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Ahmad A, Tigabu B, Ivanov A, Jerebtsova M, Ammosova T, Ramanathan P, Kumari N, Brantner CA, Pietzsch CA, Simhadri J, Abdullah G, Uversky VN, Paromov V, Popratiloff A, Widen S, Bukreyev A, Nekhai S. Ebola virus nucleoprotein interaction with host protein phosphatase-1 regulates its dimerization and capsid formation. J Biol Chem 2025; 301:108541. [PMID: 40288648 DOI: 10.1016/j.jbc.2025.108541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2025] [Revised: 04/11/2025] [Accepted: 04/15/2025] [Indexed: 04/29/2025] Open
Abstract
Ebola virus (EBOV) replication is regulated by the host protein phosphatases, PP1 and PP2A, which dephosphorylate the transcriptional cofactor of EBOV polymerase VP30. The PP1-targeting compound 1E7-03 induces VP30 phosphorylation and inhibits EBOV infection. Here, we investigate the broader role of PP1 in EBOV replication and transcription, including its interaction with nucleoprotein (NP). When EBOV-infected cells were continuously treated with 1E7-03, the NP E619K mutation was found and selected for further analysis. The NP E619K mutation moderately reduced the EBOV minigenome transcription, which was restored by the treatment with 1E7-03. Proteomics, immunoprecipitation, dimerization, split NanoBit, and colocalization analyses indicated that NP interacts with PP1 and that NP E619K mutations enhanced this binding. Treatment with 1E7-03 dissociated PP1-NP complex, but enhanced NP dimerization, which was more pronounced for NP E619K mutant. Mutation and deletion analyses pointed to several potential PP1-binding sites in NP that were located in the moderately disordered NP regions. When NP was co-expressed with VP24 and VP35, formation of EBOV capsids was impaired with NP E619K mutation. Treatment with 1E7-03 restored the capsid formation by the NP E619K mutant but inhibited capsids formed by WT NP. Our findings suggest that PP1 binds to NP and that this binding might regulate NP dimerization and capsid formation. Collectively, our results point to a new role for PP1 in EBOV replication, in which NP binding to PP1 may facilitate viral transcription by delaying capsid formation and EBOV replication.
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Affiliation(s)
- Asrar Ahmad
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA
| | - Bersabeh Tigabu
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA
| | - Marina Jerebtsova
- Department of Microbiology, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA; Department of Medicine, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Palaniappan Ramanathan
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Namita Kumari
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA; Department of Microbiology, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Christine A Brantner
- GW Nanofabrication and Imaging Center, The George Washington University, Washington, District of Columbia, USA
| | - Colette A Pietzsch
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Jyothirmai Simhadri
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA
| | - Ghadeer Abdullah
- Department of Biology, College of Art and Science, Howard University, Washington, District of Columbia, USA
| | - Vladmir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Anastas Popratiloff
- GW Nanofabrication and Imaging Center, The George Washington University, Washington, District of Columbia, USA
| | - Steve Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, Texas, USA; Department Microbiology & Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA.
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia, USA; Department of Microbiology, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Medicine, College of Medicine, Howard University, Washington, District of Columbia, USA.
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2
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Fujita-Fujiharu Y, Hu S, Hirabayashi A, Takamatsu Y, Ng YN, Houri K, Muramoto Y, Nakano M, Sugita Y, Noda T. Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24. Nat Commun 2025; 16:2171. [PMID: 40064872 PMCID: PMC11894184 DOI: 10.1038/s41467-025-57236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 02/14/2025] [Indexed: 03/14/2025] Open
Abstract
The Ebola virus, a member of the Filoviridae family, causes severe hemorrhagic fever in humans. Filamentous virions contain a helical nucleocapsid responsible for genome transcription, replication, and packaging into progeny virions. The nucleocapsid consists of a helical nucleoprotein (NP)-viral genomic RNA complex forming the core structure, to which VP24 and VP35 bind externally. Two NPs, each paired with a VP24 molecule, constitute a repeating unit. However, the detailed nucleocapsid structure remains unclear. Here, we determine the nucleocapsid-like structure within virus-like particles at 4.6 Å resolution using single-particle cryo-electron microscopy. Mutational analysis identifies specific interactions between the two NPs and two VP24s and demonstrates that each of the two VP24s in different orientations distinctively regulates nucleocapsid assembly, viral RNA synthesis, intracellular transport of the nucleocapsid, and infectious virion production. Our findings highlight the sophisticated mechanisms underlying the assembly and functional regulation of the nucleocapsid and provide insights into antiviral development.
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Affiliation(s)
- Yoko Fujita-Fujiharu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Shangfan Hu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Yuki Takamatsu
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki City, Nagasaki, 852-8102, Japan
| | - Yen Ni Ng
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Kazuya Houri
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Yukiko Muramoto
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Masahiro Nakano
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan
| | - Yukihiko Sugita
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Saitama, Kawaguchi, 332-0012, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto, 606-8501, Japan.
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3
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Bahojb Mahdavi SZ, Jebelli A, Aghbash PS, Baradaran B, Amini M, Oroojalian F, Pouladi N, Baghi HB, de la Guardia M, Mokhtarzadeh AA. A comprehensive overview on the crosstalk between microRNAs and viral pathogenesis and infection. Med Res Rev 2025; 45:349-425. [PMID: 39185567 PMCID: PMC11796338 DOI: 10.1002/med.22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 04/11/2023] [Accepted: 08/04/2024] [Indexed: 08/27/2024]
Abstract
Infections caused by viruses as the smallest infectious agents, pose a major threat to global public health. Viral infections utilize different host mechanisms to facilitate their own propagation and pathogenesis. MicroRNAs (miRNAs), as small noncoding RNA molecules, play important regulatory roles in different diseases, including viral infections. They can promote or inhibit viral infection and have a pro-viral or antiviral role. Also, viral infections can modulate the expression of host miRNAs. Furthermore, viruses from different families evade the host immune response by producing their own miRNAs called viral miRNAs (v-miRNAs). Understanding the replication cycle of viruses and their relation with host miRNAs and v-miRNAs can help to find new treatments against viral infections. In this review, we aim to outline the structure, genome, and replication cycle of various viruses including hepatitis B, hepatitis C, influenza A virus, coronavirus, human immunodeficiency virus, human papillomavirus, herpes simplex virus, Epstein-Barr virus, Dengue virus, Zika virus, and Ebola virus. We also discuss the role of different host miRNAs and v-miRNAs and their role in the pathogenesis of these viral infections.
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Affiliation(s)
- Seyedeh Zahra Bahojb Mahdavi
- Department of Biology, Faculty of Basic SciencesAzarbaijan Shahid Madani UniversityTabrizIran
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Asiyeh Jebelli
- Department of Biological Science, Faculty of Basic ScienceHigher Education Institute of Rab‐RashidTabrizIran
- Tuberculosis and Lung Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | | | - Behzad Baradaran
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad Amini
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of MedicineNorth Khorasan University of Medical SciencesBojnurdIran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic SciencesAzarbaijan Shahid Madani UniversityTabrizIran
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4
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Liu X, Stahelin RV, Pienaar E. Impact of Ebola virus nucleoprotein on VP40 virus-like particle production: a computational approach. Commun Biol 2024; 7:634. [PMID: 38796621 PMCID: PMC11128010 DOI: 10.1038/s42003-024-06300-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Ebola virus (EBOV) matrix protein VP40 can assemble and bud as virus-like particles (VLPs) when expressed alone in mammalian cells. Nucleoprotein (NP) could be recruited to VLPs as inclusion body (IB) when co-expressed, and increase VLP production. However, the mechanism behind it remains unclear. Here, we use a computational approach to study NP-VP40 interactions. Our simulations indicate that NP may enhance VLP production through stabilizing VP40 filaments and accelerating the VLP budding step. Further, both the relative timing and amount of NP expression compared to VP40 are important for the effective production of IB-containing VLPs. We predict that relative NP/VP40 expression ratio and time are important for efficient production of IB-containing VLPs. We conclude that disrupting the expression timing and amount of NP and VP40 could provide new avenues to treat EBOV infection. This work provides quantitative insights into EBOV proteins interactions and how virion generation and drug efficacy could be influenced.
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Affiliation(s)
- Xiao Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN, USA.
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5
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Collados Rodríguez M, Maillard P, Journeaux A, Komarova AV, Najburg V, David RYS, Helynck O, Guo M, Zhong J, Baize S, Tangy F, Jacob Y, Munier-Lehmann H, Meurs EF. Novel Antiviral Molecules against Ebola Virus Infection. Int J Mol Sci 2023; 24:14791. [PMID: 37834238 PMCID: PMC10573436 DOI: 10.3390/ijms241914791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Infection with Ebola virus (EBOV) is responsible for hemorrhagic fever in humans with a high mortality rate. Combined efforts of prevention and therapeutic intervention are required to tackle highly variable RNA viruses, whose infections often lead to outbreaks. Here, we have screened the 2P2I3D chemical library using a nanoluciferase-based protein complementation assay (NPCA) and isolated two compounds that disrupt the interaction of the EBOV protein fragment VP35IID with the N-terminus of the dsRNA-binding proteins PKR and PACT, involved in IFN response and/or intrinsic immunity, respectively. The two compounds inhibited EBOV infection in cell culture as well as infection by measles virus (MV) independently of IFN induction. Consequently, we propose that the compounds are antiviral by restoring intrinsic immunity driven by PACT. Given that PACT is highly conserved across mammals, our data support further testing of the compounds in other species, as well as against other negative-sense RNA viruses.
