1
|
Li Z, Xia H, Rao G, Fu Y, Chong T, Tian K, Yuan Z, Cao S. Cryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes. Nat Commun 2024; 15:2284. [PMID: 38480794 PMCID: PMC10937716 DOI: 10.1038/s41467-024-46624-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions-surrounded by 120 spikes (full virions), 60 spikes (partial virions), or no spikes (cores). BAV cores are double-layered particles similar to the cores of other non-turreted reoviruses, except for an additional protein component in the outer capsid shell, VP10. VP10 was identified to be a cementing protein that plays a pivotal role in the assembly of BAV virions by directly interacting with VP2 (inner capsid), VP8 (outer capsid), and VP4 (spike). Viral spikes (VP4/VP9 heterohexamers) are situated on top of VP10 molecules in full or partial virions. Asymmetrical electrostatic interactions between VP10 monomers and VP4 trimers are disrupted by high pH treatment, which is thus a simple way to produce BAV cores. Low pH treatment of BAV virions removes only the flexible receptor binding protein VP9 and triggers significant conformational changes in the membrane penetration protein VP4. BAV virions adopt distinct spatial organization of their surface proteins compared with other well-studied reoviruses, suggesting that BAV may have a unique mechanism of penetration of cellular endomembranes.
Collapse
Affiliation(s)
- Zhiqiang Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Han Xia
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Guibo Rao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Yan Fu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Tingting Chong
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Kexing Tian
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhiming Yuan
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China.
| | - Sheng Cao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, PR China.
| |
Collapse
|
2
|
Xue Q, Swevers L, Taning CNT. Plant and insect virus-like particles: emerging nanoparticles for agricultural pest management. PEST MANAGEMENT SCIENCE 2023; 79:2975-2991. [PMID: 37103223 DOI: 10.1002/ps.7514] [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: 12/14/2022] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 06/05/2023]
Abstract
Virus-like particles (VLPs) represent a biodegradable, biocompatible nanomaterial made from viral coat proteins that can improve the delivery of antigens, drugs, nucleic acids, and other substances, with most applications in human and veterinary medicine. Regarding agricultural viruses, many insect and plant virus coat proteins have been shown to assemble into VLPs accurately. In addition, some plant virus-based VLPs have been used in medical studies. However, to our knowledge, the potential application of plant/insect virus-based VLPs in agriculture remains largely underexplored. This review focuses on why and how to engineer coat proteins of plant/insect viruses as functionalized VLPs, and how to exploit VLPs in agricultural pest control. The first part of the review describes four different engineering strategies for loading cargo at the inner or the outer surface of VLPs depending on the type of cargo and purpose. Second, the literature on plant and insect viruses the coat proteins of which have been confirmed to self-assemble into VLPs is reviewed. These VLPs are good candidates for developing VLP-based agricultural pest control strategies. Lastly, the concepts of plant/insect virus-based VLPs for delivering insecticidal and antiviral components (e.g., double-stranded RNA, peptides, and chemicals) are discussed, which provides future prospects of VLP application in agricultural pest control. In addition, some concerns are raised about VLP production on a large scale and the short-term resistance of hosts to VLP uptake. Overall, this review is expected to stimulate interest and research exploring plant/insect virus-based VLP applications in agricultural pest management. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Qi Xue
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Clauvis Nji Tizi Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| |
Collapse
|
3
|
Zhang Q, Gao Y, Baker ML, Liu S, Jia X, Xu H, He J, Kaelber JT, Weng S, Jiang W. The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. PLoS Pathog 2023; 19:e1011341. [PMID: 37083840 PMCID: PMC10155992 DOI: 10.1371/journal.ppat.1011341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/03/2023] [Accepted: 04/02/2023] [Indexed: 04/22/2023] Open
Abstract
Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
Collapse
Affiliation(s)
- Qinfen Zhang
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhu Gao
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shanshan Liu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xudong Jia
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haidong Xu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Shaoping Weng
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| |
Collapse
|
4
|
Nottoli M, Mikhalev A, Stamm B, Lipparini F. Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library. J Phys Chem B 2022; 126:8827-8837. [PMID: 36265187 PMCID: PMC9639080 DOI: 10.1021/acs.jpcb.2c04579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations.
Collapse
Affiliation(s)
- Michele Nottoli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy
| | - Aleksandr Mikhalev
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany
| | - Benjamin Stamm
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy,E-mail:
| |
Collapse
|
5
|
Swevers L, Kontogiannatos D, Kolliopoulou A, Ren F, Feng M, Sun J. Mechanisms of Cell Entry by dsRNA Viruses: Insights for Efficient Delivery of dsRNA and Tools for Improved RNAi-Based Pest Control. Front Physiol 2021; 12:749387. [PMID: 34858204 PMCID: PMC8632066 DOI: 10.3389/fphys.2021.749387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022] Open
Abstract
While RNAi is often heralded as a promising new strategy for insect pest control, a major obstacle that still remains is the efficient delivery of dsRNA molecules within the cells of the targeted insects. However, it seems overlooked that dsRNA viruses already have developed efficient strategies for transport of dsRNA molecules across tissue barriers and cellular membranes. Besides protecting their dsRNA genomes in a protective shell, dsRNA viruses also display outer capsid layers that incorporate sophisticated mechanisms to disrupt the plasma membrane layer and to translocate core particles (with linear dsRNA genome fragments) within the cytoplasm. Because of the perceived efficiency of the translocation mechanism, it is well worth analyzing in detail the molecular processes that are used to achieve this feat. In this review, the mechanism of cell entry by dsRNA viruses belonging to the Reoviridae family is discussed in detail. Because of the large amount of progress in mammalian versus insect models, the mechanism of infections of reoviruses in mammals (orthoreoviruses, rotaviruses, orbiviruses) will be treated as a point of reference against which infections of reoviruses in insects (orbiviruses in midges, plant viruses in hemipterans, insect-specific cypoviruses in lepidopterans) will be compared. The goal of this discussion is to uncover the basic principles by which dsRNA viruses cross tissue barriers and translocate their cargo to the cellular cytoplasm; such knowledge subsequently can be incorporated into the design of dsRNA virus-based viral-like particles for optimal delivery of RNAi triggers in targeted insect pests.
Collapse
Affiliation(s)
- Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Dimitrios Kontogiannatos
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
6
|
Chang X, Wang F, Fang Q, Chen F, Yao H, Gatehouse AMR, Ye G. Virus-induced plant volatiles mediate the olfactory behaviour of its insect vectors. PLANT, CELL & ENVIRONMENT 2021; 44:2700-2715. [PMID: 33866575 DOI: 10.1111/pce.14069] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 05/19/2023]
Abstract
Plant viruses can manipulate their hosts to release odours that are attractive or repellent to their insect vectors. However, the volatile organic compounds (VOCs), either individually or as mixtures, which play a key role in the olfactory behaviour of insect vectors remains largely unknown. Our study focused on green rice leafhoppers (GRLHs) vectoring rice dwarf virus (RDV) revealed that RDV infection significantly induced the emission of (E)-β-caryophyllene and 2-heptanol by rice plants, which influenced the olfactory behaviour of both non-viruliferous and viruliferous GRLHs. (E)-β-caryophyllene attracted non-viruliferous GRLHs to settle on RDV-infected plants, but neither attracted nor repelled viruliferous GRLHs. In contrast, 2-heptanol repelled viruliferous GRLHs to settle on RDV-infected plants, but neither repelled nor attracted non-viruliferous GRLHs. Suppression of (E)-β-caryophyllene synthase OsCAS via CRISPR-Cas9 to generate oscas-1 plants enabled us to confirm the important role played by (E)-β-caryophyllene in modulating the virus-vector-host plant interaction. These novel results reveal the role of these virus-induced VOCs in modulating the behaviour of its GRLH insect vector and may facilitate the design of new strategies for disease control through manipulation of plant volatile emissions.
