1
|
Williams HM, Thorkelsson S, Vogel D, Busch C, Milewski M, Cusack S, Grünewald K, Quemin EJ, Rosenthal M. Structural snapshots of phenuivirus cap-snatching and transcription. Nucleic Acids Res 2024; 52:6049-6065. [PMID: 38709882 PMCID: PMC11162785 DOI: 10.1093/nar/gkae330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a human pathogen that is now endemic to several East Asian countries. The viral large (L) protein catalyzes viral transcription by stealing host mRNA caps via a process known as cap-snatching. Here, we establish an in vitro cap-snatching assay and present three high-quality electron cryo-microscopy (cryo-EM) structures of the SFTSV L protein in biologically relevant, transcription-specific states. In a priming-state structure, we show capped RNA bound to the L protein cap-binding domain (CBD). The L protein conformation in this priming structure is significantly different from published replication-state structures, in particular the N- and C-terminal domains. The capped-RNA is positioned in a way that it can feed directly into the RNA-dependent RNA polymerase (RdRp) ready for elongation. We also captured the L protein in an early-elongation state following primer-incorporation demonstrating that this priming conformation is retained at least in the very early stages of primer extension. This structural data is complemented by in vitro biochemical and cell-based assays. Together, these insights further our mechanistic understanding of how SFTSV and other bunyaviruses incorporate stolen host mRNA fragments into their viral transcripts thereby allowing the virus to hijack host cell translation machinery.
Collapse
Affiliation(s)
- Harry M Williams
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Sigurdur R Thorkelsson
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Carola Busch
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Morlin Milewski
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Kay Grünewald
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS) UMR9198, Gif-sur-Yvette, France
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
| |
Collapse
|
2
|
Messias TS, Silva KCP, Silva TC, Soares S. Potential of Viruses as Environmental Etiological Factors for Non-Syndromic Orofacial Clefts. Viruses 2024; 16:511. [PMID: 38675854 PMCID: PMC11053622 DOI: 10.3390/v16040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we analyzed the potential of viral infections in the species Homo sapiens as environmental causes of orofacial clefts (OFCs). A scoring system was adapted for qualitatively assessing the potential of viruses to cause cleft lip and/or palate (CL/P). This assessment considered factors such as information from the literature, nucleotide and amino acid similarities, and the presence of Endogenous Viral Elements (EVEs). The analysis involved various algorithm packages within Basic Local Alignment Search Tool 2.13.0 software and databases from the National Center for Biotechnology Information and the International Committee on Taxonomy of Viruses. Twenty significant viral species using different biosynthesis strategies were identified: Human coronavirus NL63, Rio Negro virus, Alphatorquevirus homin9, Brisavirus, Cosavirus B, Torque teno mini virus 4, Bocaparvovirus primate2, Human coronavirus HKU1, Monkeypox virus, Mammarenavirus machupoense, Volepox virus, Souris mammarenavirus, Gammapapillomavirus 7, Betainfluenzavirus influenzae, Lymphocytic choriomeningitis mammarenavirus, Ledantevirus kern, Gammainfluenzavirus influenzae, Betapolyomavirus hominis, Vesiculovirus perinet, and Cytomegalovirus humanbeta5. The evident viral etiological potential in relation to CL/P varies depending on the Baltimore class to which the viral species belongs. Given the multifactorial nature of CL/P, this relationship appears to be dynamic.
Collapse
Affiliation(s)
- Thiago S. Messias
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
| | - Kaique C. P. Silva
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Faculty of Medicine, Nove de Julho University, Bauru 17011-102, SP, Brazil
| | - Thiago C. Silva
- Faculty of Architecture, Arts, Communication and Design, São Paulo State University, Bauru 17033-360, SP, Brazil;
| | - Simone Soares
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Department of Prosthodontics and Periodontology, Bauru School of Dentistry, University of São Paulo, 9-75, Bauru 17012-901, SP, Brazil
| |
Collapse
|
3
|
Durieux Trouilleton Q, Housset D, Tarillon P, Arragain B, Malet H. Structural characterization of the oligomerization of full-length Hantaan virus polymerase into symmetric dimers and hexamers. Nat Commun 2024; 15:2256. [PMID: 38480734 PMCID: PMC10937945 DOI: 10.1038/s41467-024-46601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete cryo-electron microscopy structure of Hantaan virus polymerase in several oligomeric forms. Apo polymerase protomers can adopt two drastically different conformations, which assemble into two distinct symmetric homodimers, that can themselves gather to form hexamers. Polymerase dimerization induces the stabilization of most polymerase domains, including the C-terminal domain that contributes the most to dimer's interface, along with a lariat region that participates to the polymerase steadying. Binding to viral RNA induces significant conformational changes resulting in symmetric oligomer disruption and polymerase activation, suggesting the possible involvement of apo multimers as protecting systems that would stabilize the otherwise flexible C-terminal domains. Overall, these results provide insights into the multimerization capability of Hantavirus polymerase and may help to define antiviral compounds to counteract these life-threatening viruses.
Collapse
Affiliation(s)
| | - Dominique Housset
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Paco Tarillon
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Benoît Arragain
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
- European Molecular Biology Laboratory (EMBL), Grenoble, France.
| | - Hélène Malet
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
- Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
4
|
Rodrigues Dutra JV, Santos IA, Grosche VR, Jardim ACG, de Aguiar RS, Junior NN, José DP. L protein characterization and in silico screening of putative broad range target molecules for pathogenic mammarenaviruses from South America. J Biomol Struct Dyn 2023:1-19. [PMID: 37817533 DOI: 10.1080/07391102.2023.2268186] [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: 06/13/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
The genus Mammarenavirus belonging to the family Arenaviridae encompasses pathogenic viral species capable of triggering severe diseases in humans, causing concern for the health system due to the high fatality rate associated with them. Currently, there is a dearth of specific therapies against pathogens of the genus. Natural products isolated from plants have impacted the development of drugs against several diseases. The Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE) database offers several natural compounds with antimicrobial activities that can be used in the development of new antiviral drugs. In this context, here we modeled the arenavirus L protein, multifunctional machinery essential for the viral replicative cycle, making this enzyme a potential candidate for targeting the development of antivirals against genus pathogens. Using the modeled L protein, a virtual screening was performed, which suggested eleven molecules from the NuBBE database that binds to the active site of the L protein, which was promising in the in silico predictions of absorption and toxicity analysis. The NuBBE 1642 molecule proved to be the best candidate for four of the five species evaluated, acting as a possible broad-spectrum molecule. Additionally, our results showed that the L protein is highly conserved among species of the genus, as well as presenting close phylogenetic relationships between many of the species studied, strengthening its candidacy as a therapeutic target. The data presented here demonstrate that some NuBBE molecules are potential ligands for the L protein of arenaviruses, which may help to contain possible outbreaks.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- João Victor Rodrigues Dutra
- Federal University of Triângulo Mineiro, Iturama, Minas Gerais, Brazil
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Igor Andrade Santos
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Victória Riquena Grosche
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
- São Paulo State University, São José do Rio Preto, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
- São Paulo State University, São José do Rio Preto, Brazil
| | - Renato Santana de Aguiar
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nilson Nicolau Junior
- Laboratory of Molecular Modeling, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | | |
Collapse
|
5
|
Peng Q, Yuan B, Cheng J, Wang M, Gao S, Bai S, Zhao X, Qi J, Gao GF, Shi Y. Molecular mechanism of de novo replication by the Ebola virus polymerase. Nature 2023; 622:603-610. [PMID: 37699521 DOI: 10.1038/s41586-023-06608-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Non-segmented negative-strand RNA viruses, including Ebola virus (EBOV), rabies virus, human respiratory syncytial virus and pneumoviruses, can cause respiratory infections, haemorrhagic fever and encephalitis in humans and animals, and are considered a substantial health and economic burden worldwide1. Replication and transcription of the viral genome are executed by the large (L) polymerase, which is a promising target for the development of antiviral drugs. Here, using the L polymerase of EBOV as a representative, we show that de novo replication of L polymerase is controlled by the specific 3' leader sequence of the EBOV genome in an enzymatic assay, and that formation of at least three base pairs can effectively drive the elongation process of RNA synthesis independent of the specific RNA sequence. We present the high-resolution structures of the EBOV L-VP35-RNA complex and show that the 3' leader RNA binds in the template entry channel with a distinctive stable bend conformation. Using mutagenesis assays, we confirm that the bend conformation of the RNA is required for the de novo replication activity and reveal the key residues of the L protein that stabilize the RNA conformation. These findings provide a new mechanistic understanding of RNA synthesis for polymerases of non-segmented negative-strand RNA viruses, and reveal important targets for the development of antiviral drugs.
