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Muthuraman KR, Utomo DIS, Matsuda M, Suzuki R, Park EY. Expression of dengue capsid-like particles in silkworm and display of envelope domain III of dengue virus serotype 2. Protein Expr Purif 2024; 222:106543. [PMID: 38971211 DOI: 10.1016/j.pep.2024.106543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Dengue virus (DENV) is a considerable public health threat affecting millions of people globally. Vaccines for dengue are an important strategy to reduce the disease burden. We expressed capsid (C2) and envelope domain III of dengue virus serotype 2 (2EDIII) separately in the silkworm expression system. We conjugated them employing the monomeric streptavidin (mSA2) and biotin affinity to display the antigenic 2EDIII on the C2-forming capsid-like particle (CLP). Purified 2EDIII-displaying C2 (CLP/2EDIII) was immunogenic in BALB/c mice, eliciting neutralizing antibodies confirmed by a single-round infectious particle (SRIP) neutralization assay. Th1 cytokine levels were upregulated for the CLP/2EDIII group, and the anti-inflammatory IL-10 and pro-inflammatory IL-6 cytokine levels were also raised compared to the 2EDIII and the control groups. Elevated cytokine levels for CLP/2EDIII indicate the importance of displaying the 2EDIII as CLP/2EDIII rather than as an individual subunit. This study is the first to express the C2 protein as self-assembling CLP in vivo and 2EDIII separately in the silkworm expression system and conjugate them to form a monovalent CLP. Thus, this CLP/2EDIII display method may pave the way for an efficient tetravalent dengue vaccine candidate.
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Affiliation(s)
- Krishna Raja Muthuraman
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Doddy Irawan Setyo Utomo
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Disease, Gakuen, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Disease, Gakuen, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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2
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Jablunovsky A, Jose J. The Dynamic Landscape of Capsid Proteins and Viral RNA Interactions in Flavivirus Genome Packaging and Virus Assembly. Pathogens 2024; 13:120. [PMID: 38392858 PMCID: PMC10893219 DOI: 10.3390/pathogens13020120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The Flavivirus genus of the Flaviviridae family of enveloped single-stranded RNA viruses encompasses more than 70 members, many of which cause significant disease in humans and livestock. Packaging and assembly of the flavivirus RNA genome is essential for the formation of virions, which requires intricate coordination of genomic RNA, viral structural, and nonstructural proteins in association with virus-induced, modified endoplasmic reticulum (ER) membrane structures. The capsid (C) protein, a small but versatile RNA-binding protein, and the positive single-stranded RNA genome are at the heart of the elusive flavivirus assembly process. The nucleocapsid core, consisting of the genomic RNA encapsidated by C proteins, buds through the ER membrane, which contains viral glycoproteins prM and E organized as trimeric spikes into the lumen, forming an immature virus. During the maturation process, which involves the low pH-mediated structural rearrangement of prM and E and furin cleavage of prM in the secretory pathway, the spiky immature virus with a partially ordered nucleocapsid core becomes a smooth, mature virus with no discernible nucleocapsid. This review focuses on the mechanisms of genome packaging and assembly by examining the structural and functional aspects of C protein and viral RNA. We review the current lexicon of critical C protein features and evaluate interactions between C and genomic RNA in the context of assembly and throughout the life cycle.
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Affiliation(s)
- Anastazia Jablunovsky
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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3
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da Silva Sanches PR, Sanchez-Velazquez R, Batista MN, Carneiro BM, Bittar C, De Lorenzo G, Rahal P, Patel AH, Cilli EM. Antiviral Evaluation of New Synthetic Bioconjugates Based on GA-Hecate: A New Class of Antivirals Targeting Different Steps of Zika Virus Replication. Molecules 2023; 28:4884. [PMID: 37446546 PMCID: PMC10343505 DOI: 10.3390/molecules28134884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Re-emerging arboviruses represent a serious health problem due to their rapid vector-mediated spread, mainly in urban tropical areas. The 2013-2015 Zika virus (ZIKV) outbreak in South and Central America has been associated with cases of microcephaly in newborns and Guillain-Barret syndrome. We previously showed that the conjugate gallic acid-Hecate (GA-FALALKALKKALKKLKKALKKAL-CONH2)-is an efficient inhibitor of the hepatitis C virus. Here, we show that the Hecate peptide is degraded in human blood serum into three major metabolites. These metabolites conjugated with gallic acid were synthesized and their effect on ZIKV replication in cultured cells was evaluated. The GA-metabolite 5 (GA-FALALKALKKALKKL-COOH) was the most efficient in inhibiting two ZIKV strains of African and Asian lineage at the stage of both virus entry (virucidal and protective) and replication (post-entry). We also demonstrate that GA-metabolite 5 does not affect cell growth after 7 days of continuous treatment. Thus, this study identifies a new synthetic antiviral compound targeting different steps of ZIKV replication in vitro and with the potential for broad reactivity against other flaviviruses. Our work highlights a promising strategy for the development of new antivirals based on peptide metabolism and bioconjugation.
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Affiliation(s)
- Paulo Ricardo da Silva Sanches
- School of Pharmaceutical Science, São Paulo State University, Araraquara 14800-903, SP, Brazil
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G12 8QQ, UK; (R.S.-V.); (G.D.L.); (A.H.P.)
- Institute of Chemistry, São Paulo State University, Araraquara 14800-900, SP, Brazil
| | - Ricardo Sanchez-Velazquez
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G12 8QQ, UK; (R.S.-V.); (G.D.L.); (A.H.P.)
| | - Mariana Nogueira Batista
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065, USA; (M.N.B.)
| | - Bruno Moreira Carneiro
- School of Health Science, Federal University of Rondonópolis, Rondonópolis 78736-900, MT, Brazil;
| | - Cintia Bittar
- School of Health Science, Federal University of Rondonópolis, Rondonópolis 78736-900, MT, Brazil;
| | - Giuditta De Lorenzo
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G12 8QQ, UK; (R.S.-V.); (G.D.L.); (A.H.P.)
| | - Paula Rahal
- Institute of Bioscience, Humanities and Exact Science, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil;
| | - Arvind H. Patel
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G12 8QQ, UK; (R.S.-V.); (G.D.L.); (A.H.P.)
| | - Eduardo Maffud Cilli
- Institute of Chemistry, São Paulo State University, Araraquara 14800-900, SP, Brazil
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4
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Zhu Y, Chen S, Lurong Q, Qi Z. Recent Advances in Antivirals for Japanese Encephalitis Virus. Viruses 2023; 15:v15051033. [PMID: 37243122 DOI: 10.3390/v15051033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Culex mosquitoes are the primary vectors of the Japanese encephalitis virus (JEV). Since its discovery in 1935, Japanese encephalitis (JE), caused by JEV, has posed a significant threat to human health. Despite the widespread implementation of several JEV vaccines, the transmission chain of JEV in the natural ecosystem has not changed, and the vector of transmission cannot be eradicated. Therefore, JEV is still the focus of attention for flaviviruses. At present, there is no clinically specific drug for JE treatment. JEV infection is a complex interaction between the virus and the host cell, which is the focus of drug design and development. An overview of antivirals that target JEV elements and host factors is presented in this review. In addition, drugs that balance antiviral effects and host protection by regulating innate immunity, inflammation, apoptosis, or necrosis are reviewed to treat JE effectively.
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Affiliation(s)
- Yongzhe Zhu
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China
| | - Shenglin Chen
- Department of Clinic Laboratory Diagnostics, General Hospital of Tibet Military Area Command of PLA, Lhasa 850007, China
| | - Qilin Lurong
- Department of Geriatrics, General Hospital of Tibet Military Area Command of PLA, Lhasa 850007, China
| | - Zhongtian Qi
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China
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5
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Self-assembly of dengue virus empty capsid-like particles in solution. iScience 2023; 26:106197. [PMID: 36890794 PMCID: PMC9986514 DOI: 10.1016/j.isci.2023.106197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/11/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Nucleocapsid (NC) assembly is an essential step of the virus replication cycle. It ensures genome protection and transmission among hosts. Flaviviruses are human viruses for which envelope structure is well known, whereas no information on NC organization is available. Here we designed a dengue virus capsid protein (DENVC) mutant in which a highly positive spot conferred by arginine 85 in α4-helix was replaced by a cysteine residue, simultaneously removing the positive charge and restricting the intermolecular motion through the formation of a disulfide cross-link. We showed that the mutant self-assembles into capsid-like particles (CLP) in solution without nucleic acids. Using biophysical techniques, we investigated capsid assembly thermodynamics, showing that an efficient assembly is related to an increased DENVC stability due to α4/α4' motion restriction. To our knowledge, this is the first time that flaviviruses' empty capsid assembly is obtained in solution, revealing the R85C mutant as a powerful tool to understand the NC assembly mechanism.