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Affiliation(s)
- Mila Collados Rodríguez
- School of Infection & Immunity (SII), College of Medical, Veterinary and Life Sciences (MVLS), Sir Michael Stoker Building, MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Patrick Maillard
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Alexandra Journeaux
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France;
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Raul-Yusef Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Blizard Institute—Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Olivier Helynck
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Mingzhe Guo
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Jin Zhong
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Sylvain Baize
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Yves Jacob
- Université Paris Cité, 75013 Paris, France;
- Unité Génétique Moléculaire des Virus à ARN, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France
| | - Hélène Munier-Lehmann
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Eliane F. Meurs
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
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6
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Ahmad A, Tigabu B, Ivanov A, Jerebtsova M, Ammosova T, Ramanathan P, Kumari N, Brantner CA, Pietzsch CA, Abdullah G, Popratiloff A, Widen S, Bukreyev A, Nekhai S. Ebola Virus NP Binding to Host Protein Phosphatase-1 Regulates Capsid Formation. RESEARCH SQUARE 2023:rs.3.rs-2963943. [PMID: 37333330 PMCID: PMC10274954 DOI: 10.21203/rs.3.rs-2963943/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Ebola virus (EBOV) transcriptional regulation involves host protein phosphatases PP1 and PP2A, which dephosphorylate the transcriptional cofactor of EBOV polymerase VP30. The 1E7-03 compound, which targets PP1, induces VP30 phosphorylation and inhibits EBOV infection. This study aimed to investigate the role of PP1 in EBOV replication. When EBOV-infected cells were continuously treated with 1E7-03, the NP E619K mutation was selected. This mutation moderately reduced EBOV minigenome transcription, which was restored by the treatment with 1E7-03. Formation of EBOV capsids, when NP was co-expressed with VP24 and VP35, was impaired with NPE 619K. Treatment with 1E7-03 restored capsid formation by NP E619K mutation, but inhibited capsids formed by WT NP. The dimerization of NP E619K, tested in a split NanoBiT assay, was significantly decreased (~ 15-fold) compared to WT NP. NP E619K bound more efficiently to PP1 (~ 3-fold) but not B56 subunit of PP2A or VP30. Cross-linking and co-immunoprecipitation experiments showed fewer monomers and dimers for NP E619K which were increased with 1E7-03 treatment. NP E619K showed increased co-localization with PP1α compared to WT NP. Mutations of potential PP1 binding sites and NP deletions disrupted its interaction with PP1. Collectively, our findings suggest that PP1 binding to the NP regulates NP dimerization and capsid formation, and that NP E619K mutation, which has the enhanced PP1 binding, disrupts these processes. Our results point to a new role for PP1 in EBOV replication in which NP binding to PP1 may facilitate viral transcription by delaying capsid formation and EBOV replication.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Steve Widen
- UTMB: The University of Texas Medical Branch at Galveston
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7
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Sun W, Luan F, Wang J, Ma L, Li X, Yang G, Hao C, Qin X, Dong S. Structural insights into the interactions between lloviu virus VP30 and nucleoprotein. Biochem Biophys Res Commun 2022; 616:82-88. [PMID: 35649303 DOI: 10.1016/j.bbrc.2022.05.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
Abstract
The family Filoviridae comprises many notorious viruses, such as Ebola virus (EBOV) and Marburg virus (MARV), that can infect humans and nonhuman primates. Lloviu virus (LLOV), a less well studied filovirus, is considered a potential pathogen for humans. The VP30 C-terminal domain (CTD) of these filoviruses exhibits nucleoprotein (NP) binding and plays an essential role in viral transcription, replication and assembly. In this study, we confirmed the interactions between LLOV VP30 CTD and its NP fragment, and also determined the crystal structure of the chimeric dimeric LLOV NP-VP30 CTD at 2.50 Å resolution. The structure is highly conserved across the family Filoviridae. While in the dimer structure, only one VP30 CTD binds the NP fragment, which indicates that the interaction between LLOV VP30 CTD and NP is not strong. Our work provides a preliminary model to investigate the interactions between LLOV VP30 and NP and suggests a potential target for anti-filovirus drug development.
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Affiliation(s)
- Weiyan Sun
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Fuchen Luan
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jiajia Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Lin Ma
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xiuxiu Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China
| | - Gongxian Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China
| | - Chenyang Hao
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China.
| | - Shishang Dong
- School of Biological Science and Technology, University of Jinan, Jinan, China.
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8
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Abstract
Filovirus-infected cells are characterized by typical cytoplasmic inclusion bodies (IBs) located in the perinuclear region. The formation of these IBs is induced mainly by the accumulation of the filoviral nucleoprotein NP, which recruits the other nucleocapsid proteins, the polymerase co-factor VP35, the polymerase L, the transcription factor VP30 and VP24 via direct or indirect protein-protein interactions. Replication of the negative-strand RNA genomes by the viral polymerase L and VP35 occurs in the IBs, resulting in the synthesis of positive-strand genomes, which are encapsidated by NP, thus forming ribonucleoprotein complexes (antigenomic RNPs). These newly formed antigenomic RNPs in turn serve as templates for the synthesis of negative-strand RNA genomes that are also encapsidated by NP (genomic RNPs). Still in the IBs, genomic RNPs mature into tightly packed transport-competent nucleocapsids (NCs) by the recruitment of the viral protein VP24. NCs are tightly coiled left-handed helices whose structure is mainly determined by the multimerization of NP at its N-terminus, and these helices form the inner layer of the NCs. The RNA genome is fixed by 2 lobes of the NP N-terminus and is thus guided by individual NP molecules along the turns of the helix. Direct interaction of the NP C-terminus with the VP35 and VP24 molecules forms the outer layer of the NCs. Once formed, NCs that are located at the border of the IBs recruit actin polymerization machinery to one of their ends to drive their transport to budding sites for their envelopment and final release. Here, we review the current knowledge on the structure, assembly, and transport of filovirus NCs.
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Affiliation(s)
- Olga Dolnik
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
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Šantak M, Matić Z. The Role of Nucleoprotein in Immunity to Human Negative-Stranded RNA Viruses—Not Just Another Brick in the Viral Nucleocapsid. Viruses 2022; 14:v14030521. [PMID: 35336928 PMCID: PMC8955406 DOI: 10.3390/v14030521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 12/21/2022] Open
Abstract
Negative-stranded RNA viruses (NSVs) are important human pathogens, including emerging and reemerging viruses that cause respiratory, hemorrhagic and other severe illnesses. Vaccine design traditionally relies on the viral surface glycoproteins. However, surface glycoproteins rarely elicit effective long-term immunity due to high variability. Therefore, an alternative approach is to include conserved structural proteins such as nucleoprotein (NP). NP is engaged in myriad processes in the viral life cycle: coating and protection of viral RNA, regulation of transcription/replication processes and induction of immunosuppression of the host. A broad heterosubtypic T-cellular protection was ascribed very early to this protein. In contrast, the understanding of the humoral immunity to NP is very limited in spite of the high titer of non-neutralizing NP-specific antibodies raised upon natural infection or immunization. In this review, the data with important implications for the understanding of the role of NP in the immune response to human NSVs are revisited. Major implications of the elicited T-cell immune responses to NP are evaluated, and the possible multiple mechanisms of the neglected humoral response to NP are discussed. The intention of this review is to remind that NP is a very promising target for the development of future vaccines.
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The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:v13122465. [PMID: 34960734 PMCID: PMC8708338 DOI: 10.3390/v13122465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
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11
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Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
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12
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Wu L, Jin D, Wang D, Jing X, Gong P, Qin Y, Chen M. The two-stage interaction of Ebola virus VP40 with nucleoprotein results in a switch from viral RNA synthesis to virion assembly/budding. Protein Cell 2020; 13:120-140. [PMID: 33141416 PMCID: PMC8783937 DOI: 10.1007/s13238-020-00764-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022] Open
Abstract
Ebola virus (EBOV) is an enveloped negative-sense RNA virus and a member of the filovirus family. Nucleoprotein (NP) expression alone leads to the formation of inclusion bodies (IBs), which are critical for viral RNA synthesis. The matrix protein, VP40, not only plays a critical role in virus assembly/budding, but also can regulate transcription and replication of the viral genome. However, the molecular mechanism by which VP40 regulates viral RNA synthesis and virion assembly/budding is unknown. Here, we show that within IBs the N-terminus of NP recruits VP40 and is required for VLP-containing NP release. Furthermore, we find four point mutations (L692A, P697A, P698A and W699A) within the C-terminal hydrophobic core of NP result in a stronger VP40-NP interaction within IBs, sequestering VP40 within IBs, reducing VP40-VLP egress, abolishing the incorporation of NC-like structures into VP40-VLP, and inhibiting viral RNA synthesis, suggesting that the interaction of N-terminus of NP with VP40 induces a conformational change in the C-terminus of NP. Consequently, the C-terminal hydrophobic core of NP is exposed and binds VP40, thereby inhibiting RNA synthesis and initiating virion assembly/budding.
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Affiliation(s)
- Linjuan Wu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dongning Jin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dan Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xuping Jing
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Gong
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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13
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Monette A, Mouland AJ. Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. Viruses 2020; 12:E1179. [PMID: 33081049 PMCID: PMC7589941 DOI: 10.3390/v12101179] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
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14
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Luo M, Terrell JR, Mcmanus SA. Nucleocapsid Structure of Negative Strand RNA Virus. Viruses 2020; 12:E835. [PMID: 32751700 PMCID: PMC7472042 DOI: 10.3390/v12080835] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. In NSVs, the single strand RNA genome is encapsidated in the linear nucleocapsid throughout the viral replication cycle. Subunits of the nucleocapsid protein are parallelly aligned along the RNA genome that is sandwiched between two domains composed of conserved helix motifs. The viral RNA-dependent-RNA polymerase (vRdRp) must recognize the protein-RNA complex of the nucleocapsid and unveil the protected genomic RNA in order to initiate viral RNA synthesis. In addition, vRdRp must continuously translocate along the protein-RNA complex during elongation in viral RNA synthesis. This unique mechanism of viral RNA synthesis suggests that the nucleocapsid may play a regulatory role during NSV replication.