Collapse
Affiliation(s)
- Qi Peng
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bin Yuan
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinlong Cheng
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Siwei Gao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Suran Bai
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xuejin Zhao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
| | - George F Gao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yi Shi
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
6
|
Liu L, Wang P, Liu A, Zhang L, Yan L, Guo Y, Xiao G, Rao Z, Lou Z. Structure basis for allosteric regulation of lymphocytic choriomeningitis virus polymerase function by Z matrix protein. Protein Cell 2023; 14:703-707. [PMID: 37038286 PMCID: PMC10501185 DOI: 10.1093/procel/pwad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/29/2023] [Indexed: 04/12/2023] Open
Affiliation(s)
- Lu Liu
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Panpan Wang
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Aijun Liu
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518100, China
| | - Leike Zhang
- State key laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liming Yan
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Gengfu Xiao
- State key laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zihe Rao
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin 300350, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100105, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 200120, China
- Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
| |
Collapse
|
7
|
Meier K, Thorkelsson SR, Durieux Trouilleton Q, Vogel D, Yu D, Kosinski J, Cusack S, Malet H, Grünewald K, Quemin ERJ, Rosenthal M. Structural and functional characterization of the Sin Nombre virus L protein. PLoS Pathog 2023; 19:e1011533. [PMID: 37549153 PMCID: PMC10406178 DOI: 10.1371/journal.ppat.1011533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023] Open
Abstract
The Bunyavirales order is a large and diverse group of segmented negative-strand RNA viruses. Several virus families within this order contain important human pathogens, including Sin Nombre virus (SNV) of the Hantaviridae. Despite the high epidemic potential of bunyaviruses, specific medical countermeasures such as vaccines or antivirals are missing. The multifunctional ~250 kDa L protein of hantaviruses, amongst other functional domains, harbors the RNA-dependent RNA polymerase (RdRp) and an endonuclease and catalyzes transcription as well as replication of the viral RNA genome, making it a promising therapeutic target. The development of inhibitors targeting these key processes requires a profound understanding of the catalytic mechanisms. Here, we established expression and purification protocols of the full-length SNV L protein bearing the endonuclease mutation K124A. We applied different biochemical in vitro assays to provide an extensive characterization of the different enzymatic functions as well as the capacity of the hantavirus L protein to interact with the viral RNA. By using single-particle cryo-EM, we obtained a 3D model including the L protein core region containing the RdRp, in complex with the 5' promoter RNA. This first high-resolution model of a New World hantavirus L protein shows striking similarity to related bunyavirus L proteins. The interaction of the L protein with the 5' RNA observed in the structural model confirms our hypothesis of protein-RNA binding based on our biochemical data. Taken together, this study provides an excellent basis for future structural and functional studies on the hantavirus L protein and for the development of antiviral compounds.
Collapse
Affiliation(s)
- Kristina Meier
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Sigurdur R. Thorkelsson
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Dingquan Yu
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Hélène Malet
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
- Institut Universitaire de France (IUF), Paris, France
| | - Kay Grünewald
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
- University of Hamburg, Department of Chemistry, Hamburg, Germany
| | - Emmanuelle R. J. Quemin
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
| |
Collapse
|
8
|
Li H, Wu Y, Li M, Guo L, Gao Y, Wang Q, Zhang J, Lai Z, Zhang X, Zhu L, Lan P, Rao Z, Liu Y, Liang H. An intermediate state allows influenza polymerase to switch smoothly between transcription and replication cycles. Nat Struct Mol Biol 2023; 30:1183-1192. [PMID: 37488357 DOI: 10.1038/s41594-023-01043-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Influenza polymerase (FluPol) transcribes viral mRNA at the beginning of the viral life cycle and initiates genome replication after viral protein synthesis. However, it remains poorly understood how FluPol switches between its transcription and replication states, especially given that the structural bases of these two functions are fundamentally different. Here we propose a mechanism by which FluPol achieves functional switching between these two states through a previously unstudied conformation, termed an 'intermediate state'. Using cryo-electron microscopy, we obtained a structure of the intermediate state of H5N1 FluPol at 3.7 Å, which is characterized by a blocked cap-binding domain and a contracted core region. Structural analysis results suggest that the intermediate state may allow FluPol to transition smoothly into either the transcription or replication state. Furthermore, we show that the formation of the intermediate state is required for both the transcription and replication activities of FluPol, leading us to conclude that the transcription and replication cycles of FluPol are regulated via this intermediate state.
Collapse
Affiliation(s)
- Huanhuan Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yixi Wu
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Minke Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Lu Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yaqi Gao
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Quan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jihua Zhang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Zhaohua Lai
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Xing Zhang
- Departments of Biophysics and Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
| | - Lixin Zhu
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Lan
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zihe Rao
- Laboratory of Structural Biology, Tsinghua University, Beijing, China
| | - Yingfang Liu
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Huanhuan Liang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
| |
Collapse
|
9
|
Durieux Trouilleton Q, Barata-García S, Arragain B, Reguera J, Malet H. Structures of active Hantaan virus polymerase uncover the mechanisms of Hantaviridae genome replication. Nat Commun 2023; 14:2954. [PMID: 37221161 DOI: 10.1038/s41467-023-38555-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Hantaviruses are causing life-threatening zoonotic infections in humans. Their tripartite negative-stranded RNA genome is replicated by the multi-functional viral RNA-dependent RNA-polymerase. Here we describe the structure of the Hantaan virus polymerase core and establish conditions for in vitro replication activity. The apo structure adopts an inactive conformation that involves substantial folding rearrangement of polymerase motifs. Binding of the 5' viral RNA promoter triggers Hantaan virus polymerase reorganization and activation. It induces the recruitment of the 3' viral RNA towards the polymerase active site for prime-and-realign initiation. The elongation structure reveals the formation of a template/product duplex in the active site cavity concomitant with polymerase core widening and the opening of a 3' viral RNA secondary binding site. Altogether, these elements reveal the molecular specificities of Hantaviridae polymerase structure and uncover the mechanisms underlying replication. They provide a solid framework for future development of antivirals against this group of emerging pathogens.
Collapse
Affiliation(s)
| | | | - Benoît Arragain
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR, 7257, Marseille, France.