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6
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Murali A, Kumar S, Akshaya S, Singh SK. Drug repurposing toward the inhibition of RNA-dependent RNA polymerase of various flaviviruses through computational study. J Cell Biochem 2023; 124:127-145. [PMID: 36502494 DOI: 10.1002/jcb.30352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
Numerous pathogens affecting human is present in the flavivirus family namely west nile, dengue, yellow fever, and zika which involves in development of global burden and distressing the environment economically. Till date, no approved drugs are available for targeting these viruses. The threat which urged the identification of small molecules for the inhibition of these viruses is the spreading of serious viral diseases. The recent outbreak of zika and dengue infections postured a solemn risk to worldwide public well-being. RNA-dependent RNA polymerase (RdRp) is the supreme adaptable enzymes of all the RNA viruses which is responsible for the replication and transcription of genome among the structural and nonstructural proteins of flaviviruses. It is understood that the RdRp of the flaviviruses are similar stating that the japanese encephalitis and west nile shares 70% identity with zika whereas the dengue serotype 2 and 3 shares the identity of 76% and 81%, respectively. In this study, we investigated the binding site of four flaviviral RdRp and provided insights into various interaction of the molecules using the computational approach. Our study helps in recognizing the potent compounds that could inhibit the viral protein as a common inhibitor. Additionally, with the conformational stability analysis, we proposed the possible mechanism of inhibition of the identified common small molecule toward RdRp of flavivirus. Finally, this study could be an initiative for the identification of common inhibitors and can be explored further for understanding the mechanism of action through in vitro studies for the study on efficacy.
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Affiliation(s)
- Aarthy Murali
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sushil Kumar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
- Department of Data Sciences, Centre of Biomedical Research, Sanjay Gandhi Post Institute of Medical Sciences Campus, Lucknow, India
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7
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Yu J, Huang C, Wang Z, Kaushik RS, Sheng Z, Li F, Wang D. Development and characterization of an inducible assay system to measure Zika virus capsid interactions. J Med Virol 2022; 94:5392-5400. [PMID: 35822280 PMCID: PMC9474601 DOI: 10.1002/jmv.27991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 12/15/2022]
Abstract
The global spread of the mosquito-borne Zika virus (ZIKV) infection and its complications including Guillain-Barré syndrome and fetus microcephaly in 2015 have made ZIKV as a significant public health threat. The capsid protein plays crucial roles in ZIKV replication and thus represents an attractive therapeutic target. However, inhibitors of ZIKV capsid assembly have not been rigorously identified due to the lack of a target-based screening system. In this study, we developed a novel ZIKV capsid interaction method based on a split-luciferase complementation assay, which can be used to measure and quantify ZIKV capsid-capsid (C-C) interaction by the restored luciferase signal when capsid proteins interact with each other. Furthermore, a Tet-on inducible stable cell line was generated to screen inhibitors of capsid dimerization. By using of this system, peptides (Pep.15-24 in the N-terminal region of ZIKV capsid protein and Pep.44-58 in the α2 helix of ZIKV capsid protein) were identified to inhibit ZIKV C-C interaction. Overall, this study developed a novel inducible assay system to measure ZIKV capsid interaction and identify ZIKV capsid multimerization inhibitors, which will be applied for future discovery of ZIKV assembly inhibitors.
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Affiliation(s)
- Jieshi Yu
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Chen Huang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Zhao Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007
| | - Radhey S. Kaushik
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
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8
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Kumar S, Verma A, Yadav P, Dubey SK, Azhar EI, Maitra SS, Dwivedi VD. Molecular pathogenesis of Japanese encephalitis and possible therapeutic strategies. Arch Virol 2022; 167:1739-1762. [PMID: 35654913 PMCID: PMC9162114 DOI: 10.1007/s00705-022-05481-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/10/2022] [Indexed: 12/26/2022]
Abstract
Japanese encephalitis virus (JEV), a single-stranded, enveloped RNA virus, is a health concern across Asian countries, associated with severe neurological disorders, especially in children. Primarily, pigs, bats, and birds are the natural hosts for JEV, but humans are infected incidentally. JEV requires a few host proteins for its entry and replication inside the mammalian host cell. The endoplasmic reticulum (ER) plays a significant role in JEV genome replication and assembly. During this process, the ER undergoes stress due to its remodelling and accumulation of viral particles and unfolded proteins, leading to an unfolded protein response (UPR). Here, we review the overall strategy used by JEV to infect the host cell and various cytopathic effects caused by JEV infection. We also highlight the role of JEV structural proteins (SPs) and non-structural proteins (NSPs) at various stages of the JEV life cycle that are involved in up- and downregulation of different host proteins and are potentially relevant for developing efficient therapeutic drugs.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Akanksha Verma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Pardeep Yadav
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh 201310 India
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - S. S. Maitra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
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9
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Feng T, Zhang J, Chen Z, Pan W, Chen Z, Yan Y, Dai J. Glycosylation of viral proteins: Implication in virus-host interaction and virulence. Virulence 2022; 13:670-683. [PMID: 35436420 PMCID: PMC9037552 DOI: 10.1080/21505594.2022.2060464] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycans are among the most important cell molecular components. However, given their structural diversity, their functions have not been fully explored. Glycosylation is a vital post-translational modification for various proteins. Many bacteria and viruses rely on N-linked and O-linked glycosylation to perform critical biological functions. The diverse functions of glycosylation on viral proteins during viral infections, including Dengue, Zika, influenza, and human immunodeficiency viruses as well as coronaviruses have been reported. N-linked glycosylation is the most common form of protein modification, and it modulates folding, transportation and receptor binding. Compared to N-linked glycosylation, the functions of O-linked viral protein glycosylation have not been comprehensively evaluated. In this review, we summarize findings on viral protein glycosylation, with particular attention to studies on N-linked glycosylation in viral life cycles. This review informs the development of virus-specific vaccines or inhibitors.
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Affiliation(s)
- Tingting Feng
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jinyu Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Zhiqian Chen
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Wen Pan
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Zhengrong Chen
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
| | - Yongdong Yan
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
| | - Jianfeng Dai
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
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10
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Kumar S, Bhardwaj VK, Singh R, Das P, Purohit R. Identification of acridinedione scaffolds as potential inhibitor of DENV-2 C protein: An in silico strategy to combat dengue. J Cell Biochem 2022; 123:935-946. [PMID: 35315127 DOI: 10.1002/jcb.30237] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 12/22/2022]
Abstract
Dengue is a prominent viral disease transmitted by mosquitoes to humans that affects mainly tropical and subtropical countries worldwide. The global spread of dengue virus (DENV) is mainly occurred by Aedes aegypti and Aedes albopictus mosquitoes. The dengue virus serotypes-2 (DENV-2) is a widely prevalent serotype of DENV, that causes the hemorrhagic fever and bleeding in the mucosa, which can be fatal. In the life cycle of DENV-2, a structural capsid (DENV-2 C) protein forms the nucleocapsid assembly and bind to the viral progeny RNA. For DENV-2 maturation, the nucleocapsid is a vital component. We used virtual ligand screening to filter out the best in-house synthesized acridinedione analogs (DSPD molecules) that could efficiently bind to DENV-2 C protein. The molecular docking and dynamics simulations studies were performed to analyze the effect of DSPD molecules on DENV-2 C protein after binding. Our findings showed that DSPD molecules strongly interacted with DENV-2 C protein, as evident from molecular interactions and several time-dependent molecular dynamics-driven analyses. Moreover, this study was also supported by the thermodynamic binding free energy and steered molecular dynamics simulations. Therefore, we intend to suggest that the DSPD3 molecule could be used as a potential therapeutic molecule against dengue complications as compared to the cocrystallized inhibitor ST-148. However, further studies are required to demonstrate the ability of DSPD3 to induce DENV-2 C tetramer formation.
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Affiliation(s)
- Sachin Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vijay K Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Pralay Das
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.,Department of Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Biotechnology Division, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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11
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Mebus-Antunes NC, Ferreira WS, Barbosa GM, Neves-Martins TC, Weissmuller G, Almeida FCL, Da Poian AT. The interaction of dengue virus capsid protein with negatively charged interfaces drives the in vitro assembly of nucleocapsid-like particles. PLoS One 2022; 17:e0264643. [PMID: 35231063 PMCID: PMC8887749 DOI: 10.1371/journal.pone.0264643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/15/2022] [Indexed: 01/06/2023] Open
Abstract
Dengue virus (DENV) causes a major arthropod-borne viral disease, with 2.5 billion people living in risk areas. DENV consists in a 50 nm-diameter enveloped particle in which the surface proteins are arranged with icosahedral symmetry, while information about nucleocapsid (NC) structural organization is lacking. DENV NC is composed of the viral genome, a positive-sense single-stranded RNA, packaged by the capsid (C) protein. Here, we established the conditions for a reproducible in vitro assembly of DENV nucleocapsid-like particles (NCLPs) using recombinant DENVC. We analyzed NCLP formation in the absence or presence of oligonucleotides in solution using small angle X-ray scattering, Rayleigh light scattering as well as fluorescence anisotropy, and characterized particle structural properties using atomic force and transmission electron microscopy imaging. The experiments in solution comparing 2-, 5- and 25-mer oligonucleotides established that 2-mer is too small and 5-mer is sufficient for the formation of NCLPs. The assembly process was concentration-dependent and showed a saturation profile, with a stoichiometry of 1:1 (DENVC:oligonucleotide) molar ratio, suggesting an equilibrium involving DENVC dimer and an organized structure compatible with NCLPs. Imaging methods proved that the decrease in concentration to sub-nanomolar concentrations of DENVC allows the formation of regular spherical NCLPs after protein deposition on mica or carbon surfaces, in the presence as well as in the absence of oligonucleotides, in this latter case being surface driven. Altogether, the results suggest that in vitro assembly of DENV NCLPs depends on DENVC charge neutralization, which must be a very coordinated process to avoid unspecific aggregation. Our hypothesis is that a specific highly positive spot in DENVC α4-α4' is the main DENVC-RNA binding site, which is required to be firstly neutralized to allow NC formation.
