1
|
Mohandas S, Shete A, Sarkale P, Kumar A, Mote C, Yadav P. Genomic characterization, transcriptome analysis, and pathogenicity of the Nipah virus (Indian isolate). Virulence 2023; 14:2224642. [PMID: 37312405 PMCID: PMC10281463 DOI: 10.1080/21505594.2023.2224642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/28/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV and the substitutions observed were mostly not present in the region of any functional significance except for the phosphoprotein gene. The differential expression of viral genes was observed following infection in Vero (ATCC® CCL-81™) and BHK-21 cells. Intraperitoneal infection in the 10-12-week-old, Syrian hamster model induced dose dependant multisystemic disease characterized by prominent vascular lesions in lungs, brain, kidney and extra vascular lesions in brain and lungs. Congestion, haemorrhages, inflammatory cell infiltration, thrombosis and rarely endothelial syncitial cell formation were seen in the blood vessels. Intranasal infection resulted in respiratory tract infection characterised by pneumonia. The model showed disease characteristics resembling the human NiV infection except that of myocarditis similar to that reported by NiV-Malaysia and NiV-Bangladesh isolates in hamster model. The variation observed in the genome of the Indian isolate at the amino acid levels should be explored further for any functional significance.
Collapse
Affiliation(s)
- Sreelekshmy Mohandas
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Abhinendra Kumar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Chandrasekhar Mote
- Department of Veterinary Pathology, Krantisinh Nana Patil College of Veterinary Science, Shirwal, Maharashtra, India
| | - Pragya Yadav
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| |
Collapse
|
2
|
Chaudhuri D, Majumder S, Datta J, Giri K. In silico designing of an epitope-based peptide vaccine cocktail against Nipah virus: an Indian population-based epidemiological study. Arch Microbiol 2023; 205:380. [PMID: 37955744 DOI: 10.1007/s00203-023-03717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023]
Abstract
Nipah virus, a zoonotic virus from the family Paramyxoviridae has led to significant loss of lives till date with the most recent outbreak in India reported in Kerala. The virus has a considerably high mortality rate along with lack of characteristic symptoms which results in the delay of the virus detection. No specific vaccine is available for the virus although monoclonal antibody treatment has been seen to be effective along with favipiravir. The high mortality and complications caused by the virus underscores the necessity to develop alternative modes of vaccination. One such method has been designed in this study using peptide cocktail consisting of the immunologically important epitopes for use as vaccine. The human leucocytic antigens that are used for the study were analyzed for their presence in various ethnic Indian populations. This study may serve as a new avenue for development of more efficient peptide cocktail vaccines in recent future based on the population genetics and ethnicity.
Collapse
Affiliation(s)
- Dwaipayan Chaudhuri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Satyabrata Majumder
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Joyeeta Datta
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Kalyan Giri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India.
| |
Collapse
|
3
|
Yang S, Kar S. Are we ready to fight the Nipah virus pandemic? An overview of drug targets, current medications, and potential leads. Struct Chem 2023:1-19. [PMID: 37363045 PMCID: PMC9993391 DOI: 10.1007/s11224-023-02148-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/16/2023] [Indexed: 03/11/2023]
Abstract
Nipah virus (NiV) is a high-lethality RNA virus from the family of Paramyxoviridae and genus Henipavirus, classified under Biosafety Level-4 (BSL-4) pathogen due to the severity of pathogenicity and lack of medications and vaccines. Direct contacts or the body fluids of infected animals are the major factor of transmission of NiV. As it is not an airborne infection, the transmission rate is relatively low. Still, mutations of the NiV in the animal reservoir over the years, followed by zoonotic transfer, can make the deadliness of the virus manifold in upcoming years. Therefore, there is no denial of the possibility of a pandemic after COVID-19 considering the severe pathogenicity of NiV, and that is why we need to be prepared with possible drugs in upcoming days. Considering the time constraints, computational aided drug design (CADD) is an efficient way to study the virus and perform the drug design and test the HITs to lead experimentally. Therefore, this review focuses primarily on NiV target proteins (covering NiV and human), experimentally tested repurposed drug details, and latest computational studies on potential lead molecules, which can be explored as potential drug candidates. Computationally identified drug candidates, including their chemical structures, docking scores, amino acid level interaction with corresponding protein, and the platform used for the studies, are thoroughly discussed. The review will offer a one-stop study to access what had been performed and what can be performed in the CADD of NiV.