- INSERM, AFMB UMR, 7257, Marseille, France.
| | - Hélène Malet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
- Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
10
|
D'Antuono AL, Gallo GL, Sepulveda C, Fernández J, Brignone J, Gamboa G, Riera L, Saavedra MDC, López N. cis-Acting Element at the 5' Noncoding Region of Tacaribe Virus S RNA Modulates Genome Replication. J Virol 2023; 97:e0012523. [PMID: 36786631 PMCID: PMC10062143 DOI: 10.1128/jvi.00125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Tacaribe virus (TCRV) is the prototype of New World mammarenaviruses, a group that includes several members that cause hemorrhagic fevers in humans. The TCRV genome comprises two RNA segments, named S (small) and L (large). Both genomic segments contain noncoding regions (NCRs) at their 5' and 3' ends. While the 5'- and 3'-terminal 19-nucleotide sequences are known to be essential for promoter function, the role of their neighboring internal noncoding region (iNCR) sequences remains poorly understood. To analyze the relevance of the 5' and 3' iNCRs in TCRV S RNA synthesis, mutant S-like minigenomes and miniantigenomes were generated. Using a minireplicon assay, Northern blotting, and reverse transcription-quantitative PCR, we demonstrated that the genomic 5' iNCR is specifically engaged in minigenome replication yet is not directly involved in minigenome transcription, and we showed that the S genome 3' iNCR is barely engaged in this process. Analysis of partial deletions and point mutations, as well as total or partial substitution of the 5' iNCR sequence, led us to conclude that the integrity of the whole genomic 5' iNCR is essential and that a local predicted secondary structure or RNA-RNA interactions between the 5' and 3' iNCRs are not strictly required for viral S RNA synthesis. Furthermore, we employed a TCRV reverse genetic approach to ask whether manipulation of the S genomic 5' iNCR sequence may be suitable for viral attenuation. We found that mutagenesis of the 5' promoter-proximal subregion slightly impacted recombinant TCRV virulence in vivo. IMPORTANCE The Mammarenavirus genus of the Arenaviridae family includes several members that cause severe hemorrhagic fevers associated with high morbidity and mortality rates, for which no FDA-approved vaccines and limited therapeutic resources are available. We provide evidence demonstrating the specific involvement of the TCRV S 5' noncoding sequence adjacent to the viral promoter in replication. In addition, we examined the relevance of this region in the context of an in vivo infection. Our findings provide insight into the mechanism through which this 5' viral RNA noncoding region assists the L polymerase for efficient viral S RNA synthesis. Also, these findings expand our understanding of the effect of genetic manipulation of New World mammarenavirus sequences aimed at the rational design of attenuated recombinant virus vaccine platforms.
Collapse
Affiliation(s)
- Alejandra L. D'Antuono
- Centro de Virología Humana y Animal, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Giovanna L. Gallo
- Centro de Virología Humana y Animal, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Claudia Sepulveda
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jonás Fernández
- Centro de Virología Humana y Animal, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Julia Brignone
- Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, ANLIS-Malbran, Ministerio de Salud de la Nación, Pergamino, Buenos Aires, Argentina
| | - Graciela Gamboa
- Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, ANLIS-Malbran, Ministerio de Salud de la Nación, Pergamino, Buenos Aires, Argentina
| | - Laura Riera
- Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, ANLIS-Malbran, Ministerio de Salud de la Nación, Pergamino, Buenos Aires, Argentina
| | - María del Carmen Saavedra
- Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, ANLIS-Malbran, Ministerio de Salud de la Nación, Pergamino, Buenos Aires, Argentina
| | - Nora López
- Centro de Virología Humana y Animal, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Abierta Interamericana, Buenos Aires, Argentina
| |
Collapse
|
11
|
Whitlock AOB, Bird BH, Ghersi B, Davison AJ, Hughes J, Nichols J, Vučak M, Amara E, Bangura J, Lavalie EG, Kanu MC, Kanu OT, Sjodin A, Remien CH, Nuismer SL. Identifying the genetic basis of viral spillover using Lassa virus as a test case. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221503. [PMID: 36968239 PMCID: PMC10031424 DOI: 10.1098/rsos.221503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.
Collapse
Affiliation(s)
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emmanuel Amara
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Edwin G. Lavalie
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Marilyn C. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Osman T. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Anna Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Christopher H. Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| |
Collapse
|
12
|
Li Y. Genetic basis underlying Lassa fever endemics in the Mano River region, West Africa. Virology 2023; 579:128-136. [PMID: 36669329 DOI: 10.1016/j.virol.2023.01.006] [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: 11/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Lassa fever (LF), a haemorrhagic fever disease caused by Lassa virus (LASV), is a serious public health burden in West Africa. The Mano River region (Sierra Leone, Guinea, Liberia, and Côte d'Ivoire) has been an endemic focus of the disease over the past decades. Here, we deciphered the genetic basis underlying LF endemics in this region. Clade model and type I functional divergence analyses revealed that the major LASV group, Kenema sub-clade, which is currently circulating in the Eastern Province of Sierra Leone, has been affected by different selective pressure compared to isolates from the other areas with effects on the viral RNA-dependent RNA polymerase (L protein) and probably nucleoprotein (NP). Further, contingency analysis showed that, in the early endemic, the sub-clade has undergone adaptive diversification via acceleration of amino acid substitutions in L protein. These findings highlight the key viral factor and local adaptation regarding the endemicity of LF.
Collapse
Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, People's Republic of China.
| |
Collapse
|
13
|
Williams HM, Thorkelsson SR, Vogel D, Milewski M, Busch C, Cusack S, Grünewald K, Quemin EJ, Rosenthal M. Structural insights into viral genome replication by the severe fever with thrombocytopenia syndrome virus L protein. Nucleic Acids Res 2023; 51:1424-1442. [PMID: 36651274 PMCID: PMC9943659 DOI: 10.1093/nar/gkac1249] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a phenuivirus that has rapidly become endemic in several East Asian countries. The large (L) protein of SFTSV, which includes the RNA-dependent RNA polymerase (RdRp), is responsible for catalysing viral genome replication and transcription. Here, we present 5 cryo-electron microscopy (cryo-EM) structures of the L protein in several states of the genome replication process, from pre-initiation to late-stage elongation, at a resolution of up to 2.6 Å. We identify how the L protein binds the 5' viral RNA in a hook-like conformation and show how the distal 5' and 3' RNA ends form a duplex positioning the 3' RNA terminus in the RdRp active site ready for initiation. We also observe the L protein stalled in the early and late stages of elongation with the RdRp core accommodating a 10-bp product-template duplex. This duplex ultimately splits with the template binding to a designated 3' secondary binding site. The structural data and observations are complemented by in vitro biochemical and cell-based mini-replicon assays. Altogether, our data provide novel key insights into the mechanism of viral genome replication by the SFTSV L protein and will aid drug development against segmented negative-strand RNA viruses.
