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Molecular Determinants of Fibrillation in a Viral Amyloidogenic Domain from Combined Biochemical and Biophysical Studies. Int J Mol Sci 2022; 24:ijms24010399. [PMID: 36613842 PMCID: PMC9820236 DOI: 10.3390/ijms24010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
The Nipah and Hendra viruses (NiV and HeV) are biosafety level 4 human pathogens classified within the Henipavirus genus of the Paramyxoviridae family. In both NiV and HeV, the gene encoding the Phosphoprotein (P protein), an essential polymerase cofactor, also encodes the V and W proteins. These three proteins, which share an intrinsically disordered N-terminal domain (NTD) and have unique C-terminal domains (CTD), are all known to counteract the host innate immune response, with V and W acting by either counteracting or inhibiting Interferon (IFN) signaling. Recently, the ability of a short region within the shared NTD (i.e., PNT3) to form amyloid-like structures was reported. Here, we evaluated the relevance of each of three contiguous tyrosine residues located in a previously identified amyloidogenic motif (EYYY) within HeV PNT3 to the fibrillation process. Our results indicate that removal of a single tyrosine in this motif significantly decreases the ability to form fibrils independently of position, mainly affecting the elongation phase. In addition, we show that the C-terminal half of PNT3 has an inhibitory effect on fibril formation that may act as a molecular shield and could thus be a key domain in the regulation of PNT3 fibrillation. Finally, the kinetics of fibril formation for the two PNT3 variants with the highest and the lowest fibrillation propensity were studied by Taylor Dispersion Analysis (TDA). The results herein presented shed light onto the molecular mechanisms involved in fibril formation.
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Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-934. [PMID: 36148633 DOI: 10.1042/ebc20220045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
Measles, Nipah and Hendra viruses are severe human pathogens within the Paramyxoviridae family. Their non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the viral RNA-dependent-RNA-polymerase (RpRd) for transcription and replication. The RpRd is a complex made of the large protein (L) and of the phosphoprotein (P), the latter serving as an obligate polymerase cofactor and as a chaperon for N. Both the N and P proteins are enriched in intrinsically disordered regions (IDRs), i.e. regions devoid of stable secondary and tertiary structure. N possesses a C-terminal IDR (NTAIL), while P consists of a large, intrinsically disordered N-terminal domain (NTD) and a C-terminal domain (CTD) encompassing alternating disordered and ordered regions. The V and W proteins, two non-structural proteins that are encoded by the P gene via a mechanism of co-transcriptional edition of the P mRNA, are prevalently disordered too, sharing with P the disordered NTD. They are key players in the evasion of the host antiviral response and were shown to phase separate and to form amyloid-like fibrils in vitro. In this review, we summarize the available information on IDRs within the N, P, V and W proteins from these three model paramyxoviruses and describe their molecular partnership. We discuss the functional benefit of disorder to virus replication in light of the critical role of IDRs in affording promiscuity, multifunctionality, fine regulation of interaction strength, scaffolding functions and in promoting liquid-liquid phase separation and fibrillation.
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Pesce G, Gondelaud F, Ptchelkine D, Nilsson JF, Bignon C, Cartalas J, Fourquet P, Longhi S. Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins. Int J Mol Sci 2022; 23:ijms23020923. [PMID: 35055108 PMCID: PMC8780864 DOI: 10.3390/ijms23020923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V and W proteins which share with P their N-terminal, intrinsically disordered domain (NTD) and possess a unique C-terminal domain. Henipavirus W proteins antagonize interferon (IFN) signaling through NTD-mediated binding to STAT1 and STAT4, and prevent type I IFN expression and production of chemokines. Structural and molecular information on Henipavirus W proteins is lacking. By combining various bioinformatic approaches, we herein show that the Henipaviruses W proteins are predicted to be prevalently disordered and yet to contain short order-prone segments. Using limited proteolysis, differential scanning fluorimetry, analytical size exclusion chromatography, far-UV circular dichroism and small-angle X-ray scattering, we experimentally confirmed their overall disordered nature. In addition, using Congo red and Thioflavin T binding assays and negative-staining transmission electron microscopy, we show that the W proteins phase separate to form amyloid-like fibrils. The present study provides an additional example, among the few reported so far, of a viral protein forming amyloid-like fibrils, therefore significantly contributing to enlarge our currently limited knowledge of viral amyloids. In light of the critical role of the Henipavirus W proteins in evading the host innate immune response and of the functional role of phase separation in biology, these studies provide a conceptual asset to further investigate the functional impact of the phase separation abilities of the W proteins.