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Affiliation(s)
- Nathane C. Mebus-Antunes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wellington S. Ferreira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Glauce M. Barbosa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais C. Neves-Martins
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto Weissmuller
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C. L. Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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12
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Farelo MA, Korrou-Karava D, Brooks KF, Russell TA, Maringer K, Mayerhofer PU. Dengue and Zika Virus Capsid Proteins Contain a Common PEX19-Binding Motif. Viruses 2022; 14:v14020253. [PMID: 35215846 PMCID: PMC8874546 DOI: 10.3390/v14020253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses such as dengue virus (DENV) and Zika virus (ZIKV) have evolved sophisticated mechanisms to suppress the host immune system. For instance, flavivirus infections were found to sabotage peroxisomes, organelles with an important role in innate immunity. The current model suggests that the capsid (C) proteins of DENV and ZIKV downregulate peroxisomes, ultimately resulting in reduced production of interferons by interacting with the host protein PEX19, a crucial chaperone in peroxisomal biogenesis. Here, we aimed to explore the importance of peroxisomes and the role of C interaction with PEX19 in the flavivirus life cycle. By infecting cells lacking peroxisomes we show that this organelle is required for optimal DENV replication. Moreover, we demonstrate that DENV and ZIKV C bind PEX19 through a conserved PEX19-binding motif, which is also commonly found in cellular peroxisomal membrane proteins (PMPs). However, in contrast to PMPs, this interaction does not result in the targeting of C to peroxisomes. Furthermore, we show that the presence of C results in peroxisome loss due to impaired peroxisomal biogenesis, which appears to occur by a PEX19-independent mechanism. Hence, these findings challenge the current model of how flavivirus C might downregulate peroxisomal abundance and suggest a yet unknown role of peroxisomes in flavivirus biology.
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Affiliation(s)
- Mafalda A. Farelo
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Despoina Korrou-Karava
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Katrina F. Brooks
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Tiffany A. Russell
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Kevin Maringer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Correspondence: (K.M.); (P.U.M.)
| | - Peter U. Mayerhofer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- Correspondence: (K.M.); (P.U.M.)
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13
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Ortlieb LO, Caruso ÍP, Mebus-Antunes NC, Da Poian AT, Petronilho EDC, Figueroa-Villar JD, Nascimento CJ, Almeida FCL. Searching for drug leads targeted to the hydrophobic cleft of dengue virus capsid protein. J Enzyme Inhib Med Chem 2021; 37:287-298. [PMID: 34894959 PMCID: PMC8667904 DOI: 10.1080/14756366.2021.2004591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We synthesised and screened 18 aromatic derivatives of guanylhydrazones and oximes aromatic for their capacity to bind to dengue virus capsid protein (DENVC). The intended therapeutic target was the hydrophobic cleft of DENVC, which is a region responsible for its anchoring in lipid droplets in the infected cells. The inhibition of this process completely suppresses virus infectivity. Using NMR, we describe five compounds able to bind to the α1-α2 interface in the hydrophobic cleft. Saturation transfer difference experiments showed that the aromatic protons of the ligands are important for the interaction with DENVC. Fluorescence binding isotherms indicated that the selected compounds bind at micromolar affinities, possibly leading to binding-induced conformational changes. NMR-derived docking calculations of ligands showed that they position similarly in the hydrophobic cleft. Cytotoxicity experiments and calculations of in silico drug properties suggest that these compounds may be promising candidates in the search for antivirals targeting DENVC.
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Affiliation(s)
- Liliane O Ortlieb
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil.,Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ícaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Elaine da C Petronilho
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil
| | | | - Claudia J Nascimento
- Department of Natural Sciences, Institute of Biosciences, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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14
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Guo Y, Yao C, Cheng K, Wu Q, Xu G, Jiang L, Li C. NMR backbone resonance assignment of Japanese encephalitis virus capsid protein. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:403-407. [PMID: 34170495 DOI: 10.1007/s12104-021-10037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Japanese encephalitis virus (JEV) is a flavivirus in the same family as West Nile virus (WNV), dengue virus (DENV) and yellow fever virus (YFV), which are transmitted by mosquitoes. About 68 thousand people are infected with JEV every year. In many Asian countries, JEV is the main cause of viral encephalitis. There are no specific antiviral drugs for Japanese encephalitis. Capsid protein C is the core protein of virus particles. Many studies have revealed that capsid protein C plays an important role in the life cycle of flaviviruses. Although the structure of JEV capsid protein (JEVC) has been determined by X-ray crystallography, the mechanism of how it assembles into an inner core to encapsulate the virus genome remains elusive. What's more, the disordered N-terminal region that is reported to affect its assembly is absent in the crystal structure. NMR spectroscopy has distinct advantages over other technologies in the characterization of conformational dynamics. Here we report the backbone 1H, 13C and 15N chemical shift assignments of JEVC by heteronuclear multidimensional spectroscopy and predict its secondary structure in solution using TALOS+.
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Affiliation(s)
- Yuting Guo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Chendie Yao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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15
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Effect of siRNA targeting dengue virus genes on replication of dengue virus: an in vitro experimental study. Virusdisease 2021; 32:518-525. [PMID: 34485626 PMCID: PMC8397848 DOI: 10.1007/s13337-021-00700-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
Dengue is a notorious viral infection, which affects a large segment of world populations in absence of vaccines and anti-viral treatment. The current study evaluates role of effective siRNA in dengue virus replication. Eight siRNA were synthesized against five different genes (Capsid, CprM, NS1, NS3 and NS5) of all serotypes of dengue virus. All serotype of DV were transfected with all synthesized siRNA in vitro, using BHK-21 cell lines. Culture fluid from test and control was tested by Real time PCR for CT value comparison in siRNA treated cell line (test) and untreated cell line (controls). Percent knockdown (%KD) was calculated by ∆∆CT methods to know the difference in test and control CT value. It was found that siRNA targeted against capsid gene worked best and showed inhibition of all four DV serotypes. DV-1, DV-2, DV-3 and DV-4 showed 93.8%, 99.3%, 87.5% and 93.8% knock down (%KD) respectively by siRNA targeted against capsid gene. Additionally, Si2 (target CprM gene 60-899) and Si 6 (target NS1 gene 3007-3025) were also showing inhibition of replication. Most serotypes of DV (with few exceptions) were not inhibited by siRNA targeted against NS-1, NS-3, and NS-5 genes. Animal studies using siRNAs are warranted to establish their therapeutic role.
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16
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Sangiambut S, Promphet N, Chaiyaloom S, Puttikhunt C, Avirutnan P, Kasinrerk W, Sittisombut N, Malasit P. Increased capsid oligomerization is deleterious to dengue virus particle production. J Gen Virol 2021; 102. [PMID: 34410905 DOI: 10.1099/jgv.0.001635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The capsid protein (C) of dengue virus is required for viral infectivity as it packages viral RNA genome into infectious particles. C exists as a homodimer that forms via hydrophobic interactions between the α2 and α4 helices of monomers. To identify C region(s) important for virus particle production, a complementation system was employed in which single-round infectious particles are generated by trans-encapsidation of a viral C-deleted genome by recombinant C expressed in mosquito cells. Mutants harbouring a complete α3 deletion, or a dual Ile65-/Trp69-to-Ala substitution in the α3 helix, exhibited reduced production of infectious virus. Unexpectedly, higher proportions of oligomeric C were detected in cells expressing both mutated forms as compared with the wild-type counterpart, indicating that the α3 helix, through its internal hydrophobic residues, may down-modulate oligomerization of C during particle formation. Compared with wild-type C, the double Ile65-/Trp69 to Ala mutations appeared to hamper viral infectivity but not C and genomic RNA incorporation into the pseudo-infectious virus particles, suggesting that increased C oligomerization may impair DENV replication at the cell entry step.