Collapse
Affiliation(s)
| | | | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Morlin Milewski
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Carola Busch
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany,University of Hamburg, Hamburg, Germany
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
| | - Maria Rosenthal
- To whom correspondence should be addressed. Tel: +49 40 285380 930;
| |
Collapse
|
14
|
Malet H, Williams HM, Cusack S, Rosenthal M. The mechanism of genome replication and transcription in bunyaviruses. PLoS Pathog 2023; 19:e1011060. [PMID: 36634042 PMCID: PMC9836281 DOI: 10.1371/journal.ppat.1011060] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bunyaviruses are negative sense, single-strand RNA viruses that infect a wide range of vertebrate, invertebrate and plant hosts. WHO lists three bunyavirus diseases as priority diseases requiring urgent development of medical countermeasures highlighting their high epidemic potential. While the viral large (L) protein containing the RNA-dependent RNA polymerase is a key enzyme in the viral replication cycle and therefore a suitable drug target, our knowledge on the structure and activities of this multifunctional protein has, until recently, been very limited. However, in the last few years, facilitated by the technical advances in the field of cryogenic electron microscopy, many structures of bunyavirus L proteins have been solved. These structures significantly enhance our mechanistic understanding of bunyavirus genome replication and transcription processes and highlight differences and commonalities between the L proteins of different bunyavirus families. Here, we provide a review of our current understanding of genome replication and transcription in bunyaviruses with a focus on the viral L protein. Further, we compare within bunyaviruses and with the related influenza virus polymerase complex and highlight open questions.
Collapse
Affiliation(s)
- Hélène Malet
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
- Institut Universitaire de France (IUF), Paris, France
| | - Harry M. Williams
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
| |
Collapse
|
15
|
Mammarenavirus Genetic Diversity and Its Biological Implications. Curr Top Microbiol Immunol 2023; 439:265-303. [PMID: 36592249 DOI: 10.1007/978-3-031-15640-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.
Collapse
|
16
|
Sánchez Rodríguez F, Chojnowski G, Keegan RM, Rigden DJ. Using deep-learning predictions of inter-residue distances for model validation. Acta Crystallogr D Struct Biol 2022; 78:1412-1427. [PMID: 36458613 PMCID: PMC9716559 DOI: 10.1107/s2059798322010415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022] Open
Abstract
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data. The latest advances in the field of deep learning have enabled the increasingly accurate prediction of inter-residue distances, an advance which has played a pivotal role in the recent improvements observed in the field of protein ab initio modelling. Here, new validation methods are presented based on the use of these precise inter-residue distance predictions, which are compared with the distances observed in the protein model. Sequence-register errors are particularly clearly detected and the register shifts required for their correction can be reliably determined. The method is available in the ConKit package (https://www.conkit.org).
Collapse
Affiliation(s)
- Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ronan M. Keegan
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| |
Collapse
|
17
|
Yuan B, Peng Q, Cheng J, Wang M, Zhong J, Qi J, Gao GF, Shi Y. Structure of the Ebola virus polymerase complex. Nature 2022; 610:394-401. [PMID: 36171293 PMCID: PMC9517992 DOI: 10.1038/s41586-022-05271-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022]
Abstract
Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal antibodies have been approved to treat the Ebola virus disease1,2, there are no approved broadly reactive drugs to control diverse filovirus infection. Filovirus has a large polymerase (L) protein and the cofactor viral protein 35 (VP35), which constitute the basic functional unit responsible for virus genome RNA synthesis3. Owing to its conservation, the L-VP35 polymerase complex is a promising target for broadly reactive antiviral drugs. Here we determined the structure of Ebola virus L protein in complex with tetrameric VP35 using cryo-electron microscopy (state 1). Structural analysis revealed that Ebola virus L possesses a filovirus-specific insertion element that is essential for RNA synthesis, and that VP35 interacts extensively with the N-terminal region of L by three protomers of the VP35 tetramer. Notably, we captured the complex structure in a second conformation with the unambiguous priming loop and supporting helix away from polymerase active site (state 2). Moreover, we demonstrated that the century-old drug suramin could inhibit the activity of the Ebola virus polymerase in an enzymatic assay. The structure of the L-VP35-suramin complex reveals that suramin can bind at the highly conserved NTP entry channel to prevent substrates from entering the active site. These findings reveal the mechanism of Ebola virus replication and may guide the development of more powerful anti-filovirus drugs.
Collapse
Affiliation(s)
- Bin Yuan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinlong Cheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jin Zhong
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
18
|
Fang J, Pietzsch C, Witwit H, Tsaprailis G, Crynen G, Cho KF, Ting AY, Bukreyev A, Saphire EO, de la Torre JC. Proximity interactome analysis of Lassa polymerase reveals eRF3a/GSPT1 as a druggable target for host-directed antivirals. Proc Natl Acad Sci U S A 2022; 119:e2201208119. [PMID: 35858434 PMCID: PMC9340056 DOI: 10.1073/pnas.2201208119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/24/2022] [Indexed: 01/21/2023] Open
Abstract
Completion of the Lassa virus (LASV) life cycle critically depends on the activities of the virally encoded, RNA-dependent RNA polymerase in replication and transcription of the viral RNA genome in the cytoplasm of infected cells. The contribution of cellular proteins to these processes remains unclear. Here, we applied proximity proteomics to define the interactome of LASV polymerase in cells under conditions that recreate LASV RNA synthesis. We engineered a LASV polymerase-biotin ligase (TurboID) fusion protein that retained polymerase activity and successfully biotinylated the proximal proteome, which allowed the identification of 42 high-confidence LASV polymerase interactors. We subsequently performed a small interfering RNA (siRNA) screen to identify those interactors that have functional roles in authentic LASV infection. As proof of principle, we characterized eukaryotic peptide chain release factor subunit 3a (eRF3a/GSPT1), which we found to be a proviral factor that physically associates with LASV polymerase. Targeted degradation of GSPT1 by a small-molecule drug candidate, CC-90009, resulted in strong inhibition of LASV infection in cultured cells. Our work demonstrates the feasibility of using proximity proteomics to illuminate and characterize yet-to-be-defined host-pathogen interactome, which can reveal new biology and uncover novel targets for the development of antivirals against highly pathogenic RNA viruses.
Collapse
Affiliation(s)
- Jingru Fang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Colette Pietzsch
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550
| | - Haydar Witwit
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037
| | | | - Gogce Crynen
- Bioinformatics and Statistics Core, Scripps Research, Jupiter, FL 33458
| | | | - Alice Y. Ting
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550
| | | | | |
Collapse
|
19
|
Zadeh VR, Afowowe TO, Abe H, Urata S, Yasuda J. Potential and action mechanism of favipiravir as an antiviral against Junin virus. PLoS Pathog 2022; 18:e1010689. [PMID: 35816544 PMCID: PMC9302769 DOI: 10.1371/journal.ppat.1010689] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/21/2022] [Accepted: 06/19/2022] [Indexed: 12/26/2022] Open
Abstract
Favipiravir is a nucleoside analogue that inhibits the replication and transcription of a broad spectrum of RNA viruses, including pathogenic arenaviruses. In this study, we isolated a favipiravir-resistant mutant of Junin virus (JUNV), which is the causative agent of Argentine hemorrhagic fever, and analyzed the antiviral mechanism of favipiravir against JUNV. Two amino acid substitutions, N462D in the RNA-dependent RNA polymerase (RdRp) and A168T in the glycoprotein precursor GPC, were identified in the mutant. GPC-A168T substitution enhanced the efficiency of JUNV internalization, which explains the robust replication kinetics of the mutant in the virus growth analysis. Although RdRp-N462D substitution did not affect polymerase activity levels in a minigenome system, comparisons of RdRp error frequencies showed that the virus with RdRp-D462 possessed a significantly higher fidelity. Our next generation sequence (NGS) analysis showed a gradual accumulation of both mutations as we passaged the virus in presence of favipiravir. We also provided experimental evidence for the first time that favipiravir inhibited JUNV through the accumulation of transition mutations, confirming its role as a purine analogue against arenaviruses. Moreover, we showed that treatment with a combination of favipiravir and either ribavirin or remdesivir inhibited JUNV replication in a synergistic manner, blocking the generation of the drug-resistant mutant. Our findings provide new insights for the clinical management and treatment of Argentine hemorrhagic fever. Development of antivirals requires cautious and extensive assessment of action mechanism as well as potential for emergence of resistant phenotype of the virus. In recent years, favipiravir has been put forward as a promising candidate for the treatment of Argentine hemorrhagic fever (AHF) caused by Junin virus (JUNV). We, therefore, aimed to provide experimental evidence on action mechanism of favipiravir to help guide its clinical use. Here we show that favipiravir causes lethal mutation that impairs virus infectivity. More importantly, we demonstrate that the virus has the capability to escape favipiravir selective pressure by acquiring two amino acid substitutions on glycoprotein precursor and polymerase proteins. This observation raises concern over the use of only favipiravir in therapeutic regimens. To overcome this risk, we show that combination of favipiravir with other nucleoside analogues demonstrates a synergistic effect and suppresses the ability of JUNV to escape drug pressure. Favipiravir, ribavirin, and remdesivir have a broad spectrum of antiviral activity. Therefore, combination therapies of these drugs would be expected to have potential therapeutic effects for not only AHF but also the diseases caused by a variety of viruses, including emerging RNA viruses.
