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Shtykova EV, Dubrovin EV, Ksenofontov AL, Gifer PK, Petoukhov MV, Tokhtar VK, Sapozhnikova IM, Stavrianidi AN, Kordyukova LV, Batishchev OV. Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy. Viruses 2024; 16:427. [PMID: 38543792 PMCID: PMC10975137 DOI: 10.3390/v16030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/23/2024] Open
Abstract
The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.
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Affiliation(s)
- Eleonora V. Shtykova
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Evgeniy V. Dubrovin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Polina K. Gifer
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Maxim V. Petoukhov
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Valeriy K. Tokhtar
- Scientific and Educational Center, Botanical Garden of the National Research University “BelSU”, Belgorod 308033, Russia;
| | - Irina M. Sapozhnikova
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg 620002, Russia;
| | - Andrey N. Stavrianidi
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
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2
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Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem 2024; 7:14. [PMID: 38233506 PMCID: PMC10794713 DOI: 10.1038/s42004-024-01100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
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Affiliation(s)
- Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Chemical Sciences', Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Neža Koritnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biomedicine', Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tajda Klobučar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Vičič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ellie Holden
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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3
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Benning FMC, Jenni S, Garcia CY, Nguyen TH, Zhang X, Chao LH. Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. Nat Commun 2024; 15:250. [PMID: 38177118 PMCID: PMC10767040 DOI: 10.1038/s41467-023-44596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We use electron cryomicroscopy to determine a 3.2 Å helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a distinct protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism shows that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
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Affiliation(s)
- Friederike M C Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Coby Y Garcia
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard College, Cambridge, MA, 02138, USA
| | - Tran H Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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4
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Wang J, Hsu Y, Lee Y, Lin N. Importin α2 participates in RNA interference against bamboo mosaic virus accumulation in Nicotiana benthamiana via NbAGO10a-mediated small RNA clearance. MOLECULAR PLANT PATHOLOGY 2024; 25:e13422. [PMID: 38279848 PMCID: PMC10799208 DOI: 10.1111/mpp.13422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/29/2024]
Abstract
Karyopherins, the nucleocytoplasmic transporters, participate in multiple RNA silencing stages by transporting associated proteins into the nucleus. Importin α is a member of karyopherins and has been reported to facilitate virus infection via nuclear import of viral proteins. Unlike other RNA viruses, silencing of importin α2 (α2i) by virus-induced gene silencing (VIGS) boosted the titre of bamboo mosaic virus (BaMV) in protoplasts, and inoculated and systemic leaves of Nicotiana benthamiana. The enhanced BaMV accumulation in importin α2i plants was linked to reduced levels of RDR6-dependent secondary virus-derived small-interfering RNAs (vsiRNAs). Small RNA-seq revealed importin α2 silencing did not affect the abundance of siRNAs derived from host mRNAs but significantly reduced the 21 and 22 nucleotide vsiRNAs in BaMV-infected plants. Deletion of BaMV TGBp1, an RNA silencing suppressor, compromised importin α2i-mediated BaMV enhancement. Moreover, silencing of importin α2 upregulated NbAGO10a, a proviral protein recruited by TGBp1 for BaMV vsiRNAs clearance, but hindered the nuclear import of NbAGO10a. Taken together, these results indicate that importin α2 acts as a negative regulator of BaMV invasion by controlling the expression and nucleocytoplasmic shuttling of NbAGO10a, which removes vsiRNAs via the TGBp1-NbAGO10a-SDN1 pathway. Our findings reveal the hidden antiviral mechanism of importin α2 in countering BaMV infection in N. benthamiana.
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Affiliation(s)
- Jiun‐Da Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Yau‐Heiu Hsu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| | - Yun‐Shien Lee
- Department of BiotechnologyMing Chuan UniversityTaipeiTaiwan
| | - Na‐Sheng Lin
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
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5
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Ksenofontov AL, Baratova LA, Semenyuk PI, Fedorova NV, Badun GA. Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:2146-2156. [PMID: 38462457 DOI: 10.1134/s0006297923120167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/02/2023] [Accepted: 11/14/2023] [Indexed: 03/12/2024]
Abstract
Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/interhelix contacts were determined. For this purpose, the approach of Lee and Richards [Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400] was used. Comparison of incorporation profiles of the tritium label in the intact and trypsin-degraded PVAΔ32 revealed position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. Presence of the channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ΔN-peptide, decrease in the label incorporation within the virion (a.a. 184-200) was also observed, indicating possible structural transition leading to the virion compactization. Based on the obtained data, we can conclude that part of the surface ΔN-peptide is inserted between the coils of the virion helix thus increasing the helix pitch and providing greater flexibility of the virion, which is important for intercellular transport of the viruses in the plants.
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Affiliation(s)
- Alexander L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Ludmila A Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Pavel I Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Natalia V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Gennadii A Badun
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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6
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Benning FMC, Jenni S, Garcia CY, Nguyen TH, Zhang X, Chao LH. Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545104. [PMID: 37398449 PMCID: PMC10312762 DOI: 10.1101/2023.06.15.545104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We determined a 3.2 Å electron cryomicroscopy helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a unique protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism revealed that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
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Affiliation(s)
- Friederike M. C. Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Coby Y. Garcia
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard College, Cambridge, MA 02138, USA
| | - Tran H. Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luke H. Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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7
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Méndez-López E, Aranda MA. A regulatory role for the redox status of the pepino mosaic virus coat protein. PLoS Pathog 2023; 19:e1011732. [PMID: 37851701 PMCID: PMC10615272 DOI: 10.1371/journal.ppat.1011732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023] Open
Abstract
Cysteine oxidations play important regulatory roles during animal virus infections. Despite the importance of redox modifications during plant infections, no plant virus protein has yet been shown to be regulated by cysteine oxidation. The potexvirus pepino mosaic virus (PepMV) is pandemic in tomato crops. Previously we modeled the structure of the PepMV particle and coat protein (CP) by cryo-electron microscopy and identified critical residues of the CP RNA-binding pocket that interact with the viral RNA during particle formation and viral cell-to-cell movement. The PepMV CP has a single cysteine residue (Cys127) central to its RNA binding pocket, which is highly conserved. Here we show that the Cys127Ser replacement diminishes PepMV fitness, and that PepMV CPWT is oxidized in vivo while CPC127S is not. We also show that Cys127 gets spontaneously glutathionylated in vitro, and that S-glutathionylation blocks in vitro the formation of virion-like particles (VLPs). VLPs longer than 200 nm could be formed after in planta CPC127S overexpression, while very short and dispersed VLPs were observed after CPWT overexpression. Our results strongly suggest that the CP redox status regulates CP functions via cysteine oxidation.
