1
|
Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 DOI: 10.1128/spectrum.04199-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
Collapse
Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| |
Collapse
|
2
|
Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M. Author Correction: Structure and interactions of the endogenous human Commander complex. Nat Struct Mol Biol 2024:10.1038/s41594-024-01273-y. [PMID: 38504028 DOI: 10.1038/s41594-024-01273-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Affiliation(s)
- Saara Laulumaa
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
3
|
Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M. Structure and interactions of the endogenous human Commander complex. Nat Struct Mol Biol 2024:10.1038/s41594-024-01246-1. [PMID: 38459129 DOI: 10.1038/s41594-024-01246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/19/2024] [Indexed: 03/10/2024]
Abstract
The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.
Collapse
Affiliation(s)
- Saara Laulumaa
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
4
|
Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCrJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
Collapse
Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
| | | | | | | | | | | | | |
Collapse
|
5
|
Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ArXiv 2024:arXiv:2311.17640v3. [PMID: 38076521 PMCID: PMC10705588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
Collapse
Affiliation(s)
| | - Paul D Adams
- Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA
| | | | - Catherine L Lawson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | - Maya Topf
- Birkbeck, University of London, London, UK
| | | | | | | | | | | | | | | | - Sai J Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John D Westbrook
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Martyn D Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | | | | |
Collapse
|
6
|
Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V. Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. EMBO Rep 2023; 24:e57910. [PMID: 37983950 DOI: 10.15252/embr.202357910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
Collapse
Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Protein Biochemistry and Structural Biology, Omass Therapeutics Ltd, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ville Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
7
|
Seitz I, Saarinen S, Kumpula EP, McNeale D, Anaya-Plaza E, Lampinen V, Hytönen VP, Sainsbury F, Cornelissen JJLM, Linko V, Huiskonen JT, Kostiainen MA. DNA-origami-directed virus capsid polymorphism. Nat Nanotechnol 2023; 18:1205-1212. [PMID: 37460794 PMCID: PMC10575778 DOI: 10.1038/s41565-023-01443-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/06/2023] [Indexed: 10/15/2023]
Abstract
Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.
Collapse
Affiliation(s)
- Iris Seitz
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Sharon Saarinen
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | | | - Vili Lampinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Jeroen J L M Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, Netherlands
| | - Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
- LIBER Center of Excellence, Aalto University, Aalto, Finland
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Mauri A Kostiainen
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
| |
Collapse
|
8
|
Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
Collapse
Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
9
|
Mäkelä AR, Uğurlu H, Hannula L, Kant R, Salminen P, Fagerlund R, Mäki S, Haveri A, Strandin T, Kareinen L, Hepojoki J, Kuivanen S, Levanov L, Pasternack A, Naves RA, Ritvos O, Österlund P, Sironen T, Vapalahti O, Kipar A, Huiskonen JT, Rissanen I, Saksela K. Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants. Nat Commun 2023; 14:1637. [PMID: 36964125 PMCID: PMC10037368 DOI: 10.1038/s41467-023-37290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
The emergence of increasingly immunoevasive SARS-CoV-2 variants emphasizes the need for prophylactic strategies to complement vaccination in fighting the COVID-19 pandemic. Intranasal administration of neutralizing antibodies has shown encouraging protective potential but there remains a need for SARS-CoV-2 blocking agents that are less vulnerable to mutational viral variation and more economical to produce in large scale. Here we describe TriSb92, a highly manufacturable and stable trimeric antibody-mimetic sherpabody targeted against a conserved region of the viral spike glycoprotein. TriSb92 potently neutralizes SARS-CoV-2, including the latest Omicron variants like BF.7, XBB, and BQ.1.1. In female Balb/c mice intranasal administration of just 5 or 50 micrograms of TriSb92 as early as 8 h before but also 4 h after SARS-CoV-2 challenge can protect from infection. Cryo-EM and biochemical studies reveal triggering of a conformational shift in the spike trimer as the inhibitory mechanism of TriSb92. The potency and robust biochemical properties of TriSb92 together with its resistance against viral sequence evolution suggest that TriSb92 could be useful as a nasal spray for protecting susceptible individuals from SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Anna R Mäkelä
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Hasan Uğurlu
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
| | - Petja Salminen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Riku Fagerlund
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Sanna Mäki
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Anu Haveri
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lauri Kareinen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lev Levanov
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Arja Pasternack
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Rauno A Naves
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Olli Ritvos
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | | | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Centre, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Anja Kipar
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki, Helsinki, Finland.
- HUS Diagnostic Centre, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland.
| |
Collapse
|
10
|
Kovaleva V, Yu LY, Ivanova L, Shpironok O, Nam J, Eesmaa A, Kumpula EP, Sakson S, Toots U, Ustav M, Huiskonen JT, Voutilainen MH, Lindholm P, Karelson M, Saarma M. MANF regulates neuronal survival and UPR through its ER-located receptor IRE1α. Cell Rep 2023; 42:112066. [PMID: 36739529 DOI: 10.1016/j.celrep.2023.112066] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/20/2022] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-located protein with cytoprotective effects in neurons and pancreatic β cells in vitro and in models of neurodegeneration and diabetes in vivo. However, the exact mode of MANF action has remained elusive. Here, we show that MANF directly interacts with the ER transmembrane unfolded protein response (UPR) sensor IRE1α, and we identify the binding interface between MANF and IRE1α. The expression of wild-type MANF, but not its IRE1α binding-deficient mutant, attenuates UPR signaling by decreasing IRE1α oligomerization; phosphorylation; splicing of Xbp1, Atf6, and Txnip levels; and protecting neurons from ER stress-induced death. MANF-IRE1α interaction and not MANF-BiP interaction is crucial for MANF pro-survival activity in neurons in vitro and is required to protect dopamine neurons in an animal model of Parkinson's disease. Our data show IRE1α as an intracellular receptor for MANF and regulator of neuronal survival.
Collapse
Affiliation(s)
- Vera Kovaleva
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland.
| | - Li-Ying Yu
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Larisa Ivanova
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia
| | - Olesya Shpironok
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Jinhan Nam
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Ave Eesmaa
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Sven Sakson
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Merja H Voutilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi Lindholm
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia
| | - Mart Saarma
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
11
|
Selvaraj M, Kokate SB, Reggiano G, Kogan K, Kotila T, Kremneva E, DiMaio F, Lappalainen P, Huiskonen JT. Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms. Cell Rep 2023; 42:111900. [PMID: 36586407 DOI: 10.1016/j.celrep.2022.111900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the actin filament major groove, providing an explanation for their incapability to co-polymerize on actin filaments. We also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalyzed severing.
Collapse
Affiliation(s)
- Muniyandi Selvaraj
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Shrikant B Kokate
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Gabriella Reggiano
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Konstantin Kogan
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Tommi Kotila
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Elena Kremneva
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pekka Lappalainen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
| |
Collapse
|
12
|
Giorgi L, Niemelä A, Kumpula EP, Natri O, Parkkila P, Huiskonen JT, Koivuniemi A. Mechanistic Insights into the Activation of Lecithin–Cholesterol Acyltransferase in Therapeutic Nanodiscs Composed of Apolipoprotein A-I Mimetic Peptides and Phospholipids. Mol Pharm 2022; 19:4135-4148. [DOI: 10.1021/acs.molpharmaceut.2c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Giorgi
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Akseli Niemelä
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Ossi Natri
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Petteri Parkkila
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- Division of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Goteborg 412 96, Sweden
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Artturi Koivuniemi
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
13
|
Kelly JJ, Tranter D, Pardon E, Chi G, Kramer H, Happonen L, Knee KM, Janz JM, Steyaert J, Bulawa C, Paavilainen VO, Huiskonen JT, Yue WW. Snapshots of actin and tubulin folding inside the TRiC chaperonin. Nat Struct Mol Biol 2022; 29:420-429. [PMID: 35449234 PMCID: PMC9113939 DOI: 10.1038/s41594-022-00755-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/01/2022] [Indexed: 01/16/2023]
Abstract
The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC.