Collapse
Affiliation(s)
- Vahid Rajabali Zadeh
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tosin Oladipo Afowowe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Shuzo Urata
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- * E-mail:
| |
Collapse
|
20
|
Arragain B, Durieux Trouilleton Q, Baudin F, Provaznik J, Azevedo N, Cusack S, Schoehn G, Malet H. Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription. Nat Commun 2022; 13:902. [PMID: 35173159 PMCID: PMC8850483 DOI: 10.1038/s41467-022-28428-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 01/20/2022] [Indexed: 12/28/2022] Open
Abstract
Segmented negative-strand RNA bunyaviruses encode a multi-functional polymerase that performs genome replication and transcription. Here, we establish conditions for in vitro activity of La Crosse virus polymerase and visualize its conformational dynamics by cryo-electron microscopy, unveiling the precise molecular mechanics underlying its essential activities. We find that replication initiation is coupled to distal duplex promoter formation, endonuclease movement, prime-and-realign loop extension and closure of the polymerase core that direct the template towards the active site. Transcription initiation depends on C-terminal region closure and endonuclease movements that prompt primer cleavage prior to primer entry in the active site. Product realignment after priming, observed in replication and transcription, is triggered by the prime-and-realign loop. Switch to elongation results in polymerase reorganization and core region opening to facilitate template-product duplex formation in the active site cavity. The uncovered detailed mechanics should be helpful for the future design of antivirals counteracting bunyaviral life threatening pathogens. La Crosse is a human life threatening virus belonging to the Bunyavirales order. The structure of its polymerase solved in seven key active states by cryo-electron microscopy reveals the molecular mechanisms of viral RNA replication and transcription.
Collapse
Affiliation(s)
- Benoît Arragain
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.,European Molecular Biology Laboratory (EMBL), 38000, Grenoble, France
| | | | - Florence Baudin
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Jan Provaznik
- European Molecular Biology Laboratory (EMBL), GeneCore, 69117, Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory (EMBL), GeneCore, 69117, Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory (EMBL), 38000, Grenoble, France.
| | - Guy Schoehn
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Hélène Malet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France. .,Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
21
|
Pyle JD, Whelan SPJ, Bloyet LM. Structure and function of negative-strand RNA virus polymerase complexes. Enzymes 2021; 50:21-78. [PMID: 34861938 DOI: 10.1016/bs.enz.2021.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.
Collapse
Affiliation(s)
- Jesse D Pyle
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States; Ph.D. Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| |
Collapse
|
22
|
Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity. Nat Commun 2021; 12:7018. [PMID: 34857749 PMCID: PMC8639829 DOI: 10.1038/s41467-021-27305-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/08/2021] [Indexed: 11/08/2022] Open
Abstract
Lassa virus is endemic in West Africa and can cause severe hemorrhagic fever. The viral L protein transcribes and replicates the RNA genome via its RNA-dependent RNA polymerase activity. Here, we present nine cryo-EM structures of the L protein in the apo-, promoter-bound pre-initiation and active RNA synthesis states. We characterize distinct binding pockets for the conserved 3' and 5' promoter RNAs and show how full-promoter binding induces a distinct pre-initiation conformation. In the apo- and early elongation states, the endonuclease is inhibited by two distinct L protein peptides, whereas in the pre-initiation state it is uninhibited. In the early elongation state, a template-product duplex is bound in the active site cavity together with an incoming non-hydrolysable nucleotide and the full C-terminal region of the L protein, including the putative cap-binding domain, is well-ordered. These data advance our mechanistic understanding of how this flexible and multifunctional molecular machine is activated.
Collapse
|
23
|
Abstract
Rift Valley fever virus (RVFV) belongs to the order Bunyavirales and is the type species of genus Phlebovirus, which accounts for over 50% of family Phenuiviridae species. RVFV is mosquito-borne and causes severe diseases in both humans and livestock, and consists of three segments (S, M, L) in the genome. The L segment encodes an RNA-dependent RNA polymerase (RdRp, L protein) that is responsible for facilitating the replication and transcription of the virus. It is essential for the virus and has multiple drug targets. Here, we established an expression system and purification procedures for full-length L protein, which is composed of an endonuclease domain, RdRp domain, and cap-binding domain. A cryo-EM L protein structure was reported at 3.6 Å resolution. In this first L protein structure of genus Phlebovirus, the priming loop of RVFV L protein is distinctly different from those of other L proteins and undergoes large movements related to its replication role. Structural and biochemical analyses indicate that a single template can induce initiation of RNA synthesis, which is notably enhanced by 5' viral RNA. These findings help advance our understanding of the mechanism of RNA synthesis and provide an important basis for developing antiviral inhibitors. Importance The zoonosis RVF virus (RVFV) is one of the most serious arbovirus threats to both human and animal health. RNA-dependent RNA polymerase (RdRp) is a multifunctional enzyme catalyzing genome replication as well as viral transcription, so the RdRp is essential for studying the virus and has multiple drug targets. In our study, we report the structure of RVFV L protein at 3.6 Å resolution by cryo-EM. This is the first L protein structure of genus Phlebovirus. Strikingly, a single template can initiate RNA replication. The structure and assays provide a comprehensive and in-depth understanding of the catalytic and substrate recognition mechanism of RdRp.
Collapse
|
24
|
Abstract
Arenaviruses initiate infection by delivering a transcriptionally competent ribonucleoprotein (RNP) complex into the cytosol of host cells. The arenavirus RNP consists of the large (L) RNA-dependent RNA polymerase (RdRP) bound to a nucleoprotein (NP)-encapsidated genomic RNA (viral RNA [vRNA]) template. During transcription and replication, L must transiently displace RNA-bound NP to allow for template access into the RdRP active site. Concomitant with RNA replication, new subunits of NP must be added to the nascent complementary RNAs (cRNA) as they emerge from the product exit channel of L. Interactions between L and NP thus play a central role in arenavirus gene expression. We developed an approach to purify recombinant functional RNPs from mammalian cells in culture using a synthetic vRNA and affinity-tagged L and NP. Negative-stain electron microscopy of purified RNPs revealed they adopt diverse and flexible structures, like RNPs of other Bunyavirales members. Monodispersed L-NP and trimeric ring-like NP complexes were also obtained in excess of flexible RNPs, suggesting that these heterodimeric structures self-assemble in the absence of suitable RNA templates. This work allows for further biochemical analysis of the interaction between arenavirus L and NP proteins and provides a framework for future high-resolution structural analyses of this replication-associated complex. IMPORTANCE Arenaviruses are rodent-borne pathogens that can cause severe disease in humans. All arenaviruses begin the infection cycle with delivery of the virus replication machinery into the cytoplasm of the host cell. This machinery consists of an RNA-dependent RNA polymerase-which copies the viral genome segments and synthesizes all four viral mRNAs-bound to the two nucleoprotein-encapsidated genomic RNAs. How this complex assembles remains a mystery. Our findings provide direct evidence for the formation of diverse intracellular arenavirus replication complexes using purification strategies for the polymerase, nucleoprotein, and genomic RNA of Machupo virus, which causes Bolivian hemorrhagic fever in humans. We demonstrate that the polymerase and nucleoprotein assemble into higher-order structures within cells, providing a model for the molecular events of arenavirus RNA synthesis. These findings provide a framework for probing the architectures and functions of the arenavirus replication machinery and thus advancing antiviral strategies targeting this essential complex.
