to be a protector of the cone structure of genomic RNA, also plays an essential role in escaping innate immunity surveillance. This mini-review summarizes the function of capsid in viral immune evasion, and the comprehensive elucidation of capsid-host cell innate immunity interaction could promote our understanding of HIV-1’s pathogenic mechanism and provide insights for HIV-1 treatment in clinical therapy.
Collapse
Affiliation(s)
- Wei Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhe Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Wei
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin, China
- *Correspondence: Wei Wei,
| |
Collapse
|
31
|
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.
Collapse
|
32
|
Vrazas V, Moustafa S, Makridakis M, Karakasiliotis I, Vlahou A, Mavromara P, Katsani KR. A Proteomic Approach to Study the Biological Role of Hepatitis C Virus Protein Core+1/ARFP. Viruses 2022; 14:v14081694. [PMID: 36016316 PMCID: PMC9518822 DOI: 10.3390/v14081694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus is the major cause of chronic liver diseases and the only cytoplasmic RNA virus known to be oncogenic in humans. The viral genome gives rise to ten mature proteins and to additional proteins, which are the products of alternative translation initiation mechanisms. A protein-known as ARFP (alternative reading frame protein) or Core+1 protein-is synthesized by an open reading frame overlapping the HCV Core coding region in the (+1) frame of genotype 1a. Almost 20 years after its discovery, we still know little of the biological role of the ARFP/Core+1 protein. Here, our differential proteomic analysis of stable hepatoma cell lines expressing the Core+1/Long isoform of HCV-1a relates the expression of the Core+1/Long isoform with the progression of the pathology of HCV liver disease to cancer.
Collapse
Affiliation(s)
- Vasileios Vrazas
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Savvina Moustafa
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, Hippokration General Hospital of Athens, 11527 Athens, Greece;
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (A.V.); (M.M.)
| | - Penelope Mavromara
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
| | - Katerina R. Katsani
- Laboratory of Biochemistry and Molecular Virology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (V.V.); (P.M.)
- Correspondence:
| |
Collapse
|
33
|
MX2 Viral Substrate Breadth and Inhibitory Activity Are Regulated by Protein Phosphorylation. mBio 2022; 13:e0171422. [PMID: 35880880 PMCID: PMC9426416 DOI: 10.1128/mbio.01714-22] [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
Human immunodeficiency virus type-1 (HIV-1) infection is potently inhibited by human myxovirus resistance 2 (MX2/MxB), which binds to the viral capsid and blocks the nuclear import of viral DNA. We have recently shown that phosphorylation is a key regulator of MX2 antiviral activity, with phosphorylation of serine residues at positions 14, 17, and 18 repressing MX2 function. Here, we extend the study of MX2 posttranslational modifications and identify serine and threonine phosphorylation in all domains of MX2. By substituting these residues with aspartic acid or alanine, hence mimicking the presence or absence of a phosphate group, respectively, we identified key positions that control MX2 antiviral activity. Aspartic acid substitutions of residues Ser306 or Thr334 and alanine substitutions of Thr343 yielded proteins with substantially reduced antiviral activity, whereas the presence of aspartic acid at positions Ser28, Thr151, or Thr343 resulted in enhanced activity: referred to as hypermorphic mutants. In some cases, these hypermorphic mutations, particularly when paired with other MX2 mutations (e.g., S28D/T151D or T151D/T343A) acquired the capacity to inhibit HIV-1 capsid mutants known to be insensitive to wild-type MX2, such as P90A or T210K, as well as MX2-resistant retroviruses such as equine infectious anemia virus (EIAV) and murine leukemia virus (MLV). This work highlights the complexity and importance of MX2 phosphorylation in the regulation of antiviral activity and in the selection of susceptible viral substrates.
