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Valente AP, Moraes AH. Zika virus proteins at an atomic scale: how does structural biology help us to understand and develop vaccines and drugs against Zika virus infection? J Venom Anim Toxins Incl Trop Dis 2019; 25:e20190013. [PMID: 31523227 PMCID: PMC6727858 DOI: 10.1590/1678-9199-jvatitd-2019-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In Brazil and in other tropical areas Zika virus infection was directly associated with clinical complications as microcephaly in newborn children whose mothers were infected during pregnancy and the Guillain-Barré syndrome in adults. Recently, research has been focused on developing new vaccines and drug candidates against Zika virus infection since none of those are available. In order to contribute to vaccine and drug development efforts, it becomes important the understanding of the molecular basis of the Zika virus recognition, infection and blockade. To this purpose, it is essential the structural determination of the Zika virus proteins. The genome sequencing of the Zika virus identified ten proteins, being three structural (protein E, protein C and protein prM) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Together, these proteins are the main targets for drugs and antibody recognition. Here we examine new discoveries on high-resolution structural biology of Zika virus, observing the interactions and functions of its proteins identified via state-of-art structural methodologies as X-ray crystallography, nuclear magnetic resonance spectroscopy and cryogenic electronic microscopy. The aim of the present study is to contribute to the understanding of the structural basis of Zika virus infection at an atomic level and to point out similarities and differences to others flaviviruses.
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Affiliation(s)
- Ana Paula Valente
- National Center of Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Adolfo Henrique Moraes
- Department of Chemistry, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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Ng IHW, Chan KWK, Tan MJA, Gwee CP, Smith KM, Jeffress SJ, Saw WG, Swarbrick CMD, Watanabe S, Jans DA, Grüber G, Forwood JK, Vasudevan SG. Zika Virus NS5 Forms Supramolecular Nuclear Bodies That Sequester Importin-α and Modulate the Host Immune and Pro-Inflammatory Response in Neuronal Cells. ACS Infect Dis 2019; 5:932-948. [PMID: 30848123 DOI: 10.1021/acsinfecdis.8b00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Zika virus (ZIKV) epidemic in the Americas was alarming because of its link with microcephaly in neonates and Guillain-Barré syndrome in adults. The unusual pathologies induced by ZIKV infection and the knowledge that the flaviviral nonstructural protein 5 (NS5), the most conserved protein in the flavivirus proteome, can modulate the host immune response during ZIKV infection prompted us to investigate the subcellular localization of NS5 during ZIKV infection and explore its functional significance. A monopartite nuclear localization signal (NLS) sequence within ZIKV NS5 was predicted by the cNLS Mapper program, and we observed localization of ZIKV NS5 in the nucleus of infected cells by immunostaining with specific antibodies. Strikingly, ZIKV NS5 forms spherical shell-like nuclear bodies that exclude DNA. The putative monopartite NLS 390KRPR393 is necessary to direct FLAG-tagged NS5 to the nucleus as the NS5 390ARPA393 mutant protein accumulates in the cytoplasm. Furthermore, coimmunostaining experiments reveal that NS5 localizes with and sequesters importin-α, but not importin-β, in the observed nuclear bodies during virus infection. Structural and biochemical data demonstrate binding of ZIKV NS5 with importin-α and reveal important binding determinants required for their interaction and formation of complexes that give rise to the supramolecular nuclear bodies. Significantly, we demonstrate a neuronal-specific activation of the host immune response to ZIKV infection and a possible role of ZIKV NS5's nuclear localization toward this activation. This suggests that ZIKV pathogenesis may arise from a tissue-specific host response to ZIKV infection.
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Affiliation(s)
- Ivan H. W. Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Genome Institute of Singapore, Agency for Science & Technology Research (A*STAR), 60 Biopolis Street, Singapore 138672
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kate M. Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Sarah J. Jeffress
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Crystall M. D. Swarbrick
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - David A. Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
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53
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Saw WG, Chan KWK, Vasudevan SG, Grüber G. Zika virus nonstructural protein 5 residue R681 is critical for dimer formation and enzymatic activity. FEBS Lett 2019; 593:1272-1291. [PMID: 31090058 DOI: 10.1002/1873-3468.13437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/07/2022]
Abstract
Zika virus (ZIKV) relies on its nonstructural protein 5 (NS5) for capping and synthesis of the viral RNA. Recent small-angle X-ray scattering (SAXS) data of recombinant ZIKV NS5 protein showed that it is dimeric in solution. Here, we present insights into the critical residues responsible for its dimer formation. SAXS studies of the engineered ZIKV NS5 mutants revealed that R681A mutation on NS5 (NS5R681A ) disrupts the dimer formation and affects its RNA-dependent RNA polymerase activity as well as the subcellular localization of NS5R681A in mammalian cells. The critical residues involved in the dimer arrangement of ZIKV NS5 are discussed, and the data provide further insights into the diversity of flaviviral NS5 proteins in terms of their propensity for oligomerization.