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Affiliation(s)
- Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, Campus Universitario de Espinardo, Murcia, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, Campus Universitario de Espinardo, Murcia, Spain
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8
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Kreutzberger MAB, Cvirkaite-Krupovic V, Liu Y, Baquero DP, Liu J, Sonani RR, Calladine CR, Wang F, Krupovic M, Egelman EH. The evolution of archaeal flagellar filaments. Proc Natl Acad Sci U S A 2023; 120:e2304256120. [PMID: 37399404 PMCID: PMC10334743 DOI: 10.1073/pnas.2304256120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
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Affiliation(s)
- Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | | | - Ying Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Diana P. Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Junfeng Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Ravi R. Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Chris R. Calladine
- Department of Engineering, University of Cambridge, CambridgeCB2 1PZ, United Kingdom
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
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9
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Chase O, Javed A, Byrne MJ, Thuenemann EC, Lomonossoff GP, Ranson NA, López-Moya JJ. CryoEM and stability analysis of virus-like particles of potyvirus and ipomovirus infecting a common host. Commun Biol 2023; 6:433. [PMID: 37076658 PMCID: PMC10115852 DOI: 10.1038/s42003-023-04799-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Sweet potato feathery mottle virus (SPFMV) and Sweet potato mild mottle virus (SPMMV) are members of the genera Potyvirus and Ipomovirus, family Potyviridae, sharing Ipomoea batatas as common host, but transmitted, respectively, by aphids and whiteflies. Virions of family members consist of flexuous rods with multiple copies of a single coat protein (CP) surrounding the RNA genome. Here we report the generation of virus-like particles (VLPs) by transient expression of the CPs of SPFMV and SPMMV in the presence of a replicating RNA in Nicotiana benthamiana. Analysis of the purified VLPs by cryo-electron microscopy, gave structures with resolutions of 2.6 and 3.0 Å, respectively, showing a similar left-handed helical arrangement of 8.8 CP subunits per turn with the C-terminus at the inner surface and a binding pocket for the encapsidated ssRNA. Despite their similar architecture, thermal stability studies reveal that SPMMV VLPs are more stable than those of SPFMV.
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Affiliation(s)
- Ornela Chase
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Abid Javed
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew J Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot, Oxfordshire, OX11 0DE, UK
| | - Eva C Thuenemann
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - George P Lomonossoff
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Juan José López-Moya
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193, Cerdanyola del Vallès, Barcelona, Spain.
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10
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Huang YW, Sun CI, Hu CC, Tsai CH, Meng M, Lin NS, Dinesh-Kumar SP, Hsu YH. A viral movement protein co-opts endoplasmic reticulum luminal-binding protein and calreticulin to promote intracellular movement. PLANT PHYSIOLOGY 2023; 191:904-924. [PMID: 36459587 PMCID: PMC9922411 DOI: 10.1093/plphys/kiac547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Intracellular movement is an important step for the initial spread of virus in plants during infection. This process requires virus-encoded movement proteins (MPs) and their interaction with host factors. Despite the large number of known host factors involved in the movement of different viruses, little is known about host proteins that interact with one of the MPs encoded by potexviruses, the triple-gene-block protein 3 (TGBp3). The main obstacle lies in the relatively low expression level of potexviral TGBp3 in hosts and the weak or transient nature of interactions. Here, we used TurboID-based proximity labeling to identify the network of proteins directly or indirectly interacting with the TGBp3 of a potexvirus, Bamboo mosaic virus (BaMV). Endoplasmic reticulum (ER) luminal-binding protein 4 and calreticulin 3 of Nicotiana benthamiana (NbBiP4 and NbCRT3, respectively) associated with the functional TGBp3-containing BaMV movement complexes, but not the movement-defective mutant, TGBp3M. Fluorescent microscopy revealed that TGBp3 colocalizes with NbBiP4 or NbCRT3 and the complexes move together along ER networks to cell periphery in N. benthamiana. Loss- and gain-of-function experiments revealed that NbBiP4 or NbCRT3 is required for the efficient spread and accumulation of BaMV in infected leaves. In addition, overexpression of NbBiP4 or NbCRT3 enhanced the targeting of BaMV TGBp1 to plasmodesmata (PD), indicating that NbBiP4 and NbCRT3 interact with TGBp3 to promote the intracellular transport of virion cargo to PD that facilitates virus cell-to-cell movement. Our findings revealed additional roles for NbBiP4 and NbCRT3 in BaMV intracellular movement through ER networks or ER-derived vesicles to PD, which enhances the spread of BaMV in N. benthamiana.
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Affiliation(s)
- Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chu-I Sun
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, California 95616, USA
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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11
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Ksenofontov AL, Petoukhov MV, Matveev VV, Fedorova NV, Semenyuk PI, Arutyunyan AM, Manukhova TI, Evtushenko EA, Nikitin NA, Karpova OV, Shtykova EV. Effect of the Coat Protein N-Terminal Domain Structure on the Structure and Physicochemical Properties of Virions of Potato Virus X and Alternanthera Mosaic Virus. BIOCHEMISTRY (MOSCOW) 2023; 88:119-130. [PMID: 37068873 DOI: 10.1134/s0006297923010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The amino acid sequences of the coat proteins (CPs) of the potexviruses potato virus X (PVX) and alternanthera mosaic virus (AltMV) share ~40% identity. The N-terminal domains of these proteins differ in the amino acid sequence and the presence of the N-terminal fragment of 28 residues (ΔN peptide) in the PVX CP. Here, we determined the effect of the N-terminal domain on the structure and physicochemical properties of PVX and AltMV virions. The circular dichroism spectra of these viruses differed significantly, and the melting point of PVX virions was 10-12°C higher than that of AltMV virions. Alignment of the existing high-resolution 3D structures of the potexviral CPs showed that the RMSD value between the Cα-atoms was the largest for the N-terminal domains of the two compared models. Based on the computer modeling, the ΔN peptide of the PVX CP is fully disordered. According to the synchrotron small-angle X-ray scattering (SAXS) data, the structure of CPs from the PVX and AltMV virions differ; in particular, the PVX CP has a larger portion of crystalline regions and, therefore, is more ordered. Based on the SAXS data, the diameters of the PVX and AltMV virions and helix parameters in solution were calculated. The influence of the conformation of the PVX CP N-terminal domain and its position relative to the virion surface on the virion structure was investigated. Presumably, an increased thermal stability of PVX virions vs. AltMV is provided by the extended N-terminal domain (ΔN peptide, 28 amino acid residues), which forms additional contacts between the adjacent CP subunits in the PVX virion.
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Affiliation(s)
- Alexander L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Vladimir V Matveev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
| | - Natalia V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Pavel I Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatiana I Manukhova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Nikolai A Nikitin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Olga V Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
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12
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Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador. PLANTS 2022; 11:plants11131646. [PMID: 35807598 PMCID: PMC9268947 DOI: 10.3390/plants11131646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has been affecting babaco for decades and, since many potexviruses are serologically indistinguishable, it may have been previously misidentified as papaya mosaic virus. Based on the coat protein (CP) gene, we aimed to study the distribution and epidemiological patterns of BabMV in babaco and chamburo over the years and to model its three-dimensional structure. Sequences of the CP were obtained from thirty-six isolates from plants collected in the main babaco-producing provinces of Ecuador between 2016 and 2021. The evolution rate of BabMV was estimated at 1.21 × 10−3 nucleotide substitutions site−1 year−1 and a time of origin of the most recent common ancestor around 1958.80. From molecular dynamics simulations, compared to other proteins of BabMV—RDRP, TGB1, and Alkb domain—the CP exhibited a higher flexibility with the C and N terminals as the most flexible regions. The reconstructed viral distribution provides dispersion patterns which have implications for control approaches of BabMV.