Collapse
Affiliation(s)
- John J Kelly
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kelly M Knee
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Jay M Janz
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Christine Bulawa
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Ville O Paavilainen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK.
| | - Wyatt W Yue
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
14
|
Rissanen I, Krumm SA, Stass R, Whitaker A, Voss JE, Bruce EA, Rothenberger S, Kunz S, Burton DR, Huiskonen JT, Botten JW, Bowden TA, Doores KJ. Structural Basis for a Neutralizing Antibody Response Elicited by a Recombinant Hantaan Virus Gn Immunogen. mBio 2021; 12:e0253120. [PMID: 34225492 PMCID: PMC8406324 DOI: 10.1128/mbio.02531-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two glycoproteins, Gn and Gc, which are responsible for negotiating host cell entry and constitute key therapeutic targets. Here, we demonstrate that recombinantly derived Gn from Hantaan virus (HTNV) elicits a neutralizing antibody response (serum dilution that inhibits 50% infection [ID50], 1:200 to 1:850) in an animal model. Using antigen-specific B cell sorting, we isolated monoclonal antibodies (mAbs) exhibiting neutralizing and non-neutralizing activity, termed mAb HTN-Gn1 and mAb nnHTN-Gn2, respectively. Crystallographic analysis reveals that these mAbs target spatially distinct epitopes at disparate sites of the N-terminal region of the HTNV Gn ectodomain. Epitope mapping onto a model of the higher order (Gn-Gc)4 spike supports the immune accessibility of the mAb HTN-Gn1 epitope, a hypothesis confirmed by electron cryo-tomography of the antibody with virus-like particles. These data define natively exposed regions of the hantaviral Gn that can be targeted in immunogen design. IMPORTANCE The spillover of pathogenic hantaviruses from rodent reservoirs into the human population poses a continued threat to human health. Here, we show that a recombinant form of the Hantaan virus (HTNV) surface-displayed glycoprotein, Gn, elicits a neutralizing antibody response in rabbits. We isolated a neutralizing (HTN-Gn1) and a non-neutralizing (nnHTN-Gn2) monoclonal antibody and provide the first molecular-level insights into how the Gn glycoprotein may be targeted by the antibody-mediated immune response. These findings may guide rational vaccine design approaches focused on targeting the hantavirus glycoprotein envelope.
Collapse
Affiliation(s)
- Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Stefanie A. Krumm
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
| | - Annalis Whitaker
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Cellular, Molecular, and Biomedical Sciences Graduate Program, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - James E. Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Emily A. Bruce
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - Sylvia Rothenberger
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stefan Kunz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, Massachusetts, USA
| | - Juha T. Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, grid.59062.38University of Vermont, Burlington, Vermont, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, grid.4991.5University of Oxford, Oxford, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, King's College London, London, United Kingdom
| |
Collapse
|
15
|
Rissanen I, Stass R, Krumm SA, Seow J, Hulswit RJG, Paesen GC, Hepojoki J, Vapalahti O, Lundkvist Å, Reynard O, Volchkov V, Doores KJ, Huiskonen JT, Bowden TA. Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein. eLife 2020; 9:e58242. [PMID: 33349334 PMCID: PMC7755396 DOI: 10.7554/elife.58242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/26/2020] [Indexed: 01/22/2023] Open
Abstract
The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc)4 lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.
Collapse
Affiliation(s)
- Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Helsinki Institute of Life Science HiLIFE, University of HelsinkiHelsinkiFinland
- Molecular and Integrative Biosciences Research Programme, The Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
| | - Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Stefanie A Krumm
- Department of Infectious Diseases, King's College London, Guy's HospitalLondonUnited Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, King's College London, Guy's HospitalLondonUnited Kingdom
| | - Ruben JG Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Guido C Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Jussi Hepojoki
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of ZürichZürichSwitzerland
- Department of Virology, Medicum, Faculty of Medicine, University of HelsinkiHelsinkiFinland
| | - Olli Vapalahti
- Departments of Virology and Veterinary Biosciences, University of Helsinki and HUSLAB, Helsinki University HospitalHelsinkiFinland
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | - Olivier Reynard
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université LyonLyonFrance
| | - Viktor Volchkov
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université LyonLyonFrance
| | - Katie J Doores
- Department of Infectious Diseases, King's College London, Guy's HospitalLondonUnited Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Helsinki Institute of Life Science HiLIFE, University of HelsinkiHelsinkiFinland
- Molecular and Integrative Biosciences Research Programme, The Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| |
Collapse
|
16
|
Serris A, Stass R, Bignon EA, Muena NA, Manuguerra JC, Jangra RK, Li S, Chandran K, Tischler ND, Huiskonen JT, Rey FA, Guardado-Calvo P. The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism. Cell 2020; 183:442-456.e16. [PMID: 32937107 DOI: 10.1016/j.cell.2020.08.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square surface lattice. The envelope glycoproteins Gn and Gc form heterodimers that further assemble into tetrameric spikes, the lattice building blocks. The glycoproteins, which are the sole targets of neutralizing antibodies, drive virus entry via receptor-mediated endocytosis and endosomal membrane fusion. Here we describe the high-resolution X-ray structures of the heterodimer of Gc and the Gn head and of the homotetrameric Gn base. Docking them into an 11.4-Å-resolution cryoelectron tomography map of the hantavirus surface accounted for the complete extramembrane portion of the viral glycoprotein shell and allowed a detailed description of the surface organization of these pleomorphic virions. Our results, which further revealed a built-in mechanism controlling Gc membrane insertion for fusion, pave the way for immunogen design to protect against pathogenic hantaviruses.
Collapse
Affiliation(s)
- Alexandra Serris
- Institut Pasteur, Structural Virology Unit, and CNRS UMR 3569, Paris, France
| | - Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eduardo A Bignon
- Fundación Ciencia & Vida, Molecular Virology Laboratory, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Nicolás A Muena
- Fundación Ciencia & Vida, Molecular Virology Laboratory, Santiago, Chile
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nicole D Tischler
- Fundación Ciencia & Vida, Molecular Virology Laboratory, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Helsinki Institute of Life Science HiLIFE, Viikinkaari 1, 00014 University of Helsinki, Finland; Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, Viikinkaari 1, 00014 University of Helsinki, Finland
| | - Felix A Rey
- Institut Pasteur, Structural Virology Unit, and CNRS UMR 3569, Paris, France.
| | | |
Collapse
|
17
|
Abrishami V, Ilca SL, Gomez-Blanco J, Rissanen I, de la Rosa-Trevín JM, Reddy VS, Carazo JM, Huiskonen JT. Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog Biophys Mol Biol 2020; 160:43-52. [PMID: 32470354 DOI: 10.1016/j.pbiomolbio.2020.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 01/10/2023]
Abstract
Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.