Collapse
|
25
|
Structure of Machupo virus polymerase in complex with matrix protein Z. Nat Commun 2021; 12:6163. [PMID: 34697302 PMCID: PMC8546121 DOI: 10.1038/s41467-021-26432-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
The Arenaviridae family includes several viruses that cause severe human hemorrhagic fevers with high mortality, with no effective countermeasures currently available. The arenavirus multi-domain L protein is involved in viral transcription and replication and represents a promising target for antiviral drugs. The arenavirus matrix protein Z is a small multi-functional protein that inhibits the activities of the L protein. Here we report the structure of Machupo virus L protein in complex with Z determined by cryo-electron microscopy. The Z protein acts as a staple and binds the L protein with 1:1 stoichiometry at the intersection between the PA-C-like region, RNA-dependent RNA polymerase and PB2-N-like region. Binding of the Z protein may lock the multiple domains of L into a fixed arrangement leading to loss of catalytic activity. These results further our understanding of the inhibitory mechanism of arenavirus replication machinery and provide a novel perspective to develop antiviral drugs. The RNA polymerase L of arenaviruses is of interest for drug design and its activity is inhibited by the matrix protein Z. Here, the authors present the cryo-EM structure of the Machupo virus polymerase L in complex with matrix protein Z and discuss the inhibitory mechanism.
Collapse
|
26
|
Joseph S, Campbell KP. Lassa Fever Virus Binds Matriglycan-A Polymer of Alternating Xylose and Glucuronate-On α-Dystroglycan. Viruses 2021; 13:1679. [PMID: 34578260 PMCID: PMC8473316 DOI: 10.3390/v13091679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Lassa fever virus (LASV) can cause life-threatening hemorrhagic fevers for which there are currently no vaccines or targeted treatments. The late Prof. Stefan Kunz, along with others, showed that the high-affinity host receptor for LASV, and other Old World and clade-C New World mammarenaviruses, is matriglycan-a linear repeating disaccharide of alternating xylose and glucuronic acid that is polymerized uniquely on α-dystroglycan by like-acetylglucosaminyltransferase-1 (LARGE1). Although α-dystroglycan is ubiquitously expressed, LASV preferentially infects vascular endothelia and professional phagocytic cells, which suggests that viral entry requires additional cell-specific factors. In this review, we highlight the work of Stefan Kunz detailing the molecular mechanism of LASV binding and discuss the requirements of receptors, such as tyrosine kinases, for internalization through apoptotic mimicry.
Collapse
Affiliation(s)
| | - Kevin P. Campbell
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA;
| |
Collapse
|
27
|
Meier K, Thorkelsson SR, Quemin ERJ, Rosenthal M. Hantavirus Replication Cycle-An Updated Structural Virology Perspective. Viruses 2021; 13:1561. [PMID: 34452426 PMCID: PMC8402763 DOI: 10.3390/v13081561] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
Hantaviruses infect a wide range of hosts including insectivores and rodents and can also cause zoonotic infections in humans, which can lead to severe disease with possible fatal outcomes. Hantavirus outbreaks are usually linked to the population dynamics of the host animals and their habitats being in close proximity to humans, which is becoming increasingly important in a globalized world. Currently there is neither an approved vaccine nor a specific and effective antiviral treatment available for use in humans. Hantaviruses belong to the order Bunyavirales with a tri-segmented negative-sense RNA genome. They encode only five viral proteins and replicate and transcribe their genome in the cytoplasm of infected cells. However, many details of the viral amplification cycle are still unknown. In recent years, structural biology methods such as cryo-electron tomography, cryo-electron microscopy, and crystallography have contributed essentially to our understanding of virus entry by membrane fusion as well as genome encapsidation by the nucleoprotein. In this review, we provide an update on the hantavirus replication cycle with a special focus on structural virology aspects.
Collapse
Affiliation(s)
- Kristina Meier
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
| | - Sigurdur R. Thorkelsson
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology, University of Hamburg, 22607 Hamburg, Germany;
| | - Emmanuelle R. J. Quemin
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology, University of Hamburg, 22607 Hamburg, Germany;
| | - Maria Rosenthal
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525 Hamburg, Germany
| |
Collapse
|
28
|
Kang H, Cong J, Wang C, Ji W, Xin Y, Qian Y, Li X, Chen Y, Rao Z. Structural basis for recognition and regulation of arenavirus polymerase L by Z protein. Nat Commun 2021; 12:4134. [PMID: 34226547 PMCID: PMC8257661 DOI: 10.1038/s41467-021-24458-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and transcribes the genome of JUNV, and its regulator Z protein should provide critical clues to identify therapeutic targets for disrupting the life cycle of JUNV. Here we report the 3.54 Å cryo-EM structure of the JUNV L protein complexed with regulator Z protein. JUNV L structure reveals a conserved architecture containing signature motifs found in other L proteins. Structural analysis shows that L protein is regulated by binding of Z protein at the RNA product exit site. Based on these findings, we propose a model for the role of Z protein as a switch to turn on/off the viral RNA synthesis via its interaction with L protein. Our work unveils the mechanism of JUNV transcription, replication and regulation, which provides a framework for the rational design of antivirals for combating viral infections. Junin virus (JUNV) causes Argentine hemorrhagic fever and encodes the large protein (L) of the RNA dependent RNA polymerase (RdRp) and its regulator, the matrix zinc-binding protein (Z). Here, the authors present the 3.54 Å cryo-EM structure of the complex of JUNV L with Z, and they propose a model of how JUNV L is regulated by Z during the viral life cycle and RNA synthesis.
Collapse
Affiliation(s)
- Huiling Kang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China
| | - Jingyuan Cong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chenlong Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenxin Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuhui Xin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Qian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
29
|
Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals. Nat Microbiol 2021; 6:921-931. [PMID: 34127846 DOI: 10.1038/s41564-021-00916-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/05/2021] [Indexed: 02/05/2023]
Abstract
Zoonotic arenaviruses can lead to life-threating diseases in humans. These viruses encode a large (L) polymerase that transcribes and replicates the viral genome. At the late stage of replication, the multifunctional Z protein interacts with the L polymerase to shut down RNA synthesis and initiate virion assembly. However, the mechanism by which the Z protein regulates the activity of L polymerase is unclear. Here, we used cryo-electron microscopy to resolve the structures of both Lassa and Machupo virus L polymerases in complex with their cognate Z proteins, and viral RNA, to 3.1-3.9 Å resolutions. These structures reveal that Z protein binding induces conformational changes in two catalytic motifs of the L polymerase, and restrains their conformational dynamics to inhibit RNA synthesis, which is supported by hydrogen-deuterium exchange mass spectrometry analysis. Importantly, we show, by in vitro polymerase reactions, that Z proteins of Lassa and Machupo viruses can cross-inhibit their L polymerases, albeit with decreased inhibition efficiencies. This cross-reactivity results from a highly conserved determinant motif at the contacting interface, but is affected by other variable auxiliary motifs due to the divergent evolution of Old World and New World arenaviruses. These findings could provide promising targets for developing broad-spectrum antiviral drugs.