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13
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Lin KY, Wu SY, Hsu YH, Lin NS. MiR398-regulated antioxidants contribute to Bamboo mosaic virus accumulation and symptom manifestation. PLANT PHYSIOLOGY 2022; 188:593-607. [PMID: 34695209 PMCID: PMC9040666 DOI: 10.1093/plphys/kiab451] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Virus infections that cause mosaic or mottling in leaves commonly also induce increased levels of reactive oxygen species (ROS). However, how ROS contributes to symptoms is less well documented. Bamboo mosaic virus (BaMV) causes chlorotic mosaic symptoms in both Brachypodium distachyon and Nicotiana benthamiana. The BaMV △CPN35 mutant with an N-terminal deletion of its coat protein gene exhibits asymptomatic infection independently of virus titer. Histochemical staining of ROS in mock-, BaMV-, and BaMV△CPN35-infected leaves revealed that hydrogen peroxide (H2O2) accumulated solely in BaMV-induced chlorotic spots. Moreover, exogenous H2O2 treatment enhanced yellowish chlorosis in BaMV-infected leaves. Both BaMV and BaMV△CPN35 infection could induce the expression of Cu/Zu superoxide dismutase (CSD) antioxidants at messenger RNA and protein level. However, BaMV triggered the abundant accumulation of full-length NbCSD2 preprotein (prNbCSD2, without transit peptide cleavage), whereas BaMV△CPN35 induced a truncated prNbCSD2. Confocal microscopy showed that majority of NbCSD2-green fluorescent protein (GFP) predominantly localized in the cytosol upon BaMV infection, but BaMV△CPN35 infection tended to cause NbCSD2-GFP to remain in chloroplasts. By 5'-RNA ligase-mediated rapid amplification of cDNA ends, we validated CSDs are the targets of miR398 in vivo. Furthermore, BaMV infection increased the level of miR398, while the level of BaMV titer was regulated positively by miR398 but negatively by CSD2. In contrast, overexpression of cytosolic form NbCSD2, impairing the transport into chloroplasts, greatly enhanced BaMV accumulation. Taken together, our results indicate that induction of miR398 by BaMV infection may facilitate viral titer accumulation, and cytosolic prNbCSD2 induction may contribute to H2O2 accumulation, resulting in the development of BaMV chlorotic symptoms in plants.
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Affiliation(s)
- Kuan-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Su-Yao Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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14
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Yang MH, Hu CC, Wong CH, Liang JJ, Ko HY, He MH, Lin YL, Lin NS, Hsu YH. Convenient Auto-Processing Vector Based on Bamboo Mosaic Virus for Presentation of Antigens Through Enzymatic Coupling. Front Immunol 2021; 12:739837. [PMID: 34721406 PMCID: PMC8551676 DOI: 10.3389/fimmu.2021.739837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
We have developed a new binary epitope-presenting CVP platform based on bamboo mosaic virus (BaMV) by using the sortase A (SrtA)-mediated ligation technology. The reconstructed BaMV genome harbors two modifications: 1) a coat protein (CP) with N-terminal extension of the tobacco etch virus (TEV) protease recognition site plus 4 extra glycine (G) residues as the SrtA acceptor; and 2) a TEV protease coding region replacing that of the triple-gene-block proteins. Inoculation of such construct, pKB5G, on Nicotiana benthamiana resulted in the efficient production of filamentous CVPs ready for SrtA-mediated ligation with desired proteins. The second part of the binary platform includes an expression vector for the bacterial production of donor proteins. We demonstrated the applicability of the platform by using the recombinant envelope protein domain III (rEDIII) of Japanese encephalitis virus (JEV) as the antigen. Up to 40% of the BaMV CP subunits in each CVP were loaded with rEDIII proteins in 1 min. The rEDIII-presenting BaMV CVPs (BJLPET5G) could be purified using affinity chromatography. Immunization assays confirmed that BJLPET5G could induce the production of neutralizing antibodies against JEV infections. The binary platform could be adapted as a useful alternative for the development and mass production of vaccine candidates.
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MESH Headings
- Aminoacyltransferases/genetics
- Aminoacyltransferases/metabolism
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antigens, Viral/administration & dosage
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Cell Line
- Cysteine Endopeptidases/genetics
- Cysteine Endopeptidases/metabolism
- Disease Models, Animal
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis, Japanese/blood
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/virology
- Endopeptidases/genetics
- Endopeptidases/metabolism
- Escherichia coli/genetics
- Escherichia coli/immunology
- Escherichia coli/metabolism
- Female
- Genetic Vectors
- Immunogenicity, Vaccine
- Japanese Encephalitis Vaccines/administration & dosage
- Japanese Encephalitis Vaccines/genetics
- Japanese Encephalitis Vaccines/immunology
- Mice, Inbred BALB C
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/metabolism
- Potexvirus/enzymology
- Potexvirus/genetics
- Potexvirus/immunology
- Nicotiana/genetics
- Nicotiana/immunology
- Nicotiana/metabolism
- Virion/enzymology
- Virion/genetics
- Virion/immunology
- Mice
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Affiliation(s)
- Ming-Hao Yang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chi-Hzeng Wong
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hui-Ying Ko
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Meng-Hsun He
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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15
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Zanotti G, Grinzato A. Structure of filamentous viruses. Curr Opin Virol 2021; 51:25-33. [PMID: 34592708 DOI: 10.1016/j.coviro.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/21/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022]
Abstract
Despite filamentous viruses represent an important portion of the universe of viruses, their 3D structures available are quite limited, particularly if compared to the large number of structures of icosahedral viruses present in the Protein Data Bank. As a matter of fact, flexible filamentous viruses cannot be grown as single crystals and past structural studies have mostly been limited to X-ray fiber diffraction or to the determination of the structure of isolated viral proteins. Only very recently, several structures of filamentous viruses have become available, owing to the recent development of cryo-electron microscopy. This technique has given a strong impulse to the field and has allowed the building of reliable molecular models of entire viruses, in some cases at a nearly atomic resolution level. In this paper we briefly describe the architecture of filamentous viruses that infect bacteria, archaea, plants and humans. It is easy to foresee that more new structures of filamentous viruses will become available soon and they will allow a better understanding of the rules underlying the structural organization of these organisms so relevant for the life on our planet.
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Affiliation(s)
- Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
| | - Alessandro Grinzato
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
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16
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Huang YW, Sun CI, Hu CC, Tsai CH, Meng M, Lin NS, Hsu YH. NbPsbO1 Interacts Specifically with the Bamboo Mosaic Virus (BaMV) Subgenomic RNA (sgRNA) Promoter and Is Required for Efficient BaMV sgRNA Transcription. J Virol 2021; 95:e0083121. [PMID: 34379502 PMCID: PMC8475527 DOI: 10.1128/jvi.00831-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022] Open
Abstract
Many positive-strand (+) RNA viruses produce subgenomic RNAs (sgRNAs) in the infection cycle through the combined activities of viral replicase and host proteins. However, knowledge about host proteins involved in direct sgRNA promoter recognition is limited. Here, in the partially purified replicase complexes from Bamboo mosaic virus (BaMV)-infected tissue, we have identified the Nicotiana benthamiana photosystem II oxygen-evolving complex protein, NbPsbO1, which specifically interacted with the promoter of sgRNA but not that of genomic RNA (gRNA). Silencing of NbPsbO1 expression suppressed BaMV accumulation in N. benthamiana protoplasts without affecting viral gRNA replication. Overexpression of wild-type NbPsbO1 stimulated BaMV sgRNA accumulation. Fluorescent microscopy examination revealed that the fluorescence associated with NbPsbO1 was redistributed from chloroplast granal thylakoids to stroma in BaMV-infected cells. Overexpression of a mislocalized mutant of NbPsbO1, dTPPsbO1-T7, inhibited BaMV RNA accumulation in N. benthamiana, whereas overexpression of an NbPsbO1 derivative, sPsbO1-T7, designed to be targeted to chloroplast stroma, upregulated the sgRNA level. Furthermore, depletion of NbPsbO1 in BaMV RdRp preparation significantly inhibited sgRNA synthesis in vitro but exerted no effect on (+) or (-) gRNA synthesis, which indicates that NbPsbO1 is required for efficient sgRNA synthesis. These results reveal a novel role for NbPsbO1 in the selective enhancement of BaMV sgRNA transcription, most likely via direct interaction with the sgRNA promoter. IMPORTANCE Production of subgenomic RNAs (sgRNAs) for efficient translation of downstream viral proteins is one of the major strategies adapted for viruses that contain a multicistronic RNA genome. Both viral genomic RNA (gRNA) replication and sgRNA transcription rely on the combined activities of viral replicase and host proteins, which recognize promoter regions for the initiation of RNA synthesis. However, compared to the cis-acting elements involved in the regulation of sgRNA synthesis, the host factors involved in sgRNA promoter recognition mostly remain to be elucidated. Here, we found a chloroplast protein, NbPsbO1, which specifically interacts with Bamboo mosaic virus (BaMV) sgRNA promoter. We showed that NbPsbO1 is relocated to the BaMV replication site in BaMV-infected cells and demonstrated that NbPsbO1 is required for efficient BaMV sgRNA transcription but exerts no effect on gRNA replication. This study provides a new insight into the regulating mechanism of viral gRNA and sgRNA synthesis.