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Affiliation(s)
- Wuan-Geok Saw
- Nanyang Technological University, School of Biological Sciences, Singapore
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore
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Matsudaira PT, Verma CS. Editorial. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 143:1-4. [PMID: 30951764 DOI: 10.1016/j.pbiomolbio.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paul T Matsudaira
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore; Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; MechanoBiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore.
| | - Chandra S Verma
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, 637551, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
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Ferrero DS, Ruiz-Arroyo VM, Soler N, Usón I, Guarné A, Verdaguer N. Supramolecular arrangement of the full-length Zika virus NS5. PLoS Pathog 2019; 15:e1007656. [PMID: 30951555 PMCID: PMC6469808 DOI: 10.1371/journal.ppat.1007656] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 04/17/2019] [Accepted: 02/23/2019] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV), a member of the Flaviviridae family, has emerged as a major public health threat, since ZIKV infection has been connected to microcephaly and other neurological disorders. Flavivirus genome replication is driven by NS5, an RNA-dependent RNA polymerase (RdRP) that also contains a N-terminal methyltransferase domain essential for viral mRNA capping. Given its crucial roles, ZIKV NS5 has become an attractive antiviral target. Here, we have used integrated structural biology approaches to characterize the supramolecular arrangement of the full-length ZIKV NS5, highlighting the assembly and interfaces between NS5 monomers within a dimeric structure, as well as the dimer-dimer interactions to form higher order fibril-like structures. The relative orientation of each monomer within the dimer provides a model to explain the coordination between MTase and RdRP domains across neighboring NS5 molecules and mutational studies underscore the crucial role of the MTase residues Y25, K28 and K29 in NS5 dimerization. The basic residue K28 also participates in GTP binding and competition experiments indicate that NS5 dimerization is disrupted at high GTP concentrations. This competition represents a first glimpse at a molecular level explaining how dimerization might regulate the capping process. The lack of vaccine or antiviral drugs to combat Zika virus (ZIKV) infection has encouraged scientists to characterize in depth potential drug targets. One attractive candidate is NS5, responsible for the catalysis of the 5’-RNA capping, methylation and RNA synthesis, during flavivirus genome replication. To fulfill these activities, the methyltransferase and RNA-dependent RNA polymerase domains of NS5 need to cooperate with each other. The structural and biophysical data presented in this work demonstrate that the ZIKV NS5 protein has the ability to form dimers, as well as higher order oligomers that may participate in the fine-tuning regulation of the multiple enzyme functions in the replication complex. In addition, we have found that NS5 dimerization is disrupted at high GTP concentrations, explaining how dimerization might regulate the capping process.
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Affiliation(s)
- Diego S. Ferrero
- Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Victor M. Ruiz-Arroyo
- Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Nicolas Soler
- Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
- ICREA Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Núria Verdaguer
- Structural Biology Unit, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
- * E-mail:
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56
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018. [PMID: 30564270 DOI: 10.3389/fgene.2018.00595/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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57
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018; 9:595. [PMID: 30564270 PMCID: PMC6288177 DOI: 10.3389/fgene.2018.00595] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/15/2018] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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58
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Discovery of Novel Druggable Sites on Zika Virus NS3 Helicase Using X-ray Crystallography-Based Fragment Screening. Int J Mol Sci 2018; 19:ijms19113664. [PMID: 30463319 PMCID: PMC6274715 DOI: 10.3390/ijms19113664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/28/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
The flavivirus family contains several important human pathogens, such as Zika virus (ZIKV), dengue, West Nile, and Yellow Fever viruses, that collectively lead to a large, global disease burden. Currently, there are no approved medicines that can target these viruses. The sudden outbreak of ZIKV infections in 2015⁻2016 posed a serious threat to global public health. While the epidemic has receded, persistent reservoirs of ZIKV infection can cause reemergence. Here, we have used X-ray crystallography-based screening to discover two novel sites on ZIKV NS3 helicase that can bind drug-like fragments. Both sites are structurally conserved in other flaviviruses, and mechanistically significant. The binding poses of four fragments, two for each of the binding sites, were characterized at atomic precision. Site A is a surface pocket on the NS3 helicase that is vital to its interaction with NS5 polymerase and formation of the flaviviral replication complex. Site B corresponds to a flexible, yet highly conserved, allosteric site at the intersection of the three NS3 helicase domains. Saturation transfer difference nuclear magnetic resonance (NMR) experiments were additionally used to evaluate the binding strength of the fragments, revealing dissociation constants (KD) in the lower mM range. We conclude that the NS3 helicase of flaviviruses is a viable drug target. The data obtained open opportunities towards structure-based design of first-in-class anti-ZIKV compounds, as well as pan-flaviviral therapeutics.