Collapse
Affiliation(s)
- Xuefei Chang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Angharad M R Gatehouse
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
7
|
Rajarapu SP, Ullman DE, Uzest M, Rotenberg D, Ordaz NA, Whitfield AE. Plant–Virus–Vector Interactions. Virology 2021. [DOI: 10.1002/9781119818526.ch7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
8
|
Shao Q, Jia X, Gao Y, Liu Z, Zhang H, Tan Q, Zhang X, Zhou H, Li Y, Wu D, Zhang Q. Cryo-EM reveals a previously unrecognized structural protein of a dsRNA virus implicated in its extracellular transmission. PLoS Pathog 2021; 17:e1009396. [PMID: 33730056 PMCID: PMC7968656 DOI: 10.1371/journal.ppat.1009396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/16/2021] [Indexed: 01/15/2023] Open
Abstract
Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like viruses, with features similar to those of the Totiviridae family. Most reported members of this family infect fungi or protozoans and lack an extracellular life cycle stage. Here, we identified a new strain of OmRV and determined high-resolution structures for this virus using single-particle cryo-electron microscopy. The structures feature an unexpected protrusion at the five-fold vertex of the capsid. Disassociation of the protrusion could result in several conformational changes in the major capsid. All these structures, together with some biological results, suggest the protrusions’ associations with the extracellular transmission of OmRV. Mosquito is a reservoir of viruses, with a large amount of them perform significant research value. Omono River virus (OmRV) has been isolated from Culex mosquito and is closely related to the family Totiviridae. However, current researches have reported the extracellular transmission ability of OmRV, which is lacked in most members of Totiviridae. In the current study, we isolated a new strain, OmRV-LZ, and obtained its high-resolution cryo-electron microscopy (cryo-EM) structure. Unexpectedly, a protrusion structure has been found located at the five-fold vertex, which is unrecognized in the previous studies. Structural and molecular biological experiments were applied to try to investigate its functions. The results may be helpful to understand the extracellular transmission ability of OmRV-LZ and similar double-stranded RNA (dsRNA) viruses.
Collapse
Affiliation(s)
- Qianqian Shao
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xudong Jia
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhu Gao
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Qiqi Tan
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Xin Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Huiqiong Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Yinyin Li
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China
- * E-mail: (DW); (QZ)
| | - Qinfen Zhang
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (DW); (QZ)
| |
Collapse
|
9
|
Chen Q, Liu Y, Long Z, Yang H, Wei T. Viral Release Threshold in the Salivary Gland of Leafhopper Vector Mediates the Intermittent Transmission of Rice Dwarf Virus. Front Microbiol 2021; 12:639445. [PMID: 33613509 PMCID: PMC7890075 DOI: 10.3389/fmicb.2021.639445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/18/2021] [Indexed: 11/30/2022] Open
Abstract
Numerous piercing-sucking insects can persistently transmit viral pathogens in combination with saliva to plant phloem in an intermittent pattern. Insect vectors maintain viruliferous for life. However, the reason why insect vectors discontinuously transmit the virus remains unclear. Rice dwarf virus (RDV), a plant reovirus, was found to replicate and assemble the progeny virions in salivary gland cells of the leafhopper vector. We observed that the RDV virions moved into saliva-stored cavities in the salivary glands of leafhopper vectors via an exocytosis-like mechanism, facilitating the viral horizontal transmission to plant hosts during the feeding of leafhoppers. Interestingly, the levels of viral accumulation in the salivary glands of leafhoppers during the transmitting period were significantly lower than those of viruliferous individuals during the intermittent period. A putative viral release threshold, which was close to 1.79 × 104 copies/μg RNA was proposed from the viral titers in the salivary glands of 52 leafhoppers during the intermittent period. Thus, the viral release threshold was hypothesized to mediate the intermittent release of RDV from the salivary gland cells of leafhoppers. We anticipate that viral release threshold-mediated intermittent transmission by insect vectors is the conserved strategy for the epidemic and persistence of vector-borne viruses in nature.
Collapse
Affiliation(s)
| | | | | | | | - Taiyun Wei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Vector-borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
10
|
Mata CP, Rodríguez JM, Suzuki N, Castón JR. Structure and assembly of double-stranded RNA mycoviruses. Adv Virus Res 2020; 108:213-247. [PMID: 33837717 DOI: 10.1016/bs.aivir.2020.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycoviruses are a diverse group that includes ssRNA, dsRNA, and ssDNA viruses, with or without a protein capsid, as well as with a complex envelope. Most mycoviruses are transmitted by cytoplasmic interchange and are thought to lack an extracellular phase in their infection cycle. Structural analysis has focused on dsRNA mycoviruses, which usually package their genome in a 120-subunit T=1 icosahedral capsid, with a capsid protein (CP) dimer as the asymmetric unit. The atomic structure is available for four dsRNA mycovirus from different families: Saccharomyces cerevisiae virus L-A (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). Their capsids show structural variations of the same framework, with asymmetric or symmetric CP dimers respectively for ScV-L-A and PsV-F, dimers of similar domains of a single CP for PcV, or of two different proteins for RnQV1. The CP dimer is the building block, and assembly proceeds through dimers of dimers or pentamers of dimers, in which the genome is packed as ssRNA by interaction with CP and/or viral polymerase. These capsids remain structurally undisturbed throughout the viral cycle. The T=1 capsid participates in RNA synthesis, organizing the viral polymerase (1-2 copies) and a single loosely packaged genome segment. It also acts as a molecular sieve, to allow the passage of viral transcripts and nucleotides, but to prevent triggering of host defense mechanisms. Due to the close mycovirus-host relationship, CP evolved to allocate peptide insertions with enzyme activity, as reflected in a rough outer capsid surface.
Collapse
Affiliation(s)
- Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Javier M Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| |
Collapse
|
11
|
Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus. Structure 2020; 28:888-896.e3. [PMID: 32413288 DOI: 10.1016/j.str.2020.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/21/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023]
Abstract
Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).
Collapse
|
12
|
Fejer SN. Minimalistic coarse-grained modeling of viral capsid assembly. COMPUTATIONAL APPROACHES FOR UNDERSTANDING DYNAMICAL SYSTEMS: PROTEIN FOLDING AND ASSEMBLY 2020; 170:405-434. [DOI: 10.1016/bs.pmbts.2019.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
13
|
Konevtsova OV, Roshal DS, Lošdorfer BoŽič A, Podgornik R, Rochal S. Hidden symmetry of the anomalous bluetongue virus capsid and its role in the infection process. SOFT MATTER 2019; 15:7663-7671. [PMID: 31490506 DOI: 10.1039/c9sm01335k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clear understanding of the principles that control the arrangement of proteins and their self-assembly into viral shells is very important for the development of antiviral strategies. Here we consider the structural peculiarities and hidden symmetry of the anomalous bluetongue virus (BTV) capsid. Each of its three concentric shells violates the paradigmatic geometrical model of Caspar and Klug, which is otherwise well suited to describe most of the known icosahedral viral shells. As we show, three icosahedral spherical lattices, which are commensurate with each other and possess locally hexagonal (primitive or honeycomb) order, underlie the proteinaceous shells of the BTV capsid. This interpretation of the multishelled envelope allows us to discuss the so-called "symmetry mismatch" between its layers. We also analyze the structural stability of the considered spherical lattices on the basis of the classical theory of spherical packing and relate the proximity of the outer spherical lattice to destabilization with the fact that during infection of the cell VP2 trimers are detached from the surface of the BTV capsid. An electrostatic mechanism that can assist in this detachment is discussed in detail.