Collapse
Affiliation(s)
- Vahid Abrishami
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Serban L Ilca
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Josue Gomez-Blanco
- Biocomputing Unit, National Center for Biotechnology (CSIC), Calle Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain; Current address: Department of Anatomy & Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 0C7, Canada
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland
| | | | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, North Torrey Pines Road, La Jolla, 92037, CA, USA
| | - José-Maria Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), Calle Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| |
Collapse
|
18
|
Allen ER, Krumm SA, Raghwani J, Halldorsson S, Elliott A, Graham VA, Koudriakova E, Harlos K, Wright D, Warimwe GM, Brennan B, Huiskonen JT, Dowall SD, Elliott RM, Pybus OG, Burton DR, Hewson R, Doores KJ, Bowden TA. A Protective Monoclonal Antibody Targets a Site of Vulnerability on the Surface of Rift Valley Fever Virus. Cell Rep 2019; 25:3750-3758.e4. [PMID: 30590046 PMCID: PMC6315105 DOI: 10.1016/j.celrep.2018.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
The Gn subcomponent of the Gn-Gc assembly that envelopes the human and animal pathogen, Rift Valley fever virus (RVFV), is a primary target of the neutralizing antibody response. To better understand the molecular basis for immune recognition, we raised a class of neutralizing monoclonal antibodies (nAbs) against RVFV Gn, which exhibited protective efficacy in a mouse infection model. Structural characterization revealed that these nAbs were directed to the membrane-distal domain of RVFV Gn and likely prevented virus entry into a host cell by blocking fusogenic rearrangements of the Gn-Gc lattice. Genome sequence analysis confirmed that this region of the RVFV Gn-Gc assembly was under selective pressure and constituted a site of vulnerability on the virion surface. These data provide a blueprint for the rational design of immunotherapeutics and vaccines capable of preventing RVFV infection and a model for understanding Ab-mediated neutralization of bunyaviruses more generally.
Collapse
Affiliation(s)
- Elizabeth R Allen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stefanie A Krumm
- Kings College London, Department of Infectious Diseases, 2nd Floor, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road, Oxford OX3 7LF, UK
| | - Steinar Halldorsson
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angela Elliott
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Victoria A Graham
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Elina Koudriakova
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Wright
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7FZ, UK; Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stuart D Dowall
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Roger Hewson
- National Infection Service, Virology & Pathogenesis, Public Health England, Porton Down, Salisbury, SP4 0JG Wiltshire, UK
| | - Katie J Doores
- Kings College London, Department of Infectious Diseases, 2nd Floor, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
19
|
Wu Q, Liang S, Ochi T, Chirgadze DY, Huiskonen JT, Blundell TL. Understanding the structure and role of DNA-PK in NHEJ: How X-ray diffraction and cryo-EM contribute in complementary ways. Progress in Biophysics and Molecular Biology 2019; 147:26-32. [DOI: 10.1016/j.pbiomolbio.2019.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/12/2019] [Accepted: 03/26/2019] [Indexed: 12/13/2022]
|
20
|
Bushell SR, Pike ACW, Falzone ME, Rorsman NJG, Ta CM, Corey RA, Newport TD, Christianson JC, Scofano LF, Shintre CA, Tessitore A, Chu A, Wang Q, Shrestha L, Mukhopadhyay SMM, Love JD, Burgess-Brown NA, Sitsapesan R, Stansfeld PJ, Huiskonen JT, Tammaro P, Accardi A, Carpenter EP. The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K. Nat Commun 2019; 10:3956. [PMID: 31477691 PMCID: PMC6718402 DOI: 10.1038/s41467-019-11753-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. TMEM16K is a member of the TMEM16 family of integral membrane proteins that are either lipid scramblases or chloride channels. Here the authors combine cell biology, electrophysiology measurements, X-ray crystallography, cryo-EM and MD simulations to structurally characterize TMEM16K and show that it is an ER-resident lipid scramblase.
Collapse
Affiliation(s)
- Simon R Bushell
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Nils J G Rorsman
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,OxSyBio, Atlas Building, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Chau M Ta
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,Department of Cardiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK.,Oxford Nanopore Technologies, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics and Musculoskeletal Sciences, University of Oxford, Windmill Road, Oxford, OX3 7LD, UK
| | - Lara F Scofano
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Chitra A Shintre
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Vertex Pharmaceuticals Ltd, Milton Park, Oxfordshire, OX14 4RW, UK
| | - Annamaria Tessitore
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Nuffield Division of Clinical Laboratory Sciences, Oxford University, Oxford, OX3 9DU, UK
| | - Amy Chu
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, Oxford University, Oxford, OX1 3QT, UK
| | - Qinrui Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Leela Shrestha
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James D Love
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461-1602, USA.,Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rebecca Sitsapesan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paolo Tammaro
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Alessio Accardi
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA.,Department of Anesthesiology, Weill Cornell Medical School, 25 East 68th Street, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| |
Collapse
|
21
|
Abstract
Enveloped viruses enclose their genomes inside a lipid bilayer which is decorated by membrane proteins that mediate virus entry. These viruses display a wide range of sizes, morphologies and symmetries. Spherical viruses are often isometric and their envelope proteins follow icosahedral symmetry. Filamentous and pleomorphic viruses lack such global symmetry but their surface proteins may display locally ordered assemblies. Determining the structures of enveloped viruses, including the envelope proteins and their protein-protein interactions on the viral surface, is of paramount importance. These structures can reveal how the virions are assembled and released by budding from the infected host cell, how the progeny virions infect new cells by membrane fusion, and how antibodies bind surface epitopes to block infection. In this chapter, we discuss the uses of cryogenic electron microscopy (cryo-EM) in elucidating structures of enveloped virions. Starting from a detailed outline of data collection and processing strategies, we highlight how cryo-EM has been successfully utilized to provide unique insights into enveloped virus entry, assembly, and neutralization.
Collapse
Affiliation(s)
- Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Young Chan Kim
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Helsinki Institute of Life Science HiLIFE and Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
22
|
Ilca SL, Sun X, El Omari K, Kotecha A, de Haas F, DiMaio F, Grimes JM, Stuart DI, Poranen MM, Huiskonen JT. Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus. Nature 2019; 570:252-256. [DOI: 10.1038/s41586-019-1229-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/08/2019] [Indexed: 01/17/2023]
|
23
|
De Colibus L, Roine E, Walter TS, Ilca SL, Wang X, Wang N, Roseman AM, Bamford D, Huiskonen JT, Stuart DI. Assembly of complex viruses exemplified by a halophilic euryarchaeal virus. Nat Commun 2019; 10:1456. [PMID: 30926810 PMCID: PMC6441041 DOI: 10.1038/s41467-019-09451-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/07/2019] [Indexed: 01/27/2023] Open
Abstract
Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size. Here, the authors present the cryo-EM structure of the archaeal virus SH1 at 3.8 Å resolution and show how the major capsid proteins assemble into hetero-hexamers, providing insights into the assembly process of this and related PRD1-adeno lineage viruses.
Collapse
Affiliation(s)
- Luigi De Colibus
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Elina Roine
- Research Program in Molecular and Integrative Biosciences, Faculty of Environmental and Biological Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Serban L Ilca
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Xiangxi Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Nan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Alan M Roseman
- Division of Molecular & Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PL, UK
| | - Dennis Bamford
- Research Program in Molecular and Integrative Biosciences, Faculty of Environmental and Biological Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Juha T Huiskonen
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK. .,Research Program in Molecular and Integrative Biosciences, Faculty of Environmental and Biological Sciences, University of Helsinki, 00014, Helsinki, Finland. .,Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland.
| | - David I Stuart
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK. .,Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.
| |
Collapse
|
24
|
El Omari K, Li S, Kotecha A, Walter TS, Bignon EA, Harlos K, Somerharju P, De Haas F, Clare DK, Molin M, Hurtado F, Li M, Grimes JM, Bamford DH, Tischler ND, Huiskonen JT, Stuart DI, Roine E. The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins. Nat Commun 2019; 10:846. [PMID: 30783086 PMCID: PMC6381117 DOI: 10.1038/s41467-019-08728-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
Collapse
Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eduardo A Bignon
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Pentti Somerharju
- Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Felix De Haas
- Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands
| | - Daniel K Clare
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mika Molin
- Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland
| | - Felipe Hurtado
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Mengqiu Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Nicole D Tischler
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
| | - David I Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Elina Roine
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
| |
Collapse
|
25
|
Stass R, Ilca SL, Huiskonen JT. Beyond structures of highly symmetric purified viral capsids by cryo-EM. Curr Opin Struct Biol 2018; 52:25-31. [PMID: 30096461 DOI: 10.1016/j.sbi.2018.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Cryogenic transmission electron microscopy (cryo-EM) is widely used to determine high-resolution structures of symmetric virus capsids. The method holds promise for extending studies beyond purified capsids and their symmetric protein shells. The non-symmetric genome component has been addressed in dsRNA cypoviruses and ssRNA bacteriophages Qβ and MS2. The structure of human herpes simplex virus type 1 capsids has been determined within intact virions to resolve capsid-tegument interactions. Electron tomography under cryogenic conditions (cryo-ET), has allowed resolving an early membrane fusion intermediate of Rift Valley fever virus. Antibody-affinity based sample grids allow capturing of virions directly from cell cultures or even clinical samples. These and other emerging methods will support studies to address viral entry, assembly and neutralization processes at increasingly high resolutions and native conditions.