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Han J, Kyu Lee M, Jang Y, Cho WJ, Kim M. Repurposing of cyclophilin A inhibitors as broad-spectrum antiviral agents. Drug Discov Today 2022; 27:1895-1912. [PMID: 35609743 PMCID: PMC9123807 DOI: 10.1016/j.drudis.2022.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/30/2022] [Accepted: 05/18/2022] [Indexed: 12/28/2022]
Abstract
Cyclophilin A (CypA) is linked to diverse human diseases including viral infections. With the worldwide emergence of severe acute respiratory coronavirus 2 (SARS-CoV-2), drug repurposing has been highlighted as a strategy with the potential to speed up antiviral development. Because CypA acts as a proviral component in hepatitis C virus, coronavirus and HIV, its inhibitors have been suggested as potential treatments for these infections. Here, we review the structure of cyclosporin A and sanglifehrin A analogs as well as synthetic micromolecules inhibiting CypA; and we discuss their broad-spectrum antiviral efficacy in the context of the virus lifecycle.
Collapse
Affiliation(s)
- Jinhe Han
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yejin Jang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Won-Jea Cho
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Meeheyin Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea.
| |
Collapse
|
36
|
Serrero MC, Girault V, Weigang S, Greco TM, Ramos-Nascimento A, Anderson F, Piras A, Hickford Martinez A, Hertzog J, Binz A, Pohlmann A, Prank U, Rehwinkel J, Bauerfeind R, Cristea IM, Pichlmair A, Kochs G, Sodeik B. The interferon-inducible GTPase MxB promotes capsid disassembly and genome release of herpesviruses. eLife 2022; 11:e76804. [PMID: 35475759 PMCID: PMC9150894 DOI: 10.7554/elife.76804] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
Host proteins sense viral products and induce defence mechanisms, particularly in immune cells. Using cell-free assays and quantitative mass spectrometry, we determined the interactome of capsid-host protein complexes of herpes simplex virus and identified the large dynamin-like GTPase myxovirus resistance protein B (MxB) as an interferon-inducible protein interacting with capsids. Electron microscopy analyses showed that cytosols containing MxB had the remarkable capability to disassemble the icosahedral capsids of herpes simplex viruses and varicella zoster virus into flat sheets of connected triangular faces. In contrast, capsids remained intact in cytosols with MxB mutants unable to hydrolyse GTP or to dimerize. Our data suggest that MxB senses herpesviral capsids, mediates their disassembly, and thereby restricts the efficiency of nuclear targeting of incoming capsids and/or the assembly of progeny capsids. The resulting premature release of viral genomes from capsids may enhance the activation of DNA sensors, and thereby amplify the innate immune responses.
Collapse
Affiliation(s)
- Manutea C Serrero
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
| | | | - Sebastian Weigang
- Institute of Virology, Freiburg University Medical Center, University of FreiburgFreiburgGermany
| | - Todd M Greco
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | | | - Fenja Anderson
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Antonio Piras
- Institute of Virology, Technical University MunichMunichGermany
| | | | - Jonny Hertzog
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Anne Binz
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
| | - Anja Pohlmann
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
| | - Ute Prank
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Jan Rehwinkel
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Rudolf Bauerfeind
- Research Core Unit Laser Microscopy, Hannover Medical SchoolHannoverGermany
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Andreas Pichlmair
- Institute of Virology, Technical University MunichMunichGermany
- German Center for Infection Research (DZIF), Munich Partner siteMunichGermany
| | - Georg Kochs
- Institute of Virology, Freiburg University Medical Center, University of FreiburgFreiburgGermany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical SchoolHannoverGermany
- RESIST - Cluster of Excellence, Hannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Partner SiteHannoverGermany
| |
Collapse
|
37
|
The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 2022; 11:cells11091456. [PMID: 35563762 PMCID: PMC9100368 DOI: 10.3390/cells11091456] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/01/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500–1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
Collapse
|
38
|
Varberg JM, Unruh JR, Bestul AJ, Khan AA, Jaspersen SL. Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe. Life Sci Alliance 2022; 5:5/7/e202201423. [PMID: 35354597 PMCID: PMC8967992 DOI: 10.26508/lsa.202201423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/06/2023] Open
Abstract
Characterization of nuclear pores in Schizosaccharomyces pombe identifies regions of heterogeneous NPC density and composition and shows that NPCs are excluded near the spindle pole body by Lem2-mediated centromere tethering. The number, distribution, and composition of nuclear pore complexes (NPCs) in the nuclear envelope varies between cell types and changes during cellular differentiation and in disease. To understand how NPC density and organization are controlled, we analyzed the NPC number and distribution in the fission yeast Schizosaccharomyces pombe using structured illumination microscopy. The small size of yeast nuclei, genetic features of fungi, and our robust image analysis pipeline allowed us to study NPCs in intact nuclei under multiple conditions. Our data revealed that NPC density is maintained across a wide range of nuclear sizes. Regions of reduced NPC density are observed over the nucleolus and surrounding the spindle pole body (SPB). Lem2-mediated tethering of the centromeres to the SPB is required to maintain NPC exclusion near SPBs. These findings provide a quantitative understanding of NPC number and distribution in S. pombe and show that interactions between the centromere and the nuclear envelope influences local NPC distribution.