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Affiliation(s)
- Sutha Sangiambut
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Natcha Promphet
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Suwipa Chaiyaloom
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chunya Puttikhunt
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Panisadee Avirutnan
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Watchara Kasinrerk
- Biomedical Technology Research Center National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nopporn Sittisombut
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Prida Malasit
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Bangkok 12120, Thailand.,Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.,Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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17
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Saito A, Shofa M, Ode H, Yumiya M, Hirano J, Okamoto T, Yoshimura SH. How Do Flaviviruses Hijack Host Cell Functions by Phase Separation? Viruses 2021; 13:v13081479. [PMID: 34452345 PMCID: PMC8402827 DOI: 10.3390/v13081479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Viral proteins interact with different sets of host cell components throughout the viral life cycle and are known to localize to the intracellular membraneless organelles (MLOs) of the host cell, where formation/dissolution is regulated by phase separation of intrinsically disordered proteins and regions (IDPs/IDRs). Viral proteins are rich in IDRs, implying that viruses utilize IDRs to regulate phase separation of the host cell organelles and augment replication by commandeering the functions of the organelles and/or sneaking into the organelles to evade the host immune response. This review aims to integrate current knowledge of the structural properties and intracellular localizations of viral IDPs to understand viral strategies in the host cell. First, the properties of viral IDRs are reviewed and similarities and differences with those of eukaryotes are described. The higher IDR content in viruses with smaller genomes suggests that IDRs are essential characteristics of viral proteins. Then, the interactions of the IDRs of flaviviruses with the MLOs of the host cell are investigated with emphasis on the viral proteins localized in the nucleoli and stress granules. Finally, the possible roles of viral IDRs in regulation of the phase separation of organelles and future possibilities for antiviral drug development are discussed.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan;
| | - Maho Yumiya
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Junki Hirano
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Toru Okamoto
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
- Center for Infectious Diseases Education and Research, Osaka University, Osaka 565-0871, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Shige H. Yoshimura
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
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18
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Zhang X, Zhang Y, Jia R, Wang M, Yin Z, Cheng A. Structure and function of capsid protein in flavivirus infection and its applications in the development of vaccines and therapeutics. Vet Res 2021; 52:98. [PMID: 34193256 PMCID: PMC8247181 DOI: 10.1186/s13567-021-00966-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 01/03/2023] Open
Abstract
Flaviviruses are enveloped single positive-stranded RNA viruses. The capsid (C), a structural protein of flavivirus, is dimeric and alpha-helical, with several special structural and functional features. The functions of the C protein go far beyond a structural role in virions. It is not only responsible for encapsidation to protect the viral RNA but also able to interact with various host proteins to promote virus proliferation. Therefore, the C protein plays an important role in infected host cells and the viral life cycle. Flaviviruses have been shown to affect the health of humans and animals. Thus, there is an urgent need to effectively control flavivirus infections. The structure of the flavivirus virion has been determined, but there is relatively little information about the function of the C protein. Hence, a greater understanding of the role of the C protein in viral infections will help to discover novel antiviral strategies and provide a promising starting point for the further development of flavivirus vaccines or therapeutics.
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Affiliation(s)
- Xingcui Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Yanting Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
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19
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Li H, Zhang K, Binzel DW, Shlyakhtenko LS, Lyubchenko YL, Chiu W, Guo P. RNA nanotechnology to build a dodecahedral genome of single-stranded RNA virus. RNA Biol 2021; 18:2390-2400. [PMID: 33845711 DOI: 10.1080/15476286.2021.1915620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The quest for artificial RNA viral complexes with authentic structure while being non-replicative is on its way for the development of viral vaccines. RNA viruses contain capsid proteins that interact with the genome during morphogenesis. The sequence and properties of the protein and genome determine the structure of the virus. For example, the Pariacoto virus ssRNA genome assembles into a dodecahedron. Virus-inspired nanotechnology has progressed remarkably due to the unique structural and functional properties of viruses, which can inspire the design of novel nanomaterials. RNA is a programmable biopolymer able to self-assemble sophisticated 3D structures with rich functionalities. RNA dodecahedrons mimicking the Pariacoto virus quasi-icosahedral genome structures were constructed from both native and 2'-F modified RNA oligos. The RNA dodecahedron easily self-assembled using the stable pRNA three-way junction of bacteriophage phi29 as building blocks. The RNA dodecahedron cage was further characterized by cryo-electron microscopy and atomic force microscopy, confirming the spontaneous and homogenous formation of the RNA cage. The reported RNA dodecahedron cage will likely provide further studies on the mechanisms of interaction of the capsid protein with the viral genome while providing a template for further construction of the viral RNA scaffold to add capsid proteins for the assembly of the viral nucleocapsid as a model. Understanding the self-assembly and RNA folding of this RNA cage may offer new insights into the 3D organization of viral RNA genomes. The reported RNA cage also has the potential to be explored as a novel virus-inspired nanocarrier.
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Affiliation(s)
- Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kaiming Zhang
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Lyudmila S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Wah Chiu
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA.,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
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20
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Neves-Martins TC, Mebus-Antunes NC, Caruso IP, Almeida FCL, Da Poian AT. Unique structural features of flaviviruses' capsid proteins: new insights on structure-function relationship. Curr Opin Virol 2021; 47:106-112. [PMID: 33721656 DOI: 10.1016/j.coviro.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 10/21/2022]
Abstract
The Flaviviridae family comprises important human pathogens, including Dengue, Zika, West Nile, Yellow Fever and Japanese Encephalitis viruses. The viral genome, a positive-sense single-stranded RNA, is packaged by a single protein, the capsid protein, which is a small and highly basic protein that form intertwined homodimers in solution. Atomic-resolution structures of four flaviviruses capsid proteins were solved either in solution by nuclear magnetic resonance spectroscopy, or after protein crystallization by X-ray diffraction. Analyses of these structures revealed very particular properties, namely (i) the predominance of quaternary contacts maintaining the structure; (ii) a highly electropositive surface throughout the protein; and (iii) a flexible helix (α1). The goal of this review is to discuss the role of these features in protein structure-function relationship.
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Affiliation(s)
- Thais C Neves-Martins
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000, São José do Rio Preto, SP, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
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21
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Dey D, Poudyal S, Rehman A, Hasan SS. Structural and biochemical insights into flavivirus proteins. Virus Res 2021; 296:198343. [PMID: 33607183 DOI: 10.1016/j.virusres.2021.198343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Flaviviruses are the fastest spreading arthropod-borne viruses that cause severe symptoms such as hepatitis, hemorrhagic fever, encephalitis, and congenital deformities. Nearly 40 % of the entire human population is at risk of flavivirus epidemics. Yet, effective vaccination is restricted only to a few flaviviruses such as yellow fever and Japanese encephalitis viruses, and most recently for select cases of dengue virus infections. Despite the global spread of dengue virus, and emergence of new threats such as Zika virus and a new genotype of Japanese encephalitis virus, insights into flavivirus targets for potentially broad-spectrum vaccination are limited. In this review article, we highlight biochemical and structural differences in flavivirus proteins critical for virus assembly and host interactions. A comparative sequence analysis of pH-responsive properties of viral structural proteins identifies trends in conservation of complementary acidic-basic character between interacting viral structural proteins. This is highly relevant to the understanding of pH-sensitive differences in virus assembly in organelles such as neutral ER and acidic Golgi. Surface residues in viral interfaces identified by structural approaches are shown to demonstrate partial conservation, further reinforcing virus-specificity in assembly and interactions with host proteins. A comparative analysis of epitope conservation in emerging flaviviruses identifies therapeutic antibody candidates that have potential as broad spectrum anti-virals, thus providing a path towards development of vaccines.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - Shishir Poudyal
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette IN 47907, USA
| | - Asma Rehman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, 22. S. Greene St. Baltimore MD 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, 9600 Gudelsky Drive, Rockville MD 20850, USA.
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22
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Orba Y, Matsuno K, Nakao R, Kryukov K, Saito Y, Kawamori F, Loza Vega A, Watanabe T, Maemura T, Sasaki M, Hall WW, Hall RA, Pereira JA, Nakagawa S, Sawa H. Diverse mosquito-specific flaviviruses in the Bolivian Amazon basin. J Gen Virol 2021; 102. [PMID: 33416463 DOI: 10.1099/jgv.0.001518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The genus Flavivirus includes a range of mosquito-specific viruses in addition to well-known medically important arboviruses. Isolation and comprehensive genomic analyses of viruses in mosquitoes collected in Bolivia resulted in the identification of three novel flavivirus species. Psorophora flavivirus (PSFV) was isolated from Psorophora albigenu. The coding sequence of the PSFV polyprotein shares 60 % identity with that of the Aedes-associated lineage II insect-specific flavivirus (ISF), Marisma virus. Isolated PSFV replicates in both Aedes albopictus- and Aedes aegypti-derived cells, but not in mammalian Vero or BHK-21 cell lines. Two other flaviviruses, Ochlerotatus scapularis flavivirus (OSFV) and Mansonia flavivirus (MAFV), which were identified from Ochlerotatus scapularis and Mansonia titillans, respectively, group with the classical lineage I ISFs. The protein coding sequences of these viruses share only 60 and 40 % identity with the most closely related of known lineage I ISFs, including Xishuangbanna aedes flavivirus and Sabethes flavivirus, respectively. Phylogenetic analysis suggests that MAFV is clearly distinct from the groups of the current known Culicinae-associated lineage I ISFs. Interestingly, the predicted amino acid sequence of the MAFV capsid protein is approximately two times longer than that of any of the other known flaviviruses. Our results indicate that flaviviruses with distinct features can be found at the edge of the Bolivian Amazon basin at sites that are also home to dense populations of human-biting mosquitoes.
