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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
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2
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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.
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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
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3
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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.
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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
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Naveed M, Makhdoom SI, Ali U, Jabeen K, Aziz T, Khan AA, Jamil S, Shahzad M, Alharbi M, Alshammari A. Immunoinformatics Approach to Design Multi-Epitope-Based Vaccine against Machupo Virus Taking Viral Nucleocapsid as a Potential Candidate. Vaccines (Basel) 2022; 10:vaccines10101732. [PMID: 36298597 PMCID: PMC9609340 DOI: 10.3390/vaccines10101732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 01/09/2023] Open
Abstract
The family members of Arenaviridae include members of the genus Machupo virus, which have bi-segmented negative sense RNA inside the envelope and can be transferred to humans through rodent carriers. Machupo virus, a member of the mammarenavirus genus, causes Bolivian hemorrhage fever, its viral nucleocapsid protein being a significant virulence factor. Currently, no treatment is available for Bolivian hemorrhage fever and work to develop a protective as well as post-diagnosis treatment is underway. Adding to these efforts, this study employed a reverse-vaccinology approach to design a vaccine with B and T-cell epitopes of the viral nucleocapsid protein of the Machupo virus. Five B-cell specific, eight MHC-I restricted, and 14 MHC-II restricted epitopes were finalized for the construct based on an antigenicity score of >0.5 and non-allergenicity as a key characteristic. The poly-histidine tag was used to construct an immunogenic and stable vaccine construct and 50S ribosomal 46 protein L7/L12 adjuvant with linkers (EAAAK, GPGPG, and AYY). It covers 99.99% of the world’s population, making it highly efficient. The physicochemical properties like the aliphatic index (118.31) and the GRAVY index (0.302) showed that the vaccine is easily soluble. The overall Ramachandran score of the construct was 90.7%, and the instability index was 35.13, endorsing a stable structure. The immune simulations demonstrated a long-lasting antibody response even after the excretion of the antigen from the body in the first 5 days of injection. The IgM + IgG titers were predicted to rise to 6000 10 days post-injection and were illustrated to be stable (around 3000) after a month, elucidating that the vaccine would be effective and provide enduring protection. Lastly, the molecular interaction between the construct and the IKBKE receptor was significant and a higher eigenfactor value in MD simulations confirmed the stable molecular interaction between the receptor and the vaccine, validating our construct.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
- Correspondence: or (M.N.); or (T.A.)
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Urooj Ali
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
- Department of Biotechnology, Quaid-I-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Tariq Aziz
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- Correspondence: or (M.N.); or (T.A.)
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan
| | - Sumbal Jamil
- Rehman Medical Institute, Peshawar 25000, Pakistan
| | - Muhammad Shahzad
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Reading RG6 6AX, UK
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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5
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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.
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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.
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6
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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.
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7
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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.
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8
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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.
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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.
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9
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Fearns R. Negative‐strand RNA Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Tchesnokov EP, Bailey-Elkin BA, Mark BL, Götte M. Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein. PLoS Negl Trop Dis 2020; 14:e0008283. [PMID: 32497085 PMCID: PMC7271988 DOI: 10.1371/journal.pntd.0008283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/09/2020] [Indexed: 11/17/2022] Open
Abstract
Background The Crimean-Congo hemorrhagic fever virus (CCHFV) is a segmented negative-sense RNA virus that can cause severe human disease. The World Health Organization (WHO) has listed CCHFVas a priority pathogen with an urgent need for enhanced research activities to develop effective countermeasures. Here we adopted a biochemical approach that targets the viral RNA-dependent RNA polymerase (RdRp). The CCHFV RdRp activity is part of a multifunctional L protein that is unusually large with a molecular weight of ~450 kDa. The CCHFV L-protein also contains an ovarian tumor (OTU) domain that exhibits deubiquitinating (DUB) activity, which was shown to interfere with innate immune responses and viral replication. We report on the expression, characterization and inhibition of the CCHFV full-length L-protein and studied both RNA synthesis and DUB activity. Methodology/Principle findings Recombinant full-length CCHFV L protein was expressed in insect cells and purified to near homogeneity using affinity chromatography. RdRp activity was monitored with model primer/templates during elongation in the presence of divalent metal ions. We observed a 14-mer full length RNA product as well as the expected shorter products when omitting certain nucleotides from the reaction mixture. The D2517N mutation of the putative active site rendered the enzyme inactive. Inhibition of RNA synthesis was studies with the broad-spectrum antivirals ribavirin and favipiravir that mimic nucleotide substrates. The triphosphate form of these compounds act like ATP or GTP; however, incorporation of ATP or GTP is markedly favored over the