Collapse
Affiliation(s)
- Olga V Konevtsova
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Daria S Roshal
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - AnŽe Lošdorfer BoŽič
- Department of Theoretical Physics, JoŽef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, JoŽef Stefan Institute, SI-1000 Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia and School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Sergey Rochal
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| |
Collapse
|
14
|
SPring-8 BL44XU, a synchrotron radiation beamline for biological macromolecular assemblies, operated by the Institute for Protein Research, Osaka University. Biophys Rev 2019; 11:521-523. [PMID: 31338695 DOI: 10.1007/s12551-019-00557-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
|
15
|
Nakamichi Y, Miyazaki N, Tsutsumi K, Higashiura A, Narita H, Murata K, Nakagawa A. An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism. Structure 2018; 27:439-448.e3. [PMID: 30581044 DOI: 10.1016/j.str.2018.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 08/29/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
Abstract
Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.
Collapse
Affiliation(s)
- Yusuke Nakamichi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Kenta Tsutsumi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8551 Japan
| | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan.
| |
Collapse
|
16
|
Sato Y, Castón JR, Suzuki N. The biological attributes, genome architecture and packaging of diverse multi-component fungal viruses. Curr Opin Virol 2018; 33:55-65. [DOI: 10.1016/j.coviro.2018.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 12/19/2022]
|
17
|
Wang Q, Li J, Dang C, Chang X, Fang Q, Stanley D, Ye G. Rice dwarf virus infection alters green rice leafhopper host preference and feeding behavior. PLoS One 2018; 13:e0203364. [PMID: 30192810 PMCID: PMC6128522 DOI: 10.1371/journal.pone.0203364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/20/2018] [Indexed: 11/18/2022] Open
Abstract
Host plants, pathogens and their herbivore vectors systems have complex relationships via direct and indirect interactions. Although there are substantial gaps in understanding these systems, the dynamics of the relationships may influence the processes of virus transmission and plant disease epidemics. Rice dwarf virus (RDV) is mainly vectored by green rice leafhoppers (GRLHs), Nephotettix cincticeps (Uhler) (Hemiptera: Cicadellidae) in a persistently circulative manner. In this study, host plant selection preferences of non-viruliferous and viruliferous (carrying RDV) GRLHs between RDV-free and RDV-infected plants were tested. Non-viruliferous GRLHs preferred RDV-infected rice plants over RDV-free rice plants, and viruliferous GRLHs preferred RDV-free rice plants over RDV-infected rice plants. In odor selection preference bioassay using a four-field olfactometer, non-viruliferous GRLHs preferred odors of RDV-infected rice plants over healthy rice and viruliferous GRLHs preferred odors of RDV-free rice plants over RDV-infected ones. In 6 h plant penetration behavior bioassay using electrical penetration graphs, non-viruliferous GRLHs spent shorter time in non-penetration and much longer time in xylem feeding on RDV-infected, compared to RDV-free rice plants. Viruliferous GRLHs exhibited more salivation and stylet movement on RDV-free rice plants than on RDV-infected rice plants. We infer from these findings that RDV influences these vector behaviors by altering host plant physiology to promote viral transmission.
Collapse
Affiliation(s)
- Qianjin Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingjing Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Cong Dang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xuefei Chang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - David Stanley
- USDA/Agricultural Research Service, Biological Control of Insects Research Laboratory, Columbia MO, United States of America
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
| |
Collapse
|
18
|
Capsid Structure of dsRNA Fungal Viruses. Viruses 2018; 10:v10090481. [PMID: 30205532 PMCID: PMC6164181 DOI: 10.3390/v10090481] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/27/2023] Open
Abstract
Most fungal, double-stranded (ds) RNA viruses lack an extracellular life cycle stage and are transmitted by cytoplasmic interchange. dsRNA mycovirus capsids are based on a 120-subunit T = 1 capsid, with a dimer as the asymmetric unit. These capsids, which remain structurally undisturbed throughout the viral cycle, nevertheless, are dynamic particles involved in the organization of the viral genome and the viral polymerase necessary for RNA synthesis. The atomic structure of the T = 1 capsids of four mycoviruses was resolved: the L-A virus of Saccharomyces cerevisiae (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). These capsids show structural variations of the same framework, with 60 asymmetric or symmetric homodimers for ScV-L-A and PsV-F, respectively, monomers with a duplicated similar domain for PcV, and heterodimers of two different proteins for RnQV1. Mycovirus capsid proteins (CP) share a conserved α-helical domain, although the latter may carry different peptides inserted at preferential hotspots. Insertions in the CP outer surface are likely associated with enzymatic activities. Within the capsid, fungal dsRNA viruses show a low degree of genome compaction compared to reoviruses, and contain one to two copies of the RNA-polymerase complex per virion.
Collapse
|
19
|
Sun Z, Fan J, Li H, Liu H, Nam D, Kim C, Kim Y, Han Y, Zhang J, Yao S, Park J, Kim S, Tono K, Yabashi M, Ishikawa T, Song C, Fan C, Jiang H. Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers. ACS NANO 2018; 12:7509-7518. [PMID: 29986128 DOI: 10.1021/acsnano.8b01838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It has been proposed that the radiation damage to biological particles and soft condensed matter can be overcome by ultrafast and ultraintense X-ray free-electron lasers (FELs) with short pulse durations. The successful demonstration of the "diffraction-before-destruction" concept has made single-shot diffraction imaging a promising tool to achieve high resolutions under the native states of samples. However, the resolution is still limited because of the low signal-to-noise ratio, especially for biological specimens such as cells, viruses, and macromolecular particles. Here, we present a demonstration single-shot diffraction imaging experiment of DNA-based structures at SPring-8 Angstrom Compact Free Electron Laser (SACLA), Japan. Through quantitative analysis of the reconstructed images, the scattering abilities of gold and DNA were demonstrated. Suggestions for extracting valid DNA signals from noisy diffraction patterns were also explained and outlined. To sketch out the necessary experimental conditions for the 3D imaging of DNA origami or DNA macromolecular particles, we carried out numerical simulations with practical detector noise and experimental geometry using the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, USA. The simulated results demonstrate that it is possible to capture images of DNA-based structures at high resolutions with the technique development of current and next-generation X-ray FEL facilities.