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59
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Lei Y, Takeda K, Yu L. Impaired heterologous protein-protein interaction is an essential cause for non-viability of WNV/DENV recombinants. Virology 2018; 524:140-150. [PMID: 30195251 DOI: 10.1016/j.virol.2018.08.013] [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: 05/04/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022]
Abstract
Flavivirus RNA replication starts at 3'-end, where it folds into a highly conserved stem-loop structure. We attempted to identify the viral non-structural proteins (NSPs) that might specifically interact with the 3'-stemloop (3'SL) through a genetic approach. WNV/DENV2 chimeric recombinants that contain Dengue2 (DENV2) gene(s) in West Nile virus (WNV) backbone were tested for replication competence. Three of seven recombinant viruses, containing the DENV2 NS1, NS2A, or NS4B gene and terminated with a mutated 3'SL (MutC 3'SL), were viable. Of these three, only those bearing the DENV2 NS1 and NS2A substitutions remained infectious when the MutC 3'SL was replaced by the wildtype WNV 3'SL. However, none of the seven chimeric recombinants bearing the DENV2 3'SL were viable. We then investigated the causes for failed replication of WNV/DENV2 chimeric recombinants. Proteolytic cleavage of NS polyproteins was defective by heterologous protease NS2B/3, but was efficient by homologous DENV2 NS2B/3 protease. Whereas, the heterologous polyproteins that contained DENV2 homologous protease were found to produce abnormal vesicles. WNV/DENV2 recombinants expressing the DENV2 homologous protease did not produce infectious virus either. We examined NS protein-protein interaction (PPI) and found that heterologous PPI (hPPI) between WNV and DENV2 NSPs were impaired to various degrees. Insufficient PPIs occurred mainly between heterologous NS2B and NS3; NS2B and NS4A; NS3 and NS5, correlating to those non-viability of substitution mutants. Our results indicate that impaired PPI may decrease protease activity and affect vesicle formation, and is the essential cause for non-viability of the WNV/DENV2 recombinants.
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Affiliation(s)
- Yingfen Lei
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852, USA; Department of Microbiology, The Fourth Military Medical University, 17 Changle Xilu, Xi'an, Shaanxi 710032, PR China
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Office of Vaccines Research and Review Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Li Yu
- Division of Viral Products, Office of Vaccines Research and Review Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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60
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Saw WG, Pan A, Subramanian Manimekalai MS, Grüber A, Grüber G. Structure and flexibility of non-structural proteins 3 and -5 of Dengue- and Zika viruses in solution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:67-77. [PMID: 30171868 DOI: 10.1016/j.pbiomolbio.2018.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/16/2018] [Accepted: 08/24/2018] [Indexed: 01/17/2023]
Abstract
Dengue- (DENV) and Zika viruses (ZIKV) rely on their non-structural protein 5 (NS5) including a methyl-transferase (MTase) and a RNA-dependent RNA polymerase (RdRp) for capping and synthesis of the viral RNA, and the non-structural protein 3 (NS3) with its protease and helicase domain for polyprotein possessing, unwinding dsRNA proceeding replication, and NTPase/RTPase activities. Accumulation of data for DENV- and ZIKV NS3 and NS5 in solution during recent years provides information about their overall shape, substrate-induced alterations, oligomeric forms and flexibility, with the latter being essential for domain-domain crosstalk. The importance and differences of the linker regions that connect the two domains of NS3 or NS5 are highlighted in particular with respect to the different DENV serotypes (DENV-1 to -4) as well as to the sequence diversities between the DENV and ZIKV proteins. Novel mutants of the French Polynesia ZIKV NS3 linker presented, identify critical residues in protein stability and enzymatic activity.
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Affiliation(s)
- Wuan Geok Saw
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, 637551, Singapore
| | - Ankita Pan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, 637551, Singapore
| | | | - Ardina Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, 637551, Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, 637551, Singapore.
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61
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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: 61] [Impact Index Per Article: 10.2] [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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62
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Qadir A, Riaz M, Saeed M, Shahzad-Ul-Hussan S. Potential targets for therapeutic intervention and structure based vaccine design against Zika virus. Eur J Med Chem 2018; 156:444-460. [PMID: 30015077 DOI: 10.1016/j.ejmech.2018.07.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Continuously increasing number of reports of Zika virus (ZIKV) infections and associated severe clinical manifestations, including autoimmune abnormalities and neurological disorders such as neonatal microcephaly and Guillain-Barré syndrome have created alarming situation in various countries. To date, no specific antiviral therapy or vaccine is available against ZIKV. This review provides a comprehensive insight into the potential therapeutic targets and describes viral epitopes of broadly neutralizing antibodies (bNAbs) in vaccine design perspective. Interactions between ZIKV envelope glycoprotein E and cellular receptors mediate the viral fusion and entry to the target cell. Blocking these interactions by targeting cellular receptors or viral structural proteins mediating these interactions or viral surface glycans can inhibit viral entry to the cell. Similarly, different non-structural proteins of ZIKV and un-translated regions (UTRs) of its RNA play essential roles in viral replication cycle and potentiate for therapeutic interventions. Structure based vaccine design requires identity and structural description of the epitopes of bNAbs. We have described different conserved bNAb epitopes present in the ZIKV envelope as potential targets for structure based vaccine design. This review also highlights successes, unanswered questions and future perspectives in relation to therapeutic and vaccine development against ZIKV.
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Affiliation(s)
- Amina Qadir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Muhammad Riaz
- Department of Chemistry, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
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63
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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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64
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Dwivedi VD, Tripathi IP, Tripathi RC, Bharadwaj S, Mishra SK. Genomics, proteomics and evolution of dengue virus. Brief Funct Genomics 2018; 16:217-227. [PMID: 28073742 DOI: 10.1093/bfgp/elw040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genome of a pathogenic organism possesses a specific order of nucleotides that contains not only information about the synthesis and expression of proteomes, which are required for its growth and survival, but also about its evolution. Inhibition of any particular protein, which is required for the survival of that pathogenic organism, can be used as a potential therapeutic target for the development of effective drugs to treat its infections. In this review, the genomics, proteomics and evolution of dengue virus have been discussed, which will be helpful in better understanding of its origin, growth, survival and evolution, and may contribute toward development of new efficient anti-dengue drugs.
