1
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Volobueva AS, Fedorchenko TG, Lipunova GN, Valova MS, Sbarzaglia VA, Gladkikh AS, Kanaeva OI, Tolstykh NA, Gorshkov AN, Zarubaev VV. Leucoverdazyls as Novel Potent Inhibitors of Enterovirus Replication. Pathogens 2024; 13:410. [PMID: 38787262 PMCID: PMC11123948 DOI: 10.3390/pathogens13050410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Enteroviruses (EV) are important pathogens causing human disease with various clinical manifestations. To date, treatment of enteroviral infections is mainly supportive since no vaccination or antiviral drugs are approved for their prevention or treatment. Here, we describe the antiviral properties and mechanisms of action of leucoverdazyls-novel heterocyclic compounds with antioxidant potential. The lead compound, 1a, demonstrated low cytotoxicity along with high antioxidant and virus-inhibiting activity. A viral strain resistant to 1a was selected, and the development of resistance was shown to be accompanied by mutation of virus-specific non-structural protein 2C. This resistant virus had lower fitness when grown in cell culture. Taken together, our results demonstrate high antiviral potential of leucoverdazyls as novel inhibitors of enterovirus replication and support previous evidence of an important role of 2C proteins in EV replication.
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Affiliation(s)
| | - Tatyana G. Fedorchenko
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22/20 S. Kovalevskoi St., Yekaterinburg 620108, Russia
| | - Galina N. Lipunova
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22/20 S. Kovalevskoi St., Yekaterinburg 620108, Russia
| | - Marina S. Valova
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22/20 S. Kovalevskoi St., Yekaterinburg 620108, Russia
| | | | - Anna S. Gladkikh
- St. Petersburg Pasteur Institute, 14 Mira St., St. Petersburg 197101, Russia
| | - Olga I. Kanaeva
- St. Petersburg Pasteur Institute, 14 Mira St., St. Petersburg 197101, Russia
| | - Natalia A. Tolstykh
- St. Petersburg Pasteur Institute, 14 Mira St., St. Petersburg 197101, Russia
| | - Andrey N. Gorshkov
- Smorodintsev Influenza Research Institute, 15/17 Prof. Popova St., St. Petersburg 197376, Russia
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2
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Yin C, Zhao H, Xia X, Pan Z, Li D, Zhang L. Picornavirus 2C proteins: structure-function relationships and interactions with host factors. Front Cell Infect Microbiol 2024; 14:1347615. [PMID: 38465233 PMCID: PMC10921941 DOI: 10.3389/fcimb.2024.1347615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Abstract
Picornaviruses, which are positive-stranded, non-enveloped RNA viruses, are known to infect people and animals with a broad spectrum of diseases. Among the nonstructural proteins in picornaviruses, 2C proteins are highly conserved and exhibit multiple structural domains, including amphipathic α-helices, an ATPase structural domain, and a zinc finger structural domain. This review offers a comprehensive overview of the functional structures of picornaviruses' 2C protein. We summarize the mechanisms by which the 2C protein enhances viral replication. 2C protein interacts with various host factors to form the replication complex, ultimately promoting viral replication. We review the mechanisms through which picornaviruses' 2C proteins interact with the NF-κB, RIG-I, MDA5, NOD2, and IFN pathways, contributing to the evasion of the antiviral innate immune response. Additionally, we provide an overview of broad-spectrum antiviral drugs for treating various enterovirus infections, such as guanidine hydrochloride, fluoxetine, and dibucaine derivatives. These drugs may exert their inhibitory effects on viral infections by targeting interactions with 2C proteins. The review underscores the need for further research to elucidate the precise mechanisms of action of 2C proteins and to identify additional host factors for potential therapeutic intervention. Overall, this review contributes to a deeper understanding of picornaviruses and offers insights into the antiviral strategies against these significant viral pathogens.
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Affiliation(s)
- Chunhui Yin
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Haomiao Zhao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaoyi Xia
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zhengyang Pan
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Daoqun Li
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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3
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [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: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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4
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Kejriwal R, Evans T, Calabrese J, Swistak L, Alexandrescu L, Cohen M, Rahman N, Henriksen N, Charan Dash R, Hadden MK, Stonehouse NJ, Rowlands DJ, Kingston NJ, Hartnoll M, Dobson SJ, White SJ. Development of Enterovirus Antiviral Agents That Target the Viral 2C Protein. ChemMedChem 2023; 18:e202200541. [PMID: 36792530 DOI: 10.1002/cmdc.202200541] [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: 10/10/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
The Enterovirus (EV) genus includes several important human and animal pathogens. EV-A71, EV-D68, poliovirus (PV), and coxsackievirus (CV) outbreaks have affected millions worldwide, causing a range of upper respiratory, skin, and neuromuscular diseases, including acute flaccid myelitis, and hand-foot-and-mouth disease. There are no FDA-approved antiviral therapeutics for these enteroviruses. This study describes novel antiviral compounds targeting the conserved non-structural viral protein 2C with low micromolar to nanomolar IC50 values. The selection of resistant mutants resulted in amino acid substitutions in the viral capsid protein, implying these compounds may play a role in inhibiting the interaction of 2C and the capsid protein. The assembly and encapsidation stages of the viral life cycle still need to be fully understood, and the inhibitors reported here could be useful probes in understanding these processes.
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Affiliation(s)
- Rishabh Kejriwal
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Tristan Evans
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Joshua Calabrese
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Lea Swistak
- Institut Pasteur, Université Paris Cité Dynamics of Host-Pathogen Interactions Unit, 75015, Paris, France
| | - Lauren Alexandrescu
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Michelle Cohen
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Nahian Rahman
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Niel Henriksen
- Atomwise Inc., 717 Market St #800, San Francisco, CA 94103, USA
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06029-3092, USA
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Natalie J Kingston
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Madeline Hartnoll
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Samuel J Dobson
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon J White
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
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5
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Alhazmi A, Nekoua MP, Mercier A, Vergez I, Sane F, Alidjinou EK, Hober D. Combating coxsackievirus B infections. Rev Med Virol 2023; 33:e2406. [PMID: 36371612 DOI: 10.1002/rmv.2406] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/11/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022]
Abstract
Coxsackieviruses B (CVB) are small, non-enveloped, single-stranded RNA viruses belonging to the Enterovirus genus of the Picornaviridae family. They are common worldwide and cause a wide variety of human diseases ranging from those having relatively mild symptoms to severe acute and chronic pathologies such as cardiomyopathy and type 1 diabetes. The development of safe and effective strategies to combat these viruses remains a challenge. The present review outlines current approaches to control CVB infections and associated diseases. Various drugs targeting viral or host proteins involved in viral replication as well as vaccines have been developed and shown potential to prevent or combat CVB infections in vitro and in vivo in animal models. Repurposed drugs and alternative strategies targeting miRNAs or based on plant extracts and probiotics and their derivatives have also shown antiviral effects against CVB. In addition, clinical trials with vaccines and drugs are underway and offer hope for the prevention or treatment of CVB-induced diseases.
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Affiliation(s)
- Abdulaziz Alhazmi
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, Lille, France.,Microbiology and Parasitology Department, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia
| | | | - Ambroise Mercier
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, Lille, France
| | - Ines Vergez
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, Lille, France
| | - Famara Sane
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, Lille, France
| | | | - Didier Hober
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, Lille, France
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6
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Yeager C, Carter G, Gohara DW, Yennawar NH, Enemark E, Arnold J, Cameron CE. Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP. Nucleic Acids Res 2022; 50:11775-11798. [PMID: 36399514 PMCID: PMC9723501 DOI: 10.1093/nar/gkac1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
The enteroviral 2C protein is a therapeutic target, but the absence of a mechanistic framework for this enzyme limits our understanding of inhibitor mechanisms. Here, we use poliovirus 2C and a derivative thereof to elucidate the first biochemical mechanism for this enzyme and confirm the applicability of this mechanism to other members of the enterovirus genus. Our biochemical data are consistent with a dimer forming in solution, binding to RNA, which stimulates ATPase activity by increasing the rate of hydrolysis without impacting affinity for ATP substantially. Both RNA and DNA bind to the same or overlapping site on 2C, driven by the phosphodiester backbone, but only RNA stimulates ATP hydrolysis. We propose that RNA binds to 2C driven by the backbone, with reorientation of the ribose hydroxyls occurring in a second step to form the catalytically competent state. 2C also uses a two-step mechanism for binding to ATP. Initial binding is driven by the α and β phosphates of ATP. In the second step, the adenine base and other substituents of ATP are used to organize the active site for catalysis. These studies provide the first biochemical description of determinants driving specificity and catalytic efficiency of a picornaviral 2C ATPase.