Collapse
Affiliation(s)
- Zhibin Sun
- State Key Laboratory of Crystal Materials , Shandong University , Jinan 250100 , China
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jiadong Fan
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Haoyuan Li
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
- Department of Physics , Stanford University , Stanford , California 94305 , United States
| | - Huajie Liu
- Laboratory of Physical Biology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Daewoong Nam
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
- Department of Physics , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Chan Kim
- European XFEL GmbH , Holzkoppel 4 , Schenefeld 22869 , Germany
- Department of Physics and Photon Science & School of Materials Science and Engineering , Gwangju Institute of Science and Technology , Gwangju 61005 , Korea
| | - Yoonhee Kim
- European XFEL GmbH , Holzkoppel 4 , Schenefeld 22869 , Germany
- Department of Physics and Photon Science & School of Materials Science and Engineering , Gwangju Institute of Science and Technology , Gwangju 61005 , Korea
| | - Yubo Han
- Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , China
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Jianhua Zhang
- State Key Laboratory of Crystal Materials , Shandong University , Jinan 250100 , China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Shengkun Yao
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jaehyun Park
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5198 , Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Tetsuya Ishikawa
- RIKEN SPring-8 Center , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Changyong Song
- Department of Physics , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Chunhai Fan
- Laboratory of Physical Biology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Huaidong Jiang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| |
Collapse
|
20
|
Current Status of Single Particle Imaging with X-ray Lasers. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
21
|
Nakagawa A, Miyazaki N, Higashiura A. Hierarchical structure assembly model of rice dwarf virus particle formation. Biophys Rev 2017; 10:659-665. [PMID: 29243088 DOI: 10.1007/s12551-017-0375-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 11/25/2022] Open
Abstract
Rice dwarf virus (RDV) of the family Reoviridae and genus Phytoreovirus, is the cause of rice dwarf disease, a major negative effector of rice production throughout East Asia, including Japan. RDV has an icosahedral double-layered shell of approximately 70 nm diameter. The structural proteins constituting the capsid can self-assemble into a correct particle without requiring the help of any external factors in vitro. A total of more than 900 components assemble to make the full particle. A series of structural and functional studies of RDV, including X-ray crystallography and cryo-electron microscopy, suggest a hierarchical self-assembly mechanism involving both homologous and heterologous interactions. As such, systems for the recognition of each component should be essential for particle formation.
Collapse
Affiliation(s)
- Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
22
|
Kurta RP, Donatelli JJ, Yoon CH, Berntsen P, Bielecki J, Daurer BJ, DeMirci H, Fromme P, Hantke MF, Maia FRNC, Munke A, Nettelblad C, Pande K, Reddy HKN, Sellberg JA, Sierra RG, Svenda M, van der Schot G, Vartanyants IA, Williams GJ, Xavier PL, Aquila A, Zwart PH, Mancuso AP. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. PHYSICAL REVIEW LETTERS 2017; 119:158102. [PMID: 29077445 PMCID: PMC5757528 DOI: 10.1103/physrevlett.119.158102] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 05/19/2023]
Abstract
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
Collapse
Affiliation(s)
- Ruslan P Kurta
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Jeffrey J Donatelli
- Mathematics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter Berntsen
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Hasan DeMirci
- Biosciences Division, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Max Felix Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Kanupriya Pande
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Jonas A Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, 115409 Moscow, Russia
| | - Garth J Williams
- NSLS-II, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, USA
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter H Zwart
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | | |
Collapse
|
23
|
Brillault L, Jutras PV, Dashti N, Thuenemann EC, Morgan G, Lomonossoff GP, Landsberg MJ, Sainsbury F. Engineering Recombinant Virus-like Nanoparticles from Plants for Cellular Delivery. ACS NANO 2017; 11:3476-3484. [PMID: 28198180 DOI: 10.1021/acsnano.6b07747] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding capsid assembly following recombinant expression of viral structural proteins is critical to the design and modification of virus-like nanoparticles for biomedical and nanotechnology applications. Here, we use plant-based transient expression of the Bluetongue virus (BTV) structural proteins, VP3 and VP7, to obtain high yields of empty and green fluorescent protein (GFP)-encapsidating core-like particles (CLPs) from leaves. Single-particle cryo-electron microscopy of both types of particles revealed considerable differences in CLP structure compared to the crystal structure of infection-derived CLPs; in contrast, the two recombinant CLPs have an identical external structure. Using this insight, we exploited the unencumbered pore at the 5-fold axis of symmetry and the absence of encapsidated RNA to label the interior of empty CLPs with a fluorescent bioconjugate. CLPs containing 120 GFP molecules and those containing approximately 150 dye molecules were both shown to bind human integrin via a naturally occurring Arg-Gly-Asp motif found on an exposed loop of the VP7 trimeric spike. Furthermore, fluorescently labeled CLPs were shown to interact with a cell line overexpressing the surface receptor. Thus, BTV CLPs present themselves as a useful tool in targeted cargo delivery. These results highlight the importance of detailed structural analysis of VNPs in validating their molecular organization and the value of such analyses in aiding their design and further modification.
Collapse
Affiliation(s)
| | | | | | - Eva C Thuenemann
- Department of Biological Chemistry, John Innes Centre , Norwich Research Park, Colney, Norfolk NR4 7UH, United Kingdom
| | | | - George P Lomonossoff
- Department of Biological Chemistry, John Innes Centre , Norwich Research Park, Colney, Norfolk NR4 7UH, United Kingdom
| | | | | |
Collapse
|
24
|
Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT. Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Nat Commun 2017; 8:14814. [PMID: 28287099 PMCID: PMC5355851 DOI: 10.1038/ncomms14814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/26/2017] [Indexed: 12/30/2022] Open
Abstract
Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution. Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.
Collapse
Affiliation(s)
- Zhaoyang Sun
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kamel El Omari
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Xiaoyu Sun
- Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| | - Serban L Ilca
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Department of Biosciences, University of Helsinki, Viikinkaari 9, Helsinki 00014, Finland
| |
Collapse
|
25
|
Rochal SB, Konevtsova OV, Myasnikova AE, Lorman VL. Hidden symmetry of small spherical viruses and organization principles in "anomalous" and double-shelled capsid nanoassemblies. NANOSCALE 2016; 8:16976-16988. [PMID: 27714069 DOI: 10.1039/c6nr04930c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We propose the principles of structural organization in spherical nanoassemblies with icosahedral symmetry constituted by asymmetric protein molecules. The approach modifies the paradigmatic geometrical Caspar and Klug (CK) model of icosahedral viral capsids and demonstrates the common origin of both the "anomalous" and conventional capsid structures. In contrast to all previous models of "anomalous" viral capsids the proposed modified model conserves the basic structural principles of the CK approach and reveals the common hidden symmetry underlying all small viral shells. We demonstrate the common genesis of the "anomalous" and conventional capsids and explain their structures in the same frame. The organization principles are derived from the group theory analysis of the positional order on the spherical surface. The relationship between the modified CK geometrical model and the theory of two-dimensional spherical crystallization is discussed. We also apply the proposed approach to complex double-shelled capsids and capsids with protruding knob-like proteins. The introduced notion of commensurability for the concentric nanoshells explains the peculiarities of their organization and helps to predict analogous, but yet undiscovered, double-shelled viral capsid nanostructures.
Collapse
Affiliation(s)
- S B Rochal
- Faculty of Physics, Southern Federal University, 5 Zorge str., 344090 Rostov-on-Don, Russia.
| | - O V Konevtsova
- Faculty of Physics, Southern Federal University, 5 Zorge str., 344090 Rostov-on-Don, Russia.
| | - A E Myasnikova
- Faculty of Physics, Southern Federal University, 5 Zorge str., 344090 Rostov-on-Don, Russia.
| | - V L Lorman
- Laboratoire Charles Coulomb, UMR 5221 CNRS and Université Montpellier 2, pl. E. Bataillon, 34095 Montpellier, France
| |
Collapse
|
26
|
The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes. Sci Rep 2016; 6:33170. [PMID: 27616740 PMCID: PMC5018817 DOI: 10.1038/srep33170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023] Open
Abstract
Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short “plug” structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.