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Affiliation(s)
- Giulia Pesce
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Frank Gondelaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Denis Ptchelkine
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Juliet F. Nilsson
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Christophe Bignon
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Jérémy Cartalas
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
| | - Patrick Fourquet
- INSERM, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS), Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille University, 27 Bvd Leï Roure, CS 30059, 13273 Marseille, France;
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288 Marseille, France; (G.P.); (F.G.); (D.P.); (J.F.N.); (C.B.); (J.C.)
- Correspondence:
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Salladini E, Gondelaud F, Nilsson JF, Pesce G, Bignon C, Murrali MG, Fabre R, Pierattelli R, Kajava AV, Horvat B, Gerlier D, Mathieu C, Longhi S. Identification of a Region in the Common Amino-terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation. Biomolecules 2021; 11:1324. [PMID: 34572537 PMCID: PMC8471210 DOI: 10.3390/biom11091324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
Henipaviruses are BSL-4 zoonotic pathogens responsible in humans for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We previously showed that the Henipavirus V proteins consist of a long intrinsically disordered N-terminal domain (NTD) and a β-enriched C-terminal domain (CTD). These terminals are critical for V binding to DDB1, which is a cellular protein that is a component of the ubiquitin ligase E3 complex, as well as binding to MDA5 and LGP2, which are two host sensors of viral RNA. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquid-to-hydrogel phase transition and identified the V region responsible for this phenomenon. This region, referred to as PNT3 and encompassing residues 200-310, was further investigated using a combination of biophysical and structural approaches. Congo red binding assays, together with negative-staining transmisison electron microscopy (TEM) studies, show that PNT3 forms amyloid-like fibrils. Fibrillation abilities are dramatically reduced in a rationally designed PNT3 variant in which a stretch of three contiguous tyrosines, falling within an amyloidogenic motif, were replaced by three alanines. Worthy to note, Congo red staining experiments provided hints that these amyloid-like fibrils form not only in vitro but also in cellula after transfection or infection. The present results set the stage for further investigations aimed at assessing the functional role of phase separation and fibrillation by the Henipavirus V proteins.
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Affiliation(s)
- Edoardo Salladini
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Frank Gondelaud
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Juliet F. Nilsson
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Giulia Pesce
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Christophe Bignon
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
| | - Maria Grazia Murrali
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Roxane Fabre
- Centre d’Immunologie de Marseille-Luminy (CIML), CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille University, CEDEX 9, 13288 Marseille, France;
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy; (M.G.M.); (R.P.)
| | - Andrey V. Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, UMR 5237, CNRS, Université Montpellier, 34293 Montpellier, France;
| | - Branka Horvat
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Denis Gerlier
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Cyrille Mathieu
- Team Immunobiology of the Viral Infections, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM, U1111, CNRS, UMR 5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; (B.H.); (D.G.); (C.M.)
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (E.S.); (F.G.); (J.F.N.); (G.P.); (C.B.)