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65
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Yang X, Chen C, Tian H, Chi H, Mu Z, Zhang T, Yang K, Zhao Q, Liu X, Wang Z, Ji X, Yang H. Mechanism of ATP hydrolysis by the Zika virus helicase. FASEB J 2018; 32:5250-5257. [PMID: 29913559 DOI: 10.1096/fj.201701140r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During its life cycle, Zika virus (ZIKV), an arthropod-borne flavivirus that is associated with Guillain-Barré syndrome and causes microencephaly in fetuses and newborn children, encodes a critical and indispensable helicase domain that has 5'-triphosphatase activity and performs ATP hydrolysis to generate energy and thus, sustains unwinding of double-stranded RNA during ZIKV genome replication. Of these processes, ATP hydrolysis represents the most basic event; however, its dynamic mechanisms remain largely unknown, impeding the further understanding of the function of ZIKV helicase and the ongoing anti-ZIKV drug design. In this work, we determined the crystal structure of ZIKV helicase in complex with ADP-AlF3-Mn2+ and ADP-Mn2+ separately. The structural analysis indicates that these structures represent the intermediate state and posthydrolysis state, respectively, of the ATP hydrolysis process of ZIKV helicase. These findings, together with our earlier work, which identified the prehydrolysis state of ZIKV helicase, lead to a proposal of the ATP hydrolysis cycle for ZIKV helicase. On this basis, we used site-directed mutagenesis combined with an enzymatic study to identify successfully residues that are critical for the ATPase activity of ZIKV helicase; this will provide new ideas to understand the function for the key enzyme of ZIKV.-Yang, X., Chen, C., Tian, H., Chi, H., Mu, Z., Zhang, T., Yang, K., Zhao, Q., Liu, X., Wang, Z., Ji, X., Yang, H. Mechanism of ATP hydrolysis by the Zika virus helicase.
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Affiliation(s)
- Xiaoyun Yang
- School of Life Sciences, Tianjin University, Tianjin, China.,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Hongliang Tian
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Heng Chi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Zhongyu Mu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Tianqing Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Kailin Yang
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Xiaohua Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin, China.,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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66
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Peng M, Swarbrick CMD, Chan KWK, Luo D, Zhang W, Lai X, Li G, Vasudevan SG. Luteolin escape mutants of dengue virus map to prM and NS2B and reveal viral plasticity during maturation. Antiviral Res 2018; 154:87-96. [PMID: 29665375 DOI: 10.1016/j.antiviral.2018.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
We previously showed that luteolin, a well-known plant-derived component found in the "heat clearing" class of Traditional Chinese Medicine (TCM) herbs, is an uncompetitive inhibitor (Ki 58.6 μM) of the host proprotein convertase furin, an endoprotease that is required for maturation of flaviviruses in the trans-Golgi compartment. Luteolin also weakly inhibited recombinant dengue virus NS2B/NS3 protease (Ki 140.36 μM) non-competitively. In order to further explore the mechanism of inhibition we isolated resistant mutants by continuous passaging of DENV2 in the presence of increasing concentrations of luteolin. Nucleotide sequence analysis of the luteolin-resistant escape mutants revealed nucleotide changes that lead to amino acid substitutions in the prM (T79R) and NS2B (I114M) genes. These mutations were introduced into a DENV2 infectious clone and tested for replication in Huh-7 cells. Interestingly we found that the replication kinetics of prM T19R-NS2B I114M double-mutant (DM) was similar to wild-type virus (WT). On the other hand the prM T79R single mutant (SM1) was attenuated and the NS2B I114M single mutant (SM2) showed enhanced replication. Time of drug addition assay with luteolin showed that the mutant viruses were able to produce more mature virions than WT in the order DM > SM2>SM1>WT. Exogenous addition of furin to purified immature WT or mutant viruses revealed that luteolin blocked the prM cleavage of WT and SM2 at a similar level. On the other hand the SM1 immature virus showed some cleavage while the DM immature virus revealed efficient furin cleavage of prM even in the presence of 50 μM luteolin. Our findings suggest that luteolin inhibition of furin may occur at host/pathogen interface that permits the virus to escape the suppression by mutating key residue that may lead to an altered interface.
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Affiliation(s)
- Minhua Peng
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | | | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Wei Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaoping Lai
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Geng Li
- Center for Animal Experiment, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Subhash G Vasudevan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
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67
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Wolbachia-mediated virus blocking in mosquito cells is dependent on XRN1-mediated viral RNA degradation and influenced by viral replication rate. PLoS Pathog 2018; 14:e1006879. [PMID: 29494679 PMCID: PMC5833283 DOI: 10.1371/journal.ppat.1006879] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 12/14/2022] Open
Abstract
Wolbachia is currently being developed as a novel tool to block the transmission of dengue viruses (DENV) by Aedes aegypti. A number of mechanisms have been proposed to explain the DENV-blocking phenotype in mosquitoes, including competition for fatty acids like cholesterol, manipulation of host miRNAs and upregulation of innate immune pathways in the mosquito. We examined the various stages in the DENV infection process to better understand the mechanism of Wolbachia-mediated virus blocking (WMVB). Our results suggest that infection with Wolbachia does not inhibit DENV binding or cell entry, but reduces virus replication. In contrast to a previous report, we also observed a similar reduction in replication of West Nile virus (WNV). This reduced replication is associated with rapid viral RNA degradation in the cytoplasm. We didn't find a role for host miRNAs in WMVB. Further analysis showed that the 3' end of the virus subgenomic RNA was protected and accumulated over time suggesting that the degradation is XRN1-mediated. We also found that sub genomic flavivirus RNA accumulation inactivated XRN1 in mosquito cells in the absence of Wolbachia and led to enhancement of RNA degradation in its presence. Depletion of XRN1 decreased WMVB which was associated with a significant increase in DENV RNA. We also observed that WMVB is influenced by virus MOI and rate of virus replication. A comparatively elevated blocking was observed for slowly replicating DENV, compared to WNV. Similar results were obtained while analysing different DENV serotypes.