Collapse
Affiliation(s)
- Siyun Yang
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083 USA
| | - Supratik Kar
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083 USA
| |
Collapse
|
4
|
Becker N, Maisner A. Nipah Virus Impairs Autocrine IFN Signaling by Sequestering STAT1 and STAT2 into Inclusion Bodies. Viruses 2023; 15:554. [PMID: 36851768 PMCID: PMC9967463 DOI: 10.3390/v15020554] [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: 01/10/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes fatal infections in humans. As with most disease-causing viruses, the pathogenic potential of NiV is linked to its ability to block antiviral responses, e.g., by antagonizing IFN signaling through blocking STAT proteins. One of the STAT1/2-binding proteins of NiV is the phosphoprotein (P), but its functional role in IFN antagonism in a full viral context is not well defined. As NiV P is required for genome replication and specifically accumulates in cytosolic inclusion bodies (IBs) of infected cells, we hypothesized that this compartmentalization might play a role in P-mediated IFN antagonism. Supporting this notion, we show here that NiV can inhibit IFN-dependent antiviral signaling via a NiV P-dependent sequestration of STAT1 and STAT2 into viral IBs. Consequently, the phosphorylation/activation and nuclear translocation of STAT proteins in response to IFN is limited, as indicated by the lack of nuclear pSTAT in NiV-infected cells. Blocking autocrine IFN signaling by sequestering STAT proteins in IBs is a not yet described mechanism by which NiV could block antiviral gene expression and provides the first evidence that cytosolic NiV IBs may play a functional role in IFN antagonism.
Collapse
Affiliation(s)
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Germany
| |
Collapse
|
5
|
The pathogenesis of Nipah virus: A review. Microb Pathog 2022; 170:105693. [DOI: 10.1016/j.micpath.2022.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022]
|
6
|
The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:v13122465. [PMID: 34960734 PMCID: PMC8708338 DOI: 10.3390/v13122465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
Collapse
|
7
|
Monette A, Mouland AJ. Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. Viruses 2020; 12:E1179. [PMID: 33081049 PMCID: PMC7589941 DOI: 10.3390/v12101179] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.
Collapse
Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| |
Collapse
|
8
|
Jensen MR, Yabukarski F, Communie G, Condamine E, Mas C, Volchkova V, Tarbouriech N, Bourhis JM, Volchkov V, Blackledge M, Jamin M. Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1. Biophys J 2020; 118:2470-2488. [PMID: 32348724 PMCID: PMC7231922 DOI: 10.1016/j.bpj.2020.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022] Open
Abstract
The structural characterization of modular proteins containing long intrinsically disordered regions intercalated with folded domains is complicated by their conformational diversity and flexibility and requires the integration of multiple experimental approaches. Nipah virus (NiV) phosphoprotein, an essential component of the viral RNA transcription/replication machine and a component of the viral arsenal that hijacks cellular components and counteracts host immune responses, is a prototypical model for such modular proteins. Curiously, the phosphoprotein of NiV is significantly longer than the corresponding protein of other paramyxoviruses. Here, we combine multiple biophysical methods, including x-ray crystallography, NMR spectroscopy, and small angle x-ray scattering, to characterize the structure of this protein and provide an atomistic representation of the full-length protein in the form of a conformational ensemble. We show that full-length NiV phosphoprotein is tetrameric, and we solve the crystal structure of its tetramerization domain. Using NMR spectroscopy and small angle x-ray scattering, we show that the long N-terminal intrinsically disordered region and the linker connecting the tetramerization domain to the C-terminal X domain exchange between multiple conformations while containing short regions of residual secondary structure. Some of these transient helices are known to interact with partners, whereas others represent putative binding sites for yet unidentified proteins. Finally, using NMR spectroscopy and isothermal titration calorimetry, we map a region of the phosphoprotein, comprising residues between 110 and 140 and common to the V and W proteins, that binds with weak affinity to STAT1 and confirm the involvement of key amino acids of the viral protein in this interaction. This provides new, to our knowledge, insights into how the phosphoprotein and the nonstructural V and W proteins of NiV perform their multiple functions.
Collapse
Affiliation(s)
| | - Filip Yabukarski
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Guillaume Communie
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Eric Condamine
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble CNRS, CEA, University Grenoble Alpes, EMBL, Grenoble, France
| | - Valentina Volchkova
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Viktor Volchkov
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Martin Blackledge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Marc Jamin
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| |
Collapse
|
9
|
Guseva S, Milles S, Jensen MR, Salvi N, Kleman JP, Maurin D, Ruigrok RWH, Blackledge M. Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly. SCIENCE ADVANCES 2020; 6:eaaz7095. [PMID: 32270045 PMCID: PMC7112944 DOI: 10.1126/sciadv.aaz7095] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/09/2020] [Indexed: 05/14/2023]
Abstract
Many viruses are known to form cellular compartments, also called viral factories. Paramyxoviruses, including measles virus, colocalize their proteomic and genomic material in puncta in infected cells. We demonstrate that purified nucleoproteins (N) and phosphoproteins (P) of measles virus form liquid-like membraneless organelles upon mixing in vitro. We identify weak interactions involving intrinsically disordered domains of N and P that are implicated in this process, one of which is essential for phase separation. Fluorescence allows us to follow the modulation of the dynamics of N and P upon droplet formation, while NMR is used to investigate the thermodynamics of this process. RNA colocalizes to droplets, where it triggers assembly of N protomers into nucleocapsid-like particles that encapsidate the RNA. The rate of encapsidation within droplets is enhanced compared to the dilute phase, revealing one of the roles of liquid-liquid phase separation in measles virus replication.