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Affiliation(s)
- Yasuko Orba
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kirill Kryukov
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
| | - Yumi Saito
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Fumihiko Kawamori
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - Ariel Loza Vega
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tadashi Maemura
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - William W Hall
- Global Virus Network, Baltimore, Maryland, USA.,Centre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Juan Antonio Pereira
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, Maryland, USA.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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23
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Barnard TR, Abram QH, Lin QF, Wang AB, Sagan SM. Molecular Determinants of Flavivirus Virion Assembly. Trends Biochem Sci 2021; 46:378-390. [PMID: 33423940 DOI: 10.1016/j.tibs.2020.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/07/2023]
Abstract
Virion assembly is an important step in the life cycle of all viruses. For viruses of the Flavivirus genus, a group of enveloped positive-sense RNA viruses, the assembly step represents one of the least understood processes in the viral life cycle. While assembly is primarily driven by the viral structural proteins, recent studies suggest that several nonstructural proteins also play key roles in coordinating the assembly and packaging of the viral genome. This review focuses on describing recent advances in our understanding of flavivirus virion assembly, including the intermolecular interactions between the viral structural (capsid) and nonstructural proteins (NS2A and NS2B-NS3), host factors, as well as features of the viral genomic RNA required for efficient flavivirus virion assembly.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Quinn H Abram
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Qi Feng Lin
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Alex B Wang
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec H3G 1Y6, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
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24
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Yong XE, Raghuvamsi PV, Anand GS, Wohland T, Sharma KK. Dengue virus strain 2 capsid protein switches the annealing pathway and reduces intrinsic dynamics of the conserved 5' untranslated region. RNA Biol 2021; 18:718-731. [PMID: 33406991 PMCID: PMC8078513 DOI: 10.1080/15476286.2020.1860581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements using chaperone activity. However, the role of DENV2C during the interaction of RNA elements in the conserved 5' untranslated region (5'UTR) to the 3' untranslated region (3'UTR) is still unclear. Thus, we investigated the effect of DENV2C on the annealing mechanism of two RNA hairpin elements from the 5'UTR to their complementary sequences during (+)/(-) ds-RNAformation and (+) RNA circularization. DENV2C was found to switch the annealing pathway for RNA elements involved in (+)/(-) ds-RNA formation, but not for RNA elements related to (+) RNA circularization. In addition, we also determined that DENV2C modulates intrinsic dynamics and reduces kinetically trapped unfavourable conformations of the 5'UTR sequence. Thus, our results provide mechanistic insights by which DENV2C chaperones the interactions between RNA elements at the 5' and 3' ends during genome recombination, a prerequisite for DENV replication.
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Affiliation(s)
- Xin Ee Yong
- NUS Graduate School for integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | | | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kamal K Sharma
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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25
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Abstract
The flavivirus genus encompasses more than 75 unique viruses, including dengue virus which accounts for almost 390 million global infections annually. Flavivirus infection can result in a myriad of symptoms ranging from mild rash and flu-like symptoms, to severe encephalitis and even hemorrhagic fever. Efforts to combat the impact of these viruses have been hindered due to limited antiviral drug and vaccine development. However, the advancement of knowledge in the structural biology of flaviviruses over the last 25 years has produced unique perspectives for the identification of potential therapeutic targets. With particular emphasis on the assembly and maturation stages of the flavivirus life cycle, it is the goal of this review to comparatively analyze the structural similarities between flaviviruses to provide avenues for new research and innovation.
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Affiliation(s)
- Conrrad M R Nicholls
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States; Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States.
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26
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Silva NM, Santos NC, Martins IC. Dengue and Zika Viruses: Epidemiological History, Potential Therapies, and Promising Vaccines. Trop Med Infect Dis 2020; 5:E150. [PMID: 32977703 PMCID: PMC7709709 DOI: 10.3390/tropicalmed5040150] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/05/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
Dengue virus (DENV), which can lead to fatal hemorrhagic fever, affects 390 million people worldwide. The closely related Zika virus (ZIKV) causes microcephaly in newborns and Guillain-Barré syndrome in adults. Both viruses are mostly transmitted by Aedes albopictus and Aedes aegypti mosquitoes, which, due to globalization of trade and travel alongside climate change, are spreading worldwide, paving the way to DENV and ZIKV transmission and the occurrence of new epidemics. Local outbreaks have already occurred in temperate climates, even in Europe. As there are no specific treatments, these viruses are an international public health concern. Here, we analyze and discuss DENV and ZIKV outbreaks history, clinical and pathogenesis features, and modes of transmission, supplementing with information on advances on potential therapies and restraining measures. Taking advantage of the knowledge of the structure and biological function of the capsid (C) protein, a relatively conserved protein among flaviviruses, within a genus that includes DENV and ZIKV, we designed and patented a new drug lead, pep14-23 (WO2008/028939A1). It was demonstrated that it inhibits the interaction of DENV C protein with the host lipid system, a process essential for viral replication. Such an approach can be used to develop new therapies for related viruses, such as ZIKV.
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Affiliation(s)
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
| | - Ivo C. Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
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27
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Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020; 12:v12091057. [PMID: 32972018 PMCID: PMC7551563 DOI: 10.3390/v12091057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: ; Tel.: +1-607-255-0151
| | | | - Ian R. Tibbetts
- School of Biological Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
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28
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Araujo SC, Pereira LR, Alves RPS, Andreata-Santos R, Kanno AI, Ferreira LCS, Gonçalves VM. Anti-Flavivirus Vaccines: Review of the Present Situation and Perspectives of Subunit Vaccines Produced in Escherichia coli. Vaccines (Basel) 2020; 8:vaccines8030492. [PMID: 32878023 PMCID: PMC7564369 DOI: 10.3390/vaccines8030492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 12/14/2022] Open
Abstract
This article aims to review the present status of anti-flavivirus subunit vaccines, both those at the experimental stage and those already available for clinical use. Aspects regarding development of vaccines to Yellow Fever virus, (YFV), Dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) are highlighted, with particular emphasis on purified recombinant proteins generated in bacterial cells. Currently licensed anti-flavivirus vaccines are based on inactivated, attenuated, or virus-vector vaccines. However, technological advances in the generation of recombinant antigens with preserved structural and immunological determinants reveal new possibilities for the development of recombinant protein-based vaccine formulations for clinical testing. Furthermore, novel proposals for multi-epitope vaccines and the discovery of new adjuvants and delivery systems that enhance and/or modulate immune responses can pave the way for the development of successful subunit vaccines. Nonetheless, advances in this field require high investments that will probably not raise interest from private pharmaceutical companies and, therefore, will require support by international philanthropic organizations and governments of the countries more severely stricken by these viruses.
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Affiliation(s)
- Sergio C. Araujo
- Laboratory of Vaccine Development, Instituto Butantan, São Paulo–SP 05503-900, Brazil; (S.C.A.); (A.I.K.)
| | - Lennon R. Pereira
- Laboratory of Vaccine Development, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo–SP 05508-000, Brazil; (L.R.P.); (R.P.S.A.); (R.A.-S.)
| | - Rubens P. S. Alves
- Laboratory of Vaccine Development, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo–SP 05508-000, Brazil; (L.R.P.); (R.P.S.A.); (R.A.-S.)
| | - Robert Andreata-Santos
- Laboratory of Vaccine Development, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo–SP 05508-000, Brazil; (L.R.P.); (R.P.S.A.); (R.A.-S.)
| | - Alex I. Kanno
- Laboratory of Vaccine Development, Instituto Butantan, São Paulo–SP 05503-900, Brazil; (S.C.A.); (A.I.K.)
| | - Luis Carlos S. Ferreira
- Laboratory of Vaccine Development, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo–SP 05508-000, Brazil; (L.R.P.); (R.P.S.A.); (R.A.-S.)
- Correspondence: (L.C.S.F.); (V.M.G.)
| | - Viviane M. Gonçalves
- Laboratory of Vaccine Development, Instituto Butantan, São Paulo–SP 05503-900, Brazil; (S.C.A.); (A.I.K.)
- Correspondence: (L.C.S.F.); (V.M.G.)