Collapse
|
27
|
Abstract
Rice reoviruses, transmitted by leafhopper or planthopper vectors in a persistent propagative manner, seriously threaten the stability of rice production in Asia. Understanding the mechanisms that enable viral transmission by insect vectors is a key to controlling these viral diseases. This review describes current understanding of replication cycles of rice reoviruses in vector cell lines, transmission barriers, and molecular determinants of vector competence and persistent infection. Despite recent breakthroughs, such as the discoveries of actin-based tubule motility exploited by viruses to overcome transmission barriers and mutually beneficial relationships between viruses and bacterial symbionts, there are still many gaps in our knowledge of transmission mechanisms. Advances in genome sequencing, reverse genetics systems, and molecular technologies will help to address these problems. Investigating the multiple interaction systems among the virus, insect vector, insect symbiont, and plant during natural infection in the field is a central topic for future research on rice reoviruses.
Collapse
Affiliation(s)
- Taiyun Wei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, People's Republic of China;
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China;
| |
Collapse
|
28
|
Chen Q, Wei T. Viral receptors of the gut: insect-borne propagative plant viruses of agricultural importance. CURRENT OPINION IN INSECT SCIENCE 2016; 16:9-13. [PMID: 27720057 DOI: 10.1016/j.cois.2016.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Insect-borne propagative plant viruses of agricultural importance are transmitted by sap-sucking insects. Although the infection routes of these viruses within the bodies of insect vectors are well established, cellular receptors on the microvilli, intercellular junctions, and basal lamina for mediating viral entry or spread in insect gut epithelium have not been well identified or characterized. Recent trends in the field are opening questions on how viruses exploit actin-based tubule motility to overcome insect gut epithelium barriers after viral entry in epithelium. Advances in insect cell lines, genome sequencing, reverse genetic systems and others not yet developed technologies are needed to find and characterize the counterpart receptors in vectors and to design strategies to interfere with viral transmission.
Collapse
Affiliation(s)
- Qian Chen
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Taiyun Wei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
| |
Collapse
|
29
|
Munke A, Andreasson J, Aquila A, Awel S, Ayyer K, Barty A, Bean RJ, Berntsen P, Bielecki J, Boutet S, Bucher M, Chapman HN, Daurer BJ, DeMirci H, Elser V, Fromme P, Hajdu J, Hantke MF, Higashiura A, Hogue BG, Hosseinizadeh A, Kim Y, Kirian RA, Reddy HKN, Lan TY, Larsson DSD, Liu H, Loh ND, Maia FRNC, Mancuso AP, Mühlig K, Nakagawa A, Nam D, Nelson G, Nettelblad C, Okamoto K, Ourmazd A, Rose M, van der Schot G, Schwander P, Seibert MM, Sellberg JA, Sierra RG, Song C, Svenda M, Timneanu N, Vartanyants IA, Westphal D, Wiedorn MO, Williams GJ, Xavier PL, Yoon CH, Zook J. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Sci Data 2016; 3:160064. [PMID: 27478984 PMCID: PMC4968191 DOI: 10.1038/sdata.2016.64] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/22/2016] [Indexed: 11/09/2022] Open
Abstract
Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
Collapse
Affiliation(s)
- Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Institute of Physics ASCR, v.v.i. (FZU), ELI-Beamlines Project, Prague 182 21, Czech Republic
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Salah Awel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Kartik Ayyer
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Richard J Bean
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Peter Berntsen
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Maximilian Bucher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.,Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, Berlin 10623, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Hasan DeMirci
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Veit Elser
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Petra Fromme
- Arizona State University, School of Molecular Sciences (SMS), Tempe, Arizona 85287-1604, USA.,Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Brenda G Hogue
- Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA.,Arizona State University, School of Life Sciences (SOLS), Tempe, Arizona 85287-5401, USA.,Biodesign Center for Infectious Diseases and Vaccinology, Biodesign Institute at Arizona State University, Tempe 85287, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - Yoonhee Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA.,Arizona State University, Department of Physics, Tempe, Arizona 85287, USA
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Ti-Yen Lan
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Haiguang Liu
- Beijing Computational Science Research Center, 8 W Dongbeiwang Rd, Haidian, Beijing 100193, China
| | - N Duane Loh
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, BLK S1A, Singapore 117543, Singapore
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | | | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daewoong Nam
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Garrett Nelson
- Arizona State University, Department of Physics, Tempe, Arizona 85287, USA
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2 (Box 337), Uppsala SE-75105, Sweden
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg D-22607, Germany
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Peter Schwander
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Jonas A Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Changyong Song
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1 (Box 516), Uppsala SE-75120, Sweden
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg D-22607, Germany.,National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russia
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Max O Wiedorn
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Garth J Williams
- Brookhaven National Laboratory, NSLS-II, Upton, New York 11973, USA
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, CFEL, Hamburg 22607, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - James Zook
- Arizona State University, School of Molecular Sciences (SMS), Tempe, Arizona 85287-1604, USA.,Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA
| |
Collapse
|
30
|
Boyce M, McCrae MA, Boyce P, Kim JT. Inter-segment complementarity in orbiviruses: a driver for co-ordinated genome packaging in the Reoviridae? J Gen Virol 2016; 97:1145-1157. [PMID: 26763979 DOI: 10.1099/jgv.0.000400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The process by which eukaryotic viruses with segmented genomes select a complete set of genome segments for packaging into progeny virus particles is not understood. In this study a model based on the association of genome segments through specific RNA-RNA interactions driven by base pairing was formalized and tested in the Orbivirus genus of the Reoviridae family. A strategy combining screening of the genomic sequences for inter-segment complementarity with direct functional testing of inter-segment RNA-RNA interactions using reverse genetics is described in the type species of the Orbivirus genus, Bluetongue virus (BTV). Two examples, involving four of the ten BTV genomic segments, of specific inter-segment interaction motifs whose maintenance is essential for the generation of infectious virus, were identified. Equivalent inter-segment complementarities were found between the identified regions of the orthologous genome segments of all orbiviruses, including phylogenetically distant species. Specific interaction of the participating RNA segments was confirmed in vitro using electrophoretic mobility shift assays, with the interactions inhibited using oligonucleotides complementary to the interaction motif of one of the interacting partners, and also through mutagenesis of the motifs. In each example, the base pairing rather than the absolute sequence was critical to the formation of a functional inter-segment interaction, with mutations only being tolerated in rescued virus if compensating changes were made in the interacting partner to restore uninterrupted base pairing. The absolute sequence of the complementarity motifs varied between species, indicating that this newly identified phenomenon may contribute to the observed lack of reassortment between Orbivirus species.
Collapse
Affiliation(s)
- Mark Boyce
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK
| | | | - Paul Boyce
- Mott MacDonald, Mott MacDonald House, 8-10 Sydenham Road, Croydon, CR0 2EE
| | - Jan T Kim
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK
| |
Collapse
|
31
|
Miyazaki N, Higashiura A, Higashiura T, Akita F, Hibino H, Omura T, Nakagawa A, Iwasaki K. Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes. J Biochem 2015; 159:181-90. [PMID: 26374901 DOI: 10.1093/jb/mvv092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/30/2015] [Indexed: 02/02/2023] Open
Abstract
The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.