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68
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Strand-like structures and the nonstructural proteins 5, 3 and 1 are present in the nucleus of mosquito cells infected with dengue virus. Virology 2018; 515:74-80. [DOI: 10.1016/j.virol.2017.12.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/18/2022]
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69
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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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70
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The Dengue Virus Replication Complex: From RNA Replication to Protein-Protein Interactions to Evasion of Innate Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:115-129. [PMID: 29845529 DOI: 10.1007/978-981-10-8727-1_9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses from the Flavivirus family are the causative agents of dengue fever, Zika, Japanese encephalitis, West Nile encephalitis or Yellow fever and constitute major or emerging public health problems. A better understanding of the flavivirus replication cycle is likely to offer new opportunities for the design of antiviral therapies to treat severe conditions provoked by these viruses, but it should also help reveal fundamental biological mechanisms of the host cell. During virus replication, RNA synthesis is mediated by a dynamic and membrane-bound multi-protein assembly, named the replication complex (RC). The RC is composed of both viral and host-cell proteins that assemble within vesicles composed of the endoplasmic reticulum membrane, near the nucleus. At the heart of the flavivirus RC lies NS4B, a viral integral membrane protein that plays a role in virulence and in down-regulating the innate immune response. NS4B binds to the NS2B-NS3 protease-helicase, which itself interacts with the NS5 methyl-transferase polymerase. We present an overview of recent structural and functional data that augment our understanding of how viral RNA is replicated by dengue virus. We focus on structural data that illuminate the various roles played by proteins NS2B-NS3, NS4B and NS5. By participating in viral RNA cap methylation, the NS5 methyltransferase enables the virus to escape the host cell innate immune response. We present the molecular basis for this activity. We summarize what we know about the network of interactions established by NS2B-NS3, NS4B and NS5 (their "interactome"). This leads to a working model that is captured in the form of a rather naïve "cartoon", which we hope will be refined towards an atomic model in the near future.
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71
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The Transactions of NS3 and NS5 in Flaviviral RNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:147-163. [PMID: 29845531 DOI: 10.1007/978-981-10-8727-1_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dengue virus (DENV) replication occurs in virus-induced vesicles that contain the replication complex (RC) where viral RNA, viral proteins and host proteins participate in RNA-RNA, RNA-protein and protein-protein interactions to ensure viral genome synthesis. However, the details of the multitude of interactions involved in the biogenesis of the infectious virion are not fully understood. In this review, we will focus on the interaction between non-structural (NS) proteins NS3 and NS5, as well as their interactions with viral RNA and briefly also the interaction of NS5 with the host nuclear transport receptor protein importin-α. The multifunctional NS3 protease/helicase and NS5 methyltransferase (MTase)/RNA-dependent RNA polymerase (RdRp) contain all the enzymatic activities required to synthesize the viral RNA genome. The success stories of drug discovery and development with Hepatitis C virus (HCV), a member of the Flaviviridae family, has led to the view that DENV NS3 and NS5 may be attractive antiviral drug targets. However, more than 10 years of intensive research effort by Novatis has revealed that they are not "low hanging fruits" and therefore, the search for potent directly acting antivirals (DAAs) remains a pipeline goal for several medium to large drug discovery enterprises. The effort to discover DAAs for DENV has been boosted by the epidemic outbreak of the closely related flavivirus member - Zika virus (ZIKV). Because the viral RNA replication occurs within a molecular machine that is composed several viral and host proteins, much interest has turned to characterising functionally essential protein-protein interactions in order to identify potential allosteric inhibitor binding sites within the RC.