Collapse
|
10
|
Goh GKM, Dunker AK, Foster JA, Uversky VN. Nipah shell disorder, modes of infection, and virulence. Microb Pathog 2020; 141:103976. [PMID: 31940461 PMCID: PMC7126952 DOI: 10.1016/j.micpath.2020.103976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
Abstract
The Nipah Virus (NiV) was first isolated during a 1998-9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001-5, ~93%, 2008-12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0.93, p < 0.01, ANOVA: p < 0.01). Distinct disorder and, therefore, genetic differences can be found in all three group of strains. The fact that the transmission modes of the Malaysia strain are different from those of the Bangladesh strains suggests that the correlations may also be linked to the modes of viral transmission. Analysis of the NiV and related viruses suggests links between modes of transmission and disorder of not just the N protein but, also, of M shell protein. The links among shell disorder, transmission modes, and virulence suggest mechanisms by which viruses are attenuated as they passed through different cell hosts from different animal species. These have implications for development of vaccines and epidemiological molecular analytical tools to contain outbreaks.
Collapse
Affiliation(s)
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - James A Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow region, Russia.
| |
Collapse
|
11
|
Guseva S, Milles S, Jensen MR, Schoehn G, Ruigrok RWH, Blackledge M. Structure, dynamics and phase separation of measles virus RNA replication machinery. Curr Opin Virol 2020; 41:59-67. [DOI: 10.1016/j.coviro.2020.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
|
12
|
Sourimant J, Thakkar VD, Cox RM, Plemper RK. Viral evolution identifies a regulatory interface between paramyxovirus polymerase complex and nucleocapsid that controls replication dynamics. SCIENCE ADVANCES 2020; 6:eaaz1590. [PMID: 32181359 PMCID: PMC7056317 DOI: 10.1126/sciadv.aaz1590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/11/2019] [Indexed: 05/02/2023]
Abstract
Paramyxoviruses are negative-polarity RNA viruses of major clinical importance. The dynamic interaction of the RNA-dependent RNA polymerase (RdRP) complex with the encapsidated RNA genome is mechanistically and structurally poorly understood. Having generated recombinant measles (MeV) and canine distemper (CDV) viruses with truncated nucleocapsid (N) protein showing defects in replication kinetics, we have applied a viral evolution approach to the problem. Passaging of recombinants resulted in long-range compensatory mutations that restored RdRP bioactivity in minigenome assays and efficient replication of engineered viruses. Compensatory mutations clustered at an electronically compatible acidic loop in N-core and a basic face of the phosphoprotein X domain (P-XD). Co-affinity precipitations, biolayer interferometry, and molecular docking revealed an electrostatic-driven transiently forming interface between these domains. The compensatory mutations reduced electrostatic compatibility of these microdomains and lowered coprecipitation efficiency, consistent with a molecular checkpoint function that regulates paramyxovirus polymerase mobility through modulation of conformational stability of the P-XD assembly.
Collapse
Affiliation(s)
- Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Vidhi D. Thakkar
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Robert M. Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | | |
Collapse
|
13
|
Sen N, Kanitkar TR, Roy AA, Soni N, Amritkar K, Supekar S, Nair S, Singh G, Madhusudhan MS. Predicting and designing therapeutics against the Nipah virus. PLoS Negl Trop Dis 2019; 13:e0007419. [PMID: 31830030 PMCID: PMC6907750 DOI: 10.1371/journal.pntd.0007419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/04/2019] [Indexed: 11/28/2022] Open
Abstract
Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative peptide inhibitors (against G, F and M proteins) and 146 small molecule inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modeling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes and on 13 of the top shortlisted small molecule ligands to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To counter the threat of drug resistance, we have analysed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.