Collapse
Affiliation(s)
- Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, OX3 7BN Oxford, UK
| | - Serban L Ilca
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, OX3 7BN Oxford, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, OX3 7BN Oxford, UK; Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, Viikinkaari 1, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
26
|
Watanabe Y, Raghwani J, Allen JD, Seabright GE, Li S, Moser F, Huiskonen JT, Strecker T, Bowden TA, Crispin M. Structure of the Lassa virus glycan shield provides a model for immunological resistance. Proc Natl Acad Sci U S A 2018; 115:7320-7325. [PMID: 29941589 PMCID: PMC6048489 DOI: 10.1073/pnas.1803990115] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Lassa virus is an Old World arenavirus endemic to West Africa that causes severe hemorrhagic fever. Vaccine development has focused on the envelope glycoprotein complex (GPC) that extends from the virion envelope. The often inadequate antibody immune response elicited by both vaccine and natural infection has been, in part, attributed to the abundance of N-linked glycosylation on the GPC. Here, using a virus-like-particle system that presents Lassa virus GPC in a native-like context, we determine the composite population of each of the N-linked glycosylation sites presented on the trimeric GPC spike. Our analysis reveals the presence of underprocessed oligomannose-type glycans, which form punctuated clusters that obscure the proteinous surface of both the GP1 attachment and GP2 fusion glycoprotein subunits of the Lassa virus GPC. These oligomannose clusters are seemingly derived as a result of sterically reduced accessibility to glycan processing enzymes, and limited amino acid diversification around these sites supports their role protecting against the humoral immune response. Combined, our data provide a structure-based blueprint for understanding how glycans render the glycoprotein spikes of Lassa virus and other Old World arenaviruses immunologically resistant targets.
Collapse
Affiliation(s)
- Yasunori Watanabe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
- Division of Structural Biology, University of Oxford, OX3 7BN Oxford, United Kingdom
- Centre for Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
| | - Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7LF Oxford, United Kingdom
| | - Joel D Allen
- Centre for Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
| | - Gemma E Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
- Centre for Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
| | - Sai Li
- Division of Structural Biology, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Felipe Moser
- Division of Structural Biology, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, University of Oxford, OX3 7BN Oxford, United Kingdom
- Helsinki Institute of Life Science and Molecular and Integrative Biosciences Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Thomas Strecker
- Institute of Virology, Philipps Universität Marburg, 35043 Marburg, Germany
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, OX3 7BN Oxford, United Kingdom;
| | - Max Crispin
- Centre for Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom;
| |
Collapse
|
27
|
Halldorsson S, Li S, Li M, Harlos K, Bowden TA, Huiskonen JT. Shielding and activation of a viral membrane fusion protein. Nat Commun 2018; 9:349. [PMID: 29367607 PMCID: PMC5783950 DOI: 10.1038/s41467-017-02789-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/28/2017] [Indexed: 11/23/2022] Open
Abstract
Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. Here, we address the fusion mechanism of Rift Valley fever virus. We determine the crystal structure of the Gn glycoprotein and fit it with the Gc fusion protein into cryo-electron microscopy reconstructions of the virion. Our analysis reveals how the Gn shields the hydrophobic fusion loops of the Gc, preventing premature fusion. Electron cryotomography of virions interacting with membranes under acidic conditions reveals how the fusogenic Gc is activated upon removal of the Gn shield. Repositioning of the Gn allows extension of Gc and insertion of fusion loops in the outer leaflet of the target membrane. These data show early structural transitions that enveloped viruses undergo during host cell entry and indicate that analogous shielding mechanisms are utilized across diverse virus families. Viral fusion proteins undergo extensive conformational changes during entry but intermediate conformations often remain unknown. Here, the authors show how Gn of Rift Valley fever virus fusion protein shields hydrophobic fusion loops of Gc and how these loops embed in the target membrane at acidic conditions.
Collapse
Affiliation(s)
- Steinar Halldorsson
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Mengqiu Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK. .,Helsinki Institute of Life Science and Faculty of Environmental and Biological Sciences, University of Helsinki, Viikinkaari 1, Helsinki, 00014, Finland.
| |
Collapse
|
28
|
Malik N, Kotecha A, Gold S, Asfor A, Ren J, Huiskonen JT, Tuthill TJ, Fry EE, Stuart DI. Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation. PLoS Pathog 2017; 13:e1006607. [PMID: 28937999 PMCID: PMC5656323 DOI: 10.1371/journal.ppat.1006607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 10/25/2017] [Accepted: 08/24/2017] [Indexed: 01/21/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5) release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses) have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4), N-termini (VP1) and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers. Here we present the 8-Å resolution structure of isolated dissociated pentamers of FMDV, lacking VP4. We also found these pentamers to re-associate into a rigid, icosahedrally symmetric assembly, which enabled their structure to be solved at higher resolution (5.2 Å). In this assembly, the pentamers unexpectedly associate 'inside out', but still with their exposed hydrophobic edges buried. Stabilizing interactions occur between the HI loop of VP2 and its symmetry related partners at the icosahedral 3-fold axes, and between the BC and EF loops of VP3 with the VP2 βB-strand and the CD loop at the 2-fold axes. A relatively extensive but subtle structural rearrangement towards the periphery of the dissociated pentamer compared to that in the mature virus provides insight into the mechanism of dissociation of FMDV and the marked difference in antigenicity.
Collapse
Affiliation(s)
- Nayab Malik
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Abhay Kotecha
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Sarah Gold
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Amin Asfor
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Juha T. Huiskonen
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
- Helsinki Institute of Life Science and Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tobias J. Tuthill
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- * E-mail: (TJT); (DIS); (EEF)
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
- * E-mail: (TJT); (DIS); (EEF)
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
- * E-mail: (TJT); (DIS); (EEF)
| |
Collapse
|
29
|
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. Building bridges between cellular and molecular structural biology. eLife 2017; 6:e25835. [PMID: 28682240 PMCID: PMC5524535 DOI: 10.7554/elife.25835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/30/2017] [Indexed: 11/13/2022] Open
Abstract
The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.
Collapse
Affiliation(s)
- Ardan Patwardhan
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Sarah J Butcher
- Institute of Biotechnology and the Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - David Gault
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Corey Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrii Iudin
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - Paul K Korir
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Abraham J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingvar Lagerstedt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Catherine L Lawson
- Center for Integrative Proteomics Research and the Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, United States
| | - David Mastronarde
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, United States
| | | | - Helen Parkinson
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses, Francis Crick Institute, London, United Kingdom
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, United Kingdom
| | - Sirarat Sarntivijai
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Irene Solanes Valero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Sriram Subramaniam
- Laboratory for Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression and the Division of Computational Biology, University of Dundee, Dundee, United Kingdom
| | - Ilinca Tudose
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Gerard J Kleywegt
- Molecular and Cellular Structure Cluster, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
30
|
Kotecha A, Wang Q, Dong X, Ilca SL, Ondiviela M, Zihe R, Seago J, Charleston B, Fry EE, Abrescia NGA, Springer TA, Huiskonen JT, Stuart DI. Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Nat Commun 2017; 8:15408. [PMID: 28534487 PMCID: PMC5457520 DOI: 10.1038/ncomms15408] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/26/2017] [Indexed: 11/21/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.