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Affiliation(s)
- Ying Wen Huang
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chu I Sun
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
| | - Chung Chi Hu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Ching Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
| | - Na Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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17
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Frontiers in Bioengineering and Biotechnology: Plant Nanoparticles for Anti-Cancer Therapy. Vaccines (Basel) 2021; 9:vaccines9080830. [PMID: 34451955 PMCID: PMC8402531 DOI: 10.3390/vaccines9080830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022] Open
Abstract
Naturally occurring viral nanomaterials have gained popularity owing to their biocompatible and biodegradable nature. Plant virus nanoparticles (VNPs) can be used as nanocarriers for a number of biomedical applications. Plant VNPs are inexpensive to produce, safe to administer and efficacious as treatments. The following review describes how plant virus architecture facilitates the use of VNPs for imaging and a variety of therapeutic applications, with particular emphasis on cancer. Examples of plant viruses which have been engineered to carry drugs and diagnostic agents for specific types of cancer are provided. The drug delivery system in response to the internal conditions is known as stimuli response, recently becoming more applicable using plant viruses based VNPs. The review concludes with a perspective of the future of plant VNPs and plant virus-like particles (VLPs) in cancer research and therapy.
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18
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Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes. J Virol 2021; 95:e0067321. [PMID: 34011550 DOI: 10.1128/jvi.00673-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) has recently adopted a comprehensive, hierarchical system of virus taxa. The highest ranks in this hierarchy are realms, each of which is considered monophyletic but apparently originated independently of other realms. Here, we announce the creation of a new realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses.
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19
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Thuenemann EC, Byrne MJ, Peyret H, Saunders K, Castells-Graells R, Ferriol I, Santoni M, Steele JFC, Ranson NA, Avesani L, Lopez-Moya JJ, Lomonossoff GP. A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants. Viruses 2021; 13:885. [PMID: 34064959 PMCID: PMC8150850 DOI: 10.3390/v13050885] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient production. To examine this, we compared the accumulation of VLPs from two potexviruses, papaya mosaic virus and alternanthera mosaic virus (AltMV), when the coat proteins were expressed from a replicating potato virus X- based vector (pEff) and a non-replicating vector (pEAQ-HT). Significantly greater quantities of VLPs could be purified when pEff was used. The pEff system was also very efficient at producing VLPs of helical viruses from different virus families. Examination of the RNA content of AltMV and tobacco mosaic virus VLPs produced from pEff revealed the presence of vector-derived RNA sequences, suggesting that the replicating RNA acts as a scaffold for VLP assembly. Cryo-EM analysis of the AltMV VLPs showed they had a structure very similar to that of authentic potexvirus particles. Thus, we conclude that vectors generating replicating forms of RNA, such as pEff, are very efficient for producing helical VLPs.
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Affiliation(s)
- Eva C. Thuenemann
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Matthew J. Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (N.A.R.)
| | - Hadrien Peyret
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Keith Saunders
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Roger Castells-Graells
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Inmaculada Ferriol
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193 Cerdanyola del Vallès, Spain; (I.F.); (J.J.L.-M.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - Mattia Santoni
- Diamante srl. Strada Le Grazie, 15, 37134 Verona, Italy;
| | - John F. C. Steele
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
- Piramal Healthcare UK Ltd., Piramal Pharma Solutions, Earls Road, Grangemouth, Stirlingshire FK3 8XG, UK
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (N.A.R.)
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134 Verona, Italy;
| | - Juan Jose Lopez-Moya
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193 Cerdanyola del Vallès, Spain; (I.F.); (J.J.L.-M.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - George P. Lomonossoff
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
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20
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Stable Display of Artificially Long Foreign Antigens on Chimeric Bamboo mosaic virus Particles. Viruses 2021; 13:v13040572. [PMID: 33805417 PMCID: PMC8067224 DOI: 10.3390/v13040572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Plant viruses can be genetically modified to generate chimeric virus particles (CVPs) carrying heterologous peptides fused on the surface of coat protein (CP) subunits as vaccine candidates. However, some factors may be especially significant in determining the properties of chimeras. In this study, peptides from various sources and of various lengths were inserted into the Bamboo mosaic virus-based (BaMV) vector CP N-terminus to examine the chimeras infecting and accumulating in plants. Interestingly, it was found that the two different strains Foot-and-mouth disease virus (FMDV) VP1 antigens with flexible linker peptides (77 or 82 amino acids) were directly expressed on the BaMV CP, and the chimeric particles self-assembled and continued to express FMDV antigens. The chimeric CP, when directly fused with a large foreign protein (117 amino acids), can self-fold into incomplete virus particles or disks. The physicochemical properties of heterologus peptides N-terminus, complex strand structures of heterologus peptides C-terminus and different flexible linker peptides, can affect the chimera accumulation. Based on these findings, using plant virus-based chimeras to express foreign proteins can increase their length limitations, and engineered plant-made CVP-based vaccines have increasing potential for further development as novel vaccines.
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21
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Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments. Proc Natl Acad Sci U S A 2020; 117:19643-19652. [PMID: 32759221 DOI: 10.1073/pnas.2011125117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
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Grinzato A, Kandiah E, Lico C, Betti C, Baschieri S, Zanotti G. Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family. Nat Chem Biol 2020; 16:564-569. [DOI: 10.1038/s41589-020-0502-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 02/16/2020] [Indexed: 01/31/2023]
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23
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Abstract
Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.
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24
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Recent Advances in the Use of Plant Virus-Like Particles as Vaccines. Viruses 2020; 12:v12030270. [PMID: 32121192 DOI: 10.3390/v12030270] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
Vaccination is one of the most effective public health interventions of the 20th century. All vaccines can be classified into different types, such as vaccines against infectious diseases, anticancer vaccines and vaccines against autoimmune diseases. In recent decades, recombinant technologies have enabled the design of experimental vaccines against a wide range of diseases using plant viruses and virus-like particles as central elements to stimulate protective and long-lasting immune responses. The analysis of recent publications shows that at least 97 experimental vaccines have been constructed based on plant viruses, including 71 vaccines against infectious agents, 16 anticancer vaccines and 10 therapeutic vaccines against autoimmune disorders. Several plant viruses have already been used for the development of vaccine platforms and have been tested in human and veterinary studies, suggesting that plant virus-based vaccines will be introduced into clinical and veterinary practice in the near future.