Collapse
Affiliation(s)
- Neeladri Sen
- Indian Institute of Science Education and Research, Pune, India
| | | | | | - Neelesh Soni
- Indian Institute of Science Education and Research, Pune, India
| | | | - Shreyas Supekar
- Indian Institute of Science Education and Research, Pune, India
| | - Sanjana Nair
- Indian Institute of Science Education and Research, Pune, India
| | - Gulzar Singh
- Indian Institute of Science Education and Research, Pune, India
| | | |
Collapse
|
14
|
Ringel M, Heiner A, Behner L, Halwe S, Sauerhering L, Becker N, Dietzel E, Sawatsky B, Kolesnikova L, Maisner A. Nipah virus induces two inclusion body populations: Identification of novel inclusions at the plasma membrane. PLoS Pathog 2019; 15:e1007733. [PMID: 31034506 PMCID: PMC6488097 DOI: 10.1371/journal.ppat.1007733] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/26/2019] [Indexed: 01/31/2023] Open
Abstract
Formation of cytoplasmic inclusion bodies (IBs) is a hallmark of infections with non-segmented negative-strand RNA viruses (order Mononegavirales). We show here that Nipah virus (NiV), a bat-derived highly pathogenic member of the Paramyxoviridae family, differs from mononegaviruses of the Rhabdo-, Filo- and Pneumoviridae families by forming two types of IBs with distinct localizations, formation kinetics, and protein compositions. IBs in the perinuclear region form rapidly upon expression of the nucleocapsid proteins. These IBperi are highly mobile and associate with the aggresome marker y-tubulin. IBperi can recruit unrelated overexpressed cytosolic proteins but do not contain the viral matrix (M) protein. Additionally, NiV forms an as yet undescribed IB population at the plasma membrane (IBPM) that is y-tubulin-negative but contains the M protein. Infection studies with recombinant NiV revealed that IBPM require the M protein for their formation, and most likely represent sites of NiV assembly and budding. The identification of this novel type of plasma membrane-associated IBs not only provides new insights into NiV biology and may open new avenues to develop novel antiviral approaches to treat these highly pathogenic viruses, it also provides a basis for a more detailed characterization of IBs and their role in virus assembly and replication in infections with other Mononegavirales. Inclusion bodies (IBs) induced by non-segmented negative-strand RNA viruses (Mononegavirales) are described as mobile cytosolic compartments that concentrate viral proteins and represent the main viral replication sites in infected cells. This general concept is mainly based on studies with mononegaviruses from the Rhabdo-, Filo- and Pneumoviridae families. IBs induced by members of the Paramyxoviridae family are much less well characterized, and this study provides evidence that paramyxoviral IBs may have different compositions and functions. The main finding of this study is that Nipah virus (NiV), a highly pathogenic member of the genus Henipavirus in the family Paramyxoviridae, forms a novel type of IB whose formation at plasma membrane assembly sites depends on the viral matrix protein, and suggests a role for IBs not yet described for other Mononegavirales. This discovery clearly extents the current concept of IB functions and illustrates the need to further investigate IBs formed by other paramyxoviruses.
Collapse
Affiliation(s)
- Marc Ringel
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Anja Heiner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Laura Behner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Lucie Sauerhering
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Nico Becker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Erik Dietzel
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Bevan Sawatsky
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | | | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
- * E-mail:
| |
Collapse
|
15
|
Ranadheera C, Proulx R, Chaiyakul M, Jones S, Grolla A, Leung A, Rutherford J, Kobasa D, Carpenter M, Czub M. The interaction between the Nipah virus nucleocapsid protein and phosphoprotein regulates virus replication. Sci Rep 2018; 8:15994. [PMID: 30375468 PMCID: PMC6207681 DOI: 10.1038/s41598-018-34484-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/02/2018] [Indexed: 11/29/2022] Open
Abstract
Continued outbreaks of Henipaviruses in South Asia and Australia cause severe and lethal disease in both humans and animals. Together, with evidence of human to human transmission for Nipah virus and the lack of preventative or therapeutic measures, its threat to cause a widespread outbreak and its potential for weaponization has increased. In this study we demonstrate how overexpression of the Nipah virus nucleocapsid protein regulates viral polymerase activity and viral RNA production. By overexpressing the Nipah virus nucleocapsid protein in trans viral transcription was inhibited; however, an increase in viral genome synthesis was observed. Together, the bias of polymerase activity towards genome production led to the severe inhibition of viral progeny. We identified two domains within the nucleocapsid protein, which were each independently capable of binding the viral phosphoprotein. Evident by our data, we propose that the nucleocapsid protein’s ability to interact with the phosphoprotein of the polymerase complex causes a change in polymerase activity and subsequent deficiency in viral replication. This study not only provides insights into the dynamics of Henipavirus RNA synthesis and replication, but also provides insight into potential targets for antiviral drug development.