Collapse
Affiliation(s)
- Abhay Kotecha
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Quan Wang
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Serban L. Ilca
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Marina Ondiviela
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
| | - Rao Zihe
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | | | | | - Elizabeth E. Fry
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Timothy A. Springer
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juha T. Huiskonen
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
31
|
Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT. Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Nat Commun 2017; 8:14814. [PMID: 28287099 PMCID: PMC5355851 DOI: 10.1038/ncomms14814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/26/2017] [Indexed: 12/30/2022] Open
Abstract
Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution. Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.
Collapse
Affiliation(s)
- Zhaoyang Sun
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kamel El Omari
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Xiaoyu Sun
- Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| | - Serban L Ilca
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| |
Collapse
|
32
|
Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA. A Molecular-Level Account of the Antigenic Hantaviral Surface. Cell Rep 2016; 16:278. [PMID: 27355863 PMCID: PMC5638784 DOI: 10.1016/j.celrep.2016.06.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
33
|
Zlotnick A, Huiskonen JT. Editorial overview: Virus structure and assembly: Virions — from structure and physics to design principles. Curr Opin Virol 2016; 18:vii-viii. [DOI: 10.1016/j.coviro.2016.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
34
|
Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA. A Molecular-Level Account of the Antigenic Hantaviral Surface. Cell Rep 2016; 15:959-967. [PMID: 27117403 PMCID: PMC4858563 DOI: 10.1016/j.celrep.2016.03.082] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 11/26/2022] Open
Abstract
Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high-resolution crystal structure of the antigenic ectodomain of Gn from Puumala hantavirus (PUUV), a causative agent of hemorrhagic fever with renal syndrome. Fitting of PUUV Gn into an electron cryomicroscopy reconstruction of intact Gn-Gc spike complexes from the closely related but non-pathogenic Tula hantavirus localized Gn tetramers to the membrane-distal surface of the virion. The accuracy of the fitting was corroborated by epitope mapping and genetic analysis of available PUUV sequences. Interestingly, Gn exhibits greater non-synonymous sequence diversity than the less accessible Gc, supporting a role of the host humoral immune response in exerting selective pressure on the virus surface. The fold of PUUV Gn is likely to be widely conserved across hantaviruses. We describe the high-resolution crystal structure of a hantaviral Gn ectodomain Electron cryotomography analysis reveals the ultrastructure of Gn-Gc assembly X-ray fitting and mapping analysis reveals the antigenic hantavirus surface The Gn fold is likely to be widely conserved across this group of viruses
Collapse
Affiliation(s)
- Sai Li
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ilona Rissanen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jussi Hepojoki
- Department of Virology, Haartman Institute, University of Helsinki, 00014 Helsinki, Finland
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| |
Collapse
|
35
|
Renner M, Bertinelli M, Leyrat C, Paesen GC, Saraiva de Oliveira LF, Huiskonen JT, Grimes JM. Nucleocapsid assembly in pneumoviruses is regulated by conformational switching of the N protein. eLife 2016; 5:e12627. [PMID: 26880565 PMCID: PMC4798948 DOI: 10.7554/elife.12627] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/14/2016] [Indexed: 01/26/2023] Open
Abstract
Non-segmented, (-)RNA viruses cause serious human diseases. Human metapneumovirus (HMPV), an emerging pathogen of this order of viruses (Mononegavirales) is one of the main causes of respiratory tract illness in children. To help elucidate the assembly mechanism of the nucleocapsid (the viral RNA genome packaged by the nucleoprotein N) we present crystallographic structures of HMPV N in its assembled RNA-bound state and in a monomeric state, bound to the polymerase cofactor P. Our structures reveal molecular details of how P inhibits the self-assembly of N and how N transitions between the RNA-free and RNA-bound conformational state. Notably, we observe a role for the C-terminal extension of N in directly preventing premature uptake of RNA by folding into the RNA-binding cleft. Our structures suggest a common mechanism of how the growth of the nucleocapsid is orchestrated, and highlight an interaction site representing an important target for antivirals. DOI:http://dx.doi.org/10.7554/eLife.12627.001 Human metapneumovirus (HMPV for short) is a major cause of infections of the airways and lungs, particularly in children, elderly individuals and people with weakened immune systems. As for all viruses, HMPV cannot survive on its own. Instead, it must invade and hijack cells in order to replicate its own genetic material and form new viruses. In HMPV, this genetic information is in the form of a strand of RNA, and is protected by a shell-like structure called a nucleocapsid. Drugs that disrupt the nucleocapsid may therefore help to kill the viruses and treat the illnesses that they cause. Nucleocapsids are built out of many copies of a protein called nucleoprotein, which binds to a strand of RNA. However, viral nucleocapsids can only be built from nucleoproteins that are bound to viral RNA. Potentially, nucleoproteins could instead bind to RNA belonging to the cells that HMPV infects and they would then be trapped in a dead-end state. To prevent this type of unproductive binding, before the nucleocapsid is formed the nucleoprotein is kept unassembled with the help of another protein called the polymerase cofactor. However, it was not clear exactly how the polymerase cofactor helps to maintain this unassembled state. Using techniques called cryo-electron microscopy and X-ray crystallography, Renner et al. studied the structures formed when nucleoproteins are either bound to RNA or are unassembled and bind to the polymerase cofactor. Comparing these structures revealed that RNA normally binds to a specific cleft in the nucleoprotein. However, when nucleoprotein is bound to the polymerase cofactor a portion of the nucleoprotein folds into this cleft instead, blocking the insertion of RNA. This prevents the nucleoprotein from associating with the wrong RNA, allowing the nucleoprotein to remain in an unassembled state until it is needed for the virus. Renner et al. also found that the interactions between the nucleoprotein and the polymerase cofactor of HMPV occur at sites that are also found in several other related viruses, such as Ebola. Targeting this common region could therefore be a good strategy for developing new antiviral drugs. DOI:http://dx.doi.org/10.7554/eLife.12627.002
Collapse
Affiliation(s)
- Max Renner
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mattia Bertinelli
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Cédric Leyrat
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Guido C Paesen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Diamond Light Source, Didcot, United Kingdom
| |
Collapse
|
36
|
Li S, Sun Z, Pryce R, Parsy ML, Fehling SK, Schlie K, Siebert CA, Garten W, Bowden TA, Strecker T, Huiskonen JT. Acidic pH-Induced Conformations and LAMP1 Binding of the Lassa Virus Glycoprotein Spike. PLoS Pathog 2016; 12:e1005418. [PMID: 26849049 PMCID: PMC4743923 DOI: 10.1371/journal.ppat.1005418] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022] Open
Abstract
Lassa virus is an enveloped, bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses. Virus entry into the host cell is mediated by a tripartite surface spike complex, which is composed of two viral glycoprotein subunits, GP1 and GP2, and the stable signal peptide. Of these, GP1 binds to cellular receptors and GP2 catalyzes fusion between the viral envelope and the host cell membrane during endocytosis. The molecular structure of the spike and conformational rearrangements induced by low pH, prior to fusion, remain poorly understood. Here, we analyzed the three-dimensional ultrastructure of Lassa virus using electron cryotomography. Sub-tomogram averaging yielded a structure of the glycoprotein spike at 14-Å resolution. The spikes are trimeric, cover the virion envelope, and connect to the underlying matrix. Structural changes to the spike, following acidification, support a viral entry mechanism dependent on binding to the lysosome-resident receptor LAMP1 and further dissociation of the membrane-distal GP1 subunits.