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Affiliation(s)
- Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; (J.R.T.); (S.A.M.)
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15
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Miyake T, Farley CM, Neubauer BE, Beddow TP, Hoenen T, Engel DA. Ebola Virus Inclusion Body Formation and RNA Synthesis Are Controlled by a Novel Domain of Nucleoprotein Interacting with VP35. J Virol 2020; 94:e02100-19. [PMID: 32493824 PMCID: PMC7394894 DOI: 10.1128/jvi.02100-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/24/2020] [Indexed: 12/15/2022] Open
Abstract
Ebola virus (EBOV) inclusion bodies (IBs) are cytoplasmic sites of nucleocapsid formation and RNA replication, housing key steps in the virus life cycle that warrant further investigation. During infection, IBs display dynamic properties regarding their size and location. The contents of IBs also must transition prior to further viral maturation, assembly, and release, implying additional steps in IB function. Interestingly, the expression of the viral nucleoprotein (NP) alone is sufficient for the generation of IBs, indicating that it plays an important role in IB formation during infection. In addition to NP, other components of the nucleocapsid localize to IBs, including VP35, VP24, VP30, and the RNA polymerase L. We previously defined and solved the crystal structure of the C-terminal domain of NP (NP-Ct), but its role in virus replication remained unclear. Here, we show that NP-Ct is necessary for IB formation when NP is expressed alone. Interestingly, we find that NP-Ct is also required for the production of infectious virus-like particles (VLPs), and that defective VLPs with NP-Ct deletions are significantly reduced in viral RNA content. Furthermore, coexpression of the nucleocapsid component VP35 overcomes deletion of NP-Ct in triggering IB formation, demonstrating a functional interaction between the two proteins. Of all the EBOV proteins, only VP35 is able to overcome the defect in IB formation caused by the deletion of NP-Ct. This effect is mediated by a novel protein-protein interaction between VP35 and NP that controls both regulation of IB formation and RNA replication itself and that is mediated by a newly identified functional domain of NP, the central domain.IMPORTANCE Inclusion bodies (IBs) are cytoplasmic sites of RNA synthesis for a variety of negative-sense RNA viruses, including Ebola virus. In addition to housing important steps in the viral life cycle, IBs protect new viral RNA from innate immune attack and contain specific host proteins whose function is under study. A key viral factor in Ebola virus IB formation is the nucleoprotein, NP, which also is important in RNA encapsidation and synthesis. In this study, we have identified two domains of NP that control inclusion body formation. One of these, the central domain (CD), interacts with viral protein VP35 to control both inclusion body formation and RNA synthesis. The other is the NP C-terminal domain (NP-Ct), whose function has not previously been reported. These findings contribute to a model in which NP and its interactions with VP35 link the establishment of IBs to the synthesis of viral RNA.
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Affiliation(s)
- Tsuyoshi Miyake
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Charlotte M Farley
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Benjamin E Neubauer
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Thomas P Beddow
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Daniel A Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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16
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Ivanov A, Ramanathan P, Parry C, Ilinykh PA, Lin X, Petukhov M, Obukhov Y, Ammosova T, Amarasinghe GK, Bukreyev A, Nekhai S. Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription. Cell Mol Life Sci 2020; 77:2579-2603. [PMID: 31562565 PMCID: PMC7101265 DOI: 10.1007/s00018-019-03303-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022]
Abstract
Ebola virus (EBOV) causes severe human disease with a high case fatality rate. The balance of evidence implies that the virus circulates in bats. The molecular basis for host-viral interactions, including the role for phosphorylation during infections, is largely undescribed. To address this, and to better understand the biology of EBOV, the phosphorylation of EBOV proteins was analyzed in virions purified from infected monkey Vero-E6 cells and bat EpoNi/22.1 cells using high-resolution mass spectrometry. All EBOV structural proteins were detected with high coverage, along with phosphopeptides. Phosphorylation sites were identified in all viral structural proteins. Comparison of EBOV protein phosphorylation in monkey and bat cells showed only partial overlap of phosphorylation sites, with shared sites found in NP, VP35, and VP24 proteins, and no common sites in the other proteins. Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites. Phosphorylation of one of the identified sites in VP35, Thr-210, was demonstrated to govern the transcriptional activity of the EBOV polymerase complex. Thr-210 phosphorylation was also shown to be important for VP35 interaction with NP. This is the first study to compare phosphorylation of all EBOV virion proteins produced in primate versus bat cells, and to demonstrate the role of VP35 phosphorylation in the viral life cycle. The results uncover a novel mechanism of EBOV transcription and identify novel targets for antiviral drug development.
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Affiliation(s)
- Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Palaniappan Ramanathan
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Christian Parry
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Xionghao Lin
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- College of Dentistry, Howard University, Washington, D.C., 20059, USA
| | - Michael Petukhov
- Division of Molecular and Radiation Biophysics, Russian Nuclear Physics Institute Named After B. P. Konstantinov, National Research Center "Kurchatov Institute", Gatchina, 188300, Russia
- Russian Scientific Center of Radiology and Surgical Technologies Named After A. M. Granov, St. Petersburg, 197758, Russia
| | - Yuri Obukhov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Medicine, Howard University, Washington, D.C., 20059, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Department of Microbiology and Immunology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Galveston National Laboratory, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA.
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA.
- Department of Medicine, Howard University, Washington, D.C., 20059, USA.
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17
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Identification of interferon-stimulated genes that attenuate Ebola virus infection. Nat Commun 2020; 11:2953. [PMID: 32528005 PMCID: PMC7289892 DOI: 10.1038/s41467-020-16768-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/17/2020] [Indexed: 12/26/2022] Open
Abstract
The West Africa Ebola outbreak was the largest outbreak ever recorded, with over 28,000 reported infections; this devastating epidemic emphasized the need to understand the mechanisms to counteract virus infection. Here, we screen a library of nearly 400 interferon-stimulated genes (ISGs) against a biologically contained Ebola virus and identify several ISGs not previously known to affect Ebola virus infection. Overexpression of the top ten ISGs attenuates virus titers by up to 1000-fold. Mechanistic studies demonstrate that three ISGs interfere with virus entry, six affect viral transcription/replication, and two inhibit virion formation and budding. A comprehensive study of one ISG (CCDC92) that shows anti-Ebola activity in our screen reveals that CCDC92 can inhibit viral transcription and the formation of complete virions via an interaction with the viral protein NP. Our findings provide insights into Ebola virus infection that could be exploited for the development of therapeutics against this virus. Here, Kuroda et al. screen a library of nearly 400 interferon-stimulated genes (ISGs) and identify several ISGs that inhibit Ebola virus entry, viral transcription/replication, or virion formation. The study provides insights into interactions between Ebola and the host cells.
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18
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Herst CV, Burkholz S, Sidney J, Sette A, Harris PE, Massey S, Brasel T, Cunha-Neto E, Rosa DS, Chao WCH, Carback R, Hodge T, Wang L, Ciotlos S, Lloyd P, Rubsamen R. An effective CTL peptide vaccine for Ebola Zaire Based on Survivors' CD8+ targeting of a particular nucleocapsid protein epitope with potential implications for COVID-19 vaccine design. Vaccine 2020; 38:4464-4475. [PMID: 32418793 PMCID: PMC7186210 DOI: 10.1016/j.vaccine.2020.04.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/07/2020] [Accepted: 04/12/2020] [Indexed: 12/21/2022]
Abstract
The 2013-2016 West Africa EBOV epidemic was the biggest EBOV outbreak to date. An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. The dominant response (25/26 subjects) was specific to the EBOV nucleocapsid protein (NP). It has been suggested that epitopes on the EBOV NP could form an important part of an effective T-cell vaccine for Ebola Zaire. We show that a 9-amino-acid peptide NP44-52 (YQVNNLEEI) located in a conserved region of EBOV NP provides protection against morbidity and mortality after mouse adapted EBOV challenge. A single vaccination in a C57BL/6 mouse using an adjuvanted microsphere peptide vaccine formulation containing NP44-52 is enough to confer immunity in mice. Our work suggests that a peptide vaccine based on CD8+ T-cell immunity in EBOV survivors is conceptually sound and feasible. Nucleocapsid proteins within SARS-CoV-2 contain multiple Class I epitopes with predicted HLA restrictions consistent with broad population coverage. A similar approach to a CTL vaccine design may be possible for that virus.
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MESH Headings
- Amino Acid Sequence
- Animals
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Disease Models, Animal
- Drug Design
- Ebola Vaccines/chemistry
- Ebola Vaccines/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/prevention & control
- Humans
- Mice
- Mice, Inbred C57BL
- Nucleocapsid Proteins/chemistry
- Nucleocapsid Proteins/immunology
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- T-Lymphocytes, Cytotoxic/immunology
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Viral Vaccines/chemistry
- Viral Vaccines/immunology
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Affiliation(s)
- C V Herst
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - S Burkholz
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - J Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, CA 92037, United States
| | - A Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, CA 92037, United States
| | - P E Harris
- Endocrinology Division, Department of Medicine, School of Medicine, Columbia University, New York, NY, USA
| | - S Massey
- University of Texas, Medical Branch, 301 University Blvd, Galveston, TX 77555, United States
| | - T Brasel
- University of Texas, Medical Branch, 301 University Blvd, Galveston, TX 77555, United States
| | - E Cunha-Neto
- Laboratory of Clinical Immunology and Allergy-LIM60, University of São Paulo School of Medicine, São Paulo, Brazil; Institute for Investigation in Immunology (iii) INCT, São Paulo, Brazil; Heart Institute (Incor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - D S Rosa
- Institute for Investigation in Immunology (iii) INCT, São Paulo, Brazil; Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP/EPM), São Paulo, Brazil
| | - W C H Chao
- University of Macau, E12 Avenida da Universidade, Taipa, Macau, China
| | - R Carback
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - T Hodge
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - L Wang
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - S Ciotlos
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - P Lloyd
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States
| | - R Rubsamen
- Flow Pharma, Inc., 3451 Vincent Road, Pleasant Hill, CA 94523, United States; Massachusetts General Hospital, Department of Anesthesia, Critical Care and Pain Medicine, 55 Fruit St, Boston, MA 02114, United States.