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29
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West Nile Virus: An Update on Pathobiology, Epidemiology, Diagnostics, Control and "One Health" Implications. Pathogens 2020; 9:pathogens9070589. [PMID: 32707644 PMCID: PMC7400489 DOI: 10.3390/pathogens9070589] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
West Nile virus (WNV) is an important zoonotic flavivirus responsible for mild fever to severe, lethal neuroinvasive disease in humans, horses, birds, and other wildlife species. Since its discovery, WNV has caused multiple human and animal disease outbreaks in all continents, except Antarctica. Infections are associated with economic losses, mainly due to the cost of treatment of infected patients, control programmes, and loss of animals and animal products. The pathogenesis of WNV has been extensively investigated in natural hosts as well as in several animal models, including rodents, lagomorphs, birds, and reptiles. However, most of the proposed pathogenesis hypotheses remain contentious, and much remains to be elucidated. At the same time, the unavailability of specific antiviral treatment or effective and safe vaccines contribute to the perpetuation of the disease and regular occurrence of outbreaks in both endemic and non-endemic areas. Moreover, globalisation and climate change are also important drivers of the emergence and re-emergence of the virus and disease. Here, we give an update of the pathobiology, epidemiology, diagnostics, control, and “One Health” implications of WNV infection and disease.
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30
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Kaufman F, Dostálková A, Pekárek L, Thanh TD, Kapisheva M, Hadravová R, Bednárová L, Novotný R, Křížová I, Černý J, Grubhoffer L, Ruml T, Hrabal R, Rumlová M. Characterization and in vitro assembly of tick-borne encephalitis virus C protein. FEBS Lett 2020; 594:1989-2004. [PMID: 32510601 DOI: 10.1002/1873-3468.13857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 01/10/2023]
Abstract
Tick-borne encephalitis virus (TBEV), a member of flaviviruses, represents a serious health threat by causing human encephalitis mainly in central and eastern Europe, Russia, and northeastern Asia. As no specific therapy is available, there is an urgent need to understand all steps of the TBEV replication cycle at the molecular level. One of the critical events is the packaging of flaviviral genomic RNA by TBEV C protein to form a nucleocapsid. We purified recombinant TBEV C protein and used a combination of physical-chemical approaches, such as size-exclusion chromatography, circular dichroism, NMR spectroscopies, and transmission electron microscopy, to analyze its structural stability and its ability to dimerize/oligomerize. We compared the ability of TBEV C protein to assemble in vitro into a nucleocapsid-like structure with that of dengue C protein.
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Affiliation(s)
- Filip Kaufman
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Lukáš Pekárek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Tung Dinh Thanh
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Marina Kapisheva
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Romana Hadravová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry (IOCB) Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry (IOCB) Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radim Novotný
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic.,NMR Laboratory, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Ivana Křížová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Jiří Černý
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Prague, Czech Republic
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Richard Hrabal
- NMR Laboratory, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
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31
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Understanding Flavivirus Capsid Protein Functions: The Tip of the Iceberg. Pathogens 2020; 9:pathogens9010042. [PMID: 31948047 PMCID: PMC7168633 DOI: 10.3390/pathogens9010042] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/18/2022] Open
Abstract
Flaviviruses are enveloped positive-sense single-stranded RNA arboviruses, infectious to humans and many other animals and are transmitted primarily via tick or mosquito vectors. Capsid is the primary structural protein to interact with viral genome within virus particles and is therefore necessary for efficient packaging. However, in cells, capsid interacts with many proteins and nucleic acids and we are only beginning to understand the broad range of functions of flaviviral capsids. It is known that capsid dimers interact with the membrane of lipid droplets, aiding in both viral packaging and storage of capsid prior to packaging. However, capsid dimers can bind a range of nucleic acid templates in vitro, and likely interact with a range of targets during the flavivirus lifecycle. Capsid may interact with host RNAs, resulting in altered RNA splicing and RNA transcription. Capsid may also bind short interfering-RNAs and has been proposed to sequester these species to protect flaviviruses from the invertebrate siRNA pathways. Capsid can also be found in the nucleolus, where it wreaks havoc on ribosome biogenesis. Here we review flavivirus capsid structure, nucleic acid interactions and how these give rise to multiple functions. We also discuss how these features might be exploited either in the design of effective antivirals or novel vaccine strategies.
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32
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Rana J, Burrone OR. DENV2 Pseudoviral Particles with Unprocessed Capsid Protein Are Assembled and Infectious. Viruses 2019; 12:v12010027. [PMID: 31881703 PMCID: PMC7019998 DOI: 10.3390/v12010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/06/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022] Open
Abstract
Proteolytic processing of flavivirus polyprotein is a uniquely controlled process. To date, the sequential cleavage of the capsid anchor sequence at the junction of C-PrM has been considered essential for the production of flaviviruses. In this study, we used two experimental approaches to show the effect of unprocessed capsid on the production and infectivity of dengue virus 2 (DENV2) pseudoviral particles. The results showed that (1) both mature and unprocessed capsids of DENV2 were equally efficient in the viral RNA packaging and also in the assembly of infective particles; (2) DENV2 variants, in which the viral and host mediated cleavage of Ca peptide were independent, produced significantly higher levels of infective particles. Overall, this study demonstrated that unlike other flaviviruses, DENV2 capsid does not require a cleavable Ca sequence, and the sequential cleavage is not an obligatory requirement for the morphogenesis of infective pseudoviral particles.
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Affiliation(s)
- Jyoti Rana
- Correspondence: (J.R.); (O.R.B.); Tel.: +39-040-3757314 (J.R. & O.R.B.)
| | - Oscar R. Burrone
- Correspondence: (J.R.); (O.R.B.); Tel.: +39-040-3757314 (J.R. & O.R.B.)
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33
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Nasar S, Rashid N, Iftikhar S. Dengue proteins with their role in pathogenesis, and strategies for developing an effective anti-dengue treatment: A review. J Med Virol 2019; 92:941-955. [PMID: 31784997 DOI: 10.1002/jmv.25646] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022]
Abstract
Dengue virus is an arbovirus belonging to class Flaviviridae Its clinical manifestation ranges from asymptomatic to extreme conditions (dengue hemorrhagic fever/dengue shock syndrome). A lot of research has been done on this ailment, yet there is no effective treatment available for the disease. This review provides the systematic understanding of all dengue proteins, role of its structural proteins (C-protein, E-protein, prM) in virus entry, assembly, and secretion in host cell, and nonstructural proteins (NS1, NS2a, NS2b, NS3, NS4a, NS4b, and NS5) in viral assembly, replication, and immune evasion during dengue progression and pathogenesis. Furthermore, the review has highlighted the controversies related to the only commercially available dengue vaccine, that is, Dengvaxia, and the risk associated with it. Lastly, it provides an insight regarding various approaches for developing an effective anti-dengue treatment.
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Affiliation(s)
- Sitara Nasar
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Saima Iftikhar
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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Faheem M, Barbosa Lima JC, Jamal SB, Silva PA, Barbosa JARG. An insight into dengue virus proteins as potential drug/vaccine targets. Future Virol 2019. [DOI: 10.2217/fvl-2019-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue virus (DENV) is an arbovirus that belongs to family flaviviridae. Its genome is composed of a single stranded RNA molecule that encodes a single polyprotein. The polyprotein is processed by viral and cellular proteases to generate ten viral proteins. There are four antigenically distinct serotypes of DENV (DENV1, DENV2, DENV3 and DENV4), which are genetically related. Although protein variability is a major problem in dengue treatment, the functional and structural studies of individual proteins are equally important in treatment development. The data accumulated on dengue proteins are significant to provide detailed understanding of viral infection, replication, host-immune evasion and pathogenesis. In this review, we summarized the detailed current knowledge about DENV proteins.
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Affiliation(s)
- Muhammad Faheem
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - Jônatas Cunha Barbosa Lima
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, The Mall road, Rawalpindi, Punjab 46000, Pakistan
| | - Paula Andreia Silva
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - João Alexandre Ribeiro Gonçalves Barbosa
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
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Faustino AF, Martins AS, Karguth N, Artilheiro V, Enguita FJ, Ricardo JC, Santos NC, Martins IC. Structural and Functional Properties of the Capsid Protein of Dengue and Related Flavivirus. Int J Mol Sci 2019; 20:E3870. [PMID: 31398956 PMCID: PMC6720645 DOI: 10.3390/ijms20163870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
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Affiliation(s)
- André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nina Karguth
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Vanessa Artilheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Joana C Ricardo
- Centro de Química-Física Molecular, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
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Prasasty VD, Grazzolie K, Rosmalena R, Yazid F, Ivan FX, Sinaga E. Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches. Microorganisms 2019; 7:E226. [PMID: 31370224 PMCID: PMC6722788 DOI: 10.3390/microorganisms7080226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain-Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine.