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25
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Santoni M, Zampieri R, Avesani L. Plant Virus Nanoparticles for Vaccine Applications. Curr Protein Pept Sci 2020; 21:344-356. [PMID: 32048964 DOI: 10.2174/1389203721666200212100255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/16/2019] [Accepted: 10/19/2019] [Indexed: 12/29/2022]
Abstract
In the rapidly evolving field of nanotechnology, plant virus nanoparticles (pVNPs) are emerging as powerful tools in diverse applications ranging from biomedicine to materials science. The proteinaceous structure of plant viruses allows the capsid structure to be modified by genetic engineering and/or chemical conjugation with nanoscale precision. This means that pVNPs can be engineered to display peptides and proteins on their external surface, including immunodominant peptides derived from pathogens allowing pVNPs to be used for active immunization. In this context, pVNPs are safer than VNPs derived from mammalian viruses because there is no risk of infection or reversion to pathogenicity. Furthermore, pVNPs can be produced rapidly and inexpensively in natural host plants or heterologous production platforms. In this review, we discuss the use of pVNPs for the delivery of peptide antigens to the host immune in pre-clinical studies with the final aim of promoting systemic immunity against the corresponding pathogens. Furthermore, we described the versatility of plant viruses, with innate immunostimulatory properties, in providing a huge natural resource of carriers that can be used to develop the next generation of sustainable vaccines.
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Affiliation(s)
- Mattia Santoni
- Department of Biotechnology, University of Verona. Strada Le Grazie, 15. 37134 Verona, Italy
| | | | - Linda Avesani
- Department of Biotechnology, University of Verona. Strada Le Grazie, 15. 37134 Verona, Italy
- Diamante srl. Strada Le Grazie, 15. 37134 Verona, Italy
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26
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Martínez-Turiño S, García JA. Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more. Adv Virus Res 2020; 108:165-211. [PMID: 33837716 DOI: 10.1016/bs.aivir.2020.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.
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27
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Alazem M, He MH, Chang CH, Cheng N, Lin NS. Disrupting the Homeostasis of High Mobility Group Protein Promotes the Systemic Movement of Bamboo mosaic virus. FRONTIERS IN PLANT SCIENCE 2020; 11:597665. [PMID: 33424893 PMCID: PMC7793662 DOI: 10.3389/fpls.2020.597665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/11/2020] [Indexed: 05/21/2023]
Abstract
Viruses hijack various organelles and machineries for their replication and movement. Ever more lines of evidence indicate that specific nuclear factors are involved in systemic trafficking of several viruses. However, how such factors regulate viral systemic movement remains unclear. Here, we identify a novel role for Nicotiana benthamiana high mobility group nucleoprotein (NbHMG1/2a) in virus movement. Although infection of N. benthamiana with Bamboo mosaic virus (BaMV) decreased NbHMG1/2a expression levels, nuclear-localized NbHMG1/2a protein was shuttled out of the nucleus into cytoplasm upon BaMV infection. NbHMG1/2a knockdown or even overexpression did not affect BaMV accumulation in inoculated leaves, but it did enhance systemic movement of the virus. Interestingly, the positive regulator Rap-GTPase activation protein 1 was highly upregulated upon infection with BaMV, whereas the negative regulator thioredoxin h protein was greatly reduced, no matter if NbHMG1a/2a was silenced or overexpressed. Our findings indicate that NbHMG1/2a may have a role in plant defense responses. Once its homeostasis is disrupted, expression of relevant host factors may be perturbed that, in turn, facilitates BaMV systemic movement.
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28
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Cuesta R, Yuste-Calvo C, Gil-Cartón D, Sánchez F, Ponz F, Valle M. Structure of Turnip mosaic virus and its viral-like particles. Sci Rep 2019; 9:15396. [PMID: 31659175 PMCID: PMC6817885 DOI: 10.1038/s41598-019-51823-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 01/05/2023] Open
Abstract
Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.
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Affiliation(s)
- Rebeca Cuesta
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Carmen Yuste-Calvo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - David Gil-Cartón
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CBGP, UPM-INIA), Campus Montegancedo, 28223, Madrid, Spain
| | - Mikel Valle
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain.
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29
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Kumar S, Karmakar R, Garg DK, Gupta I, Patel AK. Elucidating the functional aspects of different domains of bean common mosaic virus coat protein. Virus Res 2019; 273:197755. [PMID: 31525400 DOI: 10.1016/j.virusres.2019.197755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
The coat protein (CP) is the only structural protein present in the polyprotein of bean common mosaic virus. The well known characteristics of the CP are self-oligomerization and nucleic acid binding activity. The studies of the coat protein mutants revealed that the oligomeric property of CP solely depends on the amino-terminal residues and the nucleic acid binding domain present at the 194-202 residue position. The 3'UTR RNA of the virus showed high binding affinity with the RNA binding domain as compared to the 5'UTR RNA. Further, the intrinsic fluorescence study of the CP also suggested that the N- and C-terminal of CP contains a highly disordered region. The present study also illustrates that the coat protein contains a conserved RNA binding pocket among the potyviruses, but displays divergent oligomerization propensities due to the difference in residue at the N- and C-terminal.
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Affiliation(s)
- Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ruma Karmakar
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Dushyant Kumar Garg
- School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Ishu Gupta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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30
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Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M. Structural basis for the multitasking nature of the potato virus Y coat protein. SCIENCE ADVANCES 2019; 5:eaaw3808. [PMID: 31328164 PMCID: PMC6636993 DOI: 10.1126/sciadv.aaw3808] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/10/2019] [Indexed: 05/02/2023]
Abstract
Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
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Affiliation(s)
- Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Martin Polák
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- University of Nova Gorica, Vipavska cesta, 5000 Nova Gorica, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Corresponding author.
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31
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Effects of Abscisic Acid and Salicylic Acid on Gene Expression in the Antiviral RNA Silencing Pathway in Arabidopsis. Int J Mol Sci 2019; 20:ijms20102538. [PMID: 31126102 PMCID: PMC6566719 DOI: 10.3390/ijms20102538] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/19/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
The RNA silencing pathways modulate responses to certain stresses, and can be partially tuned by several hormones such as salicylic acid (SA) and abscisic acid (ABA). Although SA and ABA are often antagonistic and often modulate different stress responses, they have similar effects on virus resistance, which are partially achieved through the antiviral RNA silencing pathway. Whether they play similar roles in regulating the RNA silencing pathway is unclear. By employing coexpression and promoter analyses, we found that some ABA- and SA-related transcription factors (TFs) are coexpressed with several AGO, DCL, and RDR genes, and have multiple binding sites for the identified TFs in the queried promoters. ABA and SA are antagonistic with respect to the expression of AGO1 and RDRs because ABA was able to induce these genes only in the SA mutant. Nevertheless, both hormones showed similarities in the regulation of other genes, for example, the induction of AGO2 by ABA was SA-dependent, indicating that ABA acts upstream of SA in this regulation. We inferred that the similar effects of ABA and SA on some genes resulted in the redundancy of their roles in resistance to bamboo mosaic virus, but that the two hormones are antagonistic with respect to other genes unrelated to their biosynthesis pathways.
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32
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Plant virus-based materials for biomedical applications: Trends and prospects. Adv Drug Deliv Rev 2019; 145:96-118. [PMID: 30176280 DOI: 10.1016/j.addr.2018.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022]
Abstract
Nanomaterials composed of plant viral components are finding their way into medical technology and health care, as they offer singular properties. Precisely shaped, tailored virus nanoparticles (VNPs) with multivalent protein surfaces are efficiently loaded with functional compounds such as contrast agents and drugs, and serve as carrier templates and targeting vehicles displaying e.g. peptides and synthetic molecules. Multiple modifications enable uses including vaccination, biosensing, tissue engineering, intravital delivery and theranostics. Novel concepts exploit self-organization capacities of viral building blocks into hierarchical 2D and 3D structures, and their conversion into biocompatible, biodegradable units. High yields of VNPs and proteins can be harvested from plants after a few days so that various products have reached or are close to commercialization. The article delineates potentials and limitations of biomedical plant VNP uses, integrating perspectives of chemistry, biomaterials sciences, molecular plant virology and process engineering.