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Schiavina M, Salladini E, Murrali MG, Tria G, Felli IC, Pierattelli R, Longhi S. Ensemble description of the intrinsically disordered N-terminal domain of the Nipah virus P/V protein from combined NMR and SAXS. Sci Rep 2020; 10:19574. [PMID: 33177626 PMCID: PMC7658984 DOI: 10.1038/s41598-020-76522-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Using SAXS and NMR spectroscopy, we herein provide a high-resolution description of the intrinsically disordered N-terminal domain (PNT, aa 1-406) shared by the Nipah virus (NiV) phosphoprotein (P) and V protein, two key players in viral genome replication and in evasion of the host innate immune response, respectively. The use of multidimensional NMR spectroscopy allowed us to assign as much as 91% of the residues of this intrinsically disordered domain whose size constitutes a technical challenge for NMR studies. Chemical shifts and nuclear relaxation measurements provide the picture of a highly flexible protein. The combination of SAXS and NMR information enabled the description of the conformational ensemble of the protein in solution. The present results, beyond providing an overall description of the conformational behavior of this intrinsically disordered region, also constitute an asset for obtaining atomistic information in future interaction studies with viral and/or cellular partners. The present study can thus be regarded as the starting point towards the design of inhibitors that by targeting crucial protein-protein interactions involving PNT might be instrumental to combat this deadly virus.
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Affiliation(s)
- Marco Schiavina
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Edoardo Salladini
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University and CNRS, 163 Avenue de Luminy, Case 932, Marseille, France
| | - Maria Grazia Murrali
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Giancarlo Tria
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
- Florence Center for Electron Nanoscopy (FloCEN), University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
| | - Sonia Longhi
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University and CNRS, 163 Avenue de Luminy, Case 932, Marseille, France.
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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Bloyet LM, Schramm A, Lazert C, Raynal B, Hologne M, Walker O, Longhi S, Gerlier D. Regulation of measles virus gene expression by P protein coiled-coil properties. SCIENCE ADVANCES 2019; 5:eaaw3702. [PMID: 31086822 PMCID: PMC6506246 DOI: 10.1126/sciadv.aaw3702] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 05/18/2023]
Abstract
The polymerase of negative-stranded RNA viruses consists of the large protein (L) and the phosphoprotein (P), the latter serving both as a chaperon and a cofactor for L. We mapped within measles virus (MeV) P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain (MD) of P is required for gene expression. MeV MD is kinked as a result of the presence of a stammer. Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay. By contrast, P activity is rather tolerant of substitutions within the stammer. Single substitutions at the "a" or "d" hydrophobic anchor positions with residues of variable hydrophobicity revealed that P functionality requires a narrow range of cohesiveness of its MD. Results collectively indicate that, beyond merely ensuring P oligomerization, the MD finely tunes viral gene expression through its cohesiveness.
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Affiliation(s)
- Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Antoine Schramm
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Carine Lazert
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, Paris, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
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Jordan PC, Liu C, Raynaud P, Lo MK, Spiropoulou CF, Symons JA, Beigelman L, Deval J. Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase. PLoS Pathog 2018; 14:e1006889. [PMID: 29425244 PMCID: PMC5823471 DOI: 10.1371/journal.ppat.1006889] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/22/2018] [Accepted: 01/21/2018] [Indexed: 01/27/2023] Open
Abstract
