1
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Teramoto T. Dengue virus serotypic replacement of NS3 protease or helicase domain causes chimeric viral attenuation but can be recovered by a compensated mutation at helicase domain or NS2B, respectively. J Virol 2023; 97:e0085423. [PMID: 37555662 PMCID: PMC10506484 DOI: 10.1128/jvi.00854-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 08/10/2023] Open
Abstract
Mosquito-borne dengue viruses (DENVs) have evolved to four serotypes with 69%-78% amino acid identities, resulting in incomplete immunity, where one serotype's infection does not cross-protect against secondary infections by other serotypes. Despite the amino acid differences, structural and nonstructural (NS) proteins among serotypes play similar functions. NS3 is an enzyme complex: NS3 has N-terminal protease (PRO) and C-terminal helicase (HEL) activities in addition to 5' RNA triphosphatase (5'RTP), which is involved in the RNA capping process. In this study, the effects of NS3 replacements among serotypes were tested. The replacement of NS3 full-length (FULL), PRO or HEL region suppressed viral replication in BHK-21 mammalian cells, while the single compensatory mutation improved the viral replications; P364S mutation in HEL revived PRO (DENV3)-replaced DENV1, while S68T alteration in NS2B recovered HEL (DENV1)-replaced DENV2. The results suggest that the interactions between PRO and HEL as well as HEL and NS2B are required for replication competence. Lower-frequency mutations also appeared at various locations in viral proteins, although after infecting C6/36 mosquito cells, the mutations' frequencies changed, and/or new mutations appeared. In contrast, the inter-domain region (INT, 12 amino acids)-replaced chimera quickly replicated without mutation in BHK-21 cells, although extended cell culture accumulated various mutations. These results suggest that NS3 variously interacts with DENV proteins, in which the chimeric NS3 domain replacements induced amino acid mutations, irrespective of replication efficiency. However, the viral sequences are further adjusted for replication efficiency, to fit in both mammalian cells and mosquito cells. IMPORTANCE Enzyme activities for replicating DENV 5' cap positive (+) sense RNA have been shown to reside in NS3 and NS5. However, it remains unknown how these enzymes coordinately synthesize negative (-) sense RNA, from which abundant 5' cap (+) sense RNA is produced. We previously revealed that NS5 dimerization and NS5 methyltransferase(MT)-NS3HEL interaction are important for DENV replication. Here, we found that replication incompetence due to NS3PRO or HEL replacement was compensated by a mutation at HEL or NS2B, respectively, suggesting that the interactions among NS2B, NS3PRO, and HEL are critical for DENV replication.
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Affiliation(s)
- Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
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2
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Gonzalez Lopez Ledesma MM, Costa Navarro G, Pallares HM, Paletta A, De Maio F, Iglesias NG, Gebhard L, Oviedo Rouco S, Ojeda DS, de Borba L, Giraldo M, Rajsbaum R, Ceballos A, Krogan NJ, Shah PS, Gamarnik AV. Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation. Proc Natl Acad Sci U S A 2023; 120:e2220005120. [PMID: 37252973 PMCID: PMC10266027 DOI: 10.1073/pnas.2220005120] [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: 11/23/2022] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Dengue virus (DENV) is the most important human virus transmitted by mosquitos. Dengue pathogenesis is characterized by a large induction of proinflammatory cytokines. This cytokine induction varies among the four DENV serotypes (DENV1 to 4) and poses a challenge for live DENV vaccine design. Here, we identify a viral mechanism to limit NF-κB activation and cytokine secretion by the DENV protein NS5. Using proteomics, we found that NS5 binds and degrades the host protein ERC1 to antagonize NF-κB activation, limit proinflammatory cytokine secretion, and reduce cell migration. We found that ERC1 degradation involves unique properties of the methyltransferase domain of NS5 that are not conserved among the four DENV serotypes. By obtaining chimeric DENV2 and DENV4 viruses, we map the residues in NS5 for ERC1 degradation, and generate recombinant DENVs exchanging serotype properties by single amino acid substitutions. This work uncovers a function of the viral protein NS5 to limit cytokine production, critical to dengue pathogenesis. Importantly, the information provided about the serotype-specific mechanism for counteracting the antiviral response can be applied to improve live attenuated vaccines.