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19
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Li G, Liu X, Yang M, Zhang G, Wang Z, Guo K, Gao Y, Jiao P, Sun J, Chen C, Wang H, Deng W, Xiao H, Li S, Wu H, Wang Y, Cao L, Jia Z, Shang L, Yang C, Guo Y, Rao Z. Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design. J Virol 2020; 94:e02125-19. [PMID: 32075933 PMCID: PMC7199414 DOI: 10.1128/jvi.02125-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 01/21/2023] Open
Abstract
African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs that is responsible for serious economic and production losses. It is caused by the African swine fever virus (ASFV), a large and complex icosahedral DNA virus of the Asfarviridae family. Currently, there is no effective treatment or approved vaccine against the ASFV. pS273R, a specific SUMO-1 cysteine protease, catalyzes the maturation of the pp220 and pp62 polyprotein precursors into core-shell proteins. Here, we present the crystal structure of the ASFV pS273R protease at a resolution of 2.3 Å. The overall structure of the pS273R protease is represented by two domains named the "core domain" and the N-terminal "arm domain." The "arm domain" contains the residues from M1 to N83, and the "core domain" contains the residues from N84 to A273. A structure analysis reveals that the "core domain" shares a high degree of structural similarity with chlamydial deubiquitinating enzyme, sentrin-specific protease, and adenovirus protease, while the "arm domain" is unique to ASFV. Further, experiments indicated that the "arm domain" plays an important role in maintaining the enzyme activity of ASFV pS273R. Moreover, based on the structural information of pS273R, we designed and synthesized several peptidomimetic aldehyde compounds at a submolar 50% inhibitory concentration, which paves the way for the design of inhibitors to target this severe pathogen.IMPORTANCE African swine fever virus, a large and complex icosahedral DNA virus, causes a deadly infection in domestic pigs. In addition to Africa and Europe, countries in Asia, including China, Vietnam, and Mongolia, were negatively affected by the hazards posed by ASFV outbreaks in 2018 and 2019, at which time more than 30 million pigs were culled. Until now, there has been no vaccine for protection against ASFV infection or effective treatments to cure ASF. Here, we solved the high-resolution crystal structure of the ASFV pS273R protease. The pS273R protease has a two-domain structure that distinguishes it from other members of the SUMO protease family, while the unique "arm domain" has been proven to be essential for its hydrolytic activity. Moreover, the peptidomimetic aldehyde compounds designed to target the substrate binding pocket exert prominent inhibitory effects and can thus be used in a potential lead for anti-ASFV drug development.
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Affiliation(s)
- Guobang Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Xiaoxia Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Mengyuan Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Guangshun Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Zhengyang Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Kun Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Yuxue Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Peng Jiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Weilong Deng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Huihe Xiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Sizheng Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Haoru Wu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Ying Wang
- Tianjin Crops Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- College of Life Science, Nankai University, Tianjin, People's Republic of China
| | - Zihan Jia
- College of Life Science, Nankai University, Tianjin, People's Republic of China
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Luqing Shang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
- Frontiers Science Center for Cell Responses, Nankai University, Tianjin, People's Republic of China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, People's Republic of China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China
- College of Life Science, Nankai University, Tianjin, People's Republic of China
- Frontiers Science Center for Cell Responses, Nankai University, Tianjin, People's Republic of China
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20
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Lin AE, Diehl WE, Cai Y, Finch CL, Akusobi C, Kirchdoerfer RN, Bollinger L, Schaffner SF, Brown EA, Saphire EO, Andersen KG, Kuhn JH, Luban J, Sabeti PC. Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111. Viruses 2020; 12:E105. [PMID: 31952352 PMCID: PMC7019320 DOI: 10.3390/v12010105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/17/2023] Open
Abstract
For highly pathogenic viruses, reporter assays that can be rapidly performed are critically needed to identify potentially functional mutations for further study under maximal containment (e.g., biosafety level 4 [BSL-4]). The Ebola virus nucleoprotein (NP) plays multiple essential roles during the viral life cycle, yet few tools exist to study the protein under BSL-2 or equivalent containment. Therefore, we adapted reporter assays to measure NP oligomerization and virion-like particle (VLP) production in live cells and further measured transcription and replication using established minigenome assays. As a proof-of-concept, we examined the NP-R111C substitution, which emerged during the 2013‒2016 Western African Ebola virus disease epidemic and rose to high frequency. NP-R111C slightly increased NP oligomerization and VLP budding but slightly decreased transcription and replication. By contrast, a synthetic charge-reversal mutant, NP-R111E, greatly increased oligomerization but abrogated transcription and replication. These results are intriguing in light of recent structures of NP oligomers, which reveal that the neighboring residue, K110, forms a salt bridge with E349 on adjacent NP molecules. By developing and utilizing multiple reporter assays, we find that the NP-111 position mediates a complex interplay between NP's roles in protein structure, virion budding, and transcription and replication.
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Affiliation(s)
- Aaron E. Lin
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Chidiebere Akusobi
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02120, USA;
| | | | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Stephen F. Schaffner
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth A. Brown
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kristian G. Andersen
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Pardis C. Sabeti
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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21
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Ebola virus disease: An emerging and re-emerging viral threat. J Autoimmun 2019; 106:102375. [PMID: 31806422 DOI: 10.1016/j.jaut.2019.102375] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022]
Abstract
The genus Ebolavirus from the family Filoviridae is composed of five species including Sudan ebolavirus, Reston ebolavirus, Bundibugyo ebolavirus, Taï Forest ebolavirus, and Ebola virus (previously known as Zaire ebolavirus). These viruses have a large non-segmented, negative-strand RNA of approximately 19 kb that encodes for glycoproteins (i.e., GP, sGP, ssGP), nucleoproteins, virion proteins (i.e., VP 24, 30,40) and an RNA dependent RNA polymerase. These viruses have become a global health concern because of mortality, their rapid dissemination, new outbreaks in West-Africa, and the emergence of a new condition known as "Post-Ebola virus disease syndrome" that resembles inflammatory and autoimmune conditions such as rheumatoid arthritis, systemic lupus erythematosus and spondyloarthritis with uveitis. However, there are many gaps in the understanding of the mechanisms that may induce the development of such autoimmune-like syndromes. Some of these mechanisms may include a high formation of neutrophil extracellular traps, an uncontrolled "cytokine storm", and the possible formation of auto-antibodies. The likely appearance of autoimmune phenomena in Ebola survivors suppose a new challenge in the management and control of this disease and opens a new field of research in a special subgroup of patients. Herein, the molecular biology, pathogenesis, clinical manifestations, and treatment of Ebola virus disease are reviewed and some strategies for control of disease are discussed.
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22
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Hume AJ, Mühlberger E. Distinct Genome Replication and Transcription Strategies within the Growing Filovirus Family. J Mol Biol 2019; 431:4290-4320. [PMID: 31260690 PMCID: PMC6879820 DOI: 10.1016/j.jmb.2019.06.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/31/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus genera and a sixth proposed genus. While two of these new genera are similar to the ebola- and marburgviruses, the other two, discovered in saltwater fishes, are considerably more diverse. Nonetheless, these viruses retain a number of key features of the other filoviruses. Here, we review the key characteristics of filovirus replication and transcription, highlighting similarities and differences between the viruses. In particular, we focus on key regulatory elements in the genomes, replication and transcription strategies, and the conservation of protein domains and functions among the viruses. In addition, using computational analyses, we were able to identify potential homology and functions for some of the genes of the novel filoviruses with previously unknown functions. Although none of the newly discovered filoviruses have yet been isolated, initial studies of some of these viruses using minigenome systems have yielded insights into their mechanisms of replication and transcription. In general, the Cuevavirus and proposed Dianlovirus genera appear to follow the transcription and replication strategies employed by the ebola- and marburgviruses, respectively. While our knowledge of the fish filoviruses is currently limited to sequence analysis, the lack of certain conserved motifs and even entire genes necessitates that they have evolved distinct mechanisms of replication and transcription.
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Affiliation(s)
- Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
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23
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Alvarez Paggi D, Esperante SA, Salgueiro M, Camporeale G, de Oliveira GAP, Prat Gay G. A conformational switch balances viral RNA accessibility and protection in a nucleocapsid ring model. Arch Biochem Biophys 2019; 671:77-86. [PMID: 31229488 DOI: 10.1016/j.abb.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/30/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
Virus from the Mononegavirales order share common features ranging from virion structure arrangement to mechanisms of replication and transcription. One of them is the way the nucleoprotein (N) wraps and protects the RNA genome from degradation by forming a highly ordered helical nucleocapsid. However, crystal structures from numerous Mononegavirales reveal that binding to the nucleoprotein results in occluded nucleotides that hinder base pairing necessary for transcription and replication. This hints at the existence of alternative conformations of the N protein that would impact on the protein-RNA interface, allowing for transient exposure of the nucleotides without complete RNA release. Moreover, the regulation between the alternative conformations should be finely tuned. Recombinant expression of N from the respiratory syncytial virus form regular N/RNA common among all Mononegavirales, and these constitute an ideal minimal unit for investigating the mechanisms through which these structures protect RNA so efficiently while allowing for partial accessibility during transcription and replication. Neither pH nor high ionic strength could dissociate the RNA but led to irreversible aggregation of the nucleoprotein. Low concentrations of guanidine chloride dissociated the RNA moiety but leading to irreversible aggregation of the protein moiety. On the other hand, high concentrations of urea and long incubation periods were required to remove bound RNA. Both denaturants eventually led to unfolding but converged in the formation of an RNA-free β-enriched intermediate species that remained decameric even at high denaturant concentrations. Although the N-RNA rings interact with the phosphoprotein P, the scaffold of the RNA polymerase complex, this interaction did not lead to RNA dissociation from the rings in vitro. Thus, we have uncovered complex equilibria involving changes in secondary structure of N and RNA loosening, processes that must take place in the context of RNA transcription and replication, whose detailed mechanisms and cellular and viral participants need to be established.