Paramyxoviruses represent a family of RNA viruses causing significant human diseases. These include measles virus, the most infectious virus ever reported, in addition to parainfluenza virus, and other emerging viruses. Paramyxoviruses likely share common replication machinery but their mechanisms of RNA biosynthesis activities and details of their complex polymerase structures are unknown. Mechanistic and functional details of a paramyxovirus polymerase would have sweeping implications for understanding RNA virus replication and for the development of new antiviral medicines. To study paramyxovirus polymerase structure and function, we expressed an active recombinant Nipah virus (NiV) polymerase complex assembled from the multifunctional NiV L protein bound to its phosphoprotein cofactor. NiV is an emerging highly pathogenic virus that causes severe encephalitis and has been declared a global public health concern due to its high mortality rate. Using negative-stain electron microscopy, we demonstrated NiV polymerase forms ring-like particles resembling related RNA polymerases. We identified conserved sequence elements driving recognition of the 3′-terminal genomic promoter by NiV polymerase, and leading to initiation of RNA synthesis, primer extension, and transition to elongation mode. Polyadenylation resulting from NiV polymerase stuttering provides a mechanistic basis for transcription termination. It also suggests a divergent adaptation in promoter recognition between pneumo- and paramyxoviruses. The lack of available antiviral therapy for NiV prompted us to identify the triphosphate forms of R1479 and GS-5734, two clinically relevant nucleotide analogs, as substrates and inhibitors of NiV polymerase activity by delayed chain termination. Overall, these findings provide low-resolution structural details and the mechanism of an RNA polymerase from a previously uncharacterized virus family. This work illustrates important functional differences yet remarkable similarities between the polymerases of nonsegmented negative-strand RNA viruses. RNA viruses replicate and transcribe their genomes using complex enzymatic machines known as RNA-dependent RNA polymerases. The chemical reactions driving nucleotide addition are shared among nucleic acid polymerases but the underlying mechanisms of RNA biosynthesis and the complex polymerase structures are diverse. Of these RNA viruses is the paramyxovirus family, which includes major human pathogens. Paramyxoviruses have common biological and genetic properties but little is known about their replication machinery. Insights into the structure, function, and mechanisms of RNA synthesis of one paramyxovirus polymerase will likely extend to the entire virus family. An emerging, highly pathogenic paramyxovirus is Nipah virus (NiV), which causes encephalitis in humans. We have purified NiV polymerase, probed its enzymatic and biophysical properties and developed it as a model paramyxovirus polymerase. We investigated template strand sequence elements driving RNA biosynthesis for NiV polymerase and obtained a snapshot of NiV polymerase molecular organization using electron microscopy to provide the first structural information on a paramyxovirus polymerase. This work extends previous knowledge by producing the first recombinant paramyxovirus polymerase and using this protein in enzymatic assays to highlight key functional and structural characteristics for the design of new medicines.
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Affiliation(s)
- Paul C. Jordan
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Cheng Liu
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Pauline Raynaud
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Michael K. Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Julian A. Symons
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Jerome Deval
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
- * E-mail:
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Insights into the homo-oligomerization properties of N-terminal coiled-coil domain of Ebola virus VP35 protein. Virus Res 2018; 247:61-70. [PMID: 29427597 DOI: 10.1016/j.virusres.2018.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 12/31/2022]
Abstract
The multifunctional Ebola virus (EBOV) VP35 protein is a key determinant of virulence. VP35 is essential for EBOV replication, is a component of the viral RNA polymerase and participates in nucleocapsid formation. Furthermore, VP35 contributes to EBOV evasion of the host innate immune response by suppressing RNA silencing and blocking RIG-I like receptors' pathways that lead to type I interferon (IFN) production. VP35 homo-oligomerization has been reported to be critical for its replicative function and to increase its IFN-antagonism properties. Moreover, homo-oligomerization is mediated by a predicted coiled-coil (CC) domain located within its N-terminal region. Here we report the homo-oligomerization profile of full-length recombinant EBOV VP35 (rVP35) assessed by size-exclusion chromatography and native polyacrylamide gel electrophoresis. Based on our biochemical results and in agreement with previous experimental observations, we have built an in silico 3D model of the so-far structurally unsolved EBOV VP35 CC domain and performed self-assembly homo-oligomerization simulations by means of molecular dynamics. Our model advances the understanding of how VP35 may associate in different homo-oligomeric species, a crucial process for EBOV replication and pathogenicity.