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Affiliation(s)
| | | | | | - Ana Paletta
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires-National Scientific and Technical Research Council, Buenos AiresC1121, Argentina
| | - Federico De Maio
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | | | - Leopoldo Gebhard
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | | | - Diego S. Ojeda
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | - Luana de Borba
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | - María Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX77555
| | - Ricardo Rajsbaum
- Department of Medicine, Center for Virus-Host-Innate-Immunity, Rutgers Biomedical and Health Sciences, Newark, NJ07101
| | - Ana Ceballos
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires-National Scientific and Technical Research Council, Buenos AiresC1121, Argentina
| | | | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA95616
- Department of Chemical Engineering, University of California, Davis, CA95616
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3
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Barnard TR, Landry BN, Wang AB, Sagan SM. Zika virus NS3 and NS5 proteins determine strain-dependent differences in dsRNA accumulation in a host cell type-dependent manner. J Gen Virol 2023; 104. [PMID: 37289497 DOI: 10.1099/jgv.0.001855] [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] [Indexed: 06/09/2023] Open
Abstract
For positive-sense RNA viruses, initiation of viral RNA replication represents a major target of antiviral responses to infection. Despite this, the interplay between viral replication and the innate antiviral response at early steps in the Zika virus (ZIKV) life cycle is not well understood. We have previously identified ZIKV isolates with differing levels of dsRNA accumulation, ZIKVPR (high dsRNA per infected cell) and ZIKVCDN (low dsRNA per infected cell), and we hypothesized that we could use reverse genetics to investigate how host and viral factors contribute to the establishment of viral RNA replication. We found that both the ZIKV NS3 and NS5 proteins as well as host factors were necessary to determine the dsRNA accumulation phenotype. Additionally, we show that dsRNA correlates with viral negative-strand RNA measured by strand-specific RT-qPCR, suggesting that dsRNA is an accurate readout of viral RNA replication. Interestingly, although we did not observe NS3- and NS5-dependent differences in cells with defects in interferon (IFN) production, differences in RNA accumulation precede induction of the IFN response, suggesting that RNA sensing pathways or intrinsic restriction factors may differentially restrict ZIKV in an NS3- and NS5-dependent manner. This work expands our understanding of the interplay of early steps of viral RNA replication and the induction of the innate antiviral response to ZIKV infection.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Breanna N Landry
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Alex B Wang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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4
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Teramoto T, Choi KH, Padmanabhan R. Flavivirus proteases: The viral Achilles heel to prevent future pandemics. Antiviral Res 2023; 210:105516. [PMID: 36586467 PMCID: PMC10062209 DOI: 10.1016/j.antiviral.2022.105516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
Flaviviruses are important human pathogens and include dengue (DENV), West Nile (WNV), Yellow fever virus (YFV), Japanese encephalitis (JEV) and Zika virus (ZIKV). DENV, transmitted by mosquitoes, causes diseases ranging in severity from mild dengue fever with non-specific flu-like symptoms to fatal dengue hemorrhagic fever and dengue shock syndrome. DENV infections are caused by four serotypes, DENV1-4, which interact differently with antibodies in blood serum. The incidence of DENV infection has increased dramatically in recent decades and the CDC estimates 400 million dengue infections occur each year, resulting in ∼25,000 deaths mostly among children and elderly people. Similarly, ZIKV infections are caused by infected mosquito bites to humans, can be transmitted sexually and through blood transfusions. If a pregnant woman is infected, the virus can cross the placental barrier and can spread to her fetus, causing severe brain malformations in the child including microcephaly and other birth defects. It is noteworthy that the neurological manifestations of ZIKV were also observed in DENV endemic regions, suggesting that pre-existing antibody response to DENV could augment ZIKV infection. WNV, previously unknown in the US (and known to cause only mild disease in Middle East), first arrived in New York city in 1999 (NY99) and spread throughout the US and Canada by Culex mosquitoes and birds. WNV is now endemic in North America. Thus, emerging and re-emerging flaviviruses are significant threat to human health. However, vaccines are available for only a limited number of flaviviruses, and antiviral therapies are not available for any flavivirus. Hence, there is an urgent need to develop therapeutics that interfere with essential enzymatic steps, such as protease in the flavivirus lifecycle as these viruses possess significant threat to future pandemics. In this review, we focus on our E. coli expression of NS2B hydrophilic domain (NS2BH) covalently linked to NS3 protease domain (NS3Pro) in their natural context which is processed by the combined action of both subunits of the NS2B-NS3Pro precursor. Biochemical activities of the viral protease such as solubility and autoproteolysis of NS2BH-NS3Pro linkage depended on the C-terminal portion of NS2BH linked to the NS3Pro domain. Since 2008, we also focus on the use of the recombinant protease in high throughput screens and characterization of small molecular compounds identified in these screens.