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33
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Röder J, Dickmeis C, Commandeur U. Small, Smaller, Nano: New Applications for Potato Virus X in Nanotechnology. FRONTIERS IN PLANT SCIENCE 2019; 10:158. [PMID: 30838013 PMCID: PMC6390637 DOI: 10.3389/fpls.2019.00158] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/29/2019] [Indexed: 05/08/2023]
Abstract
Nanotechnology is an expanding interdisciplinary field concerning the development and application of nanostructured materials derived from inorganic compounds or organic polymers and peptides. Among these latter materials, proteinaceous plant virus nanoparticles have emerged as a key platform for the introduction of tailored functionalities by genetic engineering and conjugation chemistry. Tobacco mosaic virus and Cowpea mosaic virus have already been developed for bioimaging, vaccination and electronics applications, but the flexible and filamentous Potato virus X (PVX) has received comparatively little attention. The filamentous structure of PVX particles allows them to carry large payloads, which are advantageous for applications such as biomedical imaging in which multi-functional scaffolds with a high aspect ratio are required. In this context, PVX achieves superior tumor homing and retention properties compared to spherical nanoparticles. Because PVX is a protein-based nanoparticle, its unique functional properties are combined with enhanced biocompatibility, making it much more suitable for biomedical applications than synthetic nanomaterials. Moreover, PVX nanoparticles have very low toxicity in vivo, and superior pharmacokinetic profiles. This review focuses on the production of PVX nanoparticles engineered using chemical and/or biological techniques, and describes current and future opportunities and challenges for the application of PVX nanoparticles in medicine, diagnostics, materials science, and biocatalysis.
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Affiliation(s)
| | | | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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34
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Richert-Pöggeler KR, Franzke K, Hipp K, Kleespies RG. Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses. Front Microbiol 2019; 9:3255. [PMID: 30666247 PMCID: PMC6330349 DOI: 10.3389/fmicb.2018.03255] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/14/2018] [Indexed: 01/29/2023] Open
Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G. Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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35
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Esfandiari N, Sefidbakht Y. An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation. Int J Biol Macromol 2018; 116:939-946. [PMID: 29777803 DOI: 10.1016/j.ijbiomac.2018.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/17/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022]
Abstract
Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate. The capsid protein (CP) structure were modeled based on homology and subjected to three independent 80 ns molecular dynamics minimization (GROMACS, OPLS force field) in the SPC water box. The RMSD, RMSF, SASA, and electrostatic properties were retrieved from the trajectories. Flexibility and hydrophilic nature of the N-terminal residues (1-34) of solvated CP could be observed in conformational changes upon minimization. The obtained structure was then docked with NbPCIP1 using ClusPro 2.0. The strong binding affinity of these two proteins (≈-16.0 Kcal mol-1) represents the formation of inclusion body and hence appearance of the symptoms.
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Affiliation(s)
- Neda Esfandiari
- Protein Research Center, Shahid Beheshti University, G.C, Tehran, Iran.
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, G.C, Tehran, Iran.
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36
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Rao G, Fu Y, Li N, Yin J, Zhang J, Wang M, Hu Z, Cao S. Controllable Assembly of Flexible Protein Nanotubes for Loading Multifunctional Modules. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25135-25145. [PMID: 29989404 DOI: 10.1021/acsami.8b07611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly of the capsid proteins (CPs) of filamentous viruses often requires the presence of DNA or RNA molecules, which has limited their applications. Here, we describe a strategy for controllable assembly of flexible bio-nanotubes consisting of Escherichia coli expressed CP of baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) in vitro. These protein-only nanotubes were studied as a new structural platform for high-density presentation of multiple active molecules on the exterior surface by direct fusion of the protein of interest to the N-terminus of HearNPV CP (HaCP). Structural characterization using cryoelectron microscopy demonstrated that the HaCP could assemble into two closely related but structurally distinct tube types, suggesting the tunable HaCP interaction network is the major contributor to the flexibility of HaCP nanotubes. Our flexible nanotubes could tolerate larger molecular modifications compared with TMV-based templates and could be used as promising candidates for versatile molecular loading applications.
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Affiliation(s)
- Guibo Rao
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | | | - Na Li
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Jiayi Yin
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Jie Zhang
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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37
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Direct imaging and computational cryo-electron microscopy of ribbons and nanotubes. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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38
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Chen I, Chen H, Huang Y, Huang H, Shenkwen L, Hsu Y, Tsai C. A thioredoxin NbTRXh2 from Nicotiana benthamiana negatively regulates the movement of Bamboo mosaic virus. MOLECULAR PLANT PATHOLOGY 2018; 19:405-417. [PMID: 28052479 PMCID: PMC6637981 DOI: 10.1111/mpp.12532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/25/2016] [Accepted: 12/29/2016] [Indexed: 05/05/2023]
Abstract
An up-regulated gene derived from Bamboo mosaic virus (BaMV)-infected Nicotiana benthamiana plants was cloned and characterized in this study. BaMV is a single-stranded, positive-sense RNA virus. This gene product, designated as NbTRXh2, was matched with sequences of thioredoxin h proteins, a group of small proteins with a conserved active-site motif WCXPC conferring disulfide reductase activity. To examine how NbTRXh2 is involved in the infection cycle of BaMV, we used the virus-induced gene silencing technique to knock down NbTRXh2 expression in N. benthamiana and inoculated the plants with BaMV. We observed that, compared with control plants, BaMV coat protein accumulation increased in knockdown plants at 5 days post-inoculation (dpi). Furthermore, BaMV coat protein accumulation did not differ significantly between NbTRXh2-knockdown and control protoplasts at 24 hpi. The BaMV infection foci in NbTRXh2-knockdown plants were larger than those in control plants. In addition, BaMV coat protein accumulation decreased when NbTRXh2 was transiently expressed in plants. These results suggest that NbTRXh2 plays a role in restricting BaMV accumulation. Moreover, confocal microscopy results showed that NbTRXh2-OFP (NbTRXh2 fused with orange fluorescent protein) localized at the plasma membrane, similar to AtTRXh9, a homologue in Arabidopsis. The expression of the mutant that did not target the substrates failed to reduce BaMV accumulation. Co-immunoprecipitation experiments revealed that the viral movement protein TGBp2 could be the target of NbTRXh2. Overall, the functional role of NbTRXh2 in reducing the disulfide bonds of targeting factors, encoded either by the host or virus (TGBp2), is crucial in restricting BaMV movement.
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Affiliation(s)
- I‐Hsuan Chen
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Hui‐Ting Chen
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Ying‐Ping Huang
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Hui‐Chen Huang
- Biotechnology CenterNational Chung Hsing UniversityTaichung402Taiwan
| | - Lin‐Ling Shenkwen
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Yau‐Heiu Hsu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Ching‐Hsiu Tsai
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
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Richert-Pöggeler KR, Franzke K, Hipp K, Kleespies RG. Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses. Front Microbiol 2018. [PMID: 30666247 DOI: 10.3389/fmicb.2018.03255.ecollection] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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Abstract
Our understanding of the viral world changed just after the first structures of icosahedral viral particles were unveiled. The structural similarities between capsid proteins of distant viral groups were not anticipated, and the findings suggested the existence of common ancestors for viruses with different host range, genomic structure and multiplication strategies. This way, diverse viruses with icosahedral particles can now be grouped based on the structural homology between their capsid proteins. In the last years, the presence of conserved folds between viral proteins in non-icosahedral viruses has also emerged. Viral particles with radically different morphologies, ranging from naked and filamentous to enveloped and pleomorphic, have shown structural homology between the nucleoproteins that bind directly to their genomes. This chapter overviews recent findings regarding the similar structure found between nucleoproteins of eukaryotic ssRNA viruses. The structural homology includes the coat proteins from all known families of flexible filamentous plant viruses, a group with monopartite (+)ssRNA genomes. Their coat proteins share a core domain with nucleoproteins of previously unrelated families of enveloped viruses that have segmented (-)ssRNA genomes. This last group consists of mostly animals viruses, including influenza virus.