Collapse
|
30
|
Wang Q, Xin Q, Shang W, Wan W, Xiao G, Zhang LK. Activation of the STAT3 Signaling Pathway by the RNA-Dependent RNA Polymerase Protein of Arenavirus. Viruses 2021; 13:v13060976. [PMID: 34070281 PMCID: PMC8225222 DOI: 10.3390/v13060976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Arenaviruses cause chronic and asymptomatic infections in their natural host, rodents, and several arenaviruses cause severe hemorrhagic fever that has a high mortality in infected humans, seriously threatening public health. There are currently no FDA-licensed drugs available against arenaviruses; therefore, it is important to develop novel antiviral strategies to combat them, which would be facilitated by a detailed understanding of the interactions between the viruses and their hosts. To this end, we performed a transcriptomic analysis on cells infected with arenavirus lymphocytic choriomeningitis virus (LCMV), a neglected human pathogen with clinical significance, and found that the signal transducer and activator of transcription 3 (STAT3) signaling pathway was activated. A further investigation indicated that STAT3 could be activated by the RNA-dependent RNA polymerase L protein (Lp) of LCMV. Our functional analysis found that STAT3 cannot affect LCMV multiplication in A549 cells. We also found that STAT3 was activated by the Lp of Mopeia virus and Junin virus, suggesting that this activation may be conserved across certain arenaviruses. Our study explored the interactions between arenaviruses and STAT3, which may help us to better understand the molecular and cell biology of arenaviruses.
Collapse
Affiliation(s)
- Qingxing Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; (Q.W.); (W.S.); (W.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qilin Xin
- UMR754, Viral Infections and Comparative Pathology, 50 Avenue Tony Garnier, CEDEX 07, 69366 Lyon, France;
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; (Q.W.); (W.S.); (W.W.)
| | - Weiwei Wan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; (Q.W.); (W.S.); (W.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; (Q.W.); (W.S.); (W.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (G.X.); (L.-K.Z.)
| | - Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; (Q.W.); (W.S.); (W.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (G.X.); (L.-K.Z.)
| |
Collapse
|
31
|
Te Velthuis AJW, Grimes JM, Fodor E. Structural insights into RNA polymerases of negative-sense RNA viruses. Nat Rev Microbiol 2021; 19:303-318. [PMID: 33495561 PMCID: PMC7832423 DOI: 10.1038/s41579-020-00501-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 01/29/2023]
Abstract
RNA viruses include many important human and animal pathogens, such as the influenza viruses, respiratory syncytial virus, Ebola virus, measles virus and rabies virus. The genomes of these viruses consist of single or multiple RNA segments that assemble with oligomeric viral nucleoprotein into ribonucleoprotein complexes. Replication and transcription of the viral genome is performed by ~250-450 kDa viral RNA-dependent RNA polymerases that also contain capping or cap-snatching activity. In this Review, we compare recent high-resolution X-ray and cryoelectron microscopy structures of RNA polymerases of negative-sense RNA viruses with segmented and non-segmented genomes, including orthomyxoviruses, peribunyaviruses, phenuiviruses, arenaviruses, rhabdoviruses, pneumoviruses and paramyxoviruses. In addition, we discuss how structural insights into these enzymes contribute to our understanding of the molecular mechanisms of viral transcription and replication, and how we can use these insights to identify targets for antiviral drug design.
Collapse
Affiliation(s)
- Aartjan J W Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
32
|
Ali F, Hussain S, Zhu YZ. A therapeutic journey of potential drugs against COVID-19. Mini Rev Med Chem 2021; 22:1876-1894. [PMID: 33845740 DOI: 10.2174/1389557521666210412161157] [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: 09/08/2020] [Revised: 01/07/2021] [Accepted: 02/15/2021] [Indexed: 11/22/2022]
Abstract
Coronavirus disease (CoVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) scrambles the world by infecting millions of peoples all over the globe. It has caused tremendous morbidity, mortality and greatly impacted the lives and economy worldwide as an outcome of mandatory quarantines or isolations. Despite the worsening trends of COVID-19, no drugs are validated to have significant efficacy in clinical treatment of COVID-19 patients in large-scale studies. Physicians and researchers throughout the world are working to understand the pathophysiology to expose the conceivable handling regimens and to determine the effective vaccines and/or therapeutic agents. Some of them re-purposed drugs for clinical trials which were primarily known to be effective against the RNA viruses including MERS-CoV and SARS-CoV-1. In the absence of a proven efficacy therapy, the current management use therapies based on antivirals, anti-inflammatory drugs, convalescent plasma, anti-parasitic agents in both oral and parenteral formulation, oxygen therapy and heparin support. What is needed at this hour, however, is a definitive drug therapy or vaccine. Different countries are rushing to find this, and various trials are already underway. We aimed to summarized the potential therapeutic strategies as a treatment options for COVID-19 that could be helpful to stop further spread of SARS-CoV-2 by effecting its structural components or modulation of immune response and also discusses the leading drugs/vaccines, which were considered as potential agents for controlling this pandemic.
Collapse
Affiliation(s)
- Fayaz Ali
- School of Pharmacy and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau SAR. China
| | - Shahid Hussain
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology Islamabad. Pakistan
| | - Yi Zhun Zhu
- School of Pharmacy and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau SAR. China
| |
Collapse
|
33
|
Structure Unveils Relationships between RNA Virus Polymerases. Viruses 2021; 13:v13020313. [PMID: 33671332 PMCID: PMC7922027 DOI: 10.3390/v13020313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.
Collapse
|
34
|
Peng Q, Peng R, Yuan B, Wang M, Zhao J, Fu L, Qi J, Shi Y. Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir. ACTA ACUST UNITED AC 2021; 2:100080. [PMID: 33521757 PMCID: PMC7834001 DOI: 10.1016/j.xinn.2021.100080] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/11/2021] [Indexed: 01/18/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into an unprecedented global pandemic. Nucleoside analogs, such as Remdesivir and Favipiravir, can serve as the first-line broad-spectrum antiviral drugs by targeting the viral polymerases. However, the underlying mechanisms for the antiviral efficacies of these drugs are far from well understood. Here, we reveal that Favipiravir, as a pyrazine derivative, could be incorporated into the viral RNA products by mimicking both adenine and guanine nucleotides. This drug thus inhibits viral replication mainly by inducing mutations in progeny RNAs, different from Remdesivir or other RNA-terminating nucleoside analogs that impair the elongation of RNA products. We further determined the cryo-EM structure of Favipiravir bound to the replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state. This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues that may explain its capacity for mimicking both adenine and guanine nucleotides. These findings shed light on the mechanism of coronavirus polymerase catalysis and provide a rational basis for developing antiviral drugs to combat the SARS-CoV-2 pandemic.