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Affiliation(s)
- D Alvarez Paggi
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
| | - S A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - M Salgueiro
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnêtica Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908-0733, USA
| | - G Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
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24
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Wang Z, Liang H, Cao H, Zhang B, Li J, Wang W, Qin S, Wang Y, Xuan L, Lai L, Shui W. Efficient ligand discovery from natural herbs by integrating virtual screening, affinity mass spectrometry and targeted metabolomics. Analyst 2019; 144:2881-2890. [PMID: 30788466 DOI: 10.1039/c8an02482k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although natural herbs have been a rich source of compounds for drug discovery, identification of bioactive components from natural herbs suffers from low efficiency and prohibitive cost of the conventional bioassay-based screening platforms. Here we develop a new strategy that integrates virtual screening, affinity mass spectrometry (MS) and targeted metabolomics for efficient discovery of herb-derived ligands towards a specific protein target site. Herb-based virtual screening conveniently selects herbs of potential bioactivity whereas affinity MS combined with targeted metabolomics readily screens candidate compounds in a high-throughput manner. This new integrated approach was benchmarked on screening chemical ligands that target the hydrophobic pocket of the nucleoprotein (NP) of Ebola viruses for which no small molecule ligands have been reported. Seven compounds identified by this approach from the crude extracts of three natural herbs were all validated to bind to the NP target in pure ligand binding assays. Among them, three compounds isolated from Piper nigrum (HJ-1, HJ-4 and HJ-6) strongly promoted the formation of large NP oligomers and reduced the protein thermal stability. In addition, cooperative binding between these chemical ligands and an endogenous peptide ligand was observed, and molecular docking was employed to propose a possible mechanism. Taken together, we established a platform integrating in silico and experimental screening approaches for efficient discovery of herb-derived bioactive ligands especially towards non-enzyme protein targets.
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Affiliation(s)
- Zhihua Wang
- College of Pharmacy, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Hao Liang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Haijie Cao
- College of Pharmacy, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Jun Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Wenqiong Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Lijiang Xuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
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25
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Pleet ML, DeMarino C, Stonier SW, Dye JM, Jacobson S, Aman MJ, Kashanchi F. Extracellular Vesicles and Ebola Virus: A New Mechanism of Immune Evasion. Viruses 2019; 11:v11050410. [PMID: 31052499 PMCID: PMC6563240 DOI: 10.3390/v11050410] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
Ebola virus (EBOV) disease can result in a range of symptoms anywhere from virtually asymptomatic to severe hemorrhagic fever during acute infection. Additionally, spans of asymptomatic persistence in recovering survivors is possible, during which transmission of the virus may occur. In acute infection, substantial cytokine storm and bystander lymphocyte apoptosis take place, resulting in uncontrolled, systemic inflammation in affected individuals. Recently, studies have demonstrated the presence of EBOV proteins VP40, glycoprotein (GP), and nucleoprotein (NP) packaged into extracellular vesicles (EVs) during infection. EVs containing EBOV proteins have been shown to induce apoptosis in recipient immune cells, as well as contain pro-inflammatory cytokines. In this manuscript, we review the current field of knowledge on EBOV EVs including the mechanisms of their biogenesis, their cargo and their effects in recipient cells. Furthermore, we discuss some of the effects that may be induced by EBOV EVs that have not yet been characterized and highlight the remaining questions and future directions.
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Affiliation(s)
- Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Spencer W Stonier
- Department, Emergent BioSolutions, Gaithersburg, MD 20879, USA.
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - John M Dye
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Steven Jacobson
- Viral Immunology Section, Neuroimmunology Branch, National Institute for Neurological Disease and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - M Javad Aman
- Department. Integrated BioTherapeutics, Inc., Gaithersburg, MD 20850, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
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26
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Kirchdoerfer RN, Saphire EO, Ward AB. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex. Acta Crystallogr F Struct Biol Commun 2019; 75:340-347. [PMID: 31045563 PMCID: PMC6497097 DOI: 10.1107/s2053230x19004424] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/01/2019] [Indexed: 02/17/2023] Open
Abstract
Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein-RNA helical filament presented here resembles previous structures determined at lower resolution, while providing improved molecular details of protein-protein and protein-RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid.
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Affiliation(s)
- Robert N. Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Jain S, Baranwal M. Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules. Med Microbiol Immunol 2019; 208:227-238. [PMID: 30790057 DOI: 10.1007/s00430-019-00584-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Immunoinformatics has come by leaps and bounds to finding potent vaccine candidates against various pathogens. In the current study, a combination of different T (CD4+ and CD8+) and B cell epitope prediction tools was applied to find peptides containing multiple epitopes against Ebola nucleoprotein (NP) and the presentation of peptides to human leukocyte antigen (HLA) molecules was analyzed by prediction, docking and population coverage tools. Further, potential peptides were analyzed by ELISA for peptide induced IFN-γ secretion in peripheral blood mononuclear cells isolated from healthy volunteers. Six peptides were obtained after merging the overlapping multiple HLA I (CD8+) and II (CD4+) restricted T cell epitopes as well as B cell epitopes and eliminating the peptides liable to generate autoimmune and allergic response. All peptides displayed 100% conservancy in Zaire ebolavirus. In other Ebola virus species (Sudan, Bundibugyo and Taï forest) and Filoviridae members (Lloviuvirus and Margburgvirus), some peptides were found to be conserved with minor variations. Prediction tools confirmed the ability of predicted peptides to bind with diverse HLA (HLA-A, HLA-B, HLA-DP, HLA-DQ and HLA-DR) alleles. CABS-dock results displayed that the average root mean square deviation (RMSD) value was less than three in majority of cases representing strong binding affinity with HLA alleles. Population coverage analysis predicted high coverage (> 85%) for expected immune response in four continents (Africa, America, Asia and Europe). Nine out of ten blood samples exhibited enhanced IFN-γ secretion for two peptides (P2 and P3). Thus, the identified NP peptides can be considered as potential synthetic vaccine candidates against Ebola virus.
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Affiliation(s)
- Sahil Jain
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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28
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Biomechanical characterization of TIM protein-mediated Ebola virus-host cell adhesion. Sci Rep 2019; 9:267. [PMID: 30670766 PMCID: PMC6342996 DOI: 10.1038/s41598-018-36449-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/21/2018] [Indexed: 01/19/2023] Open
Abstract
Since the most recent outbreak, the Ebola virus (EBOV) epidemic remains one of the world’s public health and safety concerns. EBOV is a negative-sense RNA virus that can infect humans and non-human primates, and causes hemorrhagic fever. It has been proposed that the T-cell immunoglobulin and mucin domain (TIM) family proteins act as cell surface receptors for EBOV, and that the interaction between TIM and phosphatidylserine (PS) on the surface of EBOV mediates the EBOV–host cell attachment. Despite these initial findings, the biophysical properties of the TIM-EBOV interaction, such as the mechanical strength of the TIM-PS bond that allows the virus-cell interaction to resist external mechanical perturbations, have not yet been characterized. This study utilizes single-molecule force spectroscopy to quantify the specific interaction forces between TIM-1 or TIM-4 and the following binding partners: PS, EBOV virus-like particle, and EBOV glycoprotein/vesicular stomatitis virus pseudovirion. Depending on the loading rates, the unbinding forces between TIM and ligands ranged from 40 to 100 pN, suggesting that TIM-EBOV interactions are mechanically comparable to previously reported adhesion molecule–ligand interactions. The TIM-4–PS interaction is more resistant to mechanical force than the TIM-1–PS interaction. We have developed a simple model for virus–host cell interaction that is driven by its adhesion to cell surface receptors and resisted by membrane bending (or tension). Our model identifies critical dimensionless parameters representing the ratio of deformation and adhesion energies, showing how single-molecule adhesion measurements relate quantitatively to the mechanics of virus adhesion to the cell.
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29
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Nasution MAF, Toepak EP, Alkaff AH, Tambunan USF. Flexible docking-based molecular dynamics simulation of natural product compounds and Ebola virus Nucleocapsid (EBOV NP): a computational approach to discover new drug for combating Ebola. BMC Bioinformatics 2018; 19:419. [PMID: 30453886 PMCID: PMC6245692 DOI: 10.1186/s12859-018-2387-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Ebola still remains as one of the most problematic infectious diseases in Africa with a high rate of mortality. Although this disease has been known for an almost half-century, there are no vaccines and drugs available in the market to treat Ebola. Zaire ebolavirus (EBOV), a single-stranded RNA virus which belongs to Filoviridae family and Mononegavirales order, is one of the virus causing Ebola. As one of seven proteins that EBOV encodes, Ebola virus nucleoprotein (EBOV NP) plays an imperative role in EBOV proliferation cycle. Therefore, the development of a new Ebola treatment can be targeted towards EBOV NP. Results In this work, we screened about 190,084 natural product compounds from ZINC15 database through in silico virtual screening and flexible docking simulation. Furthermore, the bioavailability and toxicity prediction have been conducted as well. Two best ligands according to the simulation and prediction tests were progressed into the molecular dynamics simulation. Conclusion In the end, we found that our proposed ligands, namely α-lipomycin (ZINC56874155) and 3-(((S)-1-amino-1,2,3,4-tetrahydroisoquinolin-5-yl)methyl)-5-((5-((5R,7S)-5,7-dihydroxy-3-oxodecyl)-2-hydroxyphenoxy) methyl)pyrrolo[3,4-b]pyrrol-5-ium (ZINC85628951), showed the promising results to be developed as a lead compounds for treating Ebola. Therefore, an experimental study is required to validate their inhibition activities against EBOV NP.