Collapse
Affiliation(s)
- Charlene Ranadheera
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada. .,Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - Roxanne Proulx
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Mark Chaiyakul
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Shane Jones
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Allen Grolla
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Anders Leung
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - John Rutherford
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.,Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael Carpenter
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.,Blood Borne Pathogens and Hepatitis, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Markus Czub
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.,Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
16
|
Possible role of the Nipah virus V protein in the regulation of the interferon beta induction by interacting with UBX domain-containing protein1. Sci Rep 2018; 8:7682. [PMID: 29769705 PMCID: PMC5955904 DOI: 10.1038/s41598-018-25815-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/17/2018] [Indexed: 02/08/2023] Open
Abstract
Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes lethal encephalitis in humans. We previously reported that the V protein, one of the three accessory proteins encoded by the P gene, is one of the key determinants of the pathogenesis of NiV in a hamster infection model. Satterfield B.A. et al. have also revealed that V protein is required for the pathogenicity of henipavirus in a ferret infection model. However, the complete functions of NiV V have not been clarified. In this study, we identified UBX domain-containing protein 1 (UBXN1), a negative regulator of RIG-I-like receptor signaling, as a host protein that interacts with NiV V. NiV V interacted with the UBX domain of UBXN1 via its proximal zinc-finger motif in the C-terminal domain. NiV V increased the level of UBXN1 protein by suppressing its proteolysis. Furthermore, NiV V suppressed RIG-I and MDA5-dependent interferon signaling by stabilizing UBXN1 and increasing the interaction between MAVS and UBXN1 in addition to directly interrupting the activation of MDA5. Our results suggest a novel molecular mechanism by which the induction of interferon is potentially suppressed by NiV V protein via UBXN1.
Collapse
|
17
|
Shang X, Chu W, Chu X, Xu L, Longhi S, Wang J. Exploration of nucleoprotein α-MoRE and XD interactions of Nipah and Hendra viruses. J Mol Model 2018; 24:113. [PMID: 29691656 DOI: 10.1007/s00894-018-3643-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/28/2018] [Indexed: 11/28/2022]
Abstract
Henipavirus, including Hendra virus (HeV) and Nipah virus (NiV), is a newly discovered human pathogen genus. The nucleoprotein of Henipavirus contains an α-helical molecular recognition element (α-MoRE) that folds upon binding to the X domain (XD) of the phosphoprotein (P). In order to explore the conformational dynamics of free α-MoREs and the underlying binding-folding mechanism with XD, atomic force field-based and hybrid structure-based MD simulations were carried out. In our empirical force field-based simulations, characteristic structures and helicities of α-MoREs reveal the co-existence of partially structured and disordered conformations, as in the case of the well characterized cognate measles virus (MeV) α-MoRE. In spite of their overall similarity, the two α-MoREs display subtle helicity differences in their C-terminal region, but much different from that of MeV. For the α-MoRE/XD complexes, the results of our hybrid structure-based simulations provide the coupled binding-folding landscapes, and unveil a wide conformational selection mechanism at early binding stages, followed by a final induce-fit mechanism selection process. However, the HeV and NiV complexes have a lower binding barrier compared to that of MeV. Moreover, the HeV α-MoRE/XD complex shows much less coupling effects between binding and folding compared to that from both NiV and MeV. Our analysis revealed that contrary to NiV and MeV, the N- and C-terminal regions of the HeV α-MoRE maintains a low helicity also in the bound form.
Collapse
Affiliation(s)
- Xu Shang
- College of Physics, Jilin University, Changchun, 130012, China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Wenting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiakun Chu
- IMDEA-Nanociencia, Campus Cantoblanco, Madrid, 28049, Spain
| | - Liufang Xu
- College of Physics, Jilin University, Changchun, 130012, China
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS and Aix-Marseille University, Marseille, France
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY, 11794, USA.