Collapse
Affiliation(s)
- Sai Li
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Zhaoyang Sun
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rhys Pryce
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Marie-Laure Parsy
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah K. Fehling
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany
| | - Katrin Schlie
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany
| | - C. Alistair Siebert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Wolfgang Garten
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas Strecker
- Institute of Virology, Philipps Universität Marburg, Marburg, Germany
| | - Juha T. Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
37
|
Abstract
Many phleboviruses (family Bunyaviridae) are emerging as medically important viruses. These viruses enter target cells by endocytosis and low pH-dependent membrane fusion in late endosomes. However, the necessary and sufficient factors for fusion have not been fully characterized. We have studied the minimal fusion requirements of a prototypic phlebovirus, Uukuniemi virus, in an in vitro virus-liposome assay. We show that efficient lipid mixing between viral and liposome membranes requires close to physiological temperatures and phospholipids with negatively charged headgroups, such as the late endosomal phospholipid bis(monoacylglycero)phosphate. We further demonstrate that bis(monoacylglycero)phosphate increases Uukuniemi virus fusion beyond the lipid mixing stage. By using electron cryotomography of viral particles in the presence or absence of liposomes, we observed that the conformation of phlebovirus glycoprotein capsomers changes from the native conformation toward a more elongated conformation at a fusion permissive pH. Our results suggest a rationale for phlebovirus entry in late endosomes.
Collapse
Affiliation(s)
- David Bitto
- From the Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Steinar Halldorsson
- From the Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Alessandro Caputo
- From the Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Juha T Huiskonen
- From the Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, United Kingdom
| |
Collapse
|
38
|
Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI, Huiskonen JT. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 2015; 6:8843. [PMID: 26534841 PMCID: PMC4667630 DOI: 10.1038/ncomms9843] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022] Open
Abstract
Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems. Electron cryomicroscopy can allow the elucidation of macromolecular structures; however, mismatches in symmetry between different components limit the attainable resolution. Here, the authors set out a computational method for extracting and retaining information from such components.
Collapse
|
39
|
Kotecha A, Seago J, Scott K, Burman A, Loureiro S, Ren J, Porta C, Ginn HM, Jackson T, Perez-Martin E, Siebert CA, Paul G, Huiskonen JT, Jones IM, Esnouf RM, Fry EE, Maree FF, Charleston B, Stuart DI. Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. Nat Struct Mol Biol 2015; 22:788-94. [PMID: 26389739 PMCID: PMC5985953 DOI: 10.1038/nsmb.3096] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/26/2015] [Indexed: 11/08/2022]
Abstract
Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.
Collapse
Affiliation(s)
- Abhay Kotecha
- Division of Structural Biology, University of Oxford, Oxford, UK
| | | | - Katherine Scott
- Transboundary Animal Disease Programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa
| | | | - Silvia Loureiro
- Animal and Microbial Sciences, University of Reading, Reading, UK
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, Oxford, UK
- The Pirbright Institute, Pirbright, UK
| | - Helen M. Ginn
- Division of Structural Biology, University of Oxford, Oxford, UK
| | | | | | | | - Guntram Paul
- Merck Sharp & Dohme Animal Health, Cologne, Germany
| | | | - Ian M. Jones
- Animal and Microbial Sciences, University of Reading, Reading, UK
| | - Robert M. Esnouf
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Francois F. Maree
- Transboundary Animal Disease Programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | | | - David I. Stuart
- Division of Structural Biology, University of Oxford, Oxford, UK
- Life Science Division, Diamond Light Source, Didcot, UK
| |
Collapse
|
40
|
Bitto D, Harvey DJ, Halldorsson S, Doores KJ, Pritchard LK, Huiskonen JT, Bowden TA, Crispin M. Determination of N-linked Glycosylation in Viral Glycoproteins by Negative Ion Mass Spectrometry and Ion Mobility. Methods Mol Biol 2015; 1331:93-121. [PMID: 26169737 PMCID: PMC4817836 DOI: 10.1007/978-1-4939-2874-3_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans.
Collapse
Affiliation(s)
- David Bitto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steinar Halldorsson
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Katie J. Doores
- King’s College London, School of Medicine at Guy’s, King’s and St Thomas’ Hospitals, Guy’s Hospital, Great Maze Pond, London, UK
| | - Laura K. Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Juha T. Huiskonen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Thomas A. Bowden
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Max Crispin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,To whom correspondence should be addressed, Max Crispin, , Tel: +44(0)1865 285445
| |
Collapse
|
41
|
Huiskonen JT, Parsy ML, Li S, Bitto D, Renner M, Bowden TA. Averaging of viral envelope glycoprotein spikes from electron cryotomography reconstructions using Jsubtomo. J Vis Exp 2014:e51714. [PMID: 25350719 PMCID: PMC4353292 DOI: 10.3791/51714] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enveloped viruses utilize membrane glycoproteins on their surface to mediate entry into host cells. Three-dimensional structural analysis of these glycoprotein ‘spikes’ is often technically challenging but important for understanding viral pathogenesis and in drug design. Here, a protocol is presented for viral spike structure determination through computational averaging of electron cryo-tomography data. Electron cryo-tomography is a technique in electron microscopy used to derive three-dimensional tomographic volume reconstructions, or tomograms, of pleomorphic biological specimens such as membrane viruses in a near-native, frozen-hydrated state. These tomograms reveal structures of interest in three dimensions, albeit at low resolution. Computational averaging of sub-volumes, or sub-tomograms, is necessary to obtain higher resolution detail of repeating structural motifs, such as viral glycoprotein spikes. A detailed computational approach for aligning and averaging sub-tomograms using the Jsubtomo software package is outlined. This approach enables visualization of the structure of viral glycoprotein spikes to a resolution in the range of 20-40 Å and study of the study of higher order spike-to-spike interactions on the virion membrane. Typical results are presented for Bunyamwera virus, an enveloped virus from the family Bunyaviridae. This family is a structurally diverse group of pathogens posing a threat to human and animal health.
Collapse
Affiliation(s)
- Juha T Huiskonen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford;
| | - Marie-Laure Parsy
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Sai Li
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - David Bitto
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Max Renner
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Thomas A Bowden
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| |
Collapse
|
42
|
Leyrat C, Renner M, Harlos K, Huiskonen JT, Grimes JM. Drastic changes in conformational dynamics of the antiterminator M2-1 regulate transcription efficiency in Pneumovirinae. eLife 2014; 3:e02674. [PMID: 24842877 PMCID: PMC4051120 DOI: 10.7554/elife.02674] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The M2-1 protein of human metapneumovirus (HMPV) is a zinc-binding transcription antiterminator which is highly conserved among pneumoviruses. We report the structure of tetrameric HMPV M2-1. Each protomer features a N-terminal zinc finger domain and an α-helical tetramerization motif forming a rigid unit, followed by a flexible linker and an α-helical core domain. The tetramer is asymmetric, three of the protomers exhibiting a closed conformation, and one an open conformation. Molecular dynamics simulations and SAXS demonstrate a dynamic equilibrium between open and closed conformations in solution. Structures of adenosine monophosphate- and DNA- bound M2-1 establish the role of the zinc finger domain in base-specific recognition of RNA. Binding to ‘gene end’ RNA sequences stabilized the closed conformation of M2-1 leading to a drastic shift in the conformational landscape of M2-1. We propose a model for recognition of gene end signals and discuss the implications of these findings for transcriptional regulation in pneumoviruses. DOI:http://dx.doi.org/10.7554/eLife.02674.001 To produce a protein from a gene, the gene must first be transcribed to make a molecule of RNA. In general, the enzyme building the RNA molecule stops building when it reaches the end of a gene and encounters a termination signal. When a virus replicates, however, it needs to transcribe all the genes in its genome, so it relies on antiterminator proteins to make the enzyme building the RNA ignore the termination signal. Therefore, medicines that stop antiterminators working could stop viral infections spreading. Human metapneumovirus (HMPV) can cause severe respiratory infections in children, the elderly and people with weakened immune systems. A protein called M2-1 that is found inside HMPV must be present for the virus to infect humans, and it was recently shown that this protein plays a role in antitermination in a virus closely related to HMPV. Using a range of techniques, including X-ray crystallography and molecular dynamics simulations, Leyrat et al. worked out the structure of M2-1 in HMPV, and showed that it can flip between ‘open’ and ‘closed’ forms. The open structure presents surfaces that could be targeted by antiviral drugs. When M2-1 binds to RNA, the closed structure is stabilized as a result of the RNA binding to two separate sites on the protein. Leyrat et al. suggest that similar antiterminator proteins in related viruses—including respiratory syncytial virus, Marburg and Ebola—could also bind in this way. Leyrat et al. also propose a model describing how M2-1 can recognize the end of a gene, which could help with the development of new antiviral treatments. DOI:http://dx.doi.org/10.7554/eLife.02674.002
Collapse
Affiliation(s)
- Cedric Leyrat
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Max Renner
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom Diamond Light Source Ltd, Didcot, United Kingdom
| |
Collapse
|
43
|
Crispin M, Harvey DJ, Bitto D, Bonomelli C, Edgeworth M, Scrivens JH, Huiskonen JT, Bowden TA. Structural plasticity of the Semliki Forest virus glycome upon interspecies transmission. J Proteome Res 2014; 13:1702-12. [PMID: 24467287 PMCID: PMC4428802 DOI: 10.1021/pr401162k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Cross-species
viral transmission subjects parent and progeny alphaviruses
to differential post-translational processing of viral envelope glycoproteins.