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Affiliation(s)
- Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
| | - Kyung H Choi
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47406, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
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5
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Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase. Nat Commun 2021; 12:2530. [PMID: 33953197 PMCID: PMC8100141 DOI: 10.1038/s41467-021-22846-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/30/2021] [Indexed: 01/07/2023] Open
Abstract
Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.
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6
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Tangudu CS, Charles J, Nunez-Avellaneda D, Hargett AM, Brault AC, Blitvich BJ. Chimeric Zika viruses containing structural protein genes of insect-specific flaviviruses cannot replicate in vertebrate cells due to entry and post-translational restrictions. Virology 2021; 559:30-39. [PMID: 33812340 DOI: 10.1016/j.virol.2021.03.014] [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: 02/08/2021] [Revised: 03/04/2021] [Accepted: 03/21/2021] [Indexed: 02/06/2023]
Abstract
Long Pine Key virus (LPKV) and Lammi virus are insect-specific flaviviruses that phylogenetically affiliate with dual-host flaviviruses. The goal of this study was to provide insight into the genetic determinants that condition this host range restriction. Chimeras were initially created by replacing select regions of the Zika virus genome, including the premembrane and envelope protein (prM-E) genes, with the corresponding regions of the LPKV genome. Of the four chimeras produced, one (the prM-E swap) yielded virus that replicated in mosquito cells. Another chimeric virus with a mosquito replication-competent phenotype was created by inserting the prM-E genes of Lammi virus into a Zika virus genetic background. Vertebrate cells did not support the replication of either chimeric virus although trace to modest amounts of viral antigen were produced, consistent with suboptimal viral entry. These data suggest that dual-host affiliated insect-specific flaviviruses cannot replicate in vertebrate cells due to entry and post-translational restrictions.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Daniel Nunez-Avellaneda
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Alissa M Hargett
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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7
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Du Pont KE, Davidson RB, McCullagh M, Geiss BJ. Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft. J Biol Chem 2020; 295:1551-1564. [PMID: 31914411 PMCID: PMC7008374 DOI: 10.1074/jbc.ra119.011922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/22/2019] [Indexed: 01/01/2023] Open
Abstract
The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential "communication hub" for this energy transduction pathway. To investigate the role of Motif V in this process, here we combined molecular dynamics, biochemistry, and virology approaches. We tested Motif V mutations in both the replicon and recombinant protein systems to investigate viral genome replication, RNA-binding affinity, ATP hydrolysis activity, and helicase-mediated unwinding activity. We found that the T407A and S411A substitutions in NS3 reduce viral replication and increase the helicase-unwinding turnover rates by 1.7- and 3.5-fold, respectively, suggesting that flaviviruses may use suboptimal NS3 helicase activity for optimal genome replication. Additionally, we used simulations of each mutant to probe structural changes within NS3 caused by each mutation. These simulations indicate that Motif V controls communication between the ATP-binding pocket and the helical gate. These results help define the linkage between ATP hydrolysis and helicase activities within NS3 and provide insight into the biophysical mechanisms for ATPase-driven NS3 helicase function.
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Affiliation(s)
- Kelly E Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Russell B Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523; School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523.
