1
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Aida-Ficken V, Kelly JA, Chatterjee P, Jenks MH, McMullan LK, Albariño CG, Montgomery JM, Seley-Radtke KL, Spiropoulou CF, Flint M. Identification of a macrocyclic compound targeting the lassa virus polymerase. Antiviral Res 2024; 228:105923. [PMID: 38844175 DOI: 10.1016/j.antiviral.2024.105923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
There are no approved vaccines or therapeutics for Lassa virus (LASV) infections. To identify compounds with anti-LASV activity, we conducted a cell-based screening campaign at biosafety level 4 and tested almost 60,000 compounds for activity against an infectious reporter LASV. Hits from this screen included several structurally related macrocycles. The most potent, Mac128, had a sub-micromolar EC50 against the reporter virus, inhibited wild-type clade IV LASV, and reduced viral titers by 4 orders of magnitude. Mechanistic studies suggested that Mac128 inhibited viral replication at the level of the polymerase.
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Affiliation(s)
- Virginia Aida-Ficken
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Jamie A Kelly
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Payel Chatterjee
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Harley Jenks
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura K McMullan
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - César G Albariño
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mike Flint
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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2
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Siegel DS, Hui HC, Pitts J, Vermillion MS, Ishida K, Rautiola D, Keeney M, Irshad H, Zhang L, Chun K, Chin G, Goyal B, Doerffler E, Yang H, Clarke MO, Palmiotti C, Vijjapurapu A, Riola NC, Stray K, Murakami E, Ma B, Wang T, Zhao X, Xu Y, Lee G, Marchand B, Seung M, Nayak A, Tomkinson A, Kadrichu N, Ellis S, Barauskas O, Feng JY, Perry JK, Perron M, Bilello JP, Kuehl PJ, Subramanian R, Cihlar T, Mackman RL. Discovery of GS-7682, a Novel 4'-Cyano-Modified C-Nucleoside Prodrug with Broad Activity against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys. J Med Chem 2024. [PMID: 39018526 DOI: 10.1021/acs.jmedchem.4c00899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
Acute respiratory viral infections, such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1), a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV (EC50 = 3-46 nM), human metapneumovirus (EC50 = 210 nM), human rhinovirus (EC50 = 54-61 nM), and enterovirus (EC50 = 83-90 nM). Prodrug optimization for cellular potency and lung cell metabolism identified 5'-methyl [(S)-hydroxy(phenoxy)phosphoryl]-l-alaninate in combination with 2',3'-diisobutyrate promoieties as being optimal for high levels of intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together, these findings support additional evaluation of 1 and its analogues as potential therapeutics for pneumo- and picornaviruses.
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Affiliation(s)
- Dustin S Siegel
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Hon C Hui
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Jared Pitts
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Meghan S Vermillion
- Gilead Sciences, Inc., Foster City, California 94404, United States
- Lovelace Biomedical, Albuquerque, New Mexico 87108, United States
| | - Kazuya Ishida
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Davin Rautiola
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Michael Keeney
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Hammad Irshad
- Lovelace Biomedical, Albuquerque, New Mexico 87108, United States
| | - Lijun Zhang
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Kwon Chun
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Gregory Chin
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Bindu Goyal
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Edward Doerffler
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Hai Yang
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Michael O Clarke
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Chris Palmiotti
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Arya Vijjapurapu
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Nicholas C Riola
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Kirsten Stray
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Eisuke Murakami
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Bin Ma
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Ting Wang
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Xiaofeng Zhao
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Yili Xu
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Gary Lee
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Bruno Marchand
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Minji Seung
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Arabinda Nayak
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Adrian Tomkinson
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Nani Kadrichu
- Inspired - Pulmonary Solutions, San Carlos, California 94070, United States
| | - Scott Ellis
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Ona Barauskas
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Joy Y Feng