Alphavirus biogenesis has been extensively studied, and the Semliki
Forest virus E1 and E2 glycoproteins have been shown to exhibit differing
degrees of processing of N-linked glycans. However the composition
of these glycans, including that arising from different host cells,
has not been determined. Here we determined the chemical composition
of the glycans from the prototypic alphavirus, Semliki Forest virus,
propagated in both arthropod and rodent cell lines, by using ion-mobility
mass spectrometry and collision-induced dissociation analysis. We
observe that both the membrane-proximal E1 fusion glycoprotein and
the protruding E2 attachment glycoprotein display heterogeneous glycosylation
that contains N-linked glycans exhibiting both limited and extensive
processing. However, E1 contained predominantly highly processed glycans
dependent on the host cell, with rodent and mosquito-derived E1 exhibiting
complex-type and paucimannose-type glycosylation, respectively. In
contrast, the protruding E2 attachment glycoprotein primarily contained
conserved under-processed oligomannose-type structures when produced
in both rodent and mosquito cell lines. It is likely that glycan processing
of E2 is structurally restricted by steric-hindrance imposed by local
viral protein structure. This contrasts E1, which presents glycans
characteristic of the host cell and is accessible to enzymes. We integrated
our findings with previous cryo-electron microscopy and crystallographic
analyses to produce a detailed model of the glycosylated mature virion
surface. Taken together, these data reveal the degree to which virally
encoded protein structure and cellular processing enzymes shape the
virion glycome during interspecies transmission of Semliki Forest
virus.
Collapse
Affiliation(s)
- Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Leyrat C, Renner M, Harlos K, Huiskonen JT, Grimes JM. Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus. Structure 2013; 22:136-48. [PMID: 24316400 PMCID: PMC3887258 DOI: 10.1016/j.str.2013.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/30/2022]
Abstract
The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca2+ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. M is a calcium binding protein Calcium stabilizes the structure of M M forms an obligate dimer in solution M self-assembles in the presence of lipids The Paramyxoviruses and the Filoviruses have a common ancestor
Collapse
Affiliation(s)
- Cedric Leyrat
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Max Renner
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Juha T Huiskonen
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
| |
Collapse
|
45
|
Maurer UE, Zeev-Ben-Mordehai T, Pandurangan AP, Cairns TM, Hannah BP, Whitbeck JC, Eisenberg RJ, Cohen GH, Topf M, Huiskonen JT, Grünewald K. The structure of herpesvirus fusion glycoprotein B-bilayer complex reveals the protein-membrane and lateral protein-protein interaction. Structure 2013; 21:1396-405. [PMID: 23850455 PMCID: PMC3737472 DOI: 10.1016/j.str.2013.05.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
Glycoprotein B (gB) is a key component of the complex herpesvirus fusion machinery. We studied membrane interaction of two gB ectodomain forms and present an electron cryotomography structure of the gB-bilayer complex. The two forms differed in presence or absence of the membrane proximal region (MPR) but showed an overall similar trimeric shape. The presence of the MPR impeded interaction with liposomes. In contrast, the MPR-lacking form interacted efficiently with liposomes. Lateral interaction resulted in coat formation on the membranes. The structure revealed that interaction of gB with membranes was mediated by the fusion loops and limited to the outer membrane leaflet. The observed intrinsic propensity of gB to cluster on membranes indicates an additional role of gB in driving the fusion process forward beyond the transient fusion pore opening and subsequently leading to fusion pore expansion. Full-length gB ectodomain has a structure similar to the ectodomain lacking the MPR The gB-bilayer structure reveals that the interaction is limited to the outer leaflet gB trimers have an intrinsic propensity to interact laterally and form protein arrays Arrays of gB trimers on membranes render the fusion pore open state irreversible
Collapse
Affiliation(s)
- Ulrike E Maurer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Bowden TA, Bitto D, McLees A, Yeromonahos C, Elliott RM, Huiskonen JT. Orthobunyavirus ultrastructure and the curious tripodal glycoprotein spike. PLoS Pathog 2013; 9:e1003374. [PMID: 23696739 PMCID: PMC3656102 DOI: 10.1371/journal.ppat.1003374] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/05/2013] [Indexed: 12/16/2022] Open
Abstract
The genus Orthobunyavirus within the family Bunyaviridae constitutes an expanding group of emerging viruses, which threaten human and animal health. Despite the medical importance, little is known about orthobunyavirus structure, a prerequisite for understanding virus assembly and entry. Here, using electron cryo-tomography, we report the ultrastructure of Bunyamwera virus, the prototypic member of this genus. Whilst Bunyamwera virions are pleomorphic in shape, they display a locally ordered lattice of glycoprotein spikes. Each spike protrudes 18 nm from the viral membrane and becomes disordered upon introduction to an acidic environment. Using sub-tomogram averaging, we derived a three-dimensional model of the trimeric pre-fusion glycoprotein spike to 3-nm resolution. The glycoprotein spike consists mainly of the putative class-II fusion glycoprotein and exhibits a unique tripod-like arrangement. Protein–protein contacts between neighbouring spikes occur at membrane-proximal regions and intra-spike contacts at membrane-distal regions. This trimeric assembly deviates from previously observed fusion glycoprotein arrangements, suggesting a greater than anticipated repertoire of viral fusion glycoprotein oligomerization. Our study provides evidence of a pH-dependent conformational change that occurs during orthobunyaviral entry into host cells and a blueprint for the structure of this group of emerging pathogens. Orthobunyaviruses comprise a group of emerging arboviruses within the Bunyaviridae, the largest family of membrane-containing viruses. In spite of the continued medical impact upon human and animal health, little is known about orthobunyavirus structure or the process of host cell entry. Here, we address this paucity of information through electron cryo-microscopy analysis of Bunyamwera virus, the prototypic representative of this genus. We reveal that Bunyamwera virions are pleomorphic and display locally-ordered lattices of viral glycoprotein spikes on the envelope surface. The three-dimensional structure of the glycoprotein spike was resolved to 3.0-nm resolution. The spike is composed of the attachment and fusion glycoproteins and comprises a unique tripodal organization. This glycoprotein arrangement contrasts those observed in other virus families. Consistent with the established pH-dependent mechanism of membrane fusion during host cell entry, we provide evidence for the disruption of this tripodal assembly upon exposure to acidic environments. These data constitute a blueprint for orthobunyavirus architecture and support a case for broadened structural diversity within the Bunyaviridae family.