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Affiliation(s)
- Calvin Yeager
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Griffin Carter
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David W Gohara
- Department of Biochemistry and Molecular Biology, St. Louis University, St. Louis, MO 63104, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Eric J Enemark
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jamie J Arnold
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig E Cameron
- To whom correspondence should be addressed. Tel: +1 919 966 9699; Fax: +1 919 962 8103;
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7
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Chen P, Wojdyla JA, Colasanti O, Li Z, Qin B, Wang M, Lohmann V, Cui S. Biochemical and structural characterization of hepatitis A virus 2C reveals an unusual ribonuclease activity on single-stranded RNA. Nucleic Acids Res 2022; 50:9470-9489. [PMID: 35947700 PMCID: PMC9458454 DOI: 10.1093/nar/gkac671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
The HAV nonstructural protein 2C is essential for virus replication; however, its precise function remains elusive. Although HAV 2C shares 24-27% sequence identity with other 2Cs, key motifs are conserved. Here, we demonstrate that HAV 2C is an ATPase but lacking helicase activity. We identified an ATPase-independent nuclease activity of HAV 2C with a preference for polyuridylic single-stranded RNAs. We determined the crystal structure of an HAV 2C fragment to 2.2 Å resolution, containing an ATPase domain, a region equivalent to enterovirus 2C zinc-finger (ZFER) and a C-terminal amphipathic helix (PBD). The PBD of HAV 2C occupies a hydrophobic pocket (Pocket) in the adjacent 2C, and we show the PBD-Pocket interaction is vital for 2C functions. We identified acidic residues that are essential for the ribonuclease activity and demonstrated mutations at these sites abrogate virus replication. We built a hexameric-ring model of HAV 2C, revealing the ribonuclease-essential residues clustering around the central pore of the ring, whereas the ATPase active sites line up at the gaps between adjacent 2Cs. Finally, we show the ribonuclease activity is shared by other picornavirus 2Cs. Our findings identified a previously unfound activity of picornavirus 2C, providing novel insights into the mechanisms of virus replication.
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Affiliation(s)
| | | | | | | | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Meitian Wang
- Swiss Light Source at the Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Volker Lohmann
- Correspondence may also be addressed to Volker Lohmann. Tel: +49 6221 56 6449; Fax: +49 6221 56 4570;
| | - Sheng Cui
- To whom correspondence should be addressed. Tel: +86 10 67828669; Fax: +86 10 67855012;
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8
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Nishikiori M, den Boon JA, Unchwaniwala N, Ahlquist P. Crowning Touches in Positive-Strand RNA Virus Genome Replication Complex Structure and Function. Annu Rev Virol 2022; 9:193-212. [PMID: 35610038 DOI: 10.1146/annurev-virology-092920-021307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Positive-strand RNA viruses, the largest genetic class of eukaryotic viruses, include coronaviruses and many other established and emerging pathogens. A major target for understanding and controlling these viruses is their genome replication, which occurs in virus-induced membrane vesicles that organize replication steps and protect double-stranded RNA intermediates from innate immune recognition. The structure of these complexes has been greatly illuminated by recent cryo-electron microscope tomography studies with several viruses. One key finding in diverse systems is the organization of crucial viral RNA replication factors in multimeric rings or crowns that among other functions serve as exit channels gating release of progeny genomes to the cytosol for translation and encapsidation. Emerging results suggest that these crowns serve additional important purposes in replication complex assembly, function, and interaction with downstream processes such as encapsidation. The findings provide insights into viral function and evolution and new bases for understanding, controlling, and engineering positive-strand RNA viruses. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Masaki Nishikiori
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Current affiliation: Assembly Biosciences, Inc., South San Francisco, California, USA
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Hurdiss DL, El Kazzi P, Bauer L, Papageorgiou N, Ferron FP, Donselaar T, van Vliet AL, Shamorkina TM, Snijder J, Canard B, Decroly E, Brancale A, Zeev-Ben-Mordehai T, Förster F, van Kuppeveld FJ, Coutard B. Fluoxetine targets an allosteric site in the enterovirus 2C AAA+ ATPase and stabilizes a ring-shaped hexameric complex. SCIENCE ADVANCES 2022; 8:eabj7615. [PMID: 34985963 PMCID: PMC8730599 DOI: 10.1126/sciadv.abj7615] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Enteroviruses are globally prevalent human pathogens responsible for many diseases. The nonstructural protein 2C is a AAA+ helicase and plays a key role in enterovirus replication. Drug repurposing screens identified 2C-targeting compounds such as fluoxetine and dibucaine, but how they inhibit 2C is unknown. Here, we present a crystal structure of the soluble and monomeric fragment of coxsackievirus B3 2C protein in complex with (S)-fluoxetine (SFX), revealing an allosteric binding site. To study the functional consequences of SFX binding, we engineered an adenosine triphosphatase (ATPase)–competent, hexameric 2C protein. Using this system, we show that SFX, dibucaine, HBB [2-(α-hydroxybenzyl)-benzimidazole], and guanidine hydrochloride inhibit 2C ATPase activity. Moreover, cryo–electron microscopy analysis demonstrated that SFX and dibucaine lock 2C in a defined hexameric state, rationalizing their mode of inhibition. Collectively, these results provide important insights into 2C inhibition and a robust engineering strategy for structural, functional, and drug-screening analysis of 2C proteins.
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Affiliation(s)
- Daniel L. Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, Netherlands
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | | | - Lisa Bauer
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, Netherlands
| | | | | | - Tim Donselaar
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, Netherlands
| | - Arno L.W. van Vliet
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Tzviya Zeev-Ben-Mordehai
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Frank J.M. van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, Netherlands
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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10
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Chen P, Li Z, Cui S. Picornaviral 2C proteins: A unique ATPase family critical in virus replication. Enzymes 2021; 49:235-264. [PMID: 34696834 DOI: 10.1016/bs.enz.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 2C proteins of Picornaviridae are unique members of AAA+ protein family. Although picornavirus 2C shares many conserved motifs with Super Family 3 DNA helicases, duplex unwinding activity of many 2C proteins remains undetected, and high-resolution structures of 2C hexamers are unavailable. All characterized 2C proteins exhibit ATPase activity, but the purpose of ATP hydrolysis is not fully understood. 2C is highly conserved among picornaviruses and plays crucial roles in nearly all steps of the virus lifecycle. It is therefore considered as an effective target for broad-spectrum antiviral drug development. Crystallographic investigation of enterovirus 2C proteins provide structural details important for the elucidation of 2C function and development of antiviral drugs. This chapter summarizes not only the findings of enzymatic activities, biochemical and structural characterizations of the 2C proteins, but also their role in virus replication, immune evasion and morphogenesis. The linkage between structure and function of the 2C proteins is discussed in detail. Inhibitors targeting the 2C proteins are also summarized to provide an overview of drug development. Finally, we raise several key questions to be addressed in this field and provide future research perspective on this unique class of ATPases.
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Affiliation(s)
- Pu Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhijian Li
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sheng Cui
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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11
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Varkey J, Zhang J, Kim J, George G, He G, Belov G, Langen R, Wang X. An Amphipathic Alpha-Helix Domain from Poliovirus 2C Protein Tubulate Lipid Vesicles. Viruses 2020; 12:v12121466. [PMID: 33353144 PMCID: PMC7766222 DOI: 10.3390/v12121466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 02/01/2023] Open
Abstract
Positive-strand RNA viruses universally remodel host intracellular membranes to form membrane-bound viral replication complexes, where viral offspring RNAs are synthesized. In the majority of cases, viral replication proteins are targeted to and play critical roles in the modulation of the designated organelle membranes. Many viral replication proteins do not have transmembrane domains, but contain single or multiple amphipathic alpha-helices. It has been conventionally recognized that these helices serve as an anchor for viral replication protein to be associated with membranes. We report here that a peptide representing the amphipathic α-helix at the N-terminus of the poliovirus 2C protein not only binds to liposomes, but also remodels spherical liposomes into tubules. The membrane remodeling ability of this amphipathic alpha-helix is similar to that recognized in other amphipathic alpha-helices from cellular proteins involved in membrane remodeling, such as BAR domain proteins. Mutations affecting the hydrophobic face of the amphipathic alpha-helix severely compromised membrane remodeling of vesicles with physiologically relevant phospholipid composition. These mutations also affected the ability of poliovirus to form plaques indicative of reduced viral replication, further underscoring the importance of membrane remodeling by the amphipathic alpha-helix in possible relation to the formation of viral replication complexes.
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Affiliation(s)
- Jobin Varkey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
| | - Jiantao Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
| | - Junghyun Kim
- Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA; (J.K.); (G.B.)
| | - Gincy George
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
| | - Guijuan He
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
| | - George Belov
- Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA; (J.K.); (G.B.)