Collapse
Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Andrew J Bestul
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Azqa A Khan
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
39
|
Serganov AA, Udi Y, Stein ME, Patel V, Fridy PC, Rice CM, Saeed M, Jacobs EY, Chait BT, Rout MP. Proteomic elucidation of the targets and primary functions of the picornavirus 2A protease. J Biol Chem 2022; 298:101882. [PMID: 35367208 PMCID: PMC9168619 DOI: 10.1016/j.jbc.2022.101882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/19/2022] Open
Abstract
Picornaviruses are small RNA viruses that hijack host cell machinery to promote their replication. During infection, these viruses express two proteases, 2Apro and 3Cpro, which process viral proteins. They also subvert a number of host functions, including innate immune responses, host protein synthesis, and intracellular transport, by utilizing poorly understood mechanisms for rapidly and specifically targeting critical host proteins. Here, we used proteomic tools to characterize 2Apro interacting partners, functions, and targeting mechanisms. Our data indicate that, initially, 2Apro primarily targets just two cellular proteins: eukaryotic translation initiation factor eIF4G (a critical component of the protein synthesis machinery) and Nup98 (an essential component of the nuclear pore complex, responsible for nucleocytoplasmic transport). The protease appears to employ two different cleavage mechanisms; it likely interacts with eIF3L, utilizing the eIF3 complex to proteolytically access the eIF4G protein but also directly binds and degrades Nup98. This Nup98 cleavage results in only a marginal effect on nuclear import of proteins, while nuclear export of proteins and mRNAs were more strongly affected. Collectively, our data indicate that 2Apro selectively inhibits protein translation, key nuclear export pathways, and cellular mRNA localization early in infection to benefit viral replication at the expense of particular cell functions.
Collapse
Affiliation(s)
- Artem A Serganov
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA.
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Valay Patel
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA; National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Massachusetts, USA.
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA; Chemistry Department, St John's University, Queens, New York, USA.
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA.
| |
Collapse
|
40
|
Yu A, Lee EMY, Briggs JAG, Ganser-Pornillos BK, Pornillos O, Voth GA. Strain and rupture of HIV-1 capsids during uncoating. Proc Natl Acad Sci U S A 2022; 119:e2117781119. [PMID: 35238630 PMCID: PMC8915963 DOI: 10.1073/pnas.2117781119] [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: 09/29/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.