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Affiliation(s)
- Mochammad Arfin Fardiansyah Nasution
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Kampus UI, Depok, 16424, Indonesia
| | - Erwin Prasetya Toepak
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Kampus UI, Depok, 16424, Indonesia
| | - Ahmad Husein Alkaff
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Kampus UI, Depok, 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Kampus UI, Depok, 16424, Indonesia.
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Sugita Y, Matsunami H, Kawaoka Y, Noda T, Wolf M. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution. Nature 2018; 563:137-140. [PMID: 30333622 DOI: 10.1038/s41586-018-0630-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA1,2. The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase1,3. The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion4,5. RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently6. Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core4,5, there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions that lead to the formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion5. The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.
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Affiliation(s)
- Yukihiko Sugita
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hideyuki Matsunami
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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Fanunza E, Frau A, Corona A, Tramontano E. Antiviral Agents Against Ebola Virus Infection: Repositioning Old Drugs and Finding Novel Small Molecules. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2018; 51:135-173. [PMID: 32287476 PMCID: PMC7112331 DOI: 10.1016/bs.armc.2018.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ebola virus (EBOV) causes a deadly hemorrhagic syndrome in humans with mortality rate up to 90%. First reported in Zaire in 1976, EBOV outbreaks showed a fluctuating trend during time and fora long period it was considered a tragic disease confined to the isolated regions of the African continent where the EBOV fear was perpetuated among the poor communities. The extreme severity of the recent 2014-16 EBOV outbreak in terms of fatality rate and rapid spread out of Africa led to the understanding that EBOV is a global health risk and highlights the necessity to find countermeasures against it. In the recent years, several small molecules have been shown to display in vitro and in vivo efficacy against EBOV and some of them have advanced into clinical trials. In addition, also existing drugs have been tested for their anti-EBOV activity and were shown to be promising candidates. However, despite the constant effort addressed to identify anti-EBOV therapeutics, no approved drugs are available against EBOV yet. In this chapter, we describe the main EBOV life cycle steps, providing a detailed picture of the druggable viral and host targets that have been explored so far by different technologies. We then summarize the small molecules, nucleic acid oligomers, and antibody-based therapies reported to have an effect either in in silico, or in biochemical and cell-based assays or in animal models and clinical trials, listing them according to their demonstrated or putative mechanism of action.
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Affiliation(s)
- Elisa Fanunza
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Genetics and Biomedical Research Institute, National Research Council, Monserrato, Italy
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Identification of a small molecule inhibitor of Ebola virus genome replication and transcription using in silico screening. Antiviral Res 2018; 156:46-54. [PMID: 29870771 PMCID: PMC6371959 DOI: 10.1016/j.antiviral.2018.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/16/2018] [Accepted: 06/01/2018] [Indexed: 02/02/2023]
Abstract
Ebola virus (EBOV) causes a severe haemorrhagic fever in humans and has a mortality rate over 50%. With no licensed drug treatments available, EBOV poses a significant threat. Investigations into possible therapeutics have been severely hampered by the classification of EBOV as a BSL4 pathogen. Here, we describe a drug discovery pathway combining in silico screening of compounds predicted to bind to a hydrophobic pocket on the nucleoprotein (NP); with a robust and rapid EBOV minigenome assay for inhibitor validation at BSL2. One compound (MCCB4) was efficacious (EC50 4.8 μM), exhibited low cytotoxicity (CC50 > 100 μM) and was specific, with no effect on either a T7 RNA polymerase driven firefly luciferase or a Bunyamwera virus minigenome. Further investigations revealed that this small molecule inhibitor was able to outcompete established replication complexes, an essential aspect for a potential EBOV treatment. An EBOV drug discovery pathway which is performed at BSL2 and successfully identifies SMIs. MCCB4 is a SMI of EBOV which is effective, specific and not cytotoxic. The effect of MCCB4 was demonstrated in two cell types. MCCB4 is able to outcompete established EBOV replication complexes. SAR analysis was performed with 2nd generation compounds.
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Gumpper RH, Li W, Castañeda CH, Scuderi MJ, Bashkin JK, Luo M. A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid. J Virol 2018; 92:e00146-18. [PMID: 29437970 PMCID: PMC5874401 DOI: 10.1128/jvi.00146-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/17/2022] Open
Abstract
Polyamides have been shown to bind double-stranded DNA by complementing the curvature of the minor groove and forming various hydrogen bonds with DNA. Several polyamide molecules have been found to have potent antiviral activities against papillomavirus, a double-stranded DNA virus. By analogy, we reason that polyamides may also interact with the structured RNA bound in the nucleocapsid of a negative-strand RNA virus. Vesicular stomatitis virus (VSV) was selected as a prototype virus to test this possibility since its genomic RNA encapsidated in the nucleocapsid forms a structure resembling one strand of an A-form RNA duplex. One polyamide molecule, UMSL1011, was found to inhibit infection of VSV. To confirm that the polyamide targeted the nucleocapsid, a nucleocapsid-like particle (NLP) was incubated with UMSL1011. The encapsidated RNA in the polyamide-treated NLP was protected from thermo-release and digestion by RNase A. UMSL1011 also inhibits viral RNA synthesis in the intracellular activity assay for the viral RNA-dependent RNA polymerase. The crystal structure revealed that UMSL1011 binds the structured RNA in the nucleocapsid. The conclusion of our studies is that the RNA in the nucleocapsid is a viable antiviral target of polyamides. Since the RNA structure in the nucleocapsid is similar in all negative-strand RNA viruses, polyamides may be optimized to target the specific RNA genome of a negative-strand RNA virus, such as respiratory syncytial virus and Ebola virus.IMPORTANCE Negative-strand RNA viruses (NSVs) include several life-threatening pathogens, such as rabies virus, respiratory syncytial virus, and Ebola virus. There are no effective antiviral drugs against these viruses. Polyamides offer an exceptional opportunity because they may be optimized to target each NSV. Our studies on vesicular stomatitis virus, an NSV, demonstrated that a polyamide molecule could specifically target the viral RNA in the nucleocapsid and inhibit viral growth. The target specificity of the polyamide molecule was proved by its inhibition of thermo-release and RNA nuclease digestion of the RNA bound in a model nucleocapsid, and a crystal structure of the polyamide inside the nucleocapsid. This encouraging observation provided the proof-of-concept rationale for designing polyamides as antiviral drugs against NSVs.
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Affiliation(s)
- Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
- Molecular Basis of Disease, Georgia State University, Atlanta, Georgia, USA
| | - Weike Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Carlos H Castañeda
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - M José Scuderi
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - James K Bashkin
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
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Ding JN, Zhang YJ, Zhong H, Ao CC, Han JG. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. J Biomol Struct Dyn 2018; 36:1009-1028. [DOI: 10.1080/07391102.2017.1307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
- Department of Clinical Medicine, Anqing Medical College, Anqing 246052, People’s Republic of China
| | - Yan-Jun Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Hui Zhong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Cheng-Cheng Ao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Ju-Guang Han
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
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Su Z, Wu C, Shi L, Luthra P, Pintilie GD, Johnson B, Porter JR, Ge P, Chen M, Liu G, Frederick TE, Binning JM, Bowman GR, Zhou ZH, Basler CF, Gross ML, Leung DW, Chiu W, Amarasinghe GK. Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly. Cell 2018; 172:966-978.e12. [PMID: 29474922 PMCID: PMC5973842 DOI: 10.1016/j.cell.2018.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 12/27/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Abstract
Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NC assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8 Å using electron cryo-microscopy and identified a new regulatory role for eNP helices α22-α23. Biochemical, biophysical, and mutational analyses revealed that inter-eNP contacts within α22-α23 are critical for viral NC assembly and regulate viral RNA synthesis. These observations suggest that the N terminus and α22-α23 of eNP function as context-dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target.
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Affiliation(s)
- Zhaoming Su
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liuqing Shi
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Grigore D Pintilie
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Britney Johnson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Justin R Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peng Ge
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gai Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thomas E Frederick
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jennifer M Binning
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wah Chiu
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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36
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Filovirus proteins for antiviral drug discovery: Structure/function of proteins involved in assembly and budding. Antiviral Res 2018; 150:183-192. [DOI: 10.1016/j.antiviral.2017.12.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/20/2017] [Accepted: 12/28/2017] [Indexed: 01/30/2023]
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Abstract
Filoviruses are highly filamentous enveloped animal viruses that can cause severe haemorrhagic fevers. The filovirus ribonucleoprotein forms a highly organized double-layered helical nucleocapsid (NC) containing five different virally encoded proteins. The inner layer consists of NP, the RNA binding protein, complexed with the monopartite linear genome. A distinctive outer layer links individual NP subunits with bridges composed of VP24-VP35 heterodimers, which achieves condensation of the NP-RNA into tight helical coils. There are no vertical connections between the outer helical layers, explaining the flexibility of the NC and its ability to bend into tight curves without breaking the genomic RNA. These properties allow the formation of enveloped virions with varying polymorphisms, including single, linear, continuous, linked, comma-shaped and torroidal forms. Virion length is modular so that just one, or two or more genome copies may be present in each virion, producing polyploid particles. The matrix protein VP40, which drives budding and envelopment, is found in a layer adjacent to the inner cytoplasmic side of viral envelope and is arranged in a 5 nm lattice structure, but its exact symmetry is unclear. There is a constant low density gap between VP40 and the nucleocapsid, so that the latter is held rigidly centred on the long axis of the viral filament. This gap likely contains a region of flexible contacts between VP40 and the NC. The unique morphology of filoviruses may be related to high titre replication, their ease of transmission, and abilities to invade a wide range of host cells and tissues.