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
- Correspondence: (R.L.); (X.W.); Tel.: +1-323-442-1323 (R.L.); +1-540-231-1868 (X.W.)
| | - Xiaofeng Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
- Correspondence: (R.L.); (X.W.); Tel.: +1-323-442-1323 (R.L.); +1-540-231-1868 (X.W.)
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12
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Zhang G, Hu B, Huo Y, Lu J, Guo J, Deng M, Li P, Wang W, Li L, Meng S, Wang Z, Shen S. Amino acid substitutions in VP2, VP1, and 2C attenuate a Coxsackievirus A16 in mice. Microb Pathog 2020; 150:104603. [PMID: 33271234 DOI: 10.1016/j.micpath.2020.104603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 09/21/2020] [Accepted: 10/30/2020] [Indexed: 11/29/2022]
Abstract
Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD), a common acute infectious disease affecting infants and young children. Severe symptoms of the central nervous system may develop and even lead to death. Here, a plaque-purified CVA16 strain, L731-P1 (P1), was serially passaged in Vero cells for six times and passage 6 (P6) stock became highly attenuated in newborn mice. Genomic sequencing of the P1 and P6 revealed seven nucleotide substitutions at positions 1434 (C to U), 2744 (A to G), 2747 (A to G), 3161 (G to A), 3182 (A to G), 4968 (C to U), and 6064 (C to U). Six of these substitutions resulted in amino acid changes at VP2-T161 M, VP1-N102D, VP1-T103A, VP1-E241K, VP1-T248A, and 2C-S297F, respectively. P1-based infectious cDNA was generated to further investigate these virulent determinants. Independent reverse transcription-polymerase chain reaction (RT-PCR) amplifications for mutant constructions and plaque-purification of the P6 for isolation of variants were performed to determine dominant mutations and strains more related to attenuation. The virulent P1, attenuated P6, as well as a plaque purified strain (PP) and other four recombinant mutants, were inoculated into one-day-old BALB/c mice and the 50% lethal dose of each strain was determined. Comparison of virulence among these strains indicated that amino acid changes of VP1-N102D, VP1-E241K and 2C-S297F might be associated more closely with a high level attenuation of CVA16-L731-P6 than other mutations. Identification of novel residues associated with virulence may contribute to understanding of molecular basis of virulence of CVA16 and other enteroviruses.
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Affiliation(s)
- Gaobo Zhang
- Wuhan Huaxia University of Technology, Wuhan, 430223, China.
| | - Bing Hu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430000, China
| | - Yuqi Huo
- The Sixth People' s Hospital of Zhengzhou, Zhengzhou, 450000, China
| | - Jia Lu
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Jing Guo
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Mi Deng
- Worldwide Safety and Regulatory Pfizer, Inc., Wuhan, 430000, China
| | - Pengfei Li
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Weishan Wang
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Li Li
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Shengli Meng
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Zejun Wang
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China.
| | - Shuo Shen
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China.
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13
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Manganaro R, Zonsics B, Bauer L, Lorenzo Lopez M, Donselaar T, Zwaagstra M, Saporito F, Ferla S, Strating JRPM, Coutard B, Hurdiss DL, van Kuppeveld FJM, Brancale A. Synthesis and antiviral effect of novel fluoxetine analogues as enterovirus 2C inhibitors. Antiviral Res 2020; 178:104781. [PMID: 32234539 DOI: 10.1016/j.antiviral.2020.104781] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022]
Abstract
Enteroviruses (EV) are a group of positive-strand RNA (+RNA) viruses that include many important human pathogens (e.g. poliovirus, coxsackievirus, echovirus, numbered enteroviruses and rhinoviruses). Fluoxetine was identified in drug repurposing screens as potent inhibitor of enterovirus B and enterovirus D replication. In this paper we are reporting the synthesis and the antiviral effect of a series of fluoxetine analogues. The results obtained offer a preliminary insight into the structure-activity relationship of its chemical scaffold and confirm the importance of the chiral configuration. We identified a racemic fluoxetine analogue, 2b, which showed a similar antiviral activity compared to (S)-fluoxetine. Investigating the stereochemistry of 2b revealed that the S-enantiomer exerts potent antiviral activity and increased the antiviral spectrum compared to the racemic mixture of 2b. In line with the observed antiviral effect, the S-enantiomer displayed a dose-dependent shift in the melting temperature in thermal shift assays, indicative for direct binding to the recombinant 2C protein.
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Affiliation(s)
- Roberto Manganaro
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Birgit Zonsics
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Lisa Bauer
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Moira Lorenzo Lopez
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Tim Donselaar
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Marleen Zwaagstra
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Fabiana Saporito
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Salvatore Ferla
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Jeroen R P M Strating
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Bruno Coutard
- Unité des Virus Emergents, (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France Aix-Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Daniel L Hurdiss
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL, Utrecht, the Netherlands
| | - Andrea Brancale
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK.
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14
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Bauer L, Manganaro R, Zonsics B, Strating JRPM, El Kazzi P, Lorenzo Lopez M, Ulferts R, van Hoey C, Maté MJ, Langer T, Coutard B, Brancale A, van Kuppeveld FJM. Fluoxetine Inhibits Enterovirus Replication by Targeting the Viral 2C Protein in a Stereospecific Manner. ACS Infect Dis 2019; 5:1609-1623. [PMID: 31305993 PMCID: PMC6747591 DOI: 10.1021/acsinfecdis.9b00179] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Enteroviruses
(family Picornaviridae) comprise a large group of
human pathogens against which no licensed antiviral therapy exists.
Drug-repurposing screens uncovered the FDA-approved drug fluoxetine
as a replication inhibitor of enterovirus B and D species. Fluoxetine
likely targets the nonstructural viral protein 2C, but detailed mode-of-action
studies are missing because structural information on 2C of fluoxetine-sensitive
enteroviruses is lacking. We here show that broad-spectrum anti-enteroviral
activity of fluoxetine is stereospecific concomitant with binding
to recombinant 2C. (S)-Fluoxetine inhibits with a
5-fold lower 50% effective concentration (EC50) than racemic
fluoxetine. Using a homology model of 2C of the fluoxetine-sensitive
enterovirus coxsackievirus B3 (CVB3) based upon a recently elucidated
structure of a fluoxetine-insensitive enterovirus, we predicted stable
binding of (S)-fluoxetine. Structure-guided mutations
disrupted binding and rendered coxsackievirus B3 (CVB3) resistant
to fluoxetine. The study provides new insights into the anti-enteroviral
mode-of-action of fluoxetine. Importantly, using only (S)-fluoxetine would allow for lower dosing in patients, thereby likely
reducing side effects.
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Affiliation(s)
- Lisa Bauer
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, The Netherlands
| | - Roberto Manganaro
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Birgit Zonsics
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Jeroen R. P. M. Strating
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, The Netherlands
| | - Priscila El Kazzi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique, Université de la Méditerranée and Université de Provence, Aix-Marseille Université, Case 925, 163 Avenue de Luminy, Marseille 3288 CEDEX 9, France
| | - Moira Lorenzo Lopez
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Rachel Ulferts
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, The Netherlands
| | - Clara van Hoey
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna A-1090, Austria
| | - Maria J. Maté
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique, Université de la Méditerranée and Université de Provence, Aix-Marseille Université, Case 925, 163 Avenue de Luminy, Marseille 3288 CEDEX 9, France
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna A-1090, Austria
| | - Bruno Coutard
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique, Université de la Méditerranée and Université de Provence, Aix-Marseille Université, Case 925, 163 Avenue de Luminy, Marseille 3288 CEDEX 9, France
- Unité des Virus Emergents, UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection, 13385 Marseille, CEDEX 5, France
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, The Netherlands
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15
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Han KR, Lee JH, Kotiguda GG, Jung KH, Chung MS, Kang S, Hwang S, Kim KH. Nucleotide triphosphatase and RNA chaperone activities of murine norovirus NS3. J Gen Virol 2018; 99:1482-1493. [PMID: 30265237 DOI: 10.1099/jgv.0.001151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Modulation of RNA structure is essential in the life cycle of RNA viruses. Immediate replication upon infection requires RNA unwinding to ensure that RNA templates are not in intra- or intermolecular duplex forms. The calicivirus NS3, one of the highly conserved nonstructural (NS) proteins, has conserved motifs common to helicase superfamily 3 among six genogroups. However, its biological functions are not fully understood. In this study we report the oligomeric state and the nucleotide triphosphatase (NTPase) and RNA chaperone activities of the recombinant full-length NS3 derived from murine norovirus (MNV). The MNV NS3 has an Mg2+-dependent NTPase activity, and site-directed mutagenesis of the conserved NTPase motifs blocked enzyme activity and viral replication in cells. Further, the NS3 was found via fluorescence resonance energy transfer (FRET)-based assays to destabilize double-stranded RNA in the presence of Mg2+ or Mn2+ in an NTP-independent manner. However, the RNA destabilization activity was not affected by mutagenesis of the conserved motifs of NTPase. These results reveal that the MNV NS3 has an NTPase-independent RNA chaperone-like activity, and that a FRET-based RNA destabilization assay has the potential to identify new antiviral drugs targeting NS3.