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8
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Infection of Aedes albopictus Mosquito C6/36 Cells with the wMelpop Strain of Wolbachia Modulates Dengue Virus-Induced Host Cellular Transcripts and Induces Critical Sequence Alterations in the Dengue Viral Genome. J Virol 2019; 93:JVI.00581-19. [PMID: 31092581 DOI: 10.1128/jvi.00581-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/06/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue virus (DENV) causes frequent epidemics infecting ∼390 million people annually in over 100 countries. There are no approved vaccines or antiviral drugs for treatment of infected patients. However, there is a novel approach to control DENV transmission by the mosquito vectors, Aedes aegypti and Aedes albopictus, using the Wolbachia symbiont. The wMelPop strain of Wolbachia suppresses DENV transmission and shortens the mosquito life span. However, the underlying mechanism is poorly understood. To clarify this mechanism, either naive A. albopictus (C6/36) or wMelPop-C6/36 cells were infected with DENV serotype 2 (DENV2). Analysis of host transcript profiles by transcriptome sequencing (RNAseq) revealed that the presence of wMelPop dramatically altered the mosquito host cell transcription in response to DENV2 infection. The viral RNA evolved from wMelPop-C6/36 cells contained low-frequency mutations (∼25%) within the coding region of transmembrane domain 1 (TMD1) of E protein. Mutations with >97% frequencies were distributed within other regions of E, the NS5 RNA-dependent RNA polymerase (NS5POL) domain, and the TMDs of NS2A, NS2B, and NS4B. Moreover, while DENV2-infected naive C6/36 cells showed syncytium formation, DENV2-infected wMelPop-C6/36 cells did not. The Wolbachia-induced mutant DENV2 can readily infect and replicate in naive C6/36 cells, whereas in mutant DENV2-infected BHK-21 or Vero cells, virus replication was delayed. In LLC-MK2 cells, the mutant failed to produce plaques. Additionally, in BHK-21 cells, many mutations in the viral genome reverted to the wild type (WT) and compensatory mutations in NS3 gene appeared. Our results indicate that wMelPop impacts significantly the interactions of DENV2 with mosquito and mammalian host cells.IMPORTANCE Mosquito-borne diseases are of global significance causing considerable morbidity and mortality throughout the world. Dengue virus (DENV; serotypes 1 to 4), a member of the Flavivirus genus of the Flaviviridae family, causes millions of infections annually. Development of a safe vaccine is hampered due to absence of cross-protection and increased risk in secondary infections due to antibody-mediated immune enhancement. Infection of vector mosquitoes with Wolbachia bacteria offers a novel countermeasure to suppress DENV transmission, but the mechanisms are poorly understood. In this study, the host transcription profiles and viral RNA sequences were analyzed in naive A. albopictus (C6/36) and wMelPop-C6/36 cells by RNAseq. Our results showed that the wMelPop symbiont caused profound changes in host transcription profiles and morphology of DENV2-infected C6/36 cells. Accumulation of several mutations throughout DENV2 RNA resulted in loss of infectivity of progeny virions. Our findings offer new insights into the mechanism of Wolbachia-mediated suppression of DENV transmission.
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Wang K, Zou C, Wang X, Huang C, Feng T, Pan W, Wu Q, Wang P, Dai J. Interferon-stimulated TRIM69 interrupts dengue virus replication by ubiquitinating viral nonstructural protein 3. PLoS Pathog 2018; 14:e1007287. [PMID: 30142214 PMCID: PMC6126873 DOI: 10.1371/journal.ppat.1007287] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 09/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
In order to eliminate viral infections, hundreds of interferon-stimulated genes (ISGs) are induced via type I interferons (IFNs). However, the functions and mechanisms of most ISGs are largely unclear. A tripartite motif (TRIM) protein encoding gene TRIM69 is induced by dengue virus (DENV) infection as an ISG. TRIM69 restricts DENV replication, and its RING domain, which has the E3 ubiquitin ligase activity, is critical for its antiviral activity. An in vivo study further confirmed that TRIM69 contributes to the control of DENV infection in immunocompetent mice. Unlike many other TRIM family members, TRIM69 is not involved in modulation of IFN signaling. Instead, TRIM69 interacts with DENV Nonstructural Protein 3 (NS3) directly and mediates its polyubiquitination and degradation. Finally, Lys104 of NS3 is identified as the target of TRIM69-mediated ubiquitination. Our study demonstrates that TRIM69 restricts DENV replication by specifically ubiquitinating a viral nonstructural protein.