| |
Collapse
|
18
|
Nipah and Hendra Virus Nucleoproteins Inhibit Nuclear Accumulation of Signal Transducer and Activator of Transcription 1 (STAT1) and STAT2 by Interfering with Their Complex Formation. J Virol 2017; 91:JVI.01136-17. [PMID: 28835499 DOI: 10.1128/jvi.01136-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
Henipaviruses, such as Nipah (NiV) and Hendra (HeV) viruses, are highly pathogenic zoonotic agents within the Paramyxoviridae family. The phosphoprotein (P) gene products of the paramyxoviruses have been well characterized for their interferon (IFN) antagonist activity and their contribution to viral pathogenicity. In this study, we demonstrated that the nucleoprotein (N) of henipaviruses also prevents the host IFN signaling response. Reporter assays demonstrated that the NiV and HeV N proteins (NiV-N and HeV-N, respectively) dose-dependently suppressed both type I and type II IFN responses and that the inhibitory effect was mediated by their core domains. Additionally, NiV-N prevented the nuclear transport of signal transducer and activator of transcription 1 (STAT1) and STAT2. However, NiV-N did not associate with Impα5, Impβ1, or Ran, which are members of the nuclear transport system for STATs. Although P protein is known as a binding partner of N protein and actively retains N protein in the cytoplasm, the IFN antagonist activity of N protein was not abolished by the coexpression of P protein. This suggests that the IFN inhibition by N protein occurs in the cytoplasm. Furthermore, we demonstrated that the complex formation of STATs was hampered in the N protein-expressing cells. As a result, STAT nuclear accumulation was reduced, causing a subsequent downregulation of interferon-stimulated genes (ISGs) due to low promoter occupancy by STAT complexes. This novel route for preventing host IFN responses by henipavirus N proteins provides new insight into the pathogenesis of these viruses.IMPORTANCE Paramyxoviruses are well known for suppressing interferon (IFN)-mediated innate immunity with their phosphoprotein (P) gene products, and the henipaviruses also possess P, V, W, and C proteins for evading host antiviral responses. There are numerous studies providing evidence for the relationship between viral pathogenicity and antagonistic activities against IFN responses by P gene products. Meanwhile, little attention has been paid to the influence of nucleoprotein (N) on host innate immune responses. In this study, we demonstrated that both the NiV and HeV N proteins have antagonistic activity against the JAK/STAT signaling pathway by preventing the nucleocytoplasmic trafficking of STAT1 and STAT2. This inhibitory effect is due to an impairment of the ability of STATs to form complexes. These results provide new insight into the involvement of N protein in viral pathogenicity via its IFN antagonism.
Collapse
|
19
|
Insights into the Hendra virus N TAIL –XD complex: Evidence for a parallel organization of the helical MoRE at the XD surface stabilized by a combination of hydrophobic and polar interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1038-53. [DOI: 10.1016/j.bbapap.2015.04.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 11/20/2022]
|
20
|
Beltrandi M, Blocquel D, Erales J, Barbier P, Cavalli A, Longhi S. Insights into the coiled-coil organization of the Hendra virus phosphoprotein from combined biochemical and SAXS studies. Virology 2015; 477:42-55. [PMID: 25637789 DOI: 10.1016/j.virol.2014.12.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 10/21/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Nipah and Hendra viruses are recently emerged paramyxoviruses belonging to the Henipavirus genus. The Henipavirus phosphoprotein (P) consists of a large intrinsically disordered domain and a C-terminal domain (PCT) containing alternating disordered and ordered regions. Among these latter is the P multimerization domain (PMD). Using biochemical, analytical ultracentrifugation and small-angle X-ray scattering (SAXS) studies, we show that Hendra virus (HeV) PMD forms an elongated coiled-coil homotrimer in solution, in agreement with our previous findings on Nipah virus (NiV) PMD. However, the orientation of the N-terminal region differs from that observed in solution for NiV PMD, consistent with the ability of this region to adopt different conformations. SAXS studies provided evidence for a trimeric organization also in the case of PCT, thus extending and strengthening our findings on PMD. The present results are discussed in light of conflicting reports in the literature pointing to a tetrameric organization of paramyxoviral P proteins.
Collapse
Affiliation(s)
- Matilde Beltrandi
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - David Blocquel
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Jenny Erales
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Pascale Barbier
- Aix-Marseille University, INSERM, CRO2 UMR_S911, Faculté de Pharmacie, 13385 Marseille, France
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
| | - Sonia Longhi
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
| |
Collapse
|
21
|
Abstract
The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.
Collapse
|
22
|
Communie G, Habchi J, Yabukarski F, Blocquel D, Schneider R, Tarbouriech N, Papageorgiou N, Ruigrok RWH, Jamin M, Jensen MR, Longhi S, Blackledge M. Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus. PLoS Pathog 2013; 9:e1003631. [PMID: 24086133 PMCID: PMC3784471 DOI: 10.1371/journal.ppat.1003631] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/01/2013] [Indexed: 11/18/2022] Open
Abstract
Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL) and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL) upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL) without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.