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Affiliation(s)
- Kang Rok Han
- 1Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, Republic of Korea.,†Present address: Konkuk University, Seoul, Republic of Korea
| | - Ji-Hye Lee
- 1Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, Republic of Korea
| | - Giri Gowda Kotiguda
- 1Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, Republic of Korea.,‡Present address: Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kyoung Ho Jung
- 1Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, Republic of Korea
| | - Mi Sook Chung
- 2Department of Food and Nutrition, Duksung Women's University, Seoul 132-714, Republic of Korea
| | - Soowon Kang
- 3Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Seungmin Hwang
- 3Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Kyung Hyun Kim
- 1Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, Republic of Korea
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16
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Guan H, Tian J, Zhang C, Qin B, Cui S. Crystal structure of a soluble fragment of poliovirus 2CATPase. PLoS Pathog 2018; 14:e1007304. [PMID: 30231078 PMCID: PMC6166989 DOI: 10.1371/journal.ppat.1007304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 10/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022] Open
Abstract
Poliovirus (PV) 2CATPase is the most studied 2C protein in the Picornaviridae family. It is involved in RNA replication, encapsidation and uncoating and many inhibitors have been found that target PV 2CATPase. Despite numerous investigations to characterize its functions, a high-resolution structure of PV 2C has not yet been determined. We report here the crystal structure of a soluble fragment of PV 2CATPase to 2.55Å, containing an ATPase domain, a zinc finger and a C-terminal helical domain but missing the N-terminal domain. The ATPase domain shares the common structural features with EV71 2C and other Superfamily 3 helicases. The C-terminal cysteine-rich motif folds into a CCCC type zinc finger in which four cysteine ligands and several auxiliary residues assist in zinc binding. By comparing with the known zinc finger fold groups, we found the zinc finger of 2C proteins belong to a new fold group, which we denote the "Enterovirus 2C-like" group. The C-terminus of PV 2CATPase forms an amphipathic helix that occupies a hydrophobic pocket located on an adjacent PV 2CATPase in the crystal lattice. The C-terminus mediated PV 2C-2C interaction promotes self-oligomerization, most likely hexamerization, which is fundamental to the ATPase activity of 2C. The zinc finger is the most structurally diverse feature in 2C proteins. Available structural and virological data suggest that the zinc finger of 2C might confer the specificity of interaction with other proteins. We built a hexameric ring model of PV 2CATPase and visualized the previously identified functional motifs and drug-resistant sites, thus providing a structure framework for antiviral drug development.
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Affiliation(s)
- Hongxin Guan
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Tian
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chu Zhang
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Qin
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sheng Cui
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail:
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17
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Song Y, Gorbatsevych O, Liu Y, Mugavero J, Shen SH, Ward CB, Asare E, Jiang P, Paul AV, Mueller S, Wimmer E. Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes. Proc Natl Acad Sci U S A 2017; 114:E8731-E8740. [PMID: 28973853 PMCID: PMC5642728 DOI: 10.1073/pnas.1714385114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Computer design and chemical synthesis generated viable variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (randomly scrambled synonymous codons). "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2Min, a variant temperature-sensitive at 33 and 39.5 °C. Compared with WT PV1, P2Min displayed a vastly reduced specific infectivity (si) (WT, 1 PFU/118 particles vs. P2Min, 1 PFU/35,000 particles), a phenotype that will be discussed broadly. Si of haploid PV presents cellular infectivity of a single genotype. We performed a comprehensive analysis of sequence and structures of the PV genome to determine if evolutionary conserved cis-acting packaging signal(s) were preserved after recoding. We showed that conserved synonymous sites and/or local secondary structures that might play a role in determining packaging specificity do not survive codon pair recoding. This makes it unlikely that numerous "cryptic, sequence-degenerate, dispersed RNA packaging signals mapping along the entire viral genome" [Patel N, et al. (2017) Nat Microbiol 2:17098] play the critical role in poliovirus packaging specificity. Considering all available evidence, we propose a two-step assembly strategy for +ssRNA viruses: step I, acquisition of packaging specificity, either (a) by specific recognition between capsid protein(s) and replication proteins (poliovirus), or (b) by the high affinity interaction of a single RNA packaging signal (PS) with capsid protein(s) (most +ssRNA viruses so far studied); step II, cocondensation of genome/capsid precursors in which an array of hairpin structures plays a role in virion formation.
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Affiliation(s)
- Yutong Song
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794;
| | - Oleksandr Gorbatsevych
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Ying Liu
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Pathology and Laboratory Medicine, Staten Island University Hospital, Staten Island, NY 10305
| | - JoAnn Mugavero
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Sam H Shen
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Charles B Ward
- Google, Inc., Mountain View, CA 94043
- Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794
| | - Emmanuel Asare
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Aniko V Paul
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Steffen Mueller
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Codagenix Inc., Stony Brook, NY 11794
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794;
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18
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Kumari N, Chaturvedi SK, Khan R, Sharma A, Khan RH, Yadav S. Characterization of CNL like protein fragment (CNL-LPF) from mature Lageneria siceraria seeds. Int J Biol Macromol 2017; 104:1194-1203. [PMID: 28676339 DOI: 10.1016/j.ijbiomac.2017.06.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
Coiled coil domain-nucleotide binding site-leucine rich repeat (CC-NBS-LRR; CNL) proteins are highly conserved family of plant disease resistance proteins, remarkably comprise of coiled-coil domain, which plays significant role in plant innate immunity. The present study reports that moderately elicited oligomerization of plant CNL like protein fragment (CNL-LPF) in presence of ATP/Mg using various biophysical methods Circular dichroism (CD) results depicted a substantial increase in β-sheet structure content of CNL-LPF. ATP/Mg induced conformational change in protein was observed by increase in blue shift with extrinsic fluorescence measurement, which indicates the exposure of hydrophobic regions of CNL-LPF and leads to self-association i.e. oligomerization. Likewise, cluster of protein oligomer and alteration in protein surface morphology were observed in presence of ATP/Mg by Transmission electron microscopy (TEM) and Atomic force microscopy (AFM), respectively. Also, augmented antiproliferation of HT1376 cells (urinary bladder cancer cell lines) was observed by CNL-LPF in presence of ATP/Mg. In conclusion, the current study illustrates that extent of CNL-LPF oligomerization was enhanced in presence of ATP/Mg (as compared to its absence). Utilization of enhanced oligomerization property of CNL-LPF as an anti-proliferative agent needs more assessment.
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Affiliation(s)
- Neha Kumari
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | | | - Rehan Khan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Alpana Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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Gunaseelan S, Chu JJH. Identifying novel antiviral targets against enterovirus 71: where are we? Future Virol 2017. [DOI: 10.2217/fvl-2016-0144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Human enterovirus 71 (HEV71) has been considered as an essential human pathogen, which causes hand, foot and mouth disease in young children. Several HEV71 outbreaks have been observed in many Asia-Pacific countries for the past two decades with significant fatalities. However, there are no competent vaccines or antivirals against HEV71 infection to date. Thus, it is of critical priority to delve into the search for anti-HEV71 agents. Prior to this, there is a need to gain knowledge about the distinct targets of HEV71 that are available and that have been exploited for antiviral therapy. This review aims to provide a better understanding of HEV71 virology and feature potential antivirals for progressive clinical development with respect to their elucidated mechanistic actions.