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Affiliation(s)
- Kezhen Wang
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Chunling Zou
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Xiujuan Wang
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Chenxiao Huang
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Tingting Feng
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Wen Pan
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
| | - Qihan Wu
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, P. R. China
| | - Penghua Wang
- Department Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Jianfeng Dai
- Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, P. R. China
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, P. R. China
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10
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Genomic changes in an attenuated genotype I Japanese encephalitis virus and comparison with virulent parental strain. Virus Genes 2018; 54:424-431. [PMID: 29605839 DOI: 10.1007/s11262-018-1559-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Genotype I Japanese encephalitis virus (JEV) strain SCYA201201 was previously isolated from brain tissues of aborted piglets. In this study, we obtained an attenuated SCYA201201-0901 strain by serial passage of strain SCYA201201-1 in Syrian baby hamster kidney cells, combined with multiple plaque purifications and selection for virulence in mice. We investigated the genetic changes associated with attenuation by comparing the entire genomes of SCYA201201-0901 and SCYA201201-1. Sequence comparisons identified 14 common amino acid substitutions in the coding region, with two nucleotide point mutations in the 5'-untranslated region (UTR) and another three in the 3'-UTR, which differed between the attenuated and virulent strains. In addition, a total of 13 silent nucleotide mutations were found after attenuation. These substitutions, alone or in combination, may be responsible for the attenuated phenotype of the SCYA201201-0901 strain in mice. This information will contribute to our understanding of attenuation and of the molecular basis of virulence in genotype I strains such as SCYA201201-0901, as well as aiding the development of safer JEV vaccines.
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11
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Swarbrick CMD, Basavannacharya C, Chan KWK, Chan SA, Singh D, Wei N, Phoo WW, Luo D, Lescar J, Vasudevan SG. NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication. Nucleic Acids Res 2018; 45:12904-12920. [PMID: 29165589 PMCID: PMC5728396 DOI: 10.1093/nar/gkx1127] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023] Open
Abstract
The protein–RNA interactions within the flavivirus replication complex (RC) are not fully understood. Our structure of dengue virus NS3 adenosine triphosphatase (ATPase)/helicase bound to the conserved 5′ genomic RNA 5′-AGUUGUUAGUCU-3′ reveals that D290 and R538 make specific interactions with G2 and G5 bases respectively. We show that single-stranded 12-mer RNA stimulates ATPase activity of NS3, however the presence of G2 and G5 leads to significantly higher activation. D290 is adjacent to the DEXH motif found in SF2 helicases like NS3 and interacts with R387, forming a molecular switch that activates the ATPase site upon RNA binding. Our structure guided mutagenesis revealed that disruption of D290–R387 interaction increases basal ATPase activity presumably as a result of higher conformational flexibility of the ATPase active site. Mutational studies also showed R538 plays a critical role in RNA interactions affecting translocation of viral RNA through dynamic interactions with bases at positions 4 and 5 of the ssRNA. Restriction of backbone flexibility around R538 through mutation of G540 to proline abolishes virus replication, indicating conformational flexibility around residue R538 is necessary for RNA translocation. The functionally critical sequence-specific contacts in NS3 RNA binding groove in subdomain III reveals potentially novel allosteric anti-viral drug targets.