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Affiliation(s)
- Mikel Valle
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, Derio, Spain.
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Chen IH, Huang YP, Tseng CH, Ni JT, Tsai CH, Hsu YH, Tsai CH. Nicotiana benthamiana Elicitor-Inducible Leucine-Rich Repeat Receptor-Like Protein Assists Bamboo Mosaic Virus Cell-to-Cell Movement. FRONTIERS IN PLANT SCIENCE 2017; 8:1736. [PMID: 29056941 PMCID: PMC5635722 DOI: 10.3389/fpls.2017.01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
For successful infection, a virus requires various host factors at different stages such as translation, targeting, replication, and spreading. One of the host genes upregulated after Nicotiana benthamiana infection with Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA potexvirus, assists in viral movement. To understand how this host protein is involved in BaMV movement, we cloned its full-length cDNA by rapid amplification of cDNA ends. The gene has 3199 nt and encodes a 969-amino acid polypeptide. The sequence of the encoded polypeptide is orthologous to that of N. tabacum elicitor-inducible leucine-rich repeat (LRR) receptor-like protein (NtEILP), a plant viral resistance gene, and is designated NbEILP. To reveal how NbEILP is involved in BaMV movement, we fused green fluorescent protein (GFP) to its C-terminus. Unfortunately, the gene's expression in N. benthamiana was beyond our detection limit possibly because of its large size (∼135 kDa). However, NbEILP at such low expression could still enhance BaMV accumulation in inoculated leaves. A short version of NbEILP was constructed to remove the LRR domain, NbEILP/ΔLRR-GFP; the expression of this deletion mutant could still enhance BaMV accumulation to 1.7-fold that of the control. Hence, the LRR domain in NbEILP is not an essential element in BaMV movement. We constructed a few deletion mutants - NbEILP/ΔLRRΔTMD (without the transmembrane domain), NbEILP/ΔLRRΔCD (without the cytoplasmic domain), and NbEILP/ΔLRRΔSP (without the signal peptide) - to examine whether these domains are involved in BaMV movement. For BaMV movement, NbEILP requires the signal peptide to target the endoplasmic reticulum and the transmembrane domain to retain on the membrane.
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Zamora M, Méndez-López E, Agirrezabala X, Cuesta R, Lavín JL, Sánchez-Pina MA, Aranda MA, Valle M. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. SCIENCE ADVANCES 2017; 3:eaao2182. [PMID: 28948231 PMCID: PMC5606705 DOI: 10.1126/sciadv.aao2182] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/18/2017] [Indexed: 05/16/2023]
Abstract
Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.
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Affiliation(s)
- Miguel Zamora
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Xabier Agirrezabala
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Rebeca Cuesta
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - José L. Lavín
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - M. Amelia Sánchez-Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Mikel Valle
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
- Corresponding author.
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Donchenko EK, Pechnikova EV, Mishyna MY, Manukhova TI, Sokolova OS, Nikitin NA, Atabekov JG, Karpova OV. Structure and properties of virions and virus-like particles derived from the coat protein of Alternanthera mosaic virus. PLoS One 2017; 12:e0183824. [PMID: 28837650 PMCID: PMC5570366 DOI: 10.1371/journal.pone.0183824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/11/2017] [Indexed: 01/01/2023] Open
Abstract
Plant viruses and their virus-like particles (VLPs) have a lot of advantages for biotechnological applications including complete safety for humans. Alternanthera mosaic virus (AltMV) is a potentially promising object for design of novel materials. The 3D structures of AltMV virions and its VLPs were obtained by single particle EM at ~13Å resolution. The comparison of the reconstructions and a trypsin treatment revealed that AltMV CPs possesses a different fold in the presence (virions) and absence of viral RNA (VLPs). For the first time, the structure of morphologically similar virions and virus-like particles based on the coat protein of a helical filamentous plant virus is shown to be different. Despite this, both AltMV virions and VLPs are stable in a wide range of conditions. To provide a large amount of AltMV for biotechnology usage the isolation procedure was modified.
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Affiliation(s)
| | - Evgeniya V. Pechnikova
- Laboratory of Electron Microscopy, V.A. Shoubnikov Institute of Crystallography of Russian Academy of Sciences, Moscow, Russia
- Nano-, Bio-, Information, Cognitive, Socio-Humanistic (NBICS) Science and Technology Center, National Research Centre "Kurchatov Institute", Moscow, Russia
| | | | | | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Olga V. Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Thérien A, Bédard M, Carignan D, Rioux G, Gauthier-Landry L, Laliberté-Gagné MÈ, Bolduc M, Savard P, Leclerc D. A versatile papaya mosaic virus (PapMV) vaccine platform based on sortase-mediated antigen coupling. J Nanobiotechnology 2017; 15:54. [PMID: 28720097 PMCID: PMC5516373 DOI: 10.1186/s12951-017-0289-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 07/10/2017] [Indexed: 02/04/2023] Open
Abstract
Background Flexuous rod-shaped nanoparticles made of the coat protein (CP) of papaya mosaic virus (PapMV) have been shown to trigger innate immunity through engagement of toll-like receptor 7 (TLR7). PapMV nanoparticles can also serve as a vaccine platform as they can increase the immune response to fused peptide antigens. Although this approach shows great potential, fusion of antigens directly to the CP open reading frame (ORF) is challenging because the fused peptides can alter the structure of the CP and its capacity to self assemble into nanoparticles—a property essential for triggering an efficient immune response to the peptide. This represents a serious limitation to the utility of this approach as fusion of small peptides only is tolerated. Results We have developed a novel approach in which peptides are fused directly to pre-formed PapMV nanoparticles. This approach is based on the use of a bacterial transpeptidase (sortase A; SrtA) that can attach the peptide directly to the nanoparticle. An engineered PapMV CP harbouring the SrtA recognition motif allows efficient coupling. To refine our engineering, and to predict the efficacy of coupling with SrtA, we modeled the PapMV structure based on the known structure of PapMV CP and on recent reports revealing the structure of two closely related potexviruses: pepino mosaic virus (PepMV) and bamboo mosaic virus (BaMV). We show that SrtA can allow the attachment of long peptides [Influenza M2e peptide (26 amino acids) and the HIV-1 T20 peptide (39 amino acids)] to PapMV nanoparticles. Consistent with our PapMV structural model, we show that around 30% of PapMV CP subunits in each nanoparticle can be fused to the peptide antigen. As predicted, engineered nanoparticles were capable of inducing a strong antibody response to the fused antigen. Finally, in a challenge study with influenza virus, we show that mice vaccinated with PapMV-M2e are protected from infection. Conclusions This technology will allow the development of vaccines harbouring long peptides containing several B and/or T cell epitopes that can contribute to a broad and robust protection from infection. The design can be fast, versatile and can be adapted to the development of vaccines for many infectious diseases as well as cancer vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12951-017-0289-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ariane Thérien
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Mikaël Bédard
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Damien Carignan
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Gervais Rioux
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Louis Gauthier-Landry
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Marie-Ève Laliberté-Gagné
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Marilène Bolduc
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada
| | - Pierre Savard
- Neurosciences, Laval University, 2705 Boul. Laurier, Québec City, PQ, G1V 4G2, Canada
| | - Denis Leclerc
- Department of Microbiology, Infectiology and Immunology, Infectious Disease Research Center, Laval University, 2705 Boul. Laurier, Quebec City, PQ, G1V 4G2, Canada.