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72
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Toh YK, Balakrishna AM, Manimekalai MSS, Chionh BB, Seetharaman RRC, Eisenhaber F, Eisenhaber B, Grüber G. Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F. Biochim Biophys Acta Gen Subj 2017; 1861:3201-3214. [DOI: 10.1016/j.bbagen.2017.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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73
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Brand C, Bisaillon M, Geiss BJ. Organization of the Flavivirus RNA replicase complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28815931 DOI: 10.1002/wrna.1437] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/09/2017] [Accepted: 07/13/2017] [Indexed: 12/20/2022]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, West Nile, yellow fever, and Zika viruses, are serious human pathogens that cause significant morbidity and mortality globally each year. Flaviviruses are single-stranded, positive-sense RNA viruses, and encode two multidomain proteins, NS3 and NS5, that possess all enzymatic activities required for genome replication and capping. NS3 and NS5 interact within virus-induced replication compartments to form the RNA genome replicase complex. Although the individual enzymatic activities of both proteins have been extensively studied and are well characterized, there are still gaps in our understanding of how they interact to efficiently coordinate their respective activities during positive-strand RNA synthesis and capping. Here, we discuss what is known about the structures and functions of the NS3 and NS5 proteins and propose a preliminary NS3:NS5:RNA interaction model based on a large body of literature about how the viral enzymes function, physical restraints between NS3 and NS5, as well as critical steps in the replication process. WIREs RNA 2017, 8:e1437. doi: 10.1002/wrna.1437 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carolin Brand
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Martin Bisaillon
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
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74
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Stephen P, Lin SX. RNA-dependent RNA polymerase: Addressing Zika outbreak by a phylogeny-based drug target study. Chem Biol Drug Des 2017. [PMID: 28636772 DOI: 10.1111/cbdd.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins.
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Affiliation(s)
- Preyesh Stephen
- Laboratory of Molecular Endocrinology, CHU Research Center, Laval University, Québec, Canada
| | - Sheng-Xiang Lin
- Laboratory of Molecular Endocrinology, CHU Research Center, Laval University, Québec, Canada
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75
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Singal B, Balakrishna AM, Nartey W, Manimekalai MSS, Jeyakanthan J, Grüber G. Crystallographic and solution structure of the N-terminal domain of the Rel protein fromMycobacterium tuberculosis. FEBS Lett 2017; 591:2323-2337. [DOI: 10.1002/1873-3468.12739] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Bharti Singal
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
| | | | - Wilson Nartey
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
| | | | | | - Gerhard Grüber
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
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76
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Ragunathan P, Sielaff H, Sundararaman L, Biuković G, Subramanian Manimekalai MS, Singh D, Kundu S, Wohland T, Frasch W, Dick T, Grüber G. The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation. J Biol Chem 2017; 292:11262-11279. [PMID: 28495884 PMCID: PMC5500794 DOI: 10.1074/jbc.m117.784959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/11/2017] [Indexed: 01/30/2023] Open
Abstract
The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide 521PDEHVEALDEDKLAKEAVKV540 of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.
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Affiliation(s)
- Priya Ragunathan
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Hendrik Sielaff
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | | | - Dhirendra Singh
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Subhashri Kundu
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Thorsten Wohland
- the Departments of Biological Sciences and Chemistry and NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore, 14 Science Drive 4, Singapore 117557, Republic of Singapore, and
| | - Wayne Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Thomas Dick
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Gerhard Grüber
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore,
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77
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Peng M, Watanabe S, Chan KWK, He Q, Zhao Y, Zhang Z, Lai X, Luo D, Vasudevan SG, Li G. Luteolin restricts dengue virus replication through inhibition of the proprotein convertase furin. Antiviral Res 2017; 143:176-185. [DOI: 10.1016/j.antiviral.2017.03.026] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/14/2017] [Accepted: 03/29/2017] [Indexed: 11/17/2022]
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78
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Pan A, Saw WG, Subramanian Manimekalai MS, Grüber A, Joon S, Matsui T, Weiss TM, Grüber G. Structural features of NS3 of Dengue virus serotypes 2 and 4 in solution and insight into RNA binding and the inhibitory role of quercetin. Acta Crystallogr D Struct Biol 2017; 73:402-419. [PMID: 28471365 PMCID: PMC5417341 DOI: 10.1107/s2059798317003849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
Dengue virus (DENV), which has four serotypes (DENV-1 to DENV-4), is the causative agent of the viral infection dengue. DENV nonstructural protein 3 (NS3) comprises a serine protease domain and an RNA helicase domain which has nucleotide triphosphatase activities that are essential for RNA replication and viral assembly. Here, solution X-ray scattering was used to provide insight into the overall structure and flexibility of the entire NS3 and its recombinant helicase and protease domains for Dengue virus serotypes 2 and 4 in solution. The DENV-2 and DENV-4 NS3 forms are elongated and flexible in solution. The importance of the linker residues in flexibility and domain-domain arrangement was shown by the compactness of the individual protease and helicase domains. Swapping of the 174PPAVP179 linker stretch of the related Hepatitis C virus (HCV) NS3 into DENV-2 NS3 did not alter the elongated shape of the engineered mutant. Conformational alterations owing to RNA binding are described in the protease domain, which undergoes substantial conformational alterations that are required for the optimal catalysis of bound RNA. Finally, the effects of ATPase inhibitors on the enzymatically active DENV-2 and DENV-4 NS3 and the individual helicases are presented, and insight into the allosteric effect of the inhibitor quercetin is provided.