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Affiliation(s)
- Crystall M D Swarbrick
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | | | - Kitti W K Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore.,Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, 117545, Singapore
| | - Shu-Ann Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Daljit Singh
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Na Wei
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 138673, Singapore.,Nanyang Institute for Structural Biology, School of Biological Sciences, Nanyang Technological University, 138673, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 138673, Singapore
| | - Julien Lescar
- Nanyang Institute for Structural Biology, School of Biological Sciences, Nanyang Technological University, 138673, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore.,Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, 117545, Singapore
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12
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Teramoto T, Balasubramanian A, Choi KH, Padmanabhan R. Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication. J Biol Chem 2017; 292:9465-9479. [PMID: 28396347 DOI: 10.1074/jbc.m117.775643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Indexed: 11/06/2022] Open
Abstract
Four serotypes of mosquito-borne dengue virus (DENV), evolved from a common ancestor, are human pathogens of global significance for which there is no vaccine or antiviral drug available. The N-terminal domain of DENV NS5 has guanylyltransferase and methyltransferase (MTase), and the C-terminal region has the polymerase (POL), all of which are important for 5'-capping and RNA replication. The crystal structure of NS5 shows it as a dimer, but the functional evidence for NS5 dimer is lacking. Our studies showed that the substitution of DENV2 NS5 MTase or POL for DENV4 NS5 within DENV2 RNA resulted in a severe attenuation of replication in the transfected BHK-21 cells. A replication-competent species was evolved with the acquired mutations in the DENV2 and DENV4 NS5 MTase or POL domain or in the DENV2 NS3 helicase domain in the DENV2 chimera RNAs by repeated passaging of infected BHK-21 or mosquito cells. The linker region of seven residues in NS5, rich in serotype-specific residues, is important for the recovery of replication fitness in the chimera RNA. Our results, taken together, provide genetic evidence for a serotype-specific interaction between NS3 and NS5 as well as specific interdomain interaction within NS5 required for RNA replication. Genome-wide RNAseq analysis revealed the distribution of adaptive mutations in RNA quasispecies. Those within NS3 and NS5 are located at the surface and/or within the NS5 dimer interface, providing a functional significance to the crystal structure NS5 dimer.
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Affiliation(s)
- Tadahisa Teramoto
- From the Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, D. C. 20057 and
| | - Anuradha Balasubramanian
- From the Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, D. C. 20057 and
| | - Kyung H Choi
- the Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-0156
| | - Radhakrishnan Padmanabhan
- From the Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, D. C. 20057 and
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13
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Chiang PY, Wu HN. The role of surface basic amino acids of dengue virus NS3 helicase in viral RNA replication and enzyme activities. FEBS Lett 2016; 590:2307-20. [DOI: 10.1002/1873-3468.12232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Pao-Yin Chiang
- Graduate Institute of Life Sciences; National Defense Medical Centre; Taipei Taiwan
- Institute of Molecular Biology; Academia Sinica; Taipei Taiwan
| | - Huey-Nan Wu
- Institute of Molecular Biology; Academia Sinica; Taipei Taiwan
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14
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Klema VJ, Ye M, Hindupur A, Teramoto T, Gottipati K, Padmanabhan R, Choi KH. Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface. PLoS Pathog 2016; 12:e1005451. [PMID: 26895240 PMCID: PMC4760774 DOI: 10.1371/journal.ppat.1005451] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/22/2016] [Indexed: 01/07/2023] Open
Abstract
Flavivirus nonstructural protein 5 (NS5) consists of methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, which catalyze 5'-RNA capping/methylation and RNA synthesis, respectively, during viral genome replication. Although the crystal structure of flavivirus NS5 is known, no data about the quaternary organization of the functional enzyme are available. We report the crystal structure of dengue virus full-length NS5, where eight molecules of NS5 are arranged as four independent dimers in the crystallographic asymmetric unit. The relative orientation of each monomer within the dimer, as well as the orientations of the MTase and RdRp domains within each monomer, is conserved, suggesting that these structural arrangements represent the biologically relevant conformation and assembly of this multi-functional enzyme. Essential interactions between MTase and RdRp domains are maintained in the NS5 dimer via inter-molecular interactions, providing evidence that flavivirus NS5 can adopt multiple conformations while preserving necessary interactions between the MTase and RdRp domains. Furthermore, many NS5 residues that reduce viral replication are located at either the inter-domain interface within a monomer or at the inter-molecular interface within the dimer. Hence the X-ray structure of NS5 presented here suggests that MTase and RdRp activities could be coordinated as a dimer during viral genome replication.