Collapse
Affiliation(s)
- Alvin Yu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Elizabeth M. Y. Lee
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637
| | - John A. G. Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
41
|
Dharan A, Campbell EM. Teaching old dogmas new tricks: recent insights into the nuclear import of HIV-1. Curr Opin Virol 2022; 53:101203. [PMID: 35121335 PMCID: PMC9175559 DOI: 10.1016/j.coviro.2022.101203] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 01/08/2023]
Abstract
A hallmark feature of lentiviruses, which separates them from other members of the retrovirus family, is their ability to infect non-dividing cells by traversing the nuclear pore complex. The viral determinant that mediates HIV-1 nuclear import is the viral capsid (CA) protein, which forms the conical core protecting the HIV-1 genome in a mature virion. Recently, a series of novel approaches developed to monitor post-fusion events in infection have challenged previous textbook models of the viral life cycle, which envisage reverse transcription and disassembly of the capsid core as events that complete in the cytoplasm. In this review, we summarize these recent findings and describe their implications on our understanding of the spatiotemporal staging of HIV-1 infection with a focus on the nuclear import and its implications in other aspects of the viral lifecycle.
Collapse
Affiliation(s)
- Adarsh Dharan
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA.
| |
Collapse
|
42
|
Huang Y, Xu F, Mei S, Liu X, Zhao F, Wei L, Fan Z, Hu Y, Wang L, Ai B, Cen S, Liang C, Guo F. MxB inhibits long interspersed element type 1 retrotransposition. PLoS Genet 2022; 18:e1010034. [PMID: 35171907 PMCID: PMC8849481 DOI: 10.1371/journal.pgen.1010034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Long interspersed element type 1 (LINE-1, also L1 for short) is the only autonomously transposable element in the human genome. Its insertion into a new genomic site may disrupt the function of genes, potentially causing genetic diseases. Cells have thus evolved a battery of mechanisms to tightly control LINE-1 activity. Here, we report that a cellular antiviral protein, myxovirus resistance protein B (MxB), restricts the mobilization of LINE-1. This function of MxB requires the nuclear localization signal located at its N-terminus, its GTPase activity and its ability to form oligomers. We further found that MxB associates with LINE-1 protein ORF1p and promotes sequestration of ORF1p to G3BP1-containing cytoplasmic granules. Since knockdown of stress granule marker proteins G3BP1 or TIA1 abolishes MxB inhibition of LINE-1, we conclude that MxB engages stress granule components to effectively sequester LINE-1 proteins within the cytoplasmic granules, thus hindering LINE-1 from accessing the nucleus to complete retrotransposition. Thus, MxB protein provides one mechanism for cells to control the mobility of retroelements. Retrotransposons occupy more than 40% of human genome, and have co-evolved with humans for millions of years. Long interspersed element type 1 (LINE-1, or L1) is the only retrotransposon that is able to jump to a new locus. LINE-1 retrotransposition causes genome instability, and is associated with genetic diseases including autoimmune diseases and cancer. To suppress this genome toxicity caused by LINE-1, humans have developed multi-layered mechanisms to control LINE-1 activity. MxB has been previously shown to inhibit LINE-1 mobility, thus contributing to host restriction of LINE-1. Here, we further demonstrate that MxB effectively restricts LINE-1 retrotransposition by sequestering LINE-1 ribonucleoprotein (RNP) within the cytoplasmic stress granules, thus guards genome stability. Hence our data attribute the restriction function of MxB to sequestering LINE-1 RNP to stress granules.
Collapse
Affiliation(s)
- Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Bin Ai
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
- * E-mail: (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (CL); (FG)
| |
Collapse
|
43
|
Albanese M, Ruhle A, Mittermaier J, Mejías-Pérez E, Gapp M, Linder A, Schmacke NA, Hofmann K, Hennrich AA, Levy DN, Humpe A, Conzelmann KK, Hornung V, Fackler OT, Keppler OT. Rapid, efficient and activation-neutral gene editing of polyclonal primary human resting CD4 + T cells allows complex functional analyses. Nat Methods 2022; 19:81-89. [PMID: 34949807 PMCID: PMC8748193 DOI: 10.1038/s41592-021-01328-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
CD4+ T cells are central mediators of adaptive and innate immune responses and constitute a major reservoir for human immunodeficiency virus (HIV) in vivo. Detailed investigations of resting human CD4+ T cells have been precluded by the absence of efficient approaches for genetic manipulation limiting our understanding of HIV replication and restricting efforts to find a cure. Here we report a method for rapid, efficient, activation-neutral gene editing of resting, polyclonal human CD4+ T cells using optimized cell cultivation and nucleofection conditions of Cas9-guide RNA ribonucleoprotein complexes. Up to six genes, including HIV dependency and restriction factors, were knocked out individually or simultaneously and functionally characterized. Moreover, we demonstrate the knock in of double-stranded DNA donor templates into different endogenous loci, enabling the study of the physiological interplay of cellular and viral components at single-cell resolution. Together, this technique allows improved molecular and functional characterizations of HIV biology and general immune functions in resting CD4+ T cells.