inhibitors. We also studied the effects of bona fide nucleotide analogues 2’-deoxy-2’-fluoro-CTP (FdC) and 2’-deoxy-2’-amino-CTP and demonstrate increased inhibitory effects due to higher rates of incorporation. We further show that the CCHFV L full-length protein and the isolated OTU domain cleave Lys48- and Lys63-linked polyubiqutin chains. Moreover, the ubiquitin analogue CC.4 inhibits the CCHFV-associated DUB activity of the full-length L protein and the isolated DUB domain to a similar extent. Inhibition of DUB activity does not affect elongation of RNA synthesis, and inhibition of RNA synthesis does not affect DUB activity. Both domains are functionally independent under these conditions. Conclusions/Significance The requirements for high biosafety measures hamper drug discovery and development efforts with infectious CCHFV. The availability of full-length CCHFV L-protein provides an important tool in this regard. High-throughput screening (HTS) campaigns are now feasible. The same enzyme preparations can be employed to identify novel polymerase and DUB inhibitors. The tick-born Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe human disease with high fatality rates. Outbreaks have been documented in a large geographic area from Africa to Asia. Unfortunately, vaccines that would prevent infection with the virus or antiviral drugs that can be administered for disease treatment are not available. Biosafety requirements further impede research in this area. The development of biochemical tools could potentially address this problem. Here we have expressed recombinant viral L-protein in insect cells. The L-protein is unusually large and exhibits RNA synthesis and deubiquitinating activities that are required for efficient viral growth. We have demonstrated that two distinct activities can be monitored in biochemical assays. Inhibition of these activities was shown with prototypic compounds. Hence, the purified L-protein provides an attractive target and tool for future drug discovery and development efforts.
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Affiliation(s)
- Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.,Li Ka Shing Institute of Virology at University of Alberta, Edmonton, Alberta, Canada
| | | | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.,Li Ka Shing Institute of Virology at University of Alberta, Edmonton, Alberta, Canada
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11
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Vogel D, Thorkelsson SR, Quemin ERJ, Meier K, Kouba T, Gogrefe N, Busch C, Reindl S, Günther S, Cusack S, Grünewald K, Rosenthal M. Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein. Nucleic Acids Res 2020; 48:5749-5765. [PMID: 32313945 PMCID: PMC7261188 DOI: 10.1093/nar/gkaa253] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
The Bunyavirales order contains several emerging viruses with high epidemic potential, including Severe fever with thrombocytopenia syndrome virus (SFTSV). The lack of medical countermeasures, such as vaccines and antivirals, is a limiting factor for the containment of any virus outbreak. To develop such antivirals a profound understanding of the viral replication process is essential. The L protein of bunyaviruses is a multi-functional and multi-domain protein performing both virus transcription and genome replication and, therefore, is an ideal drug target. We established expression and purification procedures for the full-length L protein of SFTSV. By combining single-particle electron cryo-microscopy and X-ray crystallography, we obtained 3D models covering ∼70% of the SFTSV L protein in the apo-conformation including the polymerase core region, the endonuclease and the cap-binding domain. We compared this first L structure of the Phenuiviridae family to the structures of La Crosse peribunyavirus L protein and influenza orthomyxovirus polymerase. Together with a comprehensive biochemical characterization of the distinct functions of SFTSV L protein, this work provides a solid framework for future structural and functional studies of L protein-RNA interactions and the development of antiviral strategies against this group of emerging human pathogens.
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Affiliation(s)
- Dominik Vogel
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
| | - Sigurdur Rafn Thorkelsson
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, Hamburg, Germany
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, Hamburg, Germany
| | - Kristina Meier
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
| | - Tomas Kouba
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Nadja Gogrefe
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
| | - Carola Busch
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
| | - Sophia Reindl
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany.,German Center for Infection Research (DZIF), Partner site Hamburg - Lübeck - Borstel - Riems, Hamburg 20359, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, Hamburg, Germany
| | - Maria Rosenthal
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Hamburg 20359, Germany
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Abstract
Tacaribe virus (TCRV) is the prototype of the New World arenaviruses (also known as TCRV serocomplex viruses). While TCRV is not itself a human pathogen, many closely related members of this group cause hemorrhagic fever, and thus TCRV has long served as an important BSL2 system for research into diverse areas of arenavirus biology. Due to its widespread use, a coding-complete sequence for both the S and L segments of the bipartite genome has been publically available for almost 30 years. However, more recently, this sequence has been found to contain significant discrepancies compared to other samples of the same original strain (i.e., TRVL-11573). Further, it is incomplete with respect to the genome ends, which contain critical regulatory elements for RNA synthesis. In order to rectify these issues we now present the first complete genome sequence for this important prototype arenavirus. In addition to completing the S segment 5’ end, we identified an apparent error in the L segment 3’ end as well as substantial discrepancies in the S segment intergenic region likely to affect folding. Comparison of this sequence with existing partial sequences confirmed a 12-amino-acid deletion in GP, including putative glycosylation sites, and a 4-amino-acid exchange flanking the exonuclease domain of NP. Accounting for these corrections, the TRVL-11573 strain appears to be nearly identical to that isolated in Florida in 2012. The availability of this information provides a solid basis for future molecular and genetic work on this important prototype arenavirus.