Collapse
Affiliation(s)
- Guillaume Communie
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France
- CEA, DSV, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Johnny Habchi
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Filip Yabukarski
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - David Blocquel
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Robert Schneider
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France
- CEA, DSV, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Nicolas Tarbouriech
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Nicolas Papageorgiou
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Rob W. H. Ruigrok
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Marc Jamin
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Malene Ringkjøbing Jensen
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France
- CEA, DSV, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- * E-mail: (MJ); (SL)
| | - Sonia Longhi
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
- * E-mail: (MJ); (SL)
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France
- CEA, DSV, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| |
Collapse
|
23
|
Blocquel D, Beltrandi M, Erales J, Barbier P, Longhi S. Biochemical and structural studies of the oligomerization domain of the Nipah virus phosphoprotein: evidence for an elongated coiled-coil homotrimer. Virology 2013; 446:162-72. [PMID: 24074578 DOI: 10.1016/j.virol.2013.07.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/08/2013] [Accepted: 07/24/2013] [Indexed: 12/19/2022]
Abstract
Nipah virus (NiV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The NiV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the polymerase for transcription and replication. The polymerase is recruited onto the nucleocapsid via its cofactor, the phosphoprotein (P). The NiV P protein has a modular organization, with alternating disordered and ordered domains. Among these latter, is the P multimerization domain (PMD) that was predicted to adopt a coiled-coil conformation. Using both biochemical and biophysical approaches, we show that NiV PMD forms a highly stable and elongated coiled-coil trimer, a finding in striking contrast with respect to the PMDs of Paramyxoviridae members investigated so far that were all found to tetramerize. The present results therefore represent the first report of a paramyxoviral P protein forming trimers.
Collapse
Affiliation(s)
- David Blocquel
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | | | | | | | | |
Collapse
|
24
|
Martinho M, Habchi J, El Habre Z, Nesme L, Guigliarelli B, Belle V, Longhi S. Assessing induced folding within the intrinsically disordered C-terminal domain of the Henipavirus nucleoproteins by site-directed spin labeling EPR spectroscopy. J Biomol Struct Dyn 2012; 31:453-71. [PMID: 22881220 DOI: 10.1080/07391102.2012.706068] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This work aims at characterizing structural transitions within the intrinsically disordered C-terminal domain of the nucleoprotein (NTAIL) from the Nipah and Hendra viruses, two recently emerged pathogens gathered within the Henipavirus genus. To this end, we used site-directed spin labeling combined with electron paramagnetic resonance spectroscopy to investigate the α-helical-induced folding that Henipavirus NTAIL domains undergo in the presence of the C-terminal X domain of the phosphoprotein (PXD). For each NTAIL protein, six positions located within four previously proposed molecular recognition elements (MoREs) were targeted for spin labeling, with three of these positions (475, 481, and 487) falling within the MoRE responsible for binding to PXD (Box3). A detailed analysis of the impact of the partner protein on the labeled NTAIL variants revealed a dramatic modification in the environment of the spin labels grafted within Box3, with the observed modifications supporting the formation of an induced α-helix within this region. In the free state, the slightly lower mobility of the spin labels grafted within Box3 as compared to the other positions suggests the existence of a transiently populated α-helix, as already reported for measles virus (MeV) NTAIL. Comparison with the well-characterized MeV NTAIL-PXD system, allowed us to validate the structural models of Henipavirus NTAIL-PXD complexes that we previously proposed. In addition, this study highlighted a few notable differences between the Nipah and Hendra viruses. In particular, the observation of composite spectra for the free form of the Nipah virus NTAIL variants spin labeled in Box3 supports conformational heterogeneity of this partly pre-configured α-helix, with the pre-existence of stable α-helical segments. Altogether these results provide insights into the molecular mechanisms of the Henipavirus NTAIL-PXD binding reaction.
Collapse
Affiliation(s)
- Marlène Martinho
- CNRS, Aix Marseille Université, IMM FR 3479, BIP UMR 7281, 13402 Marseille, France
| | | | | | | | | | | | | |
Collapse
|
25
|
Lo MK, Lowe L, Hummel KB, Sazzad HMS, Gurley ES, Hossain MJ, Luby SP, Miller DM, Comer JA, Rollin PE, Bellini WJ, Rota PA. Characterization of Nipah virus from outbreaks in Bangladesh, 2008-2010. Emerg Infect Dis 2012; 18:248-55. [PMID: 22304936 PMCID: PMC3310473 DOI: 10.3201/eid1802.111492] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
New genotyping scheme facilitates classification of virus sequences. Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes fatal encephalitis in humans. The initial outbreak of NiV infection occurred in Malaysia and Singapore in 1998–1999; relatively small, sporadic outbreaks among humans have occurred in Bangladesh since 2001. We characterized the complete genomic sequences of identical NiV isolates from 2 patients in 2008 and partial genomic sequences of throat swab samples from 3 patients in 2010, all from Bangladesh. All sequences from patients in Bangladesh comprised a distinct genetic group. However, the detection of 3 genetically distinct sequences from patients in the districts of Faridpur and Gopalganj indicated multiple co-circulating lineages in a localized region over a short time (January–March 2010). Sequence comparisons between the open reading frames of all available NiV genes led us to propose a standardized protocol for genotyping NiV; this protcol provides a simple and accurate way to classify current and future NiV sequences.