Collapse
Affiliation(s)
- Manuel Albanese
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany.
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy.
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Jennifer Mittermaier
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Ernesto Mejías-Pérez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Andreas Linder
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
- Department of Medicine II, University Hospital, LMU München, Munich, Germany
| | - Niklas A Schmacke
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Alexandru A Hennrich
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - David N Levy
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
| | - Andreas Humpe
- Department of Transfusion Medicine, Cell Therapeutics, and Hemostaseology, Department of Anesthesiology, University Hospital Munich, Munich, Germany
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany.
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| |
Collapse
|
44
|
Shen Q, Wu C, Freniere C, Tripler TN, Xiong Y. Nuclear Import of HIV-1. Viruses 2021; 13:2242. [PMID: 34835048 PMCID: PMC8619967 DOI: 10.3390/v13112242] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
The delivery of the HIV-1 genome into the nucleus is an indispensable step in retroviral infection of non-dividing cells, but the mechanism of HIV-1 nuclear import has been a longstanding debate due to controversial experimental evidence. It was commonly believed that the HIV-1 capsid would need to disassemble (uncoat) in the cytosol before nuclear import because the capsid is larger than the central channel of nuclear pore complexes (NPCs); however, increasing evidence demonstrates that intact, or nearly intact, HIV-1 capsid passes through the NPC to enter the nucleus. With the protection of the capsid, the HIV-1 core completes reverse transcription in the nucleus and is translocated to the integration site. Uncoating occurs while, or after, the viral genome is released near the integration site. These independent discoveries reveal a compelling new paradigm of this important step of the HIV-1 life cycle. In this review, we summarize the recent studies related to HIV-1 nuclear import, highlighting the spatial-temporal relationship between the nuclear entry of the virus core, reverse transcription, and capsid uncoating.
Collapse
Affiliation(s)
| | | | | | | | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; (Q.S.); (C.W.); (C.F.); (T.N.T.)
| |
Collapse
|
45
|
Ingram Z, Fischer DK, Ambrose Z. Disassembling the Nature of Capsid: Biochemical, Genetic, and Imaging Approaches to Assess HIV-1 Capsid Functions. Viruses 2021; 13:v13112237. [PMID: 34835043 PMCID: PMC8618418 DOI: 10.3390/v13112237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid and its disassembly, or capsid uncoating, has remained an active area of study over the past several decades. Our understanding of the HIV-1 capsid as solely a protective shell has since shifted with discoveries linking it to other complex replication events. The interplay of the HIV-1 capsid with reverse transcription, nuclear import, and integration has led to an expansion of knowledge of capsid functionality. Coincident with advances in microscopy, cell, and biochemistry assays, several models of capsid disassembly have been proposed, in which it occurs in either the cytoplasmic, nuclear envelope, or nuclear regions of the cell. Here, we discuss how the understanding of the HIV-1 capsid has evolved and the key methods that made these discoveries possible.
Collapse
Affiliation(s)
- Zachary Ingram
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; (Z.I.); (D.K.F.)
- Pittsburgh Center for HIV Protein Interactions, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Douglas K. Fischer
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; (Z.I.); (D.K.F.)
- Pittsburgh Center for HIV Protein Interactions, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; (Z.I.); (D.K.F.)