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Abstract
Negative-sense single-stranded RNA virus (NSRV) is featured by their ribonucleoprotein (RNP) complex composed by viral polymerase and genomic RNA enwrapped by nucleocapsid protein (NP). The RNP is packaged in virions and plays a central role throughout virus lifecycle. In the past decade, structural biology presents molecular insights into NPs encoded by most representative NSRVs, helping to understand the mechanism of RNP formation. Interestingly, works initiated from structural biology also reveal unexpected biological functions of virus NP beyond a structural protein. All these further the knowledge of virus NP and provide great potential for the discovery of antiviral agents to target virus RNP formation. In this chapter, we will summarize the structures and functions of viral NPs, as well as the attempt of NP-targeted antiviral development.
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Affiliation(s)
- Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China.
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Singh RK, Dhama K, Malik YS, Ramakrishnan MA, Karthik K, Khandia R, Tiwari R, Munjal A, Saminathan M, Sachan S, Desingu PA, Kattoor JJ, Iqbal HMN, Joshi SK. Ebola virus - epidemiology, diagnosis, and control: threat to humans, lessons learnt, and preparedness plans - an update on its 40 year's journey. Vet Q 2017; 37:98-135. [PMID: 28317453 DOI: 10.1080/01652176.2017.1309474] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 03/17/2017] [Indexed: 02/08/2023] Open
Abstract
Ebola virus (EBOV) is an extremely contagious pathogen and causes lethal hemorrhagic fever disease in man and animals. The recently occurred Ebola virus disease (EVD) outbreaks in the West African countries have categorized it as an international health concern. For the virus maintenance and transmission, the non-human primates and reservoir hosts like fruit bats have played a vital role. For curbing the disease timely, we need effective therapeutics/prophylactics, however, in the absence of any approved vaccine, timely diagnosis and monitoring of EBOV remains of utmost importance. The technologically advanced vaccines like a viral-vectored vaccine, DNA vaccine and virus-like particles are underway for testing against EBOV. In the absence of any effective control measure, the adaptation of high standards of biosecurity measures, strict sanitary and hygienic practices, strengthening of surveillance and monitoring systems, imposing appropriate quarantine checks and vigilance on trade, transport, and movement of visitors from EVD endemic countries remains the answer of choice for tackling the EBOV spread. Herein, we converse with the current scenario of EBOV giving due emphasis on animal and veterinary perspectives along with advances in diagnosis and control strategies to be adopted, lessons learned from the recent outbreaks and the global preparedness plans. To retrieve the evolutionary information, we have analyzed a total of 56 genome sequences of various EBOV species submitted between 1976 and 2016 in public databases.
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Affiliation(s)
- Raj Kumar Singh
- a ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Yashpal Singh Malik
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Kumaragurubaran Karthik
- e Divison of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Rekha Khandia
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Ruchi Tiwari
- g Department of Veterinary Microbiology and Immunology , College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Ashok Munjal
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Mani Saminathan
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Swati Sachan
- h Immunology Section, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Jobin Jose Kattoor
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Hafiz M N Iqbal
- i School of Engineering and Science, Tecnologico de Monterrey , Monterrey , Mexico
| | - Sunil Kumar Joshi
- j Cellular Immunology Lab , Frank Reidy Research Center for Bioelectrics , School of Medical Diagnostics & Translational Sciences, Old Dominion University , Norfolk , VA , USA
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Wan W, Kolesnikova L, Clarke M, Koehler A, Noda T, Becker S, Briggs JAG. Structure and assembly of the Ebola virus nucleocapsid. Nature 2017; 551:394-397. [PMID: 29144446 PMCID: PMC5714281 DOI: 10.1038/nature24490] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.
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Affiliation(s)
- William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Larissa Kolesnikova
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Mairi Clarke
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alexander Koehler
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Takeshi Noda
- Laboratory of Ultrastructural virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - John A. G. Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus. J Virol 2017; 91:JVI.00996-17. [PMID: 28659479 DOI: 10.1128/jvi.00996-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
Filovirus nucleoprotein (NP), viral protein 35 (VP35), and polymerase L are essential for viral replication and nucleocapsid formation. Here, we identify a 28-residue peptide (NP binding peptide [NPBP]) from Marburg virus (MARV) VP35 through sequence alignment with previously identified Ebola virus (EBOV) NPBP, which bound to the core region (residues 18 to 344) of the N-terminal portion of MARV NP with high affinity. The crystal structure of the MARV NP core/NPBP complex at a resolution of 2.6 Å revealed that NPBP binds to the C-terminal region of the NP core via electrostatic and nonpolar interactions. Further structural analysis revealed that the MARV and EBOV NP cores hold a conserved binding pocket for NPBP, and this pocket could serve as a promising target for the design of universal drugs against filovirus infection. In addition, cross-binding assays confirmed that the NP core of MARV or EBOV can bind the NPBP from the other virus, although with moderately reduced binding affinities that result from termini that are distinct between the MARV and EBOV NPBPs.IMPORTANCE Historically, Marburg virus (MARV) has caused severe disease with up to 90% lethality. Among the viral proteins produced by MARV, NP and VP35 are both multifunctional proteins that are essential for viral replication. In its relative, Ebola virus (EBOV), an N-terminal peptide from VP35 binds to the NP N-terminal region with high affinity. Whether this is a common mechanism among filoviruses is an unsolved question. Here, we present the crystal structure of a complex that consists of the core domain of MARV NP and the NPBP peptide from VP35. As we compared MARV NPBP with EBOV NPBP, several different features at the termini were identified. Although these differences reduce the affinity of the NP core for NPBPs across genera, a conserved pocket in the C-terminal region of the NP core makes cross-species binding possible. Our results expand our knowledge of filovirus NP-VP35 interactions and provide more details for therapeutic intervention.
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Yu DS, Weng TH, Wu XX, Wang FX, Lu XY, Wu HB, Wu NP, Li LJ, Yao HP. The lifecycle of the Ebola virus in host cells. Oncotarget 2017; 8:55750-55759. [PMID: 28903457 PMCID: PMC5589696 DOI: 10.18632/oncotarget.18498] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/29/2017] [Indexed: 01/01/2023] Open
Abstract
Ebola haemorrhagic fever causes deadly disease in humans and non-human primates resulting from infection with the Ebola virus (EBOV) genus of the family Filoviridae. However, the mechanisms of EBOV lifecycle in host cells, including viral entry, membrane fusion, RNP formation, GP-tetherin interaction, and VP40-inner leaflet association remain poorly understood. This review describes the biological functions of EBOV proteins and their roles in the lifecycle, summarizes the factors related to EBOV proteins or RNA expression throughout the different phases, and reviews advances with regards to the molecular events and mechanisms of the EBOV lifecycle. Furthermore, the review outlines the aspects remain unclear that urgently need to be solved in future research.
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Affiliation(s)
- Dong-Shan Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tian-Hao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao-Xin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Frederick X.C. Wang
- Department of Bioengineering, Erik Jonsson School of Engineering and Computer Science, The University of Texas at Dallas, Dallas, TX, USA
| | - Xiang-Yun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hai-Bo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus. J Virol 2017; 91:JVI.00825-17. [PMID: 28566377 DOI: 10.1128/jvi.00825-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 12/14/2022] Open
Abstract
Marburg virus (MARV) encodes a nucleoprotein (NP) to encapsidate its genome by oligomerization and form a ribonucleoprotein complex (RNP). According to previous investigation on nonsegmented negative-sense RNA viruses (nsNSV), the newly synthesized NPs must be prevented from indiscriminately binding to noncognate RNAs. During the viral RNA synthesis process, the RNPs undergo a transition from an RNA-bound form to a template-free form, to open access for the interaction between the viral polymerase and the RNA template. In filoviruses, this transition is regulated by VP35 peptide and other viral components. To further understand the dynamic process of filovirus RNP formation, we report here the structure of MARV NPcore, both in the apo form and in the VP35 peptide-chaperoned form. These structures reveal a typical bilobed structure, with a positive-charged RNA binding groove between two lobes. In the apo form, the MARV NP exists in an interesting hexameric state formed by the hydrophobic interaction within the long helix of the NPcore C-terminal region, which shows high structural flexibility among filoviruses and may imply critical function during RNP formation. Moreover, the VP35 peptide-chaperoned NPcore remains in a monomeric state and completely loses its affinity for single-stranded RNA (ssRNA). The structural comparison reveals that the RNA binding groove undergoes a transition from closed state to open state, chaperoned by VP35 peptide, thus preventing the interaction for viral RNA. Our investigation provides considerable structural insight into the filovirus RNP working mechanism and may support the development of antiviral therapies targeting the RNP formation of filovirus.IMPORTANCE Marburg virus is one of the most dangerous viruses, with high morbidity and mortality. A recent outbreak in Angola in 2005 caused the deaths of 272 persons. NP is one of the most essential proteins, as it encapsidates and protects the whole virus genome simultaneously with self-assembly oligomerization. Here we report the structures of MARV NPcore in two different forms. In the MARV NP apo form, we identify an interesting hexamer formed by hydrophobic interaction within a long helix, which is highly conserved and flexible among filoviruses and may indicate its critical function during the virus RNP formation. Moreover, the structural comparison with the NP-VP35 peptide complex reveals a structural transition chaperoned by VP35, in which the RNA binding groove undergoes a transition from closed state to open state. Finally, we discussed the high conservation and critical role of the VP35 binding pocket and its potential use for therapeutic development.