Collapse
Affiliation(s)
- Michael K Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Mondal A, Roy A, Sarkar S, Mukherjee J, Ganguly T, Chattopadhyay D. Interaction of chandipura virus N and P proteins: identification of two mutually exclusive domains of N involved in interaction with P. PLoS One 2012; 7:e34623. [PMID: 22485180 PMCID: PMC3317646 DOI: 10.1371/journal.pone.0034623] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/02/2012] [Indexed: 11/18/2022] Open
Abstract
The nucleocapsid protein (N) and the phosphoprotein (P) of nonsegmented negative-strand (NNS) RNA viruses interact with each other to accomplish two crucial events necessary for the viral replication cycle. First, the P protein binds to the aggregation prone nascent N molecules maintaining them in a soluble monomeric (N(0)) form (N(0)-P complex). It is this form that is competent for specific encapsidation of the viral genome. Second, the P protein binds to oligomeric N in the nucleoprotein complex (N-RNA-P complex), and thereby facilitates the recruitment of the viral polymerase (L) onto its template. All previous attempts to study these complexes relied on co-expression of the two proteins in diverse systems. In this study, we have characterised these different modes of N-P interaction in detail and for the first time have been able to reconstitute these complexes individually in vitro in the chandipura virus (CHPV), a human pathogenic NNS RNA virus. Using a battery of truncated mutants of the N protein, we have been able to identify two mutually exclusive domains of N involved in differential interaction with the P protein. An unique N-terminal binding site, comprising of amino acids (aa) 1-180 form the N(0)-P interacting region, whereas, C-terminal residues spanning aa 320-390 is instrumental in N-RNA-P interactions. Significantly, the ex-vivo data also supports these observations. Based on these results, we suggest that the P protein acts as N-specific chaperone and thereby partially masking the N-N self-association region, which leads to the specific recognition of viral genome RNA by N(0).
Collapse
Affiliation(s)
- Arindam Mondal
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Arunava Roy
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Sandipto Sarkar
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Jishnu Mukherjee
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Tridib Ganguly
- Department of Biological Sciences, IISER, Kolkata, West Bengal, India
| | - Dhrubajyoti Chattopadhyay
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| |
Collapse
|
27
|
Blocquel D, Habchi J, Gruet A, Blangy S, Longhi S. Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies. ACTA ACUST UNITED AC 2012; 8:392-410. [DOI: 10.1039/c1mb05401e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
28
|
Habchi J, Blangy S, Mamelli L, Jensen MR, Blackledge M, Darbon H, Oglesbee M, Shu Y, Longhi S. Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. J Biol Chem 2011; 286:13583-602. [PMID: 21317293 PMCID: PMC3075704 DOI: 10.1074/jbc.m111.219857] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/10/2011] [Indexed: 01/15/2023] Open
Abstract
The Henipavirus genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). In a previous study, we reported that in henipaviruses, the N-terminal domain of the phosphoprotein and the C-terminal domain of the nucleoprotein (N(TAIL)) are both intrinsically disordered. Here we show that Henipavirus N(TAIL) domains are also disordered in the context of full-length nucleoproteins. We also report the cloning, purification, and characterization of the C-terminal X domains (P(XD)) of Henipavirus phosphoproteins. Using isothermal titration calorimetry, we show that N(TAIL) and P(XD) form a 1:1 stoichiometric complex that is stable under NaCl concentrations as high as 1 M and has a K(D) in the μM range. Using far-UV circular dichroism and nuclear magnetic resonance, we show that P(XD) triggers an increase in the α-helical content of N(TAIL). Using fluorescence spectroscopy, we show that P(XD) has no impact on the chemical environment of a Trp residue introduced at position 527 of the Henipavirus N(TAIL) domain, thus arguing for the lack of stable contacts between the C termini of N(TAIL) and P(XD). Finally, we present a tentative structural model of the N(TAIL)-P(XD) interaction in which a short, order-prone region of N(TAIL) (α-MoRE; amino acids 473-493) adopts an α-helical conformation and is embedded between helices α2 and α3 of P(XD), leading to a relatively small interface dominated by hydrophobic contacts. The present results provide the first detailed experimental characterization of the N-P interaction in henipaviruses and designate the N(TAIL)-P(XD) interaction as a valuable target for rational antiviral approaches.
Collapse
Affiliation(s)
- Johnny Habchi
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Stéphanie Blangy
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Laurent Mamelli
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Malene Ringkjøbing Jensen
- the Protein Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA-CNRS-UJF, 41 Rue Jules Horowitz, 38027 Grenoble, France, and
| | - Martin Blackledge
- the Protein Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA-CNRS-UJF, 41 Rue Jules Horowitz, 38027 Grenoble, France, and
| | - Hervé Darbon
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Michael Oglesbee
- the Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Yaoling Shu
- the Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Sonia Longhi
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| |
Collapse
|