Collapse
Affiliation(s)
- Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi, Japan;
| | | | - Tomoko Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Fusamichi Akita
- Laboratory of Virology, National Agricultural Research Center, Tsukuba, Ibaraki, Japan; and Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama, Okayama, Japan
| | - Hiroyuki Hibino
- Laboratory of Virology, National Agricultural Research Center, Tsukuba, Ibaraki, Japan; and
| | - Toshihiro Omura
- Laboratory of Virology, National Agricultural Research Center, Tsukuba, Ibaraki, Japan; and
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan;
| |
Collapse
|
32
|
Miyazaki N, Salaipeth L, Kanematsu S, Iwasaki K, Suzuki N. Megabirnavirus structure reveals a putative 120-subunit capsid formed by asymmetrical dimers with distinctive large protrusions. J Gen Virol 2015; 96:2435-2441. [DOI: 10.1099/vir.0.000182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Naoyuki Miyazaki
- National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Lakha Salaipeth
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Satoko Kanematsu
- NARO Institute of Fruit Tree Science, 92 Shimokuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| |
Collapse
|
33
|
Chen Q, Chen H, Jia D, Mao Q, Xei L, Wei T. Nonstructural protein Pns12 of rice dwarf virus is a principal regulator for viral replication and infection in its insect vector. Virus Res 2015. [PMID: 26200955 DOI: 10.1016/j.virusres.2015.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Plant reoviruses are thought to replicate and assemble within cytoplasmic structures called viroplasms. The molecular mechanisms underling the formation of the viroplasm during infection of rice dwarf virus (RDV), a plant reovirus, in its leafhopper vector cells remain poorly understood. Viral nonstructural protein Pns12 forms viroplasm-like inclusions in the absence of viral infection, suggesting that the viroplasm matrix is basically composed of Pns12. Here, we demonstrated that core capsid protein P3 and nonstructural protein Pns11 were recruited in the viroplasm by direct interaction with Pns12, whereas nonstructural protein Pns6 was recruited through interaction with Pns11. The introduction of dsRNA from Pns12 gene into cultured insect vector cells or intact insect strongly inhibited such viroplasm formation, preventing efficient viral spread in the leafhopper in vitro and in vivo. Thus, nonstructural protein Pns12 of RDV is a principal regulator for viral replication and infection in its insect vector.
Collapse
Affiliation(s)
- Qian Chen
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Hongyan Chen
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Dongsheng Jia
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qianzhuo Mao
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lianhui Xei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
| | - Taiyun Wei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
| |
Collapse
|
34
|
Botha S, Nass K, Barends TRM, Kabsch W, Latz B, Dworkowski F, Foucar L, Panepucci E, Wang M, Shoeman RL, Schlichting I, Doak RB. Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. ACTA ACUST UNITED AC 2015; 71:387-97. [DOI: 10.1107/s1399004714026327] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/30/2014] [Indexed: 11/10/2022]
Abstract
Recent advances in synchrotron sources, beamline optics and detectors are driving a renaissance in room-temperature data collection. The underlying impetus is the recognition that conformational differences are observed in functionally important regions of structures determined using crystals kept at ambient as opposed to cryogenic temperature during data collection. In addition, room-temperature measurements enable time-resolved studies and eliminate the need to find suitable cryoprotectants. Since radiation damage limits the high-resolution data that can be obtained from a single crystal, especially at room temperature, data are typically collected in a serial fashion using a number of crystals to spread the total dose over the entire ensemble. Several approaches have been developed over the years to efficiently exchange crystals for room-temperature data collection. These includein situcollection in trays, chips and capillary mounts. Here, the use of a slowly flowing microscopic stream for crystal delivery is demonstrated, resulting in extremely high-throughput delivery of crystals into the X-ray beam. This free-stream technology, which was originally developed for serial femtosecond crystallography at X-ray free-electron lasers, is here adapted to serial crystallography at synchrotrons. By embedding the crystals in a high-viscosity carrier stream, high-resolution room-temperature studies can be conducted at atmospheric pressure using the unattenuated X-ray beam, thus permitting the analysis of small or weakly scattering crystals. The high-viscosity extrusion injector is described, as is its use to collect high-resolution serial data from native and heavy-atom-derivatized lysozyme crystals at the Swiss Light Source using less than half a milligram of protein crystals. The room-temperature serial data allowde novostructure determination. The crystal size used in this proof-of-principle experiment was dictated by the available flux density. However, upcoming developments in beamline optics, detectors and synchrotron sources will enable the use of true microcrystals. This high-throughput, high-dose-rate methodology provides a new route to investigating the structure and dynamics of macromolecules at ambient temperature.
Collapse
|
35
|
Four levels of hierarchical organization, including noncovalent chainmail, brace the mature tumor herpesvirus capsid against pressurization. Structure 2014; 22:1385-98. [PMID: 25220471 DOI: 10.1016/j.str.2014.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 05/25/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
Abstract
Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent chainmail for this purpose, but how this is achieved noncovalently in the much larger gammaherpesvirus capsid is unknown. Our cryoelectron microscopy structure of a gammaherpesvirus capsid reveals a hierarchy of four levels of organization: (1) Within a hexon capsomer, each monomer of the major capsid protein (MCP), 1,378 amino acids and six domains, interacts with its neighboring MCPs at four sites. (2) Neighboring capsomers are linked in pairs by MCP dimerization domains and in groups of three by heterotrimeric triplex proteins. (3) Small (∼280 amino acids) HK97-like domains in MCP monomers alternate with triplex heterotrimers to form a belt that encircles each capsomer. (4) One hundred sixty-two belts concatenate to form noncovalent chainmail. The triplex heterotrimer orchestrates all four levels and likely drives maturation to an angular capsid that can withstand pressurization.
Collapse
|
36
|
Yang L, Du Z, Gao F, Wu K, Xie L, Li Y, Wu Z, Wu J. Transcriptome profiling confirmed correlations between symptoms and transcriptional changes in RDV infected rice and revealed nucleolus as a possible target of RDV manipulation. Virol J 2014; 11:81. [PMID: 24885215 PMCID: PMC4032362 DOI: 10.1186/1743-422x-11-81] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/22/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Rice dwarf virus (RDV) is the causal agent of rice dwarf disease, which limits rice production in many areas of south East Asia. Transcriptional changes of rice in response to RDV infection have been characterized by Shimizu et al. and Satoh et al.. Both studies found induction of defense related genes and correlations between transcriptional changes and symptom development in RDV-infected rice. However, the same rice cultivar, namely Nipponbare belonging to the Japonic subspecies of rice was used in both studies. METHODS Gene expression changes of the indica subspecies of rice, namely Oryza sativa L. ssp. indica cv Yixiang2292 that show moderate resistance to RDV, in response to RDV infection were characterized using an Affymetrix Rice Genome Array. Differentially expressed genes (DEGs) were classified according to their Gene Ontology (GO) annotation. The effects of transient expression of Pns11 in Nicotiana benthaminana on the expression of nucleolar genes were studied using real-time PCR (RT-PCR). RESULTS 856 genes involved in defense or other physiological processes were identified to be DEGs, most of which showed up-regulation. Ribosome- and nucleolus related genes were significantly enriched in the DEGs. Representative genes related to nucleolar function exhibited altered expression in N. benthaminana plants transiently expressing Pns11 of RDV. CONCLUSIONS Induction of defense related genes is common for rice infected with RDV. There is a co-relation between symptom severity and transcriptional alteration in RDV infected rice. Besides ribosome, RDV may also target nucleolus to manipulate the translation machinery of rice. Given the tight links between nucleolus and ribosome, it is intriguing to speculate that RDV may enhance expression of ribosomal genes by targeting nucleolus through Pns11.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | | |
Collapse
|
37
|
Abstract
The mechanisms and impacts of the transmission of plant viruses by insect vectors have been studied for more than a century. The virus route within the insect vector is amply documented in many cases, but the identity, the biochemical properties, and the structure of the actual molecules (or molecule domains) ensuring compatibility between them remain obscure. Increased efforts are required both to identify receptors of plant viruses at various sites in the vector body and to design competing compounds capable of hindering transmission. Recent trends in the field are opening questions on the diversity and sophistication of viral adaptations that optimize transmission, from the manipulation of plants and vectors ultimately increasing the chances of acquisition and inoculation, to specific "sensing" of the vector by the virus while still in the host plant and the subsequent transition to a transmission-enhanced state.