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Jason K Perry
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Michel Perron
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - John P Bilello
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Philip J Kuehl
- Lovelace Biomedical, Albuquerque, New Mexico 87108, United States
| | - Raju Subramanian
- Gilead Sciences, Inc., Foster City, California 94404, United States
| | - Tomas Cihlar
- Gilead Sciences, Inc., Foster City, California 94404, United States
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3
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Gordon CJ, Walker SM, Tchesnokov EP, Kocincova D, Pitts J, Siegel DS, Perry JK, Feng JY, Bilello JP, Götte M. Mechanism and spectrum of inhibition of a 4´-cyano modified nucleotide analog against diverse RNA polymerases of prototypic respiratory RNA viruses. J Biol Chem 2024:107514. [PMID: 38945449 DOI: 10.1016/j.jbc.2024.107514] [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: 04/25/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024] Open
Abstract
The development of safe and effective broad-spectrum antivirals that target the replication machinery of respiratory viruses is of high priority in pandemic preparedness programs. Here, we studied the mechanism of action of a newly discovered nucleotide analog against diverse RNA-dependent RNA polymerases (RdRp) of prototypic respiratory viruses. GS-646939 is the active 5'-triphosphate (TP) metabolite of a 4'-cyano modified C-adenosine analog phosphoramidate prodrug GS-7682. Enzyme kinetics show that the RdRps of human rhinovirus type 16 (HRV-16) and enterovirus 71 (EV-71) incorporate GS-646939 with unprecedented selectivity; GS-646939 is incorporated 20-50-fold more efficiently than its natural ATP counterpart. The RdRp complex of respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) incorporate GS-646939 and ATP with similar efficiency. In contrast, influenza B RdRp shows a clear preference for ATP and human mitochondrial RNA polymerase (h-mtRNAP) does not show significant incorporation of GS-646939. Once incorporated into the nascent RNA strand, GS-646939 acts as a chain-terminator although higher NTP concentrations can partially overcome inhibition for some polymerases. Modeling and biochemical data suggest that the 4'-modification inhibits RdRp translocation. Comparative studies with GS-443902, the active triphosphate form of the 1'-cyano modified prodrugs remdesivir and obeldesivir, reveal not only different mechanisms of inhibition, but also differences in the spectrum of inhibition of viral polymerases. In conclusion, 1'-cyano and 4'-cyano modifications of nucleotide analogs provide complementary strategies to target the polymerase of several families of respiratory RNA viruses.
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Affiliation(s)
- Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Simon M Walker
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Dana Kocincova
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jared Pitts
- Gilead Sciences, Inc., Foster City, California, USA
| | | | | | - Joy Y Feng
- Gilead Sciences, Inc., Foster City, California, USA
| | | | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
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4
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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.
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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
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5
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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.
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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.
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6
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Cao D, Gao Y, Chen Z, Gooneratne I, Roesler C, Mera C, D'Cunha P, Antonova A, Katta D, Romanelli S, Wang Q, Rice S, Lemons W, Ramanathan A, Liang B. Structures of the promoter-bound respiratory syncytial virus polymerase. Nature 2024; 625:611-617. [PMID: 38123676 PMCID: PMC10794133 DOI: 10.1038/s41586-023-06867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten viral mRNAs and replicates full-length viral genomic and antigenomic RNAs1. The RSV polymerase initiates RNA synthesis by binding to the conserved 3'-terminal RNA promoters of the genome or antigenome2. However, the lack of a structure of the RSV polymerase bound to the RNA promoter has impeded the mechanistic understanding of RSV RNA synthesis. Here we report cryogenic electron microscopy structures of the RSV polymerase bound to its genomic and antigenomic viral RNA promoters, representing two of the first structures of an RNA-dependent RNA polymerase in complex with its RNA promoters in non-segmented negative-sense RNA viruses. The overall structures of the promoter-bound RSV polymerases are similar to that of the unbound (apo) polymerase. Our structures illustrate the interactions between the RSV polymerase and the RNA promoters and provide the structural basis for the initiation of RNA synthesis at positions 1 and 3 of the RSV promoters. These structures offer a deeper understanding of the pre-initiation state of the RSV polymerase and could aid in antiviral research against RSV.