Collapse
Affiliation(s)
- Qi Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bin Yuan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingru Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lifeng Fu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
- College of Basic Medicine, Jilin University, Changchun, China
- Corresponding author
| |
Collapse
|
35
|
Brothers in Arms: Structure, Assembly and Function of Arenaviridae Nucleoprotein. Viruses 2020; 12:v12070772. [PMID: 32708976 PMCID: PMC7411964 DOI: 10.3390/v12070772] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 02/08/2023] Open
Abstract
Arenaviridae is a family of viruses harbouring important emerging pathogens belonging to the Bunyavirales order. Like in other segmented negative strand RNA viruses, the nucleoprotein (NP) is a major actor of the viral life cycle being both (i) the necessary co-factor of the polymerase present in the L protein, and (ii) the last line of defence of the viral genome (vRNA) by physically hiding its presence in the cytoplasm. The NP is also one of the major players interfering with the immune system. Several structural studies of NP have shown that it features two domains: a globular RNA binding domain (NP-core) in its N-terminal and an exonuclease domain (ExoN) in its C-terminal. Further studies have observed that significant conformational changes are necessary for RNA encapsidation. In this review we revisited the most recent structural and functional data available on Arenaviridae NP, compared to other Bunyavirales nucleoproteins and explored the structural and functional implications. We review the variety of structural motif extensions involved in NP–NP binding mode. We also evaluate the major functional implications of NP interactome and the role of ExoN, thus making the NP a target of choice for future vaccine and antiviral therapy.
Collapse
|
36
|
Arragain B, Effantin G, Gerlach P, Reguera J, Schoehn G, Cusack S, Malet H. Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Nat Commun 2020; 11:3590. [PMID: 32681014 PMCID: PMC7368059 DOI: 10.1038/s41467-020-17349-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/25/2020] [Indexed: 11/22/2022] Open
Abstract
Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and transcription of the RNA genome constitute essential processes performed by the virally encoded multi-domain RNA-dependent RNA polymerase. Here, we describe the complete high-resolution cryo-EM structure of La Crosse virus polymerase. It reveals the presence of key protruding C-terminal domains, notably the cap-binding domain, which undergoes large movements related to its role in transcription initiation, and a zinc-binding domain that displays a fold not previously observed. We capture the polymerase structure at pre-initiation and elongation states, uncovering the coordinated movement of the priming loop, mid-thumb ring linker and lid domain required for the establishment of a ten-base-pair template-product RNA duplex before strand separation into respective exit tunnels. These structural details and the observed dynamics of key functional elements will be instrumental for structure-based development of polymerase inhibitors. RNA-dependent RNA polymerases from segmented negative stranded RNA viruses catalyze genome replication and viral transcription. Here, the authors present the cryo-EM structure of full-length La Crosse virus polymerase and structurally characterize the pre-initiation and elongation states, which is of interest for the development of polymerase inhibitors.
Collapse
Affiliation(s)
- Benoît Arragain
- Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), F-38000, Grenoble, France
| | - Grégory Effantin
- Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), F-38000, Grenoble, France
| | - Piotr Gerlach
- European Molecular Biology Laboratory, Grenoble, France.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Juan Reguera
- European Molecular Biology Laboratory, Grenoble, France.,Aix-Marseille Université, CNRS, INSERM, AFMB UMR 7257, 13288, Marseille, France
| | - Guy Schoehn
- Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), F-38000, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France.
| | - Hélène Malet
- Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), F-38000, Grenoble, France.
| |
Collapse
|
37
|
Mutation of an Influenza Virus Polymerase 3' RNA Promoter Binding Site Inhibits Transcription Elongation. J Virol 2020; 94:JVI.00498-20. [PMID: 32295915 DOI: 10.1128/jvi.00498-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Influenza viruses encode a viral RNA-dependent RNA polymerase (FluPol), which is responsible for transcribing and replicating the negative-sense viral RNA (vRNA) genome. FluPol transcribes vRNA using a host-capped mRNA primer and replicates it by synthesizing a positive-sense cRNA intermediate, which is copied back into vRNA. To carry out these functions, FluPol interacts with vRNA and cRNA using conserved promoter elements at the 5' and 3' termini. Recent structural studies have identified a new surface binding site for the 3' vRNA and cRNA promoters on FluPol, referred to as the mode B site. However, the role of this binding site in FluPol function is unknown. In this study, we used a combination of cell-based and biochemical assays to show that the mode B site is important for both viral genome transcription and replication in influenza A virus. Furthermore, we show that the mode B site is not needed for initiating transcription in vitro but is required to synthesize a full-length product. This is consistent with a model in which the 3' terminus of the vRNA template binds in the mode B site during elongation. Our data provide the first functional insights into the role of the mode B site on FluPol, which advances our understanding of FluPol function and influenza virus replication.IMPORTANCE Influenza viruses are responsible for up to 650,000 deaths per year through seasonal epidemics, and pandemics have caused tens of millions of deaths in the past. Most current therapeutics suffer from widespread resistance, creating a need for new drug targets against influenza virus. The virus encodes an RNA-dependent RNA polymerase, which replicates and transcribes the vRNA genome. The polymerase interacts with vRNA and the complementary replicative intermediate cRNA using several specific binding sites; however, the functions associated with these binding sites remain unknown. Here, we functionally characterize a binding site for the 3' vRNA and cRNA promoters. Our data offer insight into the mechanism of viral genome transcription by the influenza virus polymerase and may be applicable to other related viruses.
Collapse
|
38
|
Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Wang Q, Sun Y, Fan Z, Qi J, Gao GF, Shi Y. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2. Cell Rep 2020; 31:107774. [PMID: 32531208 PMCID: PMC7260489 DOI: 10.1016/j.celrep.2020.107774] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/23/2020] [Accepted: 05/26/2020] [Indexed: 01/18/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). The viral polymerase is a promising antiviral target. Here, we describe the near-atomic-resolution structure of the SARS-CoV-2 polymerase complex consisting of the nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases and suggests a mechanism of activation by cofactors. Biochemical studies reveal reduced activity of the core polymerase complex and lower thermostability of individual subunits of SARS-CoV-2 compared with SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate adaptation of SARS-CoV-2 toward humans with a relatively lower body temperature than the natural bat hosts. Cryo-EM structure of SARS-CoV-2 nsp12-nsp7-nsp8 core polymerase complex The core complex of SARS-CoV-2 has lower enzymatic activity than SARS-CoV SARS-CoV-2 nsp7-8-12 subunits are less thermostable than the SARS-CoV counterpart
Collapse
Affiliation(s)
- Qi Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yuan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xixi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Sun
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), 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; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of the Chinese Academy of Sciences, Chongqing 400013, China; College of Basic Medicine, Jilin University, Changchun, Jilin 130021, China.
| |
Collapse
|
39
|
Abstract
Lassa fever was first described as a clinical entity fifty years ago. The causative agent Lassa virus was isolated from these first known cases. This chapter reviews the key publications on Lassa fever research that appeared in the scientific literature at that time and over the ensuing decades.
Collapse
Affiliation(s)
- Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70118, USA. .,Zalgen Labs, LLC, 20271 Goldenrod Lane, Suite 2083, Germantown, MD, 20876, USA.
| |
Collapse
|
40
|
Abstract
The ongoing COVID-19 pandemic has made us to consider the emergence of potential viral diseases in the future. Animals can carry vast and diverse virus species, most of which we do not understand yet, and the spillover events of the viruses from the unknown pool in animals to human population always occurred in the past. To effectively prevent and control the emerging viral diseases, we should make efforts to explore the unknown virus species in nature and prepare in advance.
Collapse
Affiliation(s)
- Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|