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Structural dissection of human metapneumovirus phosphoprotein using small angle x-ray scattering. Sci Rep 2017; 7:14865. [PMID: 29093501 PMCID: PMC5665942 DOI: 10.1038/s41598-017-14448-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/10/2017] [Indexed: 12/21/2022] Open
Abstract
The phosphoprotein (P) is the main and essential cofactor of the RNA polymerase (L) of non-segmented, negative‐strand RNA viruses. P positions the viral polymerase onto its nucleoprotein–RNA template and acts as a chaperone of the nucleoprotein (N), thereby preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of human metapneumovirus (HMPV) forms homotetramers composed of a stable oligomerization domain (Pcore) flanked by large intrinsically disordered regions (IDRs). Here we combined x-ray crystallography of Pcore with small angle x-ray scattering (SAXS)-based ensemble modeling of the full-length P protein and several of its fragments to provide a structural description of P that captures its dynamic character, and highlights the presence of varyingly stable structural elements within the IDRs. We discuss the implications of the structural properties of HMPV P for the assembly and functioning of the viral transcription/replication machinery.
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11
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Longhi S, Bloyet LM, Gianni S, Gerlier D. How order and disorder within paramyxoviral nucleoproteins and phosphoproteins orchestrate the molecular interplay of transcription and replication. Cell Mol Life Sci 2017; 74:3091-3118. [PMID: 28600653 PMCID: PMC11107670 DOI: 10.1007/s00018-017-2556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023]
Abstract
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail. By having a significant residual disorder, NTAIL-XD complexes are illustrative examples of "fuzziness", whose possible functional significance is discussed. Finally, the relevance of N-P interactions as promising targets for innovative antiviral approaches is underscored, and the functional advantages of structural disorder for paramyxoviruses are pinpointed.
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Affiliation(s)
- Sonia Longhi
- Aix-Marseille Univ, AFMB UMR 7257, 163, avenue de Luminy, Case 932, 13288, Marseille Cedex 09, France.
- CNRS, AFMB UMR 7257, 13288, Marseille, France.
| | - Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
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12
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Salladini E, Delauzun V, Longhi S. The Henipavirus V protein is a prevalently unfolded protein with a zinc-finger domain involved in binding to DDB1. ACTA ACUST UNITED AC 2017; 13:2254-2267. [DOI: 10.1039/c7mb00488e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PNT remains disordered also within the V protein. V binds to DDB1, with the ZnFD playing an important role.
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Affiliation(s)
- Edoardo Salladini
- Aix-Marseille Univ
- CNRS
- Architecture et Fonction des Macromolécules Biologiques (AFMB)
- UMR 7257
- 13288 Marseille Cedex 09
| | - Vincent Delauzun
- Aix-Marseille Univ
- CNRS
- Architecture et Fonction des Macromolécules Biologiques (AFMB)
- UMR 7257
- 13288 Marseille Cedex 09
| | - Sonia Longhi
- Aix-Marseille Univ
- CNRS
- Architecture et Fonction des Macromolécules Biologiques (AFMB)
- UMR 7257
- 13288 Marseille Cedex 09
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13
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Noval MG, Esperante SA, Molina IG, Chemes LB, Prat-Gay GD. Intrinsic Disorder to Order Transitions in the Scaffold Phosphoprotein P from the Respiratory Syncytial Virus RNA Polymerase Complex. Biochemistry 2016; 55:1441-54. [PMID: 26901160 DOI: 10.1021/acs.biochem.5b01332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsic disorder is at the center of biochemical regulation and is particularly overrepresented among the often multifunctional viral proteins. Replication and transcription of the respiratory syncytial virus (RSV) relies on a RNA polymerase complex with a phosphoprotein cofactor P as the structural scaffold, which consists of a four-helix bundle tetramerization domain flanked by two domains predicted to be intrinsically disordered. Because intrinsic disorder cannot be reduced to a defined atomic structure, we tackled the experimental dissection of the disorder-order transitions of P by a domain fragmentation approach. P remains as a tetramer above 70 °C but shows a pronounced reversible secondary structure transition between 10 and 60 °C. While the N-terminal module behaves as a random coil-like IDP in a manner independent of tetramerization, the isolated C-terminal module displays a cooperative and reversible metastable transition. When linked to the tetramerization domain, the C-terminal module becomes markedly more structured and stable, with strong ANS binding. Therefore, the tertiary structure in the C-terminal module is not compact, conferring "late" molten globule-like IDP properties, stabilized by interactions favored by tetramerization. The presence of a folded structure highly sensitive to temperature, reversibly and almost instantly formed and broken, suggests a temperature sensing activity. The marginal stability allows for exposure of protein binding sites, offering a thermodynamic and kinetic fine-tuning in order-disorder transitions, essential for the assembly and function of the RSV RNA polymerase complex.