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Abstract
RosettaES, an algorithm that uses a fragment-based sampling strategy, improves macromolecular structure modeling from cryo-EM data at 3–5-Å resolution. Accurate atomic modeling of macromolecular structures into cryo-electron microscopy (cryo-EM) maps is a major challenge, as the moderate resolution makes accurate placement of atoms difficult. We present Rosetta enumerative sampling (RosettaES), an automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3–5-Å resolution. On a benchmark set of nine proteins, RosettaES was able to identify near-native conformations in 85% of segments. RosettaES was also used to determine models for three challenging macromolecular structures.
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46
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Chang KC, Chang LT, Huang YW, Lai YC, Lee CW, Liao JT, Lin NS, Hsu YH, Hu CC. Transmission of Bamboo mosaic virus in Bamboos Mediated by Insects in the Order Diptera. Front Microbiol 2017; 8:870. [PMID: 28559888 PMCID: PMC5432563 DOI: 10.3389/fmicb.2017.00870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
Abstract
Bamboo mosaic virus (BaMV), a member of the genus Potexvirus, is the major threat to bamboo cultivation. Similar to most potexviruses, the transmission of BaMV by insect vectors has not been documented previously. However, field observations of BaMV disease incidences suggested that insect vectors might be involved. In this study, we aimed to investigate the possibility of insect-mediated transmission of BaMV among bamboo clumps, in order to provide further insights into the infection cycles of BaMV for the development of effective disease management measures. From the major insects collected from infected bamboo plantations, BaMV genomic RNAs were detected inside the bodies of two dipteran insects, Gastrozona fasciventris and Atherigona orientalis, but not in thrips (Scirtothrips dorsalis). Artificial feeding assays using green fluorescent protein-tagged BaMV virions revealed that BaMV could enter the digestive systems and survive in the regurgitant and excretion of the dipterans. BaMV RNA could be retained in the dipterans for up to 4 weeks. Insect-mediated transmission assays indicated that both dipterans could transmit BaMV to bamboo seedlings through artificially created wounds with low infection efficiency (14 - 41%), suggesting that the dipterans may mediate the transmission in a mechanical-like manner. These results demonstrated that dipterans with sponge-like mouthparts may also serve as vectors for at least one potexvirus, BaMV, among bamboo plants. The finding suggested that dipteran insect control should be integrated into the disease management measures against BaMV infections.
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Affiliation(s)
- Kuo-Chen Chang
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Ling-Teng Chang
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Yi-Chin Lai
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Chin-Wei Lee
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Jia-Teh Liao
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Na-Sheng Lin
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan.,Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
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Wang IN, Yeh WB, Lin NS. Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA. Front Microbiol 2017; 8:886. [PMID: 28588562 PMCID: PMC5440514 DOI: 10.3389/fmicb.2017.00886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.
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Affiliation(s)
- Ing-Nang Wang
- Department of Biological Sciences, University at Albany, AlbanyNY, United States
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsin UniversityTaichung, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
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Chen TH, Hu CC, Liao JT, Lee YL, Huang YW, Lin NS, Lin YL, Hsu YH. Production of Japanese Encephalitis Virus Antigens in Plants Using Bamboo Mosaic Virus-Based Vector. Front Microbiol 2017; 8:788. [PMID: 28515719 PMCID: PMC5413549 DOI: 10.3389/fmicb.2017.00788] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
Japanese encephalitis virus (JEV) is among the major threats to public health in Asia. For disease control and prevention, the efficient production of safe and effective vaccines against JEV is in urgent need. In this study, we produced a plant-made JEV vaccine candidate using a chimeric virus particle (CVP) strategy based on bamboo mosaic virus (BaMV) for epitope presentation. The chimeric virus, designated BJ2A, was constructed by fusing JEV envelope protein domain III (EDIII) at the N-terminus of BaMV coat protein, with an insertion of the foot-and-mouth disease virus 2A peptide to facilitate the production of both unfused and epitope-presenting for efficient assembly of the CVP vaccine candidate. The strategy allowed stable maintenance of the fusion construct over long-term serial passages in plants. Immuno-electron microscopy examination and immunization assays revealed that BJ2A is able to present the EDIII epitope on the surface of the CVPs, which stimulated effective neutralizing antibodies against JEV infection in mice. This study demonstrates the efficient production of an effective CVP vaccine candidate against JEV in plants by the BaMV-based epitope presentation system.
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Affiliation(s)
- Tsung-Hsien Chen
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Jia-Teh Liao
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Yi-Ling Lee
- Institute of Biomedical Sciences, Academia SinicaTaipei, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Na-Sheng Lin
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan.,Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia SinicaTaipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
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Alazem M, He MH, Moffett P, Lin NS. Abscisic Acid Induces Resistance against Bamboo Mosaic Virus through Argonaute2 and 3. PLANT PHYSIOLOGY 2017; 174:339-355. [PMID: 28270624 PMCID: PMC5411131 DOI: 10.1104/pp.16.00015] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/03/2017] [Indexed: 05/21/2023]
Abstract
Plant resistance to pathogens is tuned by defense-related hormones. Of these, abscisic acid (ABA) is well documented to moderate resistance against fungi and bacteria. However, ABA's contribution to resistance against viruses is pleiotropic. ABA affects callose deposition at plasmodesmata (therefore hindering the viral cell-to-cell movement), but here, we show that when callose synthase is down-regulated, ABA still induces resistance against infection with Bamboo mosaic virus (BaMV). By examining the potential connections between the ABA and RNA-silencing pathways in Arabidopsis (Arabidopsis thaliana), we showed that ABA regulates the expression of almost the whole ARGONAUTE (AGO) gene family, of which some are required for plant resistance against BaMV Our data show that BaMV infection and ABA treatment regulate the same set of AGOs, with positive effects on AGO1, AGO2, and AGO3, no effect on AGO7, and negative effects on AGO4 and AGO10 The BaMV-mediated regulation of AGO1, AGO2, and AGO3 is ABA dependent, because the accumulation of these AGOs in BaMV-infected ABA mutants did not reach the levels observed in infected wild-type plants. In addition, the AGO1-miR168a complex is dispensable for BaMV resistance, while AGO2 and AGO3 were important for ABA-mediated resistance. While most ago mutants showed increased susceptibility to BaMV infection (except ago10), ago1-27 showed reduced BaMV titers, which was attributed to the up-regulated levels of AGO2, AGO3, and AGO4 We have established that ABA regulates the expression of several members of the AGO family, and this regulation partially contributes to ABA-mediated resistance against BaMV These findings reveal another role for ABA in plants.
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Affiliation(s)
- Mazen Alazem
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Meng-Hsun He
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Peter Moffett
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
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Model-based structural and functional characterization of the Rice stripe tenuivirus nucleocapsid protein interacting with viral genomic RNA. Virology 2017; 506:73-83. [PMID: 28359901 DOI: 10.1016/j.virol.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/21/2022]
Abstract
Rice stripe tenuivirus (RSV) is a filamentous, negative-strand RNA virus causing severe diseases on rice in Asian countries. The viral particle is composed predominantly of a nucleocapsid protein (NP) and genomic RNA. However, the molecular details of how the RSV NP interacts with genomic RNA during particle assembly remain largely unknown. Here, we modeled the NP-RNA complex and show that polar amino acids within a predicted groove of NP are critical for RNA binding and protecting the RNA from RNase digestion. RSV NP formed pentamers, hexamers, heptamers, and octamers. By modeling the higher-order structures, we found that oligomer formation was driven by the N-terminal amino arm of the NP. Deletion of this arm abolished oligomerization; the N-terminally truncated NP was less able to interact with RNA and protect RNA than was the wild type. These findings afford valuable new insights into molecular mechanism of RSV NPs interacting with genomic RNA.
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