Collapse
Affiliation(s)
- Thomas A. Bowden
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
| | - David Bitto
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Angela McLees
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
| | - Christelle Yeromonahos
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Richard M. Elliott
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
| | - Juha T. Huiskonen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
47
|
Karotki L, Huiskonen JT, Stefan CJ, Ziółkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC. Eisosome proteins assemble into a membrane scaffold. ACTA ACUST UNITED AC 2012; 195:889-902. [PMID: 22123866 PMCID: PMC3257569 DOI: 10.1083/jcb.201104040] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Membrane organization by eisosomes is mediated by self-assembly of its main components into a membrane-bound protein scaffold with lipid-binding specificity. Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to efficiently orchestrate the many reactions occurring there simultaneously. Despite the almost universal presence of membrane domains, mechanisms of their formation are often unclear. Yeast cells feature prominent plasma membrane domain organization, which is at least partially mediated by eisosomes. Eisosomes are large protein complexes that are primarily composed of many subunits of two Bin–Amphiphysin–Rvs domain–containing proteins, Pil1 and Lsp1. In this paper, we show that these proteins self-assemble into higher-order structures and bind preferentially to phosphoinositide-containing membranes. Using a combination of electron microscopy approaches, we generate structural models of Pil1 and Lsp1 assemblies, which resemble eisosomes in cells. Our data suggest that the mechanism of membrane organization by eisosomes is mediated by self-assembly of its core components into a membrane-bound protein scaffold with lipid-binding specificity.
Collapse
Affiliation(s)
- Lena Karotki
- Organelle Architecture and Dynamics, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Ibiricu I, Huiskonen JT, Döhner K, Bradke F, Sodeik B, Grünewald K. Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons. PLoS Pathog 2011; 7:e1002406. [PMID: 22194682 PMCID: PMC3240593 DOI: 10.1371/journal.ppat.1002406] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 10/13/2011] [Indexed: 11/23/2022] Open
Abstract
During herpes simplex virus 1 (HSV1) egress in neurons, viral particles travel from the neuronal cell body along the axon towards the synapse. Whether HSV1 particles are transported as enveloped virions as proposed by the ‘married’ model or as non-enveloped capsids suggested by the ‘separate’ model is controversial. Specific viral proteins may form a recruitment platform for microtubule motors that catalyze such transport. However, their subviral location has remained elusive. Here we established a system to analyze herpesvirus egress by cryo electron tomography. At 16 h post infection, we observed intra-axonal transport of progeny HSV1 viral particles in dissociated hippocampal neurons by live-cell fluorescence microscopy. Cryo electron tomography of frozen-hydrated neurons revealed that most egressing capsids were transported independently of the viral envelope. Unexpectedly, we found not only DNA-containing capsids (cytosolic C-capsids), but also capsids lacking DNA (cytosolic A-/B-capsids) in mid-axon regions. Subvolume averaging revealed lower amounts of tegument on cytosolic A-/B-capsids than on C-capsids. Nevertheless, all capsid types underwent active axonal transport. Therefore, even few tegument proteins on the capsid vertices seemed to suffice for transport. Secondary envelopment of capsids was observed at axon terminals. On their luminal face, the enveloping vesicles were studded with typical glycoprotein-like spikes. Furthermore, we noted an accretion of tegument density at the concave cytosolic face of the vesicle membrane in close proximity to the capsids. Three-dimensional analysis revealed that these assembly sites lacked cytoskeletal elements, but that filamentous actin surrounded them and formed an assembly compartment. Our data support the ‘separate model’ for HSV1 egress, i.e. progeny herpes viruses being transported along axons as subassemblies and not as complete virions within transport vesicles. Herpes simplex virus 1 (HSV1) establishes lifelong latent infections in the peripheral nervous system. After reactivation, progeny viral particles travel within sensory neurons towards sites of initial infection. There are conflicting reports what type of viral structures are transported: some studies observed non-enveloped capsids traveling while others reported transport of fully enveloped viruses within vesicles. Here, we used cryo electron tomography to analyze the three-dimensional architecture of HSV1 in axons of hippocampal neurons. In mid-axonal regions we found predominantly non-enveloped capsids. Interestingly, we observed both genome-containing and empty capsids that differed significantly in the amount of bound proteins. Viral protein recruitment thus varied between the different cytosolic capsid types, but effective transport occurred despite these differences. Furthermore, we observed three-dimensional snapshots of secondary capsid envelopment in axon terminals. Altogether, this study provides valuable structural detail on axonal HSV1 particles supporting the notion that viral subassemblies are conveyed along the axons to be assembled only after axonal transport.
Collapse
Affiliation(s)
- Iosune Ibiricu
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Juha T. Huiskonen
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Katinka Döhner
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Frank Bradke
- Research Group Axonal Growth and Regeneration, Max Planck Institute of Neurobiology, Martinsried, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Kay Grünewald
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
49
|
Ziółkowska NE, Karotki L, Rehman M, Huiskonen JT, Walther TC. Eisosome-driven plasma membrane organization is mediated by BAR domains. Nat Struct Mol Biol 2011; 18:854-6. [PMID: 21685922 DOI: 10.1038/nsmb.2080] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 04/27/2011] [Indexed: 11/09/2022]
Abstract
Plasma membranes are organized into domains of different protein and lipid composition. Eisosomes are key complexes for yeast plasma membrane organization, containing primarily Pil1 and Lsp1. Here we show that both proteins consist mostly of a banana-shaped BAR domain common to membrane sculpting proteins, most similar to the ones of amphiphysin, arfaptin 2 and endophilin 2. Our data reveal a previously unrecognized family of BAR-domain proteins involved in plasma membrane organization.
Collapse
Affiliation(s)
- Natasza E Ziółkowska
- Max Planck Institute of Biochemistry, Organelle Architecture and Dynamics, Martinsried, Germany
| | | | | | | | | |
Collapse
|
50
|
Habjan M, Penski N, Wagner V, Spiegel M, Overby AK, Kochs G, Huiskonen JT, Weber F. Efficient production of Rift Valley fever virus-like particles: The antiviral protein MxA can inhibit primary transcription of bunyaviruses. Virology 2009; 385:400-8. [PMID: 19155037 DOI: 10.1016/j.virol.2008.12.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 10/30/2008] [Accepted: 12/08/2008] [Indexed: 11/15/2022]
Abstract
Rift Valley fever virus (RVFV) is a highly pathogenic member of the family Bunyaviridae that needs to be handled under biosafety level (BSL) 3 conditions. Here, we describe reverse genetics systems to measure RVFV polymerase activity in mammalian cells and to generate virus-like particles (VLPs). Recombinant polymerase (L) and nucleocapsid protein (N), expressed together with a minireplicon RNA, formed transcriptionally active nucleocapsids. These could be packaged into VLPs by additional expression of viral glycoproteins. The VLPs resembled authentic virus particles and were able to infect new cells. After infection, VLP-associated nucleocapsids autonomously performed primary transcription, and co-expression of L and N in VLP-infected cells allowed subsequent replication and secondary transcription. Bunyaviruses are potently inhibited by a human interferon-induced protein, MxA. However, the affected step in the infection cycle is not entirely characterized. Using the VLP system, we demonstrate that MxA inhibits both primary and secondary transcriptions of RVFV. A set of infection assays distinguishing between virus attachment, entry, and subsequent RNA synthesis confirmed that MxA is able to target immediate early RNA synthesis of incoming RVFV particles. Thus, our reverse genetics systems are useful for dissecting individual steps of RVFV infection under non-BSL3 conditions.
Collapse
Affiliation(s)
- Matthias Habjan
- Department of Virology, University of Freiburg, D-79008 Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|