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Affiliation(s)
- Saravanan Gunaseelan
- Laboratory of Molecular RNA Virology & Antiviral Strategies, Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University Health System, 5 Science Drive 2, National University of Singapore, 117597 Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology & Antiviral Strategies, Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University Health System, 5 Science Drive 2, National University of Singapore, 117597 Singapore
- Institute of Molecular & Cell Biology, Agency for Science, Technology & Research (A*STAR), 61 Biopolis Drive, Proteos #06–05, Singapore 138673
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20
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Guan H, Tian J, Qin B, Wojdyla JA, Wang B, Zhao Z, Wang M, Cui S. Crystal structure of 2C helicase from enterovirus 71. SCIENCE ADVANCES 2017; 3:e1602573. [PMID: 28508043 PMCID: PMC5409451 DOI: 10.1126/sciadv.1602573] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Enterovirus 71 (EV71) is the major pathogen responsible for outbreaks of hand, foot, and mouth disease. EV71 nonstructural protein 2C participates in many critical events throughout the virus life cycle; however, its precise role is not fully understood. Lack of a high-resolution structure made it difficult to elucidate 2C activity and prevented inhibitor development. We report the 2.5 Å-resolution crystal structure of the soluble part of EV71 2C, containing an adenosine triphosphatase (ATPase) domain, a cysteine-rich zinc finger with an unusual fold, and a carboxyl-terminal helical domain. Unlike other AAA+ ATPases, EV71 2C undergoes a carboxyl terminus-mediated self-oligomerization, which is dependent on a specific interaction between the carboxyl-terminal helix of one monomer and a deep pocket formed between the ATPase and the zinc finger domains of the neighboring monomer. The carboxyl terminus-mediated self-oligomerization is fundamental to 2C ATPase activity and EV71 replication. Our findings suggest a strategy for inhibition of enterovirus replication by disruption of the self-oligomerization interface of 2C.
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Affiliation(s)
- Hongxin Guan
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Juan Tian
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Bo Qin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | | | - Bei Wang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Zhendong Zhao
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
| | - Meitian Wang
- Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Sheng Cui
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dong Dan San Tiao, Beijing 100730, China
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21
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A Single Amino Acid Substitution in Poliovirus Nonstructural Protein 2CATPase Causes Conditional Defects in Encapsidation and Uncoating. J Virol 2016; 90:6174-6186. [PMID: 27076638 PMCID: PMC4936127 DOI: 10.1128/jvi.02877-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/28/2016] [Indexed: 12/11/2022] Open
Abstract
The specificity of encapsidation of C-cluster enteroviruses depends on an interaction between capsid proteins and nonstructural protein 2CATPase. In particular, residue N252 of poliovirus 2CATPase interacts with VP3 of coxsackievirus A20, in the context of a chimeric virus. Poliovirus 2CATPase has important roles both in RNA replication and encapsidation. In this study, we searched for additional sites in 2CATPase, near N252, that are required for encapsidation. Accordingly, segments adjacent to N252 were analyzed by combining triple and single alanine mutations to identify residues required for function. Two triple alanine mutants exhibited defects in RNA replication. The remaining two mutations, located in secondary structures in a predicted three-dimensional model of 2CATPase, caused lethal growth phenotypes. Most single alanine mutants, derived from the lethal variants, were either quasi-infectious and yielded variants with wild-type (wt) or temperature-sensitive (ts) growth phenotypes or had a lethal growth phenotype due to defective RNA replication. The K259A mutation, mapping to an α helix in the predicted structure of 2CATPase, resulted in a cold-sensitive virus. In vivo protein synthesis and virus production were strikingly delayed at 33°C relative to the wt, suggesting a defect in uncoating. Studies with a reporter virus indicated that this mutant is also defective in encapsidation at 33°C. Cell imaging confirmed a much-reduced production of K259A mature virus at 33°C relative to the wt. In conclusion, we have for the first time linked a cold-sensitive encapsidation defect in 2CATPase (K259A) to a subsequent delay in uncoating of the virus particle at 33°C during the next cycle of infection. IMPORTANCE Enterovirus morphogenesis, which involves the encapsidation of newly made virion RNA, is a process still poorly understood. Elucidation of this process is important for future drug development for a large variety of diseases caused by these agents. We have previously shown that the specificity of encapsidation of poliovirus and of C-cluster coxsackieviruses, which are prototypes of enteroviruses, is dependent on an interaction of capsid proteins with the multifunctional nonstructural protein 2CATPase. In this study, we have searched for residues in poliovirus 2CATPase, near a presumed capsid-interacting site, important for encapsidation. An unusual cold-sensitive mutant of 2CATPase possessed a defect in encapsidation at 37°C and subsequently in uncoating during the next cycle of infection at 33°C. These studies not only reveal a new site in 2CATPase that is involved in encapsidation but also identify a link between encapsidation and uncoating.
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22
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Gao Y, Sun SQ, Guo HC. Biological function of Foot-and-mouth disease virus non-structural proteins and non-coding elements. Virol J 2016; 13:107. [PMID: 27334704 PMCID: PMC4917953 DOI: 10.1186/s12985-016-0561-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) represses host translation machinery, blocks protein secretion, and cleaves cellular proteins associated with signal transduction and the innate immune response to infection. Non-structural proteins (NSPs) and non-coding elements (NCEs) of FMDV play a critical role in these biological processes. The FMDV virion consists of capsid and nucleic acid. The virus genome is a positive single stranded RNA and encodes a single long open reading frame (ORF) flanked by a long structured 5ʹ-untranslated region (5ʹ-UTR) and a short 3ʹ-UTR. The ORF is translated into a polypeptide chain and processed into four structural proteins (VP1, VP2, VP3, and VP4), 10 NSPs (Lpro, 2A, 2B, 2C, 3A, 3B1–3, 3Cpro, and 3Dpol), and some cleavage intermediates. In the past decade, an increasing number of studies have begun to focus on the molecular pathogenesis of FMDV NSPs and NCEs. This review collected recent research progress on the biological functions of these NSPs and NCEs on the replication and host cellular regulation of FMDV to understand the molecular mechanism of host–FMDV interactions and provide perspectives for antiviral strategy and development of novel vaccines.
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Affiliation(s)
- Yuan Gao
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Shi-Qi Sun
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Hui-Chen Guo
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China.
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23
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Agudo R, de la Higuera I, Arias A, Grande-Pérez A, Domingo E. Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism. Virology 2016; 494:257-66. [PMID: 27136067 PMCID: PMC7111656 DOI: 10.1016/j.virol.2016.04.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 02/05/2023]
Abstract
We previously characterized a foot-and-mouth disease virus (FMDV) with three amino acid replacements in its polymerase (3D) that conferred resistance to the mutagenic nucleoside analogue ribavirin. Here we show that passage of this mutant in the presence of high ribavirin concentrations resulted in selection of viruses with the additional replacement I248T in 2C. This 2C substitution alone (even in the absence of replacements in 3D) increased FMDV fitness mainly in the presence of ribavirin, prevented an incorporation bias in favor of A and U associated with ribavirin mutagenesis, and conferred the ATPase activity of 2C decreased sensitivity to ribavirin-triphosphate. Since in previous studies we described that 2C with I248T was selected under different selective pressures, this replacement qualifies as a joker substitution in FMDV evolution. The results have identified a role of 2C in nucleotide incorporation, and have unveiled a new polymerase-independent mechanism of virus escape to lethal mutagenesis. A replacement in FMDV protein 2C confers reduced sensitivity to the mutagen ribavirin. The effect of the replacement is to prevent a mutational bias evoked by ribavirin. 2C has an effect in nucleotide incorporation by the FMDV polymerase. We describe a new molecular mechanism of escape to ribavirin-mediated extinction.
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Affiliation(s)
- Rubén Agudo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Ignacio de la Higuera
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Armando Arias
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
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24
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Screening of a Library of FDA-Approved Drugs Identifies Several Enterovirus Replication Inhibitors That Target Viral Protein 2C. Antimicrob Agents Chemother 2016; 60:2627-38. [PMID: 26856848 PMCID: PMC4862474 DOI: 10.1128/aac.02182-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/29/2016] [Indexed: 11/20/2022] Open
Abstract
Enteroviruses (EVs) represent many important pathogens of humans. Unfortunately, no antiviral compounds currently exist to treat infections with these viruses. We screened the Prestwick Chemical Library, a library of approved drugs, for inhibitors of coxsackievirus B3, identified pirlindole as a potent novel inhibitor, and confirmed the inhibitory action of dibucaine, zuclopenthixol, fluoxetine, and formoterol. Upon testing of viruses of several EV species, we found that dibucaine and pirlindole inhibited EV-B and EV-D and that dibucaine also inhibited EV-A, but none of them inhibited EV-C or rhinoviruses (RVs). In contrast, formoterol inhibited all enteroviruses and rhinoviruses tested. All compounds acted through the inhibition of genome replication. Mutations in the coding sequence of the coxsackievirus B3 (CV-B3) 2C protein conferred resistance to dibucaine, pirlindole, and zuclopenthixol but not formoterol, suggesting that 2C is the target for this set of compounds. Importantly, dibucaine bound to CV-B3 protein 2C in vitro, whereas binding to a 2C protein carrying the resistance mutations was reduced, providing an explanation for how resistance is acquired.