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Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S. A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Cell 2020; 181:877-893.e21. [PMID: 32304664 DOI: 10.1016/j.cell.2020.03.061] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/18/2020] [Accepted: 03/26/2020] [Indexed: 11/16/2022]
Abstract
Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP.
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Affiliation(s)
- Joanna M Wandzik
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Tomas Kouba
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Alexander Pflug
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Petra Drncova
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Jan Provaznik
- European Molecular Biology Laboratory, GeneCore, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, GeneCore, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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14
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Peng R, Xu X, Jing J, Wang M, Peng Q, Liu S, Wu Y, Bao X, Wang P, Qi J, Gao GF, Shi Y. Structural insight into arenavirus replication machinery. Nature 2020; 579:615-619. [PMID: 32214249 DOI: 10.1038/s41586-020-2114-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 01/14/2020] [Indexed: 01/10/2023]
Abstract
Arenaviruses can cause severe haemorrhagic fever and neurological diseases in humans and other animals, exemplified by Lassa mammarenavirus, Machupo mammarenavirus and lymphocytic choriomeningitis virus, posing great threats to public health1-4. These viruses encode a large multi-domain RNA-dependent RNA polymerase for transcription and replication of the viral genome5. Viral polymerases are one of the leading antiviral therapeutic targets. However, the structure of arenavirus polymerase is not yet known. Here we report the near-atomic resolution structures of Lassa and Machupo virus polymerases in both apo and promoter-bound forms. These structures display a similar overall architecture to influenza virus and bunyavirus polymerases but possess unique local features, including an arenavirus-specific insertion domain that regulates the polymerase activity. Notably, the ordered active site of arenavirus polymerase is inherently switched on, without the requirement for allosteric activation by 5'-viral RNA, which is a necessity for both influenza virus and bunyavirus polymerases6,7. Moreover, dimerization could facilitate the polymerase activity. These findings advance our understanding of the mechanism of arenavirus replication and provide an important basis for developing antiviral therapeutics.
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Affiliation(s)
- Ruchao Peng
- 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
| | - Xin Xu
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jiamei Jing
- 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
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Peng
- 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
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 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
| | - Sheng Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xichen Bao
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Peiyi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 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
| | - George F Gao
- 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.
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 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.
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 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.
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 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.
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15
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Wendt L, Bostedt L, Hoenen T, Groseth A. High-throughput screening for negative-stranded hemorrhagic fever viruses using reverse genetics. Antiviral Res 2019; 170:104569. [PMID: 31356830 DOI: 10.1016/j.antiviral.2019.104569] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/28/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Abstract
Viral hemorrhagic fevers (VHFs) cause thousands of fatalities every year, but the treatment options for their management remain very limited. In particular, the development of therapeutic interventions is restricted by the lack of commercial viability of drugs targeting individual VHF agents. This makes approaches like drug repurposing and/or the identification of broad range therapies (i.e. those directed at host responses or common proviral factors) highly attractive. However, the identification of candidates for such antiviral repurposing or of host factors/pathways important for the virus life cycle is reliant on high-throughput screening (HTS). Recently, such screening work has been increasingly facilitated by the availability of reverse genetics-based approaches, including tools such as full-length clone (FLC) systems to generate reporter-expressing viruses or various life cycle modelling (LCM) systems, many of which have been developed and/or greatly improved during the last years. In particular, since LCM systems are capable of modelling specific steps in the life cycle, they are a valuable tool for both targeted screening (i.e. for inhibitors of a specific pathway) and mechanism of action studies. This review seeks to summarize the currently available reverse genetics systems for negative-sense VHF causing viruses (i.e. arenaviruses, bunyaviruses and filoviruses), and to highlight the recent advancements made in applying these systems for HTS to identify either antivirals or new virus-host interactions that might hold promise for the development of future treatments for the infections caused by these deadly but neglected virus groups.
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Affiliation(s)
- Lisa Wendt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Linus Bostedt
- Junior Research Group - Arenavirus Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany.
| | - Allison Groseth
- Junior Research Group - Arenavirus Biology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany.
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