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Affiliation(s)
- Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhenhang Chen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Inesh Gooneratne
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Claire Roesler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cristopher Mera
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul D'Cunha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna Antonova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Katta
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Romanelli
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Qi Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Samantha Rice
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Wesley Lemons
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita Ramanathan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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7
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Sänger L, Williams HM, Yu D, Vogel D, Kosinski J, Rosenthal M, Uetrecht C. RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment. J Am Chem Soc 2023; 145:27958-27974. [PMID: 38104324 PMCID: PMC10755698 DOI: 10.1021/jacs.3c07325] [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: 07/10/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Lassa virus is a negative-strand RNA virus with only four structural proteins that causes periodic outbreaks in West Africa. The nucleoprotein (NP) encapsidates the viral genome, forming ribonucleoprotein complexes (RNPs) together with the viral RNA and the L protein. RNPs must be continuously restructured during viral genome replication and transcription. The Z protein is important for membrane recruitment of RNPs, viral particle assembly, and budding and has also been shown to interact with the L protein. However, the interaction of NP, viral RNA, and Z is poorly understood. Here, we characterize the interactions between Lassa virus NP, Z, and RNA using structural mass spectrometry. We identify the presence of RNA as the driver for the disassembly of ring-like NP trimers, a storage form, into monomers to subsequently form higher order RNA-bound NP assemblies. We locate the interaction site of Z and NP and demonstrate that while NP binds Z independently of the presence of RNA, this interaction is pH-dependent. These data improve our understanding of RNP assembly, recruitment, and release in Lassa virus.
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Affiliation(s)
- Lennart Sänger
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Harry M. Williams
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
| | - Dingquan Yu
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
| | - Dominik Vogel
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Jan Kosinski
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Maria Rosenthal
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
- Faculty
V: School of Life Sciences, University of
Siegen, Am Eichenhang 50, 57076 Siegen, Germany
- Deutsches
Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
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8
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Arragain B, Pelosse M, Thompson A, Cusack S. Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Nat Commun 2023; 14:8145. [PMID: 38066000 PMCID: PMC10709604 DOI: 10.1038/s41467-023-44044-x] [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: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated.
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Affiliation(s)
- Benoit Arragain
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Martin Pelosse
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Albert Thompson
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
- The Francis Crick Institute, London, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.
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9
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Hastie KM, Melnik LI, Cross RW, Klitting RM, Andersen KG, Saphire EO, Garry RF. The Arenaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J Infect Dis 2023; 228:S359-S375. [PMID: 37849403 PMCID: PMC10582522 DOI: 10.1093/infdis/jiac266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Lassa virus (LASV), Junin virus (JUNV), and several other members of the Arenaviridae family are capable of zoonotic transfer to humans and induction of severe viral hemorrhagic fevers. Despite the importance of arenaviruses as potential pandemic pathogens, numerous gaps exist in scientific knowledge pertaining to this diverse family, including gaps in understanding replication, immunosuppression, receptor usage, and elicitation of neutralizing antibody responses, that in turn complicates development of medical countermeasures. A further challenge to the development of medical countermeasures for arenaviruses is the requirement for use of animal models at high levels of biocontainment, where each model has distinct advantages and limitations depending on, availability of space, animals species-specific reagents, and most importantly the ability of the model to faithfully recapitulate human disease. Designation of LASV and JUNV as prototype pathogens can facilitate progress in addressing the public health challenges posed by members of this important virus family.
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Affiliation(s)
- Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston National Laboratory, Galveston, Texas, USA
| | - Raphaëlle M Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Research Translational Institute, La Jolla, California, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Scripps Research Translational Institute, La Jolla, California, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
- Zalgen Labs LLC, Frederick, Maryland, USA
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10
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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.
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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.