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25
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Xia H, Wang P, Wang GC, Yang J, Sun X, Wu W, Qiu Y, Shu T, Zhao X, Yin L, Qin CF, Hu Y, Zhou X. Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone. PLoS Pathog 2015. [PMID: 26218680 PMCID: PMC4517893 DOI: 10.1371/journal.ppat.1005067] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our understanding of enteroviruses and the two types of RNA remodeling activities. Enteroviruses contain a large number of closely related human pathogens, including poliovirus, EV71, and coxsackie viruses, and cause ~3 billion infections annually. Among the nonstructural proteins of enteroviruses or picornaviruses, protein 2CATPase is the most conserved and complex but the least understood. On the basis of sequence analyses, this protein has been predicted as a putative superfamily 3 (SF3) helicase that supposedly plays a pivotal role in enteroviral RNA replication. However, attempts to determine the helicase activity associated with 2CATPase have been unsuccessful. We found that eukaryotically expressed EV71 or CAV16 2CATPase does possess an ATP-dependent RNA helicase activity that 3′→5′ unwinds RNA helices like other SF3 helicases; surprisingly, it also functions as an RNA chaperone that remodels RNA structures in an ATP-independent manner. Moreover, we determined the domain requirements for these two RNA remodeling activities associated with 2CATPase and provide both in vitro and cellular evidence of their potential roles during viral RNA replication. Additionally, our study provides the first evidence that RNA helicase and chaperoning activities can be integrated within one protein, thereby introducing an extended view of RNA remodeling proteins.
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Affiliation(s)
- Hongjie Xia
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peipei Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Guang-Chuan Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jie Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xianlin Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenzhe Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yang Qiu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ting Shu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaolu Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lei Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuanyang Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- * E-mail:
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26
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Paul AV, Wimmer E. Initiation of protein-primed picornavirus RNA synthesis. Virus Res 2015; 206:12-26. [PMID: 25592245 DOI: 10.1016/j.virusres.2014.12.028] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/16/2014] [Accepted: 12/24/2014] [Indexed: 12/14/2022]
Abstract
Plus strand RNA viruses use different mechanisms to initiate the synthesis of their RNA chains. The Picornaviridae family constitutes a large group of plus strand RNA viruses that possess a small terminal protein (VPg) covalently linked to the 5'-end of their genomes. The RNA polymerases of these viruses use VPg as primer for both minus and plus strand RNA synthesis. In the first step of the initiation reaction the RNA polymerase links a UMP to the hydroxyl group of a tyrosine in VPg using as template a cis-replicating element (cre) positioned in different regions of the viral genome. In this review we will summarize what is known about the initiation reaction of protein-primed RNA synthesis by the RNA polymerases of the Picornaviridae. As an example we will use the RNA polymerase of poliovirus, the prototype of Picornaviridae. We will also discuss models of how these nucleotidylylated protein primers might be used, together with viral and cellular replication proteins and other cis-replicating RNA elements, during minus and plus strand RNA synthesis.
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Affiliation(s)
- Aniko V Paul
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, United States.
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, United States
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27
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Wang C, Ma HC, Wimmer E, Jiang P, Paul AV. A C-terminal, cysteine-rich site in poliovirus 2C(ATPase) is required for morphogenesis. J Gen Virol 2014; 95:1255-1265. [PMID: 24558221 DOI: 10.1099/vir.0.062497-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The morphogenesis of viruses belonging to the genus Enterovirus in the family Picornaviridae is still poorly understood despite decades-long investigations. However, we recently provided evidence that 2C(ATPase) gives specificity to poliovirus encapsidation through an interaction with capsid protein VP3. The polypeptide 2C(ATPase) is a highly conserved non-structural protein of enteroviruses with important roles in RNA replication, encapsidation and uncoating. We have identified a site (K279/R280) near the C terminus of the polypeptide that is required for morphogenesis. The aim of the current project was to search for additional functional sites near the C terminus of the 2C(ATPase) polypeptide, with particular interest in those that are required for encapsidation. We selected for analysis a cysteine-rich site of the polypeptide and constructed four mutants in which cysteines or a histidine was changed to an alanine. The RNA transcripts were transfected into HeLa cells yielding two lethal, one temperature-sensitive and one quasi-infectious mutants. All four mutants exhibited normal protein translation in vitro and three of them possessed severe RNA replication defects. The quasi-infectious mutant (C286A) yielded variants with a pseudo-reversion at the original site (A286D), but some also contained one additional mutation: A138V or M293V. The temperature-sensitive mutant (C272A/H273A) exhibited an encapsidation and possibly also an uncoating defect at 37 °C. Variants of this mutant revealed suppressor mutations at three different sites in the 2C(ATPase) polypeptide: A138V, M293V and K295R. We concluded that the cysteine-rich site near the C terminus of 2C(ATPase) is involved in encapsidation, possibly through an interaction with an upstream segment located between boxes A and B of the nucleotide-binding domain.
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Affiliation(s)
- Chunling Wang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hsin-Chieh Ma
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aniko V Paul
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
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28
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Tan CW, Lai JKF, Sam IC, Chan YF. Recent developments in antiviral agents against enterovirus 71 infection. J Biomed Sci 2014; 21:14. [PMID: 24521134 PMCID: PMC3924904 DOI: 10.1186/1423-0127-21-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/09/2014] [Indexed: 12/13/2022] Open
Abstract
Enterovirus 71 (EV-71) is the main etiological agent of hand, foot and mouth disease (HFMD). Recent EV-71 outbreaks in Asia-Pacific were not limited to mild HFMD, but were associated with severe neurological complications such as aseptic meningitis and brainstem encephalitis, which may lead to cardiopulmonary failure and death. The absence of licensed therapeutics for clinical use has intensified research into anti-EV-71 development. This review highlights the potential antiviral agents targeting EV-71 attachment, entry, uncoating, translation, polyprotein processing, virus-induced formation of membranous RNA replication complexes, and RNA-dependent RNA polymerase. The strategies for antiviral development include target-based synthetic compounds, anti-rhinovirus and poliovirus libraries screening, and natural compound libraries screening. Growing knowledge of the EV-71 life cycle will lead to successful development of antivirals. The continued effort to develop antiviral agents for treatment is crucial in the absence of a vaccine. The coupling of antivirals with an effective vaccine will accelerate eradication of the disease.
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Affiliation(s)
| | | | | | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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29
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Strategies for purifying variants of human rhinovirus 14 2C protein. Protein Expr Purif 2013; 95:28-37. [PMID: 24316192 DOI: 10.1016/j.pep.2013.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/14/2013] [Accepted: 11/25/2013] [Indexed: 11/22/2022]
Abstract
The positive strand RNA genome of picornaviruses, including human rhinovirus (HRV), poliovirus (PV) and foot-and-mouth disease virus, is translated immediately into a polyprotein that is cleaved by virally encoded proteinases into 10-13 mature proteins. These include the four proteins required to assemble the viral particle as well as 3D(pol) (the viral RNA polymerase) and 2C, an ATPase and putative helicase. 2C is a protein which is responsible, together with 2B and 3A, for anchoring the replication complexes to membranous structures in the infected cell on which RNA replication takes place. Additionally, expression of 2C and its precursor 2BC in mammalian cells leads to vesicle formation observed in infected cells. 2C is encoded by all picornaviruses; nevertheless, its exact role in viral replication remains unclear. A contributing factor is the absence of structural data for this hydrophobic protein the generation of which has been hampered by an inability to produce soluble and stable material. Here, we compare 2C from several genera and show that the 2C protein has considerable heterogeneity. Using protein structure meta-analysis, we developed models of HRV14 2C that should be useful for mutational analysis. Based on these analyses, we expressed and purified two domains of HRV14 2C using three different protocols and examined the folding by thermal denaturation or (1)H NMR. Both domains were concentrated sufficiently to allow crystal screens or NMR pilot experiments to be performed. This work provides a platform to explore 2C proteins from all picornaviral genera to generate candidates for structural analysis.
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30
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Springer CL, Huntoon HP, Peersen OB. Polyprotein context regulates the activity of poliovirus 2CATPase bound to bilayer nanodiscs. J Virol 2013; 87:5994-6004. [PMID: 23514879 PMCID: PMC3648184 DOI: 10.1128/jvi.03491-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/11/2013] [Indexed: 12/26/2022] Open
Abstract
Positive-strand RNA viruses generally replicate in large membrane-associated complexes. For poliovirus, these replication complexes are anchored to the membrane via the viral 2B, 2C, and 3A proteins. 2C is an AAA+ family ATPase that plays a key role in host cell membrane rearrangement, is a putative helicase, and is implicated in virion assembly and packaging. However, the membrane-binding characteristics of all of these viral proteins have made it difficult to elucidate their exact roles in virus replication. We show here that small lipid bilayers known as nanodiscs can be used to chaperone the in vitro expression of soluble poliovirus 2C, 2BC, and 2BC3AB polyproteins in a membrane-bound form. ATPase assays on these proteins show that the activity of the core 2C domain is stimulated ~0-fold compared to the larger 2BC3AB polyprotein, with most of this stimulation occurring upon removal of 2B. The proteins are active over a wide range of salt concentrations, exhibit slight lipid headgroup dependence, and show significant stimulation by acetate. Our data lead to a model wherein the replication complex can be assembled with a minimally active form of 2C that then becomes fully activated by proteolytic cleavage from the adjacent 2B viroporin domain.