Collapse
Affiliation(s)
- Stéphane Blanc
- INRA, UMR BGPI, CIRAD-INRA-SupAgro, CIRAD TA-A54K, Campus International de Baillarguet, 34398 Montpellier Cedex 05, France; , ,
| | | | | |
Collapse
|
38
|
Abstract
The family Reoviridae separates two subfamilies and consists of 15 genera. Fourteen viruses in three genera (Phytoreovirus, Oryzavirus, and Fijivirus) infect plants. The outbreaks of the plant-infecting reoviruses cause sometime the serious yield loss of rice and maize, and are a menace to safe and efficient food production in the Southeast Asia. The plant-infecting reoviruses are double-shelled icosahedral particles, from 50 to 80nm in diameter, and include from 10 to 12 segmented double-stranded genomic RNAs depending on the viruses. These viruses are transmitted in a persistent manner by the vector insects and replicated in both plants and in their vectors. This review provides a brief overview of the plant-infecting reoviruses and their recent research progresses including the strategy for viral controls using transgenic rice plants.
Collapse
Affiliation(s)
- Takahide Sasaya
- Agro-Environment Research Division,NARO Kyushu Okinawa Agricultural Research Center
| |
Collapse
|
39
|
Miyazaki N, Akita F, Nakagawa A, Murata K, Omura T, Iwasaki K. Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:826-8. [PMID: 24121321 PMCID: PMC3795537 DOI: 10.1107/s090904951302219x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
It is well known that viruses utilize the host cellular systems for their infection and replication processes. However, the molecular mechanisms underlying these processes are poorly understood for most viruses. To understand these molecular mechanisms, it is essential to observe the viral and virus-related structures and analyse their molecular interactions within a cellular context. Cryo-electron microscopy and tomography offer the potential to observe macromolecular structures and to analyse their molecular interactions within the cell. Here, using cryo-electron microscopy and tomography, the structures of Rice dwarf virus are reported within fully hydrated insect vector cells grown on electron microscopy grids towards revealing the viral infection and replication mechanisms.
Collapse
Affiliation(s)
- Naoyuki Miyazaki
- National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fusamichi Akita
- National Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
- Division of Bioscience, Graduate School of Natural Science and Technology, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Toshihiro Omura
- National Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
40
|
Miyazaki N, Nakagawa A, Iwasaki K. Life cycle of phytoreoviruses visualized by electron microscopy and tomography. Front Microbiol 2013; 4:306. [PMID: 24137159 PMCID: PMC3797527 DOI: 10.3389/fmicb.2013.00306] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022] Open
Abstract
Rice dwarf virus and Rice gall dwarf virus, members of the genus Phytoreovirus in the family Reoviridae,are known as agents of rice disease, because their spread results in substantial economic damage in many Asian countries. These viruses are transmitted via insect vectors, and they multiply both in the plants and in the insect vectors. Structural information about the viruses and their interactions with cellular components in the life cycle are essential for understanding viral infection and replication mechanisms. The life cycle of the viruses involves various cellular events such as cell entry, synthesis of viral genome and proteins, assembly of viral components, viral egress from infected cells, and intra- and intercellular transports. This review focuses on the major events underlying the life cycle of phytoreoviruses, which has been visualized by various electron microscopy (EM) imaging techniques, including cryo-electron microscopy and tomography, and demonstrates the advantage of the advanced EM imaging techniques to investigate the viral infection and replication mechanisms.
Collapse
Affiliation(s)
- Naoyuki Miyazaki
- Institute for Protein Research, Osaka University Osaka, Japan ; National Institute for Physiological Sciences Okazaki, Japan
| | | | | |
Collapse
|
41
|
Nemecek D, Boura E, Wu W, Cheng N, Plevka P, Qiao J, Mindich L, Heymann JB, Hurley JH, Steven AC. Subunit folds and maturation pathway of a dsRNA virus capsid. Structure 2013; 21:1374-83. [PMID: 23891288 PMCID: PMC3742642 DOI: 10.1016/j.str.2013.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/08/2013] [Accepted: 06/14/2013] [Indexed: 12/24/2022]
Abstract
The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine.
Collapse
Affiliation(s)
- Daniel Nemecek
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Evzen Boura
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2. 16600 Prague 6, Czech Republic
| | - Weimin Wu
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
| | - Naiqian Cheng
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907
| | - Jian Qiao
- Department of Microbiology, Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, 225 Warren Street, Newark, NJ 07103
| | - Leonard Mindich
- Department of Microbiology, Public Health Research Institute Center, University of Medicine and Dentistry of New Jersey, 225 Warren Street, Newark, NJ 07103
| | - J. Bernard Heymann
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
| | - James H. Hurley
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
| | - Alasdair C. Steven
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr, Bethesda, MD 20892
| |
Collapse
|
42
|
Castón JR, Luque D, Gómez-Blanco J, Ghabrial SA. Chrysovirus structure: repeated helical core as evidence of gene duplication. Adv Virus Res 2013; 86:87-108. [PMID: 23498904 DOI: 10.1016/b978-0-12-394315-6.00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Chrysoviruses are double-stranded RNA viruses with a multipartite genome. Structure of two fungal chrysoviruses, Penicillium chrysogenum virus and Cryphonectria nitschkei chrysovirus 1, has been determined by three-dimensional cryo-electron microscopy analysis and in hydrodynamic studies. The capsids of both viruses are based on a T=1 lattice containing 60 subunits, remain structurally undisturbed throughout the viral cycle, and participate in genome metabolism. The capsid protein is formed by a repeated α-helical core, indicative of gene duplication. Whereas the chrysovirus capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The arrangement of the chrysovirus α-helical core is conserved in the totivirus L-A capsid protein, suggesting a shared basic fold. The encapsidated genome is organized in concentric shells; whereas inner dsRNA shells are diffuse, the outermost layer is organized into a dodecahedral cage beneath the protein capsid. This genome ordering could constitute a framework for dsRNA transcription in the capsid interior and/or have a structural role for capsid stability.