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Affiliation(s)
- Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia.
| | - Karel Grazzolie
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Rosmalena Rosmalena
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fatmawaty Yazid
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fransiskus Xaverius Ivan
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Ernawati Sinaga
- Faculty of Biology, Universitas Nasional, Jakarta 12520, Indonesia
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Poonsiri T, Wright GSA, Solomon T, Antonyuk SV. Crystal Structure of the Japanese Encephalitis Virus Capsid Protein. Viruses 2019; 11:E623. [PMID: 31284608 PMCID: PMC6669762 DOI: 10.3390/v11070623] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/29/2022] Open
Abstract
Japanese encephalitis (JE) is inflammation and swelling of the brain caused by the JE virus (JEV), a mosquito-borne member of the Flavivirus family. There are around 68,000 JE cases worldwide each year, many of which result in permanent brain damage and death. There is no specific treatment for JE. Here we present the crystal structure of the JEV capsid protein, a potential drug target, at 1.98 Å, and compare it to other flavivirus capsid proteins. The JEV capsid has a helical secondary structure (α helixes 1-4) and a similar protein fold to the dengue virus (DENV), the West Nile virus (WNV), and the Zika virus (ZIKV) capsid proteins. It forms a homodimer by antiparallel pairing with another subunit (') through α-helix 1-1', 2-2', and 4-4' interactions. This dimeric form is believed to be the building block of the nucleocapsid. The flexibility of the N-terminal α helix-1 allows the formation of closed and open conformations with possible functional importance. The basic C-terminal pairing of α4-4' forms a coiled-coil-like structure, indicating possible nucleic acid binding functionality. However, a comparison with other nucleic acid interacting domains indicates that homodimerization would preclude binding. This is the first JEV capsid protein to be described and is an addition to the structural biology of the Flavivirus.
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Affiliation(s)
- Thanalai Poonsiri
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK
- Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Gareth S A Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK
| | - Tom Solomon
- Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
- Walton Centre NHS Foundation Trust, L9 7LJ Liverpool, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK.
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Figueira-Mansur J, Aguilera EA, Stoque RM, Ventura GT, Mohana-Borges R. Mutations in the dimer interfaces of the dengue virus capsid protein affect structural stability and impair RNA-capsid interaction. Sci Rep 2019; 9:2829. [PMID: 30808916 PMCID: PMC6391532 DOI: 10.1038/s41598-019-39185-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/08/2019] [Indexed: 11/09/2022] Open
Abstract
The dengue virus 2 capsid protein (DENV2C) plays a primary structural role in the protection of the viral genome and is crucial for nucleocapsid assembly. In this study, we generated single mutants of DENV2C at L50 and L54 residues of the α2 helix, which was shown to interfere with the integration of the capsid into lipid droplets, and at residues L81 and I88 located in the α4 helix, which was shown to affect viral assembly. We demonstrated that the oligomeric states of DENV2C and its mutants exist primarily in the dimeric state in solution. All single-point mutations introduced in DENV2C promoted reduction in protein stability, an effect that was more pronounced for the L81N and I88N mutants, but not protein unfolding. All the single-point mutations affected the ability of DEN2C to interact with RNA. We concluded that mutations in the α2-α2' and α4-α4' dimer interfaces of DENV2C affect the structural stability of the protein and impair RNA-capsid interaction. These effects were more pronounced for mutations at the L81 and I88 residues in the α4 helix. These results indicate the importance of the α4-α4' dimer interface, which could be studied as a potential target for drug design in the future.
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Affiliation(s)
- Janaina Figueira-Mansur
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Estefania A Aguilera
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael M Stoque
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo T Ventura
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Lazo L, Valdes I, Guillén G, Hermida L, Gil L. Aiming at the heart: the capsid protein of dengue virus as a vaccine candidate. Expert Rev Vaccines 2019; 18:161-173. [PMID: 30677305 DOI: 10.1080/14760584.2019.1574575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Dengue fever remains as a health problem worldwide. Although Dengvaxia®, was registered in several countries, the results after the immunization of people suggest an increase of risk in non-immune persons and children younger than 9 years old. No other vaccine is registered so far, thus the development of a safe and effective vaccine continues to be a priority for the WHO and the scientific community. AREAS COVERED This work reviews the structural and antigenic properties of the capsid protein of Dengue virus, along with results of studies performed to assess the immunogenicity and protective capacity in animals of vaccine candidates based on this protein. EXPERT OPINION The generation of a memory cellular immune response alone, after vaccination against Dengue virus, could be advantageous, as there would not be risk of increasing viral infectivity through sub-neutralizing antibodies. However, it is improbable to achieving sterilizing immunity. In this scenario, an infection could stablished but without the appearance of the severe disease. The cell-mediated immunity should keep the virus at bay. The capsid protein induces a protective immune response in animals without the induction of virus-binding antibodies. Vaccine candidates based on this protein could be an attractive strategy to induce protection against the severe Dengue disease.
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Affiliation(s)
- Laura Lazo
- a Vaccine Department , Center for Genetic Engineering and Biotechnology (CIGB) , Havana , Cuba
| | - Iris Valdes
- a Vaccine Department , Center for Genetic Engineering and Biotechnology (CIGB) , Havana , Cuba
| | - Gerardo Guillén
- a Vaccine Department , Center for Genetic Engineering and Biotechnology (CIGB) , Havana , Cuba
| | - Lisset Hermida
- a Vaccine Department , Center for Genetic Engineering and Biotechnology (CIGB) , Havana , Cuba
| | - Lázaro Gil
- a Vaccine Department , Center for Genetic Engineering and Biotechnology (CIGB) , Havana , Cuba
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40
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Fast NMR method to probe solvent accessibility and disordered regions in proteins. Sci Rep 2019; 9:1647. [PMID: 30733478 PMCID: PMC6367444 DOI: 10.1038/s41598-018-37599-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 12/10/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1H-15N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.
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Martins AS, Carvalho FA, Faustino AF, Martins IC, Santos NC. West Nile Virus Capsid Protein Interacts With Biologically Relevant Host Lipid Systems. Front Cell Infect Microbiol 2019; 9:8. [PMID: 30788291 PMCID: PMC6372508 DOI: 10.3389/fcimb.2019.00008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 01/27/2023] Open
Abstract
West Nile and dengue viruses are closely related flaviviruses, originating mosquito-borne viral infections for which there are no effective and specific treatments. Their capsid proteins sequence and structure are particularly similar, forming highly superimposable α-helical homodimers. Measuring protein-ligand interactions at the single-molecule level yields detailed information of biological and biomedical relevance. In this work, such an approach was successfully applied on the characterization of the West Nile virus capsid protein interaction with host lipid systems, namely intracellular lipid droplets (an essential step for dengue virus replication) and blood plasma lipoproteins. Dynamic light scattering measurements show that West Nile virus capsid protein binds very low-density lipoproteins, but not low-density lipoproteins, and this interaction is dependent of potassium ions. Zeta potential experiments show that the interaction with lipid droplets is also dependent of potassium ions as well as surface proteins. The forces involved on the binding of the capsid protein with lipid droplets and lipoproteins were determined using atomic force microscopy-based force spectroscopy, proving that these interactions are K+-dependent rather than a general dependence of ionic strength. The capsid protein interaction with host lipid systems may be targeted in future therapeutic strategies against different flaviviruses. The biophysical and nanotechnology approaches employed in this study may be applied to characterize the interactions of other important proteins from different viruses, in order to understand their life cycles, as well as to find new strategies to inhibit them.
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Affiliation(s)
- Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Filomena A Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Boon PLS, Saw WG, Lim XX, Raghuvamsi PV, Huber RG, Marzinek JK, Holdbrook DA, Anand GS, Grüber G, Bond PJ. Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble. ACS Chem Biol 2018; 13:1621-1630. [PMID: 29792674 DOI: 10.1021/acschembio.8b00231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and colocalizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins. We show that the use of MD force fields (FFs) optimized for intrinsically disordered proteins (IDPs) is necessary to capture their conformational landscape and validate the computationally generated ensembles with reference to SAXS and HDXMS data. Representative ensembles of the C protein dimer are characterized by alternating, clamp-like exposure and occlusion of the internal hydrophobic patch, as well as by residual helical structure at the disordered N-terminus previously identified as a potential source of autoinhibition. Such dynamics are likely to determine the multifunctionality of the C protein during the flavivirus life cycle and hence impact the design of novel antiviral compounds.