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11
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Bezerra EHS, Melo-Hanchuk TD, Marques RE. Structural and molecular biology of Sabiá virus. Exp Biol Med (Maywood) 2023; 248:1624-1634. [PMID: 37937408 PMCID: PMC10723027 DOI: 10.1177/15353702231199071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Brazilian mammarenavirus, or Sabiá virus (SABV), is a New World (NW) arenavirus associated with fulminant hemorrhagic disease in humans and the sole biosafety level 4 microorganism ever isolated in Brazil. Since the isolation of SABV in the 1990s, studies on viral biology have been scarce, with no available countermeasures against SABV infection or disease. Here we provide a comprehensive review of SABV biology, including key aspects of SABV replication, and comparisons with related Old World and NW arenaviruses. SABV is most likely a rodent-borne virus, transmitted to humans, through exposure to urine and feces in peri-urban areas. Using protein structure prediction methods and alignments, we analyzed shared and unique features of SABV proteins (GPC, NP, Z, and L) that could be explored in search of therapeutic strategies, including repurposing intended application against arenaviruses. Highly conserved catalytic activities present in L protein could be targeted for broad-acting antiviral activity among arenaviruses, while protein-protein interactions, such as those between L and the matrix protein Z, have evolved in NW arenaviruses and should be specific to SABV. The nucleoprotein (NP) also shares targetable interaction interfaces with L and Z and exhibits exonuclease activity in the C-terminal domain, which may be involved in multiple aspects of SABV replication. Envelope glycoproteins GP1 and GP2 have been explored in the development of promising cross-reactive neutralizing antibodies and vaccines, some of which could be repurposed for SABV. GP1 remains a challenging target in SABV as evolutive pressures render it the most variable viral protein in terms of both sequence and structure, while antiviral strategies targeting the Z protein remain to be validated. In conclusion, the prediction and analysis of protein structures should revolutionize research on viruses such as SABV by facilitating the rational design of countermeasures while reducing dependence on sophisticated laboratory infrastructure for experimental validation.
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Affiliation(s)
| | | | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo 13083-100, Brazil
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12
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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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13
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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.
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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.
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14
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Garry RF. Lassa Virus Structural Biology and Replication. Curr Top Microbiol Immunol 2023. [PMID: 37100973 DOI: 10.1007/82_2023_262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Lassa virus (LASV) is the causative agent of Lassa fever, an often-fatal hemorrhagic fever that is endemic in West Africa. LASV virions are enveloped and contain two single-stranded RNA genome segments. Both segments are ambisense and encode two proteins. The nucleoprotein associates with viral RNAs forming ribonucleoprotein complexes. The glycoprotein complex mediates viral attachment and entry. The Zinc protein serves as the matrix protein. Large is a polymerase that catalyzes viral RNA transcription and replication. LASV virion entry occurs via a clathrin-independent endocytic pathway usually involving alpha-dystroglycan and lysosomal associated membrane protein 1 as surface and intracellular receptors, respectively. Advances in understanding LASV structural biology and replication have facilitated development of promising vaccine and drug candidates.
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Affiliation(s)
- Robert F Garry
- School of Medicine, Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA.
- Zalgen Labs, Frederick, MD, 21703, USA.
- Global Virus Network (GVN), Baltimore, MD, 21201, USA.
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15
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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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16
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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.
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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
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17
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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.
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Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, People's Republic of China.
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18
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Abstract
Lassa virus (LASV) is endemic in the rodent populations of Sierra Leone, Nigeria and other countries in West Africa. Spillover to humans occurs frequently and results in Lassa fever, a viral haemorrhagic fever (VHF) associated with a high case fatality rate. Despite advances, fundamental gaps in knowledge of the immunology, epidemiology, ecology and pathogenesis of Lassa fever persist. More frequent outbreaks, the potential for further geographic expansion of Mastomys natalensis and other rodent reservoirs, the ease of procurement and possible use and weaponization of LASV, the frequent importation of LASV to North America and Europe, and the emergence of novel LASV strains in densely populated West Africa have driven new initiatives to develop countermeasures for LASV. Although promising candidates are being evaluated, as yet there are no approved vaccines or therapeutics for human use. This Review discusses the virology of LASV, the clinical course of Lassa fever and the progress towards developing medical countermeasures.