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Affiliation(s)
- Courtney L Springer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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31
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The nonstructural protein 2C of a Picorna-like virus displays nucleic acid helix destabilizing activity that can be functionally separated from its ATPase activity. J Virol 2013; 87:5205-18. [PMID: 23449794 DOI: 10.1128/jvi.00245-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Picorna-like viruses in the Picornavirales order are a large group of positive-strand RNA viruses that include numerous important pathogens for plants, insects, and humans. In these viruses, nonstructural protein 2C is one of the most conserved proteins and contains ATPase activity and putative RNA helicase activity. Here we expressed 2C protein of Ectropis obliqua picorna-like virus (EoV; genus Iflavirus, family Iflaviridae, order Picornavirales) in a eukaryotic expression system and determined that EoV 2C displays ATP-independent nucleic acid helix destabilizing and strand annealing acceleration activity in a concentration-dependent manner, indicating that this picornaviral 2C is more like an RNA chaperone than like the previously predicted RNA helicase. Our further characterization of EoV 2C revealed that divalent metal ions, such as Mg(2+) and Zn(2+), inhibit 2C-mediated helix destabilization to different extents. Moreover, we determined that EoV 2C also contains ATPase activity like that of other picornaviral 2C proteins and further assessed the functional relevance between its RNA chaperone-like and ATPase activities using mutational analysis as well as their responses to Mg(2+). Our data show that, when one of the two 2C activities was dramatically inhibited or almost abolished, the other activity could remain intact, showing that the RNA chaperone-like and ATPase activities of EoV 2C can be functionally separated. This report reveals that a picorna-like virus 2C protein displays RNA helix destabilizing and strand annealing acceleration activity, which may be critical for picornaviral replication and pathogenesis, and should foster our understanding of picorna-like viruses and viral RNA chaperones.
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Selective serotonin reuptake inhibitor fluoxetine inhibits replication of human enteroviruses B and D by targeting viral protein 2C. Antimicrob Agents Chemother 2013; 57:1952-6. [PMID: 23335743 DOI: 10.1128/aac.02084-12] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although the genus Enterovirus contains many important human pathogens, there is no licensed drug for either the treatment or the prophylaxis of enterovirus infections. We report that fluoxetine (Prozac)--a selective serotonin reuptake inhibitor--inhibits the replication of human enterovirus B (HEV-B) and HEV-D but does not affect the replication of HEV-A and HEV-C or human rhinovirus A or B. We show that fluoxetine interferes with viral RNA replication, and we identified viral protein 2C as the target of this compound.
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Effantin G, Dordor A, Sandrin V, Martinelli N, Sundquist WI, Schoehn G, Weissenhorn W. ESCRT-III CHMP2A and CHMP3 form variable helical polymers in vitro and act synergistically during HIV-1 budding. Cell Microbiol 2012; 15:213-26. [PMID: 23051622 DOI: 10.1111/cmi.12041] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/03/2012] [Accepted: 10/04/2012] [Indexed: 12/23/2022]
Abstract
The endosomal sorting complex required for transport-III (ESCRT-III) proteins are essential for budding of some enveloped viruses, for the formation of intraluminal vesicles at the endosome and for the abscission step of cytokinesis. ESCRT-III proteins form polymers that constrict membrane tubes, leading to fission. We have used electron cryomicroscopy to determine the molecular organization of pleiomorphic ESCRT-III CHMP2A-CHMP3 polymers. The three-dimensional reconstruction at 22 Å resolution reveals a helical organization of filaments of CHMP molecules organized in a head-to-tail fashion. Protease susceptibility experiments indicate that polymerization is achieved via conformational changes that increase the protomer stability. Combinatorial siRNA knockdown experiments indicate that CHMP3 contributes synergistically to HIV-1 budding, and the CHMP3 contribution is ~ 10-fold more pronounced in concert with CHMP2A than with CHMP2B. This is consistent with surface plasmon resonance affinity measurements that suggest sequential CHMP4B-CHMP3-CHMP2A recruitment while showing that both CHMP2A and CHMP2B interact with CHMP4B, in agreement with their redundant functions in HIV-1 budding. Our data thus indicate that the CHMP2A-CHMP3 polymer observed in vitro contributes to HIV-1 budding by assembling on CHMP4B polymers.
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Affiliation(s)
- Grégory Effantin
- Unit of Virus Host Cell Interactions, UMI 3265, Université Joseph Fourier-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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Selection and characterisation of guanidine-resistant mutants of human enterovirus 71. Virus Res 2012; 169:72-9. [PMID: 22814431 DOI: 10.1016/j.virusres.2012.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 06/29/2012] [Accepted: 07/10/2012] [Indexed: 11/22/2022]
Abstract
The replication of human enterovirus 71 (HEV71) in cell culture is inhibited by concentrations of guanidine that do not have an observable adverse effect on host cell metabolism. Although the HEV71 non-structural protein 2C is known to play an important role in viral RNA replication, its precise biochemical activities and structure have not been fully determined. Here we describe amino acid substitutions in HEV71 protein 2C that confer resistance to guanidine. Three guanidine-resistant virus populations were independently isolated and found to contain five mutations in protein 2C, one of which, A4657T (2C-M193L), was present in two of the independently selected populations. This mutation was introduced into a HEV71 infectious cDNA clone and was sufficient to confer complete resistance to growth inhibition in the presence of 4mM guanidine. In the first guanidine-resistant population selected, the 2C-M193L mutation occurred in association with an additional mutation, A4459G (2C-I127V), located in the putative cis-acting replication element (cre) of coding region 2C. This mutation conferred only partial guanidine resistance when introduced into the HEV71-26M infectious clone. When the 2C-I127V and 2C-M193L mutations were introduced into HEV71-26M together, the 2C-I127V mutation did not increase the level of guanidine resistance due to the 2C-M193L mutation alone. This study confirms that guanidine resistance can be readily selected in HEV71 and is attributable to mutations within protein 2C.
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Alanine scanning of poliovirus 2CATPase reveals new genetic evidence that capsid protein/2CATPase interactions are essential for morphogenesis. J Virol 2012; 86:9964-75. [PMID: 22761387 DOI: 10.1128/jvi.00914-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polypeptide 2C(ATPase) is one of the most thoroughly studied but least understood proteins in the life cycle of poliovirus. Within the protein, multiple functional domains important for uncoating, host cell membrane alterations, and RNA replication and encapsidation have previously been identified. In this study, charged to alanine-scanning mutagenesis was used to generate conditional-lethal mutations in hitherto-uncharacterized domains of the 2C(ATPase) polypeptide, particularly those involved in morphogenesis. Adjacent or clustered charged amino acids (2 to 4), scattered along the 2C(ATPase) coding sequence, were replaced with alanines. RNA transcripts of mutant poliovirus cDNA clones were transfected into HeLa cells. Subsequently, 10 lethal, 1 severely temperature-sensitive, 2 quasi-infectious, and 3 wild type-like mutants were identified. Using a luciferase-containing reporter virus, we demonstrated RNA replication defects in all lethal and quasi-infectious mutants. Temperature-sensitive mutants were defective in RNA replication only at the restricted temperatures. Furthermore, we characterized a quasi-infectious mutant (K(6)A/K(7)A) that produced a suppressor mutation (G(1)R) and a novel 2B^2C(ATPase) cleavage site (Q^R). Surprisingly, this cleavage site mutation did not interfere with normal processing of the polyprotein. These mutants have led to the identification of several new sites within the 2C(ATPase) polypeptide that are required for RNA replication. In addition, analysis of the suppressor mutants has revealed a new domain near the C terminus of 2C(ATPase) that is involved in encapsidation, possibly achieved through interaction with an amino acid sequence between NTP binding motifs A and B of 2C(ATPase). Most importantly, the identification of suppressor mutations in both 2C(ATPase) and the capsid domains (VP1 and VP3) of poliovirus has confirmed that an interaction between 2C(ATPase) and capsid proteins is involved in viral morphogenesis.