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Affiliation(s)
- Valerie J. Klema
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Mengyi Ye
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Aditya Hindupur
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D.C., United States of America
| | - Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D.C., United States of America
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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15
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Klema VJ, Padmanabhan R, Choi KH. Flaviviral Replication Complex: Coordination between RNA Synthesis and 5'-RNA Capping. Viruses 2015; 7:4640-56. [PMID: 26287232 PMCID: PMC4576198 DOI: 10.3390/v7082837] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 12/28/2022] Open
Abstract
Genome replication in flavivirus requires (-) strand RNA synthesis, (+) strand RNA synthesis, and 51-RNA capping and methylation. To carry out viral genome replication, flavivirus assembles a replication complex, consisting of both viral and host proteins, on the cytoplasmic side of the endoplasmic reticulum (ER) membrane. Two major components of the replication complex are the viral non-structural (NS) proteins NS3 and NS5. Together they possess all the enzymatic activities required for genome replication, yet how these activities are coordinated during genome replication is not clear. We provide an overview of the flaviviral genome replication process, the membrane-bound replication complex, and recent crystal structures of full-length NS5. We propose a model of how NS3 and NS5 coordinate their activities in the individual steps of (-) RNA synthesis, (+) RNA synthesis, and 51-RNA capping and methylation.
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Affiliation(s)
- Valerie J Klema
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC 20057, USA.
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA.
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16
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Bullard KM, Gullberg RC, Soltani E, Steel JJ, Geiss BJ, Keenan SM. Murine Efficacy and Pharmacokinetic Evaluation of the Flaviviral NS5 Capping Enzyme 2-Thioxothiazolidin-4-One Inhibitor BG-323. PLoS One 2015; 10:e0130083. [PMID: 26075394 PMCID: PMC4468182 DOI: 10.1371/journal.pone.0130083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/15/2015] [Indexed: 12/25/2022] Open
Abstract
Arthropod-borne flavivirus infection continues to cause significant morbidity and mortality worldwide. Identification of drug targets and novel antiflaviviral compounds to treat these diseases has become a global health imperative. A previous screen of 235,456 commercially available small molecules identified the 2-thioxothiazolidin-4-one family of compounds as inhibitors of the flaviviral NS5 capping enzyme, a promising target for antiviral drug development. Rational drug design methodologies enabled identification of lead compound BG-323 from this series. We have shown previously that BG-323 potently inhibits NS5 capping enzyme activity, displays antiviral effects in dengue virus replicon assays and inhibits growth of West Nile and yellow fever viruses with low cytotoxicity in vitro. In this study we further characterized BG-323’s antiviral activity in vitro and in vivo. We found that BG-323 was able to reduce replication of WNV (NY99) and Powassan viruses in culture, and we were unable to force resistance into WNV (Kunjin) in long-term culture experiments. We then evaluated the antiviral activity of BG-323 in a murine model. Mice were challenged with WNV NY99 and administered BG-323 or mock by IP inoculation immediately post challenge and twice daily thereafter. Mice were bled and viremia was quantified on day three. No significant differences in viremia were observed between BG-323-treated and control groups and clinical scores indicated both BG-323-treated and control mice developed signs of illness on approximately the same day post challenge. To determine whether differences in in vitro and in vivo efficacy were due to unfavorable pharmacokinetic properties of BG-323, we conducted a pharmacokinetic evaluation of this small molecule. Insights from pharmacokinetic studies indicate that BG-323 is cell permeable, has a low efflux ratio and does not significantly inhibit two common cytochrome P450 (CYP P450) isoforms thus suggesting this molecule may be less likely to cause adverse drug interactions. However, the T1/2 of BG-323 was suboptimal and the percent of drug bound to plasma binding proteins was high. Future studies with BG-323 will be aimed at increasing the T1/2 and determining strategies for mitigating the effects of high plasma protein binding, which likely contribute to low in vivo efficacy.
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Affiliation(s)
- Kristen M. Bullard
- University of Northern Colorado, School of Biological Sciences, Greeley, CO, United States of America
| | - Rebekah C. Gullberg
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Elnaz Soltani
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - J. Jordan Steel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail: (SMK); (BJG)
| | - Susan M. Keenan
- University of Northern Colorado, School of Biological Sciences, Greeley, CO, United States of America
- * E-mail: (SMK); (BJG)
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