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Affiliation(s)
- Ankita Pan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Ardina Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shin Joon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laboratory, Menlo Park, California, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laboratory, Menlo Park, California, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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79
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El Sahili A, Lescar J. Dengue Virus Non-Structural Protein 5. Viruses 2017; 9:E91. [PMID: 28441781 PMCID: PMC5408697 DOI: 10.3390/v9040091] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/15/2017] [Accepted: 04/20/2017] [Indexed: 12/17/2022] Open
Abstract
The World Health Organization estimates that the yearly number of dengue cases averages 390 million. This mosquito-borne virus disease is endemic in over 100 countries and will probably continue spreading, given the observed trend in global warming. So far, there is no antiviral drug available against dengue, but a vaccine has been recently marketed. Dengue virus also serves as a prototype for the study of other pathogenic flaviviruses that are emerging, like West Nile virus and Zika virus. Upon viral entry into the host cell and fusion of the viral lipid membrane with the endosomal membrane, the viral RNA is released and expressed as a polyprotein, that is then matured into three structural and seven non-structural (NS) proteins. The envelope, membrane and capsid proteins form the viral particle while NS1-NS2A-NS2B-NS3-NS4A-NS4B and NS5 assemble inside a cellular replication complex, which is embedded in endoplasmic reticulum (ER)-derived vesicles. In addition to their roles in RNA replication within the infected cell, NS proteins help the virus escape the host innate immunity and reshape the host-cell inner structure. This review focuses on recent progress in characterizing the structure and functions of NS5, a protein responsible for the replication and capping of viral RNA that represents a promising drug target.
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Affiliation(s)
- Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
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80
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Oliveira AFCDS, Teixeira RR, Oliveira ASD, Souza APMD, Silva MLD, Paula SOD. Potential Antivirals: Natural Products Targeting Replication Enzymes of Dengue and Chikungunya Viruses. Molecules 2017; 22:E505. [PMID: 28327521 PMCID: PMC6155337 DOI: 10.3390/molecules22030505] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/09/2017] [Accepted: 03/17/2017] [Indexed: 11/16/2022] Open
Abstract
Dengue virus (DENV) and chikungunya virus (CHIKV) are reemergent arboviruses that are transmitted by mosquitoes of the Aedes genus. During the last several decades, these viruses have been responsible for millions of cases of infection and thousands of deaths worldwide. Therefore, several investigations were conducted over the past few years to find antiviral compounds for the treatment of DENV and CHIKV infections. One attractive strategy is the screening of compounds that target enzymes involved in the replication of both DENV and CHIKV. In this review, we describe advances in the evaluation of natural products targeting the enzymes involved in the replication of these viruses.
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Affiliation(s)
- Ana Flávia Costa da Silveira Oliveira
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
- Instituto Federal de Educação, Ciência e Tecnologia do Norte de Minas, 39900-000 Almenara, MG, Brazil.
| | - Róbson Ricardo Teixeira
- Departamento de Química, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
| | - André Silva de Oliveira
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
- Instituto Federal de Educação, Ciência e Tecnologia do Norte de Minas, 39900-000 Almenara, MG, Brazil.
| | - Ana Paula Martins de Souza
- Departamento de Química, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
| | - Milene Lopes da Silva
- Departamento de Química, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
| | - Sérgio Oliveira de Paula
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P.H. Rolfs, S/N, 36570-900 Viçosa, MG, Brazil.
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81
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Liu J, Kong X, Lee YM, Zhang MK, Guo LY, Lin Y, Lim TK, Lin Q, Xu XQ. Stk38 Modulates Rbm24 Protein Stability to Regulate Sarcomere Assembly in Cardiomyocytes. Sci Rep 2017; 7:44870. [PMID: 28322254 PMCID: PMC5359592 DOI: 10.1038/srep44870] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/13/2017] [Indexed: 01/12/2023] Open
Abstract
RNA-binding protein Rbm24 is a key regulator of heart development and required for sarcomere assembly and heart contractility. Yet, its underlying mechanism remains unclear. Here, we link serine/threonine kinase 38 (Stk38) signaling to the regulation of Rbm24 by showing that Rbm24 phosphorylation and its function could be modulated by Stk38. Using co-immunoprecipitation coupled with mass spectrometry technique, we identified Stk38 as an endogenous binding partner of Rbm24. Stk38 knockdown resulted in decreased Rbm24 protein level in cardiomyocytes. Further studies using Stk38 kinase inhibitor or activator showed that Rbm24 protein stability was regulated in a kinase activity-dependent manner. Deficiency of Stk38 caused reduction of sarcomere proteins and disarrangement of sarcomere, suggesting that Stk38 is essential for Rbm24 to regulate sarcomere assembly. Our results revealed that Stk38 kinase catalyzes the phosphorylation of Rbm24 during sarcomerogensis and this orchestrates accurate sarcomere alignment. This furthers our understanding of the regulatory mechanism of cardiac sarcomere assembly in both physiologic and pathologic contexts, and uncovers a potential novel pathway to cardiomyopathy through modulating the Stk38/Rbm24 protein activity.