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Affiliation(s)
- Robert F Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.
- Zalgen Labs, Frederick, MD, USA.
- Global Viral Network, Baltimore, MD, USA.
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19
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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.
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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;
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20
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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.
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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
- * E-mail:
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21
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Olenyi T, Marquet C, Heinzinger M, Kröger B, Nikolova T, Bernhofer M, Sändig P, Schütze K, Littmann M, Mirdita M, Steinegger M, Dallago C, Rost B. LambdaPP: Fast and accessible protein-specific phenotype predictions. Protein Sci 2023; 32:e4524. [PMID: 36454227 PMCID: PMC9793974 DOI: 10.1002/pro.4524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/09/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first internet server making AI protein predictions available in 1992. Given a protein sequence as input, LambdaPP provides easily accessible visualizations of protein 3D structure, along with predictions at the protein level (GeneOntology, subcellular location), and the residue level (binding to metal ions, small molecules, and nucleotides; conservation; intrinsic disorder; secondary structure; alpha-helical and beta-barrel transmembrane segments; signal-peptides; variant effect) in seconds. The structure prediction provided by LambdaPP-leveraging ColabFold and computed in minutes-is based on MMseqs2 multiple sequence alignments. All other feature prediction methods are based on the pLM ProtT5. Queried by a protein sequence, LambdaPP computes protein and residue predictions almost instantly for various phenotypes, including 3D structure and aspects of protein function. LambdaPP is freely available for everyone to use under embed.predictprotein.org, the interactive results for the case study can be found under https://embed.predictprotein.org/o/Q9NZC2. The frontend of LambdaPP can be found on GitHub (github.com/sacdallago/embed.predictprotein.org), and can be freely used and distributed under the academic free use license (AFL-2). For high-throughput applications, all methods can be executed locally via the bio-embeddings (bioembeddings.com) python package, or docker image at ghcr.io/bioembeddings/bio_embeddings, which also includes the backend of LambdaPP.
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Affiliation(s)
- Tobias Olenyi
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany,TUM Graduate SchoolCenter of Doctoral Studies in Informatics and its Applications (CeDoSIA)GarchingGermany
| | - Céline Marquet
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany,TUM Graduate SchoolCenter of Doctoral Studies in Informatics and its Applications (CeDoSIA)GarchingGermany
| | - Michael Heinzinger
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany,TUM Graduate SchoolCenter of Doctoral Studies in Informatics and its Applications (CeDoSIA)GarchingGermany
| | - Benjamin Kröger
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany
| | - Tiha Nikolova
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany
| | - Michael Bernhofer
- TUM Graduate SchoolCenter of Doctoral Studies in Informatics and its Applications (CeDoSIA)GarchingGermany
| | - Philip Sändig
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany
| | - Konstantin Schütze
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany
| | - Maria Littmann
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany
| | - Milot Mirdita
- School of Biological SciencesSeoul National UniversitySeoulSouth Korea
| | - Martin Steinegger
- School of Biological SciencesSeoul National UniversitySeoulSouth Korea,Korea Artificial Intelligence InstituteSeoul National UniversitySeoulSouth Korea,Korea Institute of Molecular Biology and GeneticsSeoul National UniversitySeoulSouth Korea
| | - Christian Dallago
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany,VantAINew YorkUSA
| | - Burkhard Rost
- TUM (Technical University of Munich) Department of InformaticsBioinformatics‐ & Computational Biology—i12GarchingGermany,Institute for Advanced Study (TUM‐IAS)Lichtenbergstr. 2a, 85748 Garching/Munich, Germany & TUM School of Life Sciences Weihenstephan (WZW)FreisingGermany
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22
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Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies. Viruses 2022; 14:v14102200. [PMID: 36298755 PMCID: PMC9612308 DOI: 10.3390/v14102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022] Open
Abstract
RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
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