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Affiliation(s)
- María G Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Sebastian A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Ivana G Molina
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.,CNPq, Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro, RJ, Brazil
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14
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Habchi J, Longhi S. Structural Disorder within Paramyxoviral Nucleoproteins and Phosphoproteins in Their Free and Bound Forms: From Predictions to Experimental Assessment. Int J Mol Sci 2015; 16:15688-726. [PMID: 26184170 PMCID: PMC4519920 DOI: 10.3390/ijms160715688] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/10/2023] Open
Abstract
We herein review available computational and experimental data pointing to the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed molecular description of the mechanisms governing the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (PXD) of the homologous P proteins. We also show that NTAIL-PXD complexes are "fuzzy", i.e., they possess a significant residual disorder, and discuss the possible functional significance of this fuzziness. Finally, we emphasize the relevance of N-P interactions involving intrinsically disordered proteins as promising targets for new antiviral approaches, and end up summarizing the general functional advantages of disorder for viruses.
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
| | - Sonia Longhi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
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15
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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.
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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.
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16
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Order and Disorder in the Replicative Complex of Paramyxoviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:351-81. [PMID: 26387109 DOI: 10.1007/978-3-319-20164-1_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this review we summarize available data showing the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous P proteins. We also show that a significant flexibility persists within NTAIL-XD complexes, which therefore provide illustrative examples of "fuzziness". The functional implications of structural disorder for viral transcription and replication are discussed in light of the ability of disordered regions to establish a complex molecular partnership and to confer a considerable reach to the elements of the replicative machinery.
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17
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Baronti L, Erales J, Habchi J, Felli IC, Pierattelli R, Longhi S. Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy. Chembiochem 2014; 16:268-76. [DOI: 10.1002/cbic.201402534] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 12/12/2022]
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18
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Blocquel D, Habchi J, Durand E, Sevajol M, Ferron F, Erales J, Papageorgiou N, Longhi S. Coiled-coil deformations in crystal structures: the measles virus phosphoprotein multimerization domain as an illustrative example. ACTA ACUST UNITED AC 2014; 70:1589-603. [PMID: 24914970 DOI: 10.1107/s139900471400234x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/31/2014] [Indexed: 01/02/2023]
Abstract
The structures of two constructs of the measles virus (MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communie et al. (2013), J. Virol. 87, 7166-7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal. These results show that crystal packing can bias conclusions about function and mechanism based on analysis of a single crystal structure, and they challenge to some extent the assumption according to which coiled-coil structures can be reliably predicted from the amino-acid sequence. Structural comparison also highlighted significant differences in the extent of disorder in the C-terminal region of each monomer. The differential flexibility of the C-terminal region is also supported by size-exclusion chromatography and small-angle X-ray scattering studies, which showed that MeV PMD exists in solution as a dynamic equilibrium between two tetramers of different compaction. Finally, the possible functional implications of the flexibility of the C-terminal region of PMD are discussed.
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Affiliation(s)
- David Blocquel
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Johnny Habchi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Eric Durand
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Marion Sevajol
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Jenny Erales
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | | | - Sonia Longhi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
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19
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Xue B, Blocquel D, Habchi J, Uversky AV, Kurgan L, Uversky VN, Longhi S. Structural disorder in viral proteins. Chem Rev 2014; 114:6880-911. [PMID: 24823319 DOI: 10.1021/cr4005692] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, College of Fine Arts and Sciences, and ‡Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , Tampa, Florida 33620, United States
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20
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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.
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