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Papageorgiou N, Coutard B, Lantez V, Gautron E, Chauvet O, Baronti C, Norder H, de Lamballerie X, Heresanu V, Ferté N, Veesler S, Gorbalenya AE, Canard B. The 2C putative helicase of echovirus 30 adopts a hexameric ring-shaped structure. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1116-20. [PMID: 20944244 DOI: 10.1107/s090744491002809x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/14/2010] [Indexed: 11/10/2022]
Abstract
The 2C protein, which is an essential ATPase and one of the most conserved proteins across the Picornaviridae family, is an emerging antiviral target for which structural and functional characterization remain elusive. Based on a distant relationship to helicases of small DNA viruses, piconavirus 2C proteins have been predicted to unwind double-stranded RNAs. Here, a terminally extended variant of the 2C protein from echovirus 30 has been studied by means of enzymatic activity assays, transmission electron microscopy, atomic force microscopy and dynamic light scattering. The transmission electron-microscopy technique showed the existence of ring-shaped particles with ∼12 nm external diameter. Image analysis revealed that these particles were hexameric and resembled those formed by superfamily 3 DNA virus helicases.
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Affiliation(s)
- Nicolas Papageorgiou
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique, Université de la Méditerranée and Université de Provence, Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
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Direct interaction between two viral proteins, the nonstructural protein 2C and the capsid protein VP3, is required for enterovirus morphogenesis. PLoS Pathog 2010; 6:e1001066. [PMID: 20865167 PMCID: PMC2928791 DOI: 10.1371/journal.ppat.1001066] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 07/26/2010] [Indexed: 12/27/2022] Open
Abstract
In spite of decades-long studies, the mechanism of morphogenesis of plus-stranded RNA viruses belonging to the genus Enterovirus of Picornaviridae, including poliovirus (PV), is not understood. Numerous attempts to identify an RNA encapsidation signal have failed. Genetic studies, however, have implicated a role of the non-structural protein 2C(ATPase) in the formation of poliovirus particles. Here we report a novel mechanism in which protein-protein interaction is sufficient to explain the specificity in PV encapsidation. Making use of a novel "reporter virus", we show that a quasi-infectious chimera consisting of the capsid precursor of C-cluster coxsackie virus 20 (C-CAV20) and the nonstructural proteins of the closely related PV translated and replicated its genome with wild type kinetics, whereas encapsidation was blocked. On blind passages, encapsidation of the chimera was rescued by a single mutation either in capsid protein VP3 of CAV20 or in 2C(ATPase) of PV. Whereas each of the single-mutation variants expressed severe proliferation phenotypes, engineering both mutations into the chimera yielded a virus encapsidating with wild type kinetics. Biochemical analyses provided strong evidence for a direct interaction between 2C(ATPase) and VP3 of PV and CAV20. Chimeras of other C-CAVs (CAV20/CAV21 or CAV18/CAV20) were blocked in encapsidation (no virus after blind passages) but could be rescued if the capsid and 2C(ATPase) coding regions originated from the same virus. Our novel mechanism explains the specificity of encapsidation without apparent involvement of an RNA signal by considering that (i) genome replication is known to be stringently linked to translation, (ii) morphogenesis is known to be stringently linked to genome replication, (iii) newly synthesized 2C(ATPase) is an essential component of the replication complex, and (iv) 2C(ATPase) has specific affinity to capsid protein(s). These conditions lead to morphogenesis at the site where newly synthesized genomes emerge from the replication complex.
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Sweeney TR, Cisnetto V, Bose D, Bailey M, Wilson JR, Zhang X, Belsham GJ, Curry S. Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism. J Biol Chem 2010; 285:24347-59. [PMID: 20507978 PMCID: PMC2915670 DOI: 10.1074/jbc.m110.129940] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV), a positive sense, single-stranded RNA virus, causes a highly contagious disease in cloven-hoofed livestock. Like other picornaviruses, FMDV has a conserved 2C protein assigned to the superfamily 3 helicases a group of AAA+ ATPases that has a predicted N-terminal membrane-binding amphipathic helix attached to the main ATPase domain. In infected cells, 2C is involved in the formation of membrane vesicles, where it co-localizes with viral RNA replication complexes, but its precise role in virus replication has not been elucidated. We show here that deletion of the predicted N-terminal amphipathic helix enables overexpression in Escherichia coli of a highly soluble truncated protein, 2C(34–318), that has ATPase and RNA binding activity. ATPase activity was abrogated by point mutations in the Walker A (K116A) and B (D160A) motifs and Motif C (N207A) in the active site. Unliganded 2C(34–318) exhibits concentration-dependent self-association to yield oligomeric forms, the largest of which is tetrameric. Strikingly, in the presence of ATP and RNA, FMDV 2C(34–318) containing the N207A mutation, which binds but does not hydrolyze ATP, was found to oligomerize specifically into hexamers. Visualization of FMDV 2C-ATP-RNA complexes by negative stain electron microscopy revealed hexameric ring structures with 6-fold symmetry that are characteristic of AAA+ ATPases. ATPase assays performed by mixing purified active and inactive 2C(34–318) subunits revealed a coordinated mechanism of ATP hydrolysis. Our results provide new insights into the structure and mechanism of picornavirus 2C proteins that will facilitate new investigations of their roles in infection.
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Affiliation(s)
- Trevor R Sweeney
- Biophysics Section, Blackett Laboratory, Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, United Kingdom
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Effantin G, Maurizi MR, Steven AC. Binding of the ClpA unfoldase opens the axial gate of ClpP peptidase. J Biol Chem 2010; 285:14834-40. [PMID: 20236930 PMCID: PMC2863180 DOI: 10.1074/jbc.m109.090498] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/06/2010] [Indexed: 11/06/2022] Open
Abstract
ClpP is a serine protease whose active sites are sequestered in a cavity enclosed between two heptameric rings of subunits. The ability of ClpP to process folded protein substrates depends on its being partnered by an AAA+ ATPase/unfoldase, ClpA or ClpX. In active complexes, substrates are unfolded and fed along an axial channel to the degradation chamber inside ClpP. We have used cryoelectron microscopy at approximately 11-A resolution to investigate the three-dimensional structure of ClpP complexed with either one or two end-mounted ClpA hexamers. In the absence of ClpA, the apical region of ClpP is sealed; however, it opens on ClpA binding, creating an access channel. This region is occupied by the N-terminal loops (residues 1-17) of ClpP, which tend to be poorly visible in crystal structures, indicative of conformational variability. Nevertheless, we were able to model the closed-to-open transition that accompanies ClpA binding in terms of movements of these loops; in particular, "up" conformations of the loops correlate with the open state. The main part of ClpP, the barrel formed by 14 copies of residues 18-193, is essentially unchanged by the interaction with ClpA. Using difference mapping, we localized the binding site for ClpA to a peripheral pocket between adjacent ClpP subunits. Based on these observations, we propose that access to the ClpP degradation chamber is controlled allosterically by hinged movements of its N-terminal loops, which the symmetry-mismatched binding of ClpA suffices to induce.
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Affiliation(s)
| | - Michael R. Maurizi
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
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Conversion of VPg into VPgpUpUOH before and during poliovirus negative-strand RNA synthesis. J Virol 2009; 83:12660-70. [PMID: 19812161 DOI: 10.1128/jvi.01676-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are two protein primers involved in picornavirus RNA replication, VPg, the viral protein of the genome, and VPgpUpU(OH). A cis-acting replication element (CRE) within the open reading frame of poliovirus (PV) RNA allows the viral RNA-dependent RNA polymerase 3D(Pol) to catalyze the conversion of VPg into VPgpUpU(OH). In this study, we used preinitiation RNA replication complexes (PIRCs) to determine when CRE-dependent VPg uridylylation occurs relative to the sequential synthesis of negative- and positive-strand RNA. Guanidine HCl (2 mM), a reversible inhibitor of PV 2C(ATPase), prevented CRE-dependent VPgpUpU(OH) synthesis and the initiation of negative-strand RNA synthesis. VPgpUpU(OH) and nascent negative-strand RNA molecules were synthesized coincident in time following the removal of guanidine, consistent with PV RNA functioning simultaneously as a template for CRE-dependent VPgpUpU(OH) synthesis and negative-strand RNA synthesis. The amounts of [(32)P]UMP incorporated into VPgpUpU(OH) and negative-strand RNA products indicated that 100 to 400 VPgpUpU(OH) molecules were made coincident in time with each negative-strand RNA. 3'-dCTP inhibited the elongation of nascent negative-strand RNAs without affecting CRE-dependent VPg uridylylation. A 3' nontranslated region mutation which inhibited negative-strand RNA synthesis did not inhibit CRE-dependent VPg uridylylation. Together, the data implicate 2C(ATPase) in the mechanisms whereby PV RNA functions as a template for reiterative CRE-dependent VPg uridylylation before and during negative-strand RNA synthesis.
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