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Affiliation(s)
- Priscilla L. S. Boon
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, #05-01, 28 Medical Drive, Singapore 117456
| | - Wuan Geok Saw
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Xin Xiang Lim
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Palur Venkata Raghuvamsi
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Roland G. Huber
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Jan K. Marzinek
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Daniel A. Holdbrook
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Ganesh S. Anand
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Gerhard Grüber
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Peter J. Bond
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
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43
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Structural insight into the Zika virus capsid encapsulating the viral genome. Cell Res 2018; 28:497-499. [PMID: 29467384 DOI: 10.1038/s41422-018-0007-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022] Open
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Kumar R, Singh N, Abdin MZ, Patel AH, Medigeshi GR. Dengue Virus Capsid Interacts with DDX3X-A Potential Mechanism for Suppression of Antiviral Functions in Dengue Infection. Front Cell Infect Microbiol 2018; 7:542. [PMID: 29387631 PMCID: PMC5776122 DOI: 10.3389/fcimb.2017.00542] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/26/2017] [Indexed: 11/28/2022] Open
Abstract
Dengue virus is a pathogen of global concern and has a huge impact on public health system in low- and middle-income countries. The capsid protein of dengue virus is least conserved among related flavivirus and there is very limited information on the role of cytosolic proteins that interact with dengue virus capsid. We identified DEAD (Asp-Glu-Ala-Asp) Box Helicase 3, an X-Linked (DDX3X), cytosolic ATP-dependent RNA helicase as a dengue virus capsid-interacting protein. We show that the N-terminal region of capsid is important for interaction with DDX3X, while the N-terminal domain of DDX3X seems to be involved in interaction with dengue capsid. DDX3X was down-regulated in dengue virus infected cells at later stages of infection. Our results show that DDX3X is an antiviral protein as suppression of DDX3X expression by siRNA led to an increase in viral titers and overexpression of DDX3X led to inhibition of viral replication. Knock-down of DDX3X did not affect induction of type I interferon response upon infection suggesting that the effect of DDX3X knock-down is independent of the interferon-dependent pathways that DDX3X modulates under normal conditions. Thus, our study identifies DDX3X as a dengue virus capsid interacting protein and indicates a potential link between the antiviral functions of DDX3X and dengue capsid at later stages of dengue infection.
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Affiliation(s)
- Rinki Kumar
- Clinical and Cellular Virology Lab, Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Nirpendra Singh
- Regional Center for Biotechnology, NCR-Biotech Science Cluster, Faridabad, India
| | - Malik Z Abdin
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Guruprasad R Medigeshi
- Clinical and Cellular Virology Lab, Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, India
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45
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Genome-Wide Mutagenesis of Dengue Virus Reveals Plasticity of the NS1 Protein and Enables Generation of Infectious Tagged Reporter Viruses. J Virol 2017; 91:JVI.01455-17. [PMID: 28956770 DOI: 10.1128/jvi.01455-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/21/2017] [Indexed: 12/21/2022] Open
Abstract
Dengue virus (DENV) is a major global pathogen that causes significant morbidity and mortality in tropical and subtropical areas worldwide. An improved understanding of the regions within the DENV genome and its encoded proteins that are required for the virus replication cycle will expedite the development of urgently required therapeutics and vaccines. We subjected an infectious DENV genome to unbiased insertional mutagenesis and used next-generation sequencing to identify sites that tolerate 15-nucleotide insertions during the virus replication cycle in hepatic cell culture. This revealed that the regions within capsid, NS1, and the 3' untranslated region were the most tolerant of insertions. In contrast, prM- and NS2A-encoding regions were largely intolerant of insertions. Notably, the multifunctional NS1 protein readily tolerated insertions in regions within the Wing, connector, and β-ladder domains with minimal effects on viral RNA replication and infectious virus production. Using this information, we generated infectious reporter viruses, including a variant encoding the APEX2 electron microscopy tag in NS1 that uniquely enabled high-resolution imaging of its localization to the surface and interior of viral replication vesicles. In addition, we generated a tagged virus bearing an mScarlet fluorescent protein insertion in NS1 that, despite an impact on fitness, enabled live cell imaging of NS1 localization and traffic in infected cells. Overall, this genome-wide profile of DENV genome flexibility may be further dissected and exploited in reporter virus generation and antiviral strategies.IMPORTANCE Regions of genetic flexibility in viral genomes can be exploited in the generation of reporter virus tools and should arguably be avoided in antiviral drug and vaccine design. Here, we subjected the DENV genome to high-throughput insertional mutagenesis to identify regions of genetic flexibility and enable tagged reporter virus generation. In particular, the viral NS1 protein displayed remarkable tolerance of small insertions. This genetic flexibility enabled generation of several novel NS1-tagged reporter viruses, including an APEX2-tagged virus that we used in high-resolution imaging of NS1 localization in infected cells by electron microscopy. For the first time, this analysis revealed the localization of NS1 within viral replication factories known as "vesicle packets" (VPs), in addition to its acknowledged localization to the luminal surface of these VPs. Together, this genetic profile of DENV may be further refined and exploited in the identification of antiviral targets and the generation of reporter virus tools.
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Hou W, Cruz-Cosme R, Armstrong N, Obwolo LA, Wen F, Hu W, Luo MH, Tang Q. Molecular cloning and characterization of the genes encoding the proteins of Zika virus. Gene 2017; 628:117-128. [PMID: 28720531 DOI: 10.1016/j.gene.2017.07.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/18/2017] [Accepted: 07/14/2017] [Indexed: 01/06/2023]
Abstract
Zika virus (ZIKV) encodes a precursor protein (also called polyprotein) of about 3424 amino acids that is processed by proteases to generate 10 mature proteins and a small peptide. In the present study, we characterized the chemical features, suborganelle distribution and potential function of each protein using Flag-tagged protein expression system. Western blot analysis revealed the molecular weight of the proteins and the polymerization of E, NS1, and NS3 proteins. In addition, we performed multi-labeled fluorescent immunocytochemistry and subcellular fractionation to determine the subcellular localization of these proteins in host cells. We found that 1) the capsid protein colocalizes with 3 different cellular organelles: nucleoli, Golgi apparatus, and lipid droplet; NS2b and NS4a are associated with the Golgi apparatus; 2) the capsid and NS1proteins distribute in both cytoplasm and nucleus, NS5 is a nuclear protein; 3) NS3 protein colocalizes with tubulin and affects Lamin A; 4) Envelope, PrM, and NS2a proteins co-localize with the endoplasmic reticulum; 5) NS1 is associated with autophagosomes and NS4b is related to early endosome; 6) NS5 forms punctate structures in the nucleus that associate with splicing compartments shown by SC35, leading to reduction of SC35 protein level and trafficking of SC35 from the nucleus to the cytoplasm. These data suggest that ZIKV generates 10 functional viral proteins that exhibit distinctive subcellular distribution in host cells.
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Affiliation(s)
- Wangheng Hou
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States
| | - Najealicka Armstrong
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States
| | - Lilian Akello Obwolo
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States
| | - Fayuan Wen
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad Street, Philadelphia, PA 19140, United States
| | - Min-Hua Luo
- State Key Laboratory of Virology, Wuhan, Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Seeley Mudd Building, 520 W Street, NW, Washington, DC 20059, United States.
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Lopez-Denman AJ, Mackenzie JM. The IMPORTance of the Nucleus during Flavivirus Replication. Viruses 2017; 9:v9010014. [PMID: 28106839 PMCID: PMC5294983 DOI: 10.3390/v9010014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation. In this review, we discuss the current understanding of flavivirus nuclear localisation, and the function it has during flavivirus infection. We also describe-while closely related-the functional differences between similar viral proteins in their nuclear translocation.
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Affiliation(s)
- Adam J Lopez-Denman
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne 3086, Australia.
| | - Jason M Mackenzie
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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The flavivirus capsid protein: Structure, function and perspectives towards drug design. Virus Res 2017; 227:115-123. [DOI: 10.1016/j.virusres.2016.10.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/29/2016] [Accepted: 10/12/2016] [Indexed: 12/12/2022]
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Abstract
The re-emergence of Zika virus (ZIKV) and its suspected link with various disorders in newborns and adults led the World Health Organization to declare a global health emergency. In response, the stem cell field quickly established platforms for modeling ZIKV exposure using human pluripotent stem cell-derived neural progenitors and brain organoids, fetal tissues, and animal models. These efforts provided significant insight into cellular targets, pathogenesis, and underlying biological mechanisms of ZIKV infection as well as platforms for drug testing. Here we review the remarkable progress in stem cell-based ZIKV research and discuss current challenges and future opportunities.
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Affiliation(s)
- Guo-Li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA. Proc Natl Acad Sci U S A 2016; 113:13863-13868. [PMID: 27849599 DOI: 10.1073/pnas.1600544113] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-borne flaviviruses, including yellow fever virus (YFV), Zika virus (ZIKV), and West Nile virus (WNV), profoundly affect human health. The successful transmission of these viruses to a human host depends on the pathogen's ability to overcome a potentially sterilizing immune response in the vector mosquito. Similar to other invertebrate animals and plants, the mosquito's RNA silencing pathway comprises its primary antiviral defense. Although a diverse range of plant and insect viruses has been found to encode suppressors of RNA silencing, the mechanisms by which flaviviruses antagonize antiviral small RNA pathways in disease vectors are unknown. Here we describe a viral suppressor of RNA silencing (VSR) encoded by the prototype flavivirus, YFV. We show that the YFV capsid (YFC) protein inhibits RNA silencing in the mosquito Aedes aegypti by interfering with Dicer. This VSR activity appears to be broadly conserved in the C proteins of other medically important flaviviruses, including that of ZIKV. These results suggest that a molecular "arms race" between vector and pathogen underlies the continued existence of flaviviruses in nature.
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