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Filovirus proteins for antiviral drug discovery: Structure/function bases of the replication cycle. Antiviral Res 2017; 141:48-61. [PMID: 28192094 DOI: 10.1016/j.antiviral.2017.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/12/2017] [Accepted: 02/07/2017] [Indexed: 12/26/2022]
Abstract
Filoviruses are important pathogens that cause severe and often fatal hemorrhagic fever in humans, for which no approved vaccines and antiviral treatments are yet available. In an earlier article (Martin et al., Antiviral Research, 2016), we reviewed the role of the filovirus surface glycoprotein in replication and as a target for drugs and vaccines. In this review, we focus on recent findings on the filovirus replication machinery and how they could be used for the identification of new therapeutic targets and the development of new antiviral compounds. First, we summarize the recent structural and functional advances on the molecules involved in filovirus replication/transcription cycle, particularly the NP, VP30, VP35 proteins, and the "large" protein L, which harbors the RNA-dependent RNA polymerase (RdRp) and mRNA capping activities. These proteins are essential for viral mRNA synthesis and genome replication, and consequently they constitute attractive targets for drug design. We then describe how these insights into filovirus replication mechanisms and the structure/function characterization of the involved proteins have led to the development of new and innovative antiviral strategies that may help reduce the filovirus disease case fatality rate through post-exposure or prophylactic treatments.
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Kirchdoerfer RN, Wasserman H, Amarasinghe GK, Saphire EO. Filovirus Structural Biology: The Molecules in the Machine. Curr Top Microbiol Immunol 2017; 411:381-417. [PMID: 28795188 DOI: 10.1007/82_2017_16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter, we describe what is known thus far about the structures and functions of the handful of proteins encoded by filovirus genomes. Amongst the fascinating findings of the last decade is the plurality of functions and structures that these polypeptides can adopt. Many of the encoded proteins can play multiple, distinct roles in the virus life cycle, although the mechanisms by which these functions are determined and controlled remain mostly veiled. Further, some filovirus proteins are multistructural: adopting different oligomeric assemblies and sometimes, different tertiary structures to achieve their separate, and equally essential functions. Structures, and the functions they dictate, are described for components of the nucleocapsid, the matrix, and the surface and secreted glycoproteins.
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Affiliation(s)
- Robert N Kirchdoerfer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hal Wasserman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, The Skaggs Institute for Chemical Biology, La Jolla, CA, 92037, USA.
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Jamin M, Yabukarski F. Nonsegmented Negative-Sense RNA Viruses-Structural Data Bring New Insights Into Nucleocapsid Assembly. Adv Virus Res 2016; 97:143-185. [PMID: 28057258 DOI: 10.1016/bs.aivir.2016.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Viruses with a nonsegmented negative-sense RNA genome (NNVs) include important human pathogens as well as life-threatening zoonotic viruses. These viruses share a common RNA replication complex, including the genomic RNA and three proteins, the nucleoprotein (N), the phosphoprotein (P), and the RNA-dependent RNA polymerase (L). During genome replication, the RNA polymerase complex first synthesizes positive-sense antigenomes, which in turn serve as template for the production of negative-sense progeny genomes. These newly synthesized antigenomic and genomic RNAs must be encapsidated by N, and the source of soluble, RNA-free N, competent for the encapsidation is a complex between N and P, named the N0-P complex. In this review, we summarize recent progress made in the structural characterization of the different components of this peculiar RNA polymerase machinery. We discuss common features and replication strategies and highlight idiosyncrasies encountered in different viruses, along with the key role of the dual ordered/disordered architecture of protein components and the dynamics of the viral polymerase machinery. In particular, we focus on the N0-P complex and its role in the nucleocapsid assembly process. These new results provide evidence that the mechanism of NC assembly is conserved between the different families and thus support a divergent evolution from a common ancestor. In addition, the successful inhibition of infection due to different NNVs by peptides derived from P suggests that the mechanism of NC assembly is a potential target for antiviral development.
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Affiliation(s)
- M Jamin
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
| | - F Yabukarski
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
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In vitro assembly of Ebola virus nucleocapsid-like complex expressed in E. coli. Protein Cell 2016; 7:888-898. [PMID: 27650953 PMCID: PMC5205660 DOI: 10.1007/s13238-016-0314-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/12/2016] [Indexed: 11/02/2022] Open
Abstract
Ebola virus (EBOV) harbors an RNA genome encapsidated by nucleoprotein (NP) along with other viral proteins to form a nucleocapsid complex. Previous Cryo-eletron tomography and biochemical studies have shown the helical structure of EBOV nucleocapsid at nanometer resolution and the first 450 amino-acid of NP (NPΔ451-739) alone is capable of forming a helical nucleocapsid-like complex (NLC). However, the structural basis for NP-NP interaction and the dynamic procedure of the nucleocapsid assembly is yet poorly understood. In this work, we, by using an E. coli expression system, captured a series of images of NPΔ451-739 conformers at different stages of NLC assembly by negative-stain electron microscopy, which allowed us to picture the dynamic procedure of EBOV nucleocapsid assembly. Along with further biochemical studies, we showed the assembly of NLC is salt-sensitive, and also established an indispensible role of RNA in this process. We propose the diverse modes of NLC elongation might be the key determinants shaping the plasticity of EBOV virions. Our findings provide a new model for characterizing the self-oligomerization of viral nucleoproteins and studying the dynamic assembly process of viral nucleocapsid in vitro.
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Binding of RNA by the Nucleoproteins of Influenza Viruses A and B. Viruses 2016; 8:v8090247. [PMID: 27649229 PMCID: PMC5035961 DOI: 10.3390/v8090247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022] Open
Abstract
This paper describes a biochemical study for making complexes between the nucleoprotein of influenza viruses A and B (A/NP and B/NP) and small RNAs (polyUC RNAs from 5 to 24 nucleotides (nt)), starting from monomeric proteins. We used negative stain electron microscopy, size exclusion chromatography-multi-angle laser light scattering (SEC-MALLS) analysis, and fluorescence anisotropy measurements to show how the NP-RNA complexes evolve. Both proteins make small oligomers with 24-nt RNAs, trimers for A/NP, and dimers, tetramers, and larger complexes for B/NP. With shorter RNAs, the affinities of NP are all in the same range at 50 mM NaCl, showing that the RNAs bind on the same site. The affinity of B/NP for a 24-nt RNA does not change with salt. However, the affinity of A/NP for a 24-nt RNA is lower at 150 and 300 mM NaCl, suggesting that the RNA binds to another site, either on the same protomer or on a neighbour protomer. For our fluorescence anisotropy experiments, we used 6-fluorescein amidite (FAM)-labelled RNAs. By using a (UC)6-FAM3′ RNA with 150 mM NaCl, we observed an interesting phenomenon that gives macromolecular complexes similar to the ribonucleoprotein particles purified from the viruses.
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Novel Chemical Ligands to Ebola Virus and Marburg Virus Nucleoproteins Identified by Combining Affinity Mass Spectrometry and Metabolomics Approaches. Sci Rep 2016; 6:29680. [PMID: 27403722 PMCID: PMC4940736 DOI: 10.1038/srep29680] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022] Open
Abstract
The nucleoprotein (NP) of Ebola virus (EBOV) and Marburg virus (MARV) is an essential component of the viral ribonucleoprotein complex and significantly impacts replication and transcription of the viral RNA genome. Although NP is regarded as a promising antiviral druggable target, no chemical ligands have been reported to interact with EBOV NP or MARV NP. We identified two compounds from a traditional Chinese medicine Gancao (licorice root) that can bind both NPs by combining affinity mass spectrometry and metabolomics approaches. These two ligands, 18β-glycyrrhetinic acid and licochalcone A, were verified by defined compound mixture screens and further characterized with individual ligand binding assays. Accompanying biophysical analyses demonstrate that binding of 18β-glycyrrhetinic acid to EBOV NP significantly reduces protein thermal stability, induces formation of large NP oligomers, and disrupts the critical association of viral ssRNA with NP complexes whereas the compound showed no such activity on MARV NP. Our study has revealed the substantial potential of new analytical techniques in ligand discovery from natural herb resources. In addition, identification of a chemical ligand that influences the oligomeric state and RNA-binding function of EBOV NP sheds new light on antiviral drug development.
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Wang H, Shi Y, Song J, Qi J, Lu G, Yan J, Gao GF. Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1. Cell 2016; 164:258-268. [PMID: 26771495 PMCID: PMC7111281 DOI: 10.1016/j.cell.2015.12.044] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/30/2015] [Accepted: 12/23/2015] [Indexed: 02/05/2023]
Abstract
Filoviruses, including Ebola and Marburg, cause fatal hemorrhagic fever in humans and primates. Understanding how these viruses enter host cells could help to develop effective therapeutics. An endosomal protein, Niemann-Pick C1 (NPC1), has been identified as a necessary entry receptor for this process, and priming of the viral glycoprotein (GP) to a fusion-competent state is a prerequisite for NPC1 binding. Here, we have determined the crystal structure of the primed GP (GPcl) of Ebola virus bound to domain C of NPC1 (NPC1-C) at a resolution of 2.3 Å. NPC1-C utilizes two protruding loops to engage a hydrophobic cavity on head of GPcl. Upon enzymatic cleavage and NPC1-C binding, conformational change in the GPcl further affects the state of the internal fusion loop, triggering membrane fusion. Our data therefore provide structural insights into filovirus entry in the late endosome and the molecular basis for design of therapeutic inhibitors of viral entry. Structural basis of Ebola virus endosomal-receptor binding NPC1 domain C (NPC1-C) displays a helical core structure with two protruding loops NPC1-C binds to the primed Ebola virus GP (GPcl) protein with a low affinity NPC1-C utilizes two protruding loops to engage a hydrophobic cavity on head of GPcl
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Affiliation(s)
- Han Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early-warning, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Jian Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Microbial Physiology and Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early-warning, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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