- Pittsburgh Center for HIV Protein Interactions, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Correspondence:
| |
Collapse
|
46
|
Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
Collapse
Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| |
Collapse
|
47
|
The journey of herpesvirus capsids and genomes to the host cell nucleus. Curr Opin Virol 2021; 50:147-158. [PMID: 34464845 DOI: 10.1016/j.coviro.2021.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/04/2023]
Abstract
Starting a herpesviral infection is a steeplechase across membranes, cytosol, and nuclear envelopes and against antiviral defence mechanisms. Here, we highlight recent insights on capsid stabilization at the portals during assembly, early capsid-host interactions ensuring nuclear targeting of incoming capsids, and genome uncoating. After fusion with a host membrane, incoming capsids recruit microtubule motors for traveling to the centrosome, and by unknown mechanisms get forward towards the nucleus. The interaction of capsid-associated tegument proteins with nucleoporins orients the capsid portal towards the nuclear pore, and presumably after removal of the portal caps the genomes that have been packaged under pressure can be injected into the nucleoplasm for transcription and replication. Some cell types disarm the incoming capsids or silence the incoming genomes to reduce the likelihood of infection.
Collapse
|
48
|
Semmelink MFW, Steen A, Veenhoff LM. Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS. Int J Mol Sci 2021; 22:9217. [PMID: 34502125 PMCID: PMC8431710 DOI: 10.3390/ijms22179217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research.
Collapse
Affiliation(s)
| | | | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (M.F.W.S.); (A.S.)
| |
Collapse
|
49
|
Abstract
Viral infection is intrinsically linked to the capacity of the virus to generate progeny. Many DNA and some RNA viruses need to access the nuclear machinery and therefore transverse the nuclear envelope barrier through the nuclear pore complex. Viral genomes then become chromatinized either in their episomal form or upon integration into the host genome. Interactions with host DNA, transcription factors or nuclear bodies mediate their replication. Often interfering with nuclear functions, viruses use nuclear architecture to ensure persistent infections. Discovering these multiple modes of replication and persistence served in unraveling many important nuclear processes, such as nuclear trafficking, transcription, and splicing. Here, by using examples of DNA and RNA viral families, we portray the nucleus with the virus inside.
Collapse
Affiliation(s)
- Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ines J de Castro
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| |
Collapse
|
50
|
Betancor G, Jimenez-Guardeño JM, Lynham S, Antrobus R, Khan H, Sobala A, Dicks MDJ, Malim MH. MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation. Nat Microbiol 2021; 6:1031-1042. [PMID: 34282309 PMCID: PMC7611661 DOI: 10.1038/s41564-021-00937-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/17/2021] [Indexed: 01/24/2023]
Abstract
The antiviral cytokine interferon activates expression of interferon-stimulated genes to establish an antiviral state. Myxovirus resistance 2 (MX2, also known as MxB) is an interferon-stimulated gene that inhibits the nuclear import of HIV-1 and interacts with the viral capsid and cellular nuclear transport machinery. Here, we identified the myosin light chain phosphatase (MLCP) subunits myosin phosphatase target subunit 1 (MYPT1) and protein phosphatase 1 catalytic subunit-β (PPP1CB) as positively-acting regulators of MX2, interacting with its amino-terminal domain. We demonstrated that serine phosphorylation of the N-terminal domain at positions 14, 17 and 18 suppresses MX2 antiviral function, prevents interactions with the HIV-1 capsid and nuclear transport factors, and is reversed by MLCP. Notably, serine phosphorylation of the N-terminal domain also impedes MX2-mediated inhibition of nuclear import of cellular karyophilic cargo. We also found that interferon treatment reduces levels of phosphorylation at these serine residues and outline a homeostatic regulatory mechanism in which repression of MX2 by phosphorylation, together with MLCP-mediated dephosphorylation, balances the deleterious effects of MX2 on normal cell function with innate immunity against HIV-1.
Collapse
Affiliation(s)
- Gilberto Betancor
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, The James Black Centre, King's College London, London, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hataf Khan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Andrew Sobala
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Matthew D J Dicks
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
| |
Collapse
|