Collapse
|
43
|
Kawata M, Sato C. Multi-reference-based multiple alignment statistics enables accurate protein-particle pickup from noisy images. Microscopy (Oxf) 2012; 62:303-15. [PMID: 23172700 DOI: 10.1093/jmicro/dfs075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Data mining from noisy data/images is one of the most important themes in modern science and technology. Statistical image processing is a promising technique for analysing such data. Automation of particle pickup from noisy electron micrographs is essential, especially when improvement of the resolution of single particle analysis requires a huge number of particle images. For such a purpose, reference-based matching using primary three-dimensional (3D) model projections is mainly adopted. In the matching, however, the highest peaks of the correlation may not accurately indicate particles when the image is very noisy. In contrast, the density and the heights of the peaks should reflect the probability distribution of the particles. To statistically determine the particle positions from the peak distributions, we have developed a density-based peak search followed by a peak selection based on average peak height, using multi-reference alignment (MRA). Its extension, using multi-reference multiple alignment (MRMA), was found to enable particle pickup at higher accuracy even from extremely noisy images with a signal-to-noise ratio of 0.001. We refer to these new methods as stochastic pickup with MRA (MRA-StoPICK) or with MRMA (MRMA-StoPICK). MRMA-StoPICK has a higher pickup accuracy and furthermore, is almost independent of parameter settings. They were successfully applied to cryo-electron micrographs of Rice dwarf virus. Because current computational resources and parallel data processing environments allow somewhat CPU-intensive MRA-StoPICK and MRMA-StoPICK to be performed in a short period, these methods are expected to allow high-resolution analysis of the 3D structure of particles.
Collapse
Affiliation(s)
- Masaaki Kawata
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, Tsukuba 305-8568, Japan
| | | |
Collapse
|
44
|
Saha M, Morais MC. FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps. ACTA ACUST UNITED AC 2012; 28:3265-73. [PMID: 23131460 DOI: 10.1093/bioinformatics/bts616] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. RESULT Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.
Collapse
Affiliation(s)
- Mitul Saha
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 7555-0647, USA.
| | | |
Collapse
|
45
|
Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML. Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking. Structure 2012; 20:450-63. [PMID: 22405004 DOI: 10.1016/j.str.2012.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 12/16/2011] [Accepted: 01/03/2012] [Indexed: 11/26/2022]
Abstract
A significant number of macromolecular structures solved by electron cryo-microscopy and X-ray crystallography obtain resolutions of 3.5-6Å, at which direct atomistic interpretation is difficult. To address this, we developed pathwalking, a semi-automated protocol to enumerate reasonable Cα models from near-atomic resolution density maps without a structural template or sequence-structure correspondence. Pathwalking uses an approach derived from the Traveling Salesman Problem to rapidly generate an ensemble of initial models for individual proteins, which can later be optimized to produce full atomic models. Pathwalking can also be used to validate and identify potential structural ambiguities in models generated from near-atomic resolution density maps. In this work, examples from the EMDB and PDB are used to assess the broad applicability and accuracy of our method. With the growing number of near-atomic resolution density maps from cryo-EM and X-ray crystallography, pathwalking can become an important tool in modeling protein structures.
Collapse
Affiliation(s)
- Mariah R Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | |
Collapse
|
46
|
Abstract
Is it possible to meaningfully comprehend the diversity of the viral world? We propose that it is. This is based on the observation that, although there is immense genomic variation, every infective virion is restricted by strict constraints in structure space (i.e., there are a limited number of ways to fold a protein chain, and only a small subset of these have the potential to construct a virion, the hallmark of a virus). We have previously suggested the use of structure for the higher-order classification of viruses, where genomic similarities are no longer observable. Here, we summarize the arguments behind this proposal, describe the current status of structural work, highlighting its power to infer common ancestry, and discuss the limitations and obstacles ahead of us. We also reflect on the future opportunities for a more concerted effort to provide high-throughput methods to facilitate the large-scale sampling of the virosphere.
Collapse
|
47
|
Assembly of Large Icosahedral Double-Stranded RNA Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:379-402. [DOI: 10.1007/978-1-4614-0980-9_17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
48
|
Wei T, Miyazaki N, Uehara-Ichiki T, Hibino H, Shimizu T, Netsu O, Kikuchi A, Sasaya T, Iwasaki K, Omura T. Three-dimensional analysis of the association of viral particles with mitochondria during the replication of Rice gall dwarf virus. J Mol Biol 2011; 410:436-46. [PMID: 21635897 DOI: 10.1016/j.jmb.2011.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/28/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
Examination of cultured insect vector cells that had been infected with Rice gall dwarf virus (RGDV), using transmission electron microscopy and confocal microscopy, revealed the presence of clusters of virus-coated mitochondria around viroplasms in which replication and assembly of RGDV occurred, suggesting a role for mitochondria in supplying the energy required for viral morphogenetic processes. Electron tomography revealed that RGDV particles on the surface of mitochondria are arrayed in an orderly but loose manner, unlike tightly packaged particles in vesicular compartments, suggesting the presence of counterpart molecules on the surface of mitochondria. The viral particles in close proximity to mitochondria were aligned along intermediate filaments, which might serve as scaffolds for the anchorage of these particles. RGDV has a putative mitochondrion-targeting sequence on the outer surface of the outer-capsid protein P8. The arrangement of RGDV particles around mitochondria suggests that the region of the P8 protein containing the mitochondrion-targeting sequence might attach to a molecule like a receptor on the outer mitochondrial membrane. Our analysis demonstrates the three-dimensional arrangement and molecular basis for the mitochondrial proximity of RGDV particles during viral replication.
Collapse
Affiliation(s)
- Taiyun Wei
- National Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Tanaka T, Sun L, Tsutani K, Suzuki N. Rearrangements of mycoreovirus 1 S1, S2 and S3 induced by the multifunctional protein p29 encoded by the prototypic hypovirus Cryphonectria hypovirus 1 strain EP713. J Gen Virol 2011; 92:1949-1959. [PMID: 21508189 DOI: 10.1099/vir.0.031138-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mycoreovirus 1 (MyRV1), a member of the family Reoviridae possessing a genome consisting of 11 dsRNA segments (S1-S11), infects the chestnut blight fungus and reduces its virulence (hypovirulence). Studies have previously demonstrated reproducible induction of intragenic rearrangements of MyRV1 S6 (S6L: almost full-length duplication) and S10 (S10ss: internal deletion of three-quarters of the ORF), mediated by the multifunctional protein p29 encoded by the prototype hypovirus, Cryphonectria hypovirus 1 (CHV1) strain EP713, of the family Hypoviridae with ssRNA genomes. The current study showed that CHV1 p29 also induced rearrangements of the three largest MyRV1 segments, S1, S2 and S3, which encode structural proteins. These rearranged segments involved in-frame extensions of almost two-thirds of the ORFs (S1L, S2L and S3L, respectively), which is rare for a reovirus rearrangement. MyRV1 variants carrying S1L, S2L or S3L always contained S10ss (MyRV1/S1L+S10ss2, MyRV1/S2L+S10ss2 or MyRV1/S3L+S10ss2). Levels of mRNAs for the rearranged and co-existing unaltered genome segments in fungal colonies infected with each of the MyRV1 variants appeared to be comparable to those for the corresponding normal segments in wild-type MyRV1-infected colonies, suggesting that the rearranged segments were fully competent for packaging and transcription. Protein products of the rearranged segments were detectable in fungal colonies infected with S2L MyRV1/S2L+S10ss2 and S3L MyRV1/S3L+S10ss2, whilst S1L-encoded protein remained undetectable. S1L, S2L and S3L were associated with enhancement of the aerial hyphae growth rate. This study has provided additional examples of MyRV1 intragenic rearrangements induced by p29, and suggests that normal S1, S2 and S3 are required for the symptoms caused by MyRV1.
Collapse
Affiliation(s)
- Toru Tanaka
- Agrivirology Laboratory, Institute of Plant Science and Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Liying Sun
- Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Kouhei Tsutani
- Agrivirology Laboratory, Institute of Plant Science and Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| |
Collapse
|
50
|
Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol 2011; 174:360-73. [PMID: 21296162 DOI: 10.1016/j.jsb.2011.01.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.
Collapse
Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|