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Affiliation(s)
- Jing Liu
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China.,Fujian Key Laboratory of Organ and Tissue Regeneration, Medical College, Xiamen University, 361100, P.R. China
| | - Xu Kong
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China
| | - Yew Mun Lee
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Meng Kai Zhang
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China
| | - Li Yan Guo
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China
| | - Yu Lin
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Xiu Qin Xu
- The Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, 361100, P.R. China.,Fujian Key Laboratory of Organ and Tissue Regeneration, Medical College, Xiamen University, 361100, P.R. China
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82
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Duan W, Song H, Wang H, Chai Y, Su C, Qi J, Shi Y, Gao GF. The crystal structure of Zika virus NS5 reveals conserved drug targets. EMBO J 2017; 36:919-933. [PMID: 28254839 DOI: 10.15252/embj.201696241] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/16/2017] [Accepted: 02/02/2017] [Indexed: 12/31/2022] Open
Abstract
Zika virus (ZIKV) has emerged as major health concern, as ZIKV infection has been shown to be associated with microcephaly, severe neurological disease and possibly male sterility. As the largest protein component within the ZIKV replication complex, NS5 plays key roles in the life cycle and survival of the virus through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains. Here, we present the crystal structures of ZIKV NS5 MTase in complex with an RNA cap analogue (m7GpppA) and the free NS5 RdRp. We have identified the conserved features of ZIKV NS5 MTase and RdRp structures that could lead to development of current antiviral inhibitors being used against flaviviruses, including dengue virus and West Nile virus, to treat ZIKV infection. These results should inform and accelerate the structure-based design of antiviral compounds against ZIKV.
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Affiliation(s)
- Wenqian Duan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Haiyuan Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Su
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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83
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Structural features of Zika virus non-structural proteins 3 and -5 and its individual domains in solution as well as insights into NS3 inhibition. Antiviral Res 2017; 141:73-90. [PMID: 28202376 DOI: 10.1016/j.antiviral.2017.02.005] [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: 11/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/20/2022]
Abstract
Zika virus (ZIKV) has emerged as a pathogen of major health concern. The virus relies on its non-structural protein 5 (NS5) including a methyl-transferase (MTase) and a RNA-dependent RNA polymerase (RdRp) for capping and synthesis of the viral RNA and the nonstructural protein 3 (NS3) with its protease and helicase domain for polyprotein possessing, unwinding dsRNA proceeding replication, and NTPase/RTPase activities. In this study we present for the first time insights into the overall structure of the entire French Polynesia ZIKV NS3 in solution. The protein is elongated and flexible in solution. Solution studies of the individual protease- and helicase domains show the compactness of the two monomeric enzymes as well as the contribution of the 10-residues linker region to the flexibility of the entire NS3. We show also the solution X-ray scattering data of the French Polynesia ZIKV NS5, which is dimeric in solution and switches to oligomers in a concentration-dependent manner. The solution shapes of the MTase and RdRp domains are described. The dimer arrangement of ZIKV NS5 is discussed in terms of its importance for MTase-RdRp communication and concerted interaction with its flexible and monomeric counterpart NS3 during viral replication and capping. The comparison of ZIKV NS3 and -NS5 solution data with the related DENV nonstructural proteins shed light into the similarities and diversities of these classes of enzymes. Finally, the effect of ATPase inhibitors to the enzymatic active ZIKV NS3 and the individual helicase are provided.
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84
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Abstract
Viruses are major pathogenic agents that can cause a variety of diseases, such as AIDS, hepatitis, respiratory diseases, and many more, in humans, plants, and animals. The most prominent of them have been adenoviruses, alphaviruses, flaviviruses, hepatitis C virus, herpesviruses, human immunodeficiency virus of type 1, and picornaviruses. This chapter presents an introductory remark on such viruses, mechanisms of their invasion, and diseases related to them. The inhibition of these viruses is of great concern to human beings. Each of these viruses encodes one or more proteases that play crucial roles in their replication, and thus they are important targets for the design and development of potent antiviral agents. The chapter, therefore, also introduces the readers to such proteases and their structures and functions. This chapter is thus a prelude to the remaining chapters in the book, which present in detail about the different viruses and their proteases.
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Affiliation(s)
- Anjana Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
| | - Satya P. Gupta
- National Institute of Technical Teachers’ Training and Research, Bhopal, Madhya Pradesh, India
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85
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Cao X, Li Y, Jin X, Li Y, Guo F, Jin T. Molecular mechanism of divalent-metal-induced activation of NS3 helicase and insights into Zika virus inhibitor design. Nucleic Acids Res 2016; 44:10505-10514. [PMID: 27915293 PMCID: PMC5137455 DOI: 10.1093/nar/gkw941] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/03/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Zika virus has attracted increasing attention because of its potential for causing human neural disorders, including microcephaly in infants and Guillain–Barré syndrome. Its NS3 helicase domain plays critical roles in NTP-dependent RNA unwinding and translocation during viral replication. Our structural analysis revealed a pre-activation state of NS3 helicase in complex with GTPγS, in which the triphosphate adopts a compact conformation in the absence of any divalent metal ions. In contrast, in the presence of a divalent cation, GTPγS adopts an extended conformation, and the Walker A motif undergoes substantial conformational changes. Both features contribute to more extensive interactions between the GTPγS and the enzyme. Thus, this study provides structural evidence on the allosteric modulation of MgNTP2− on the NS3 helicase activity. Furthermore, the compact conformation of inhibitory NTP identified in this study provides precise information for the rational drug design of small molecule inhibitors for the treatment of ZIKV infection.
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Affiliation(s)
- Xiaocong Cao
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yajuan Li
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangyu Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yuelong Li
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Feng Guo
- School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
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86
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Tay MYF, Smith K, Ng IHW, Chan KWK, Zhao Y, Ooi EE, Lescar J, Luo D, Jans DA, Forwood JK, Vasudevan SG. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production. PLoS Pathog 2016; 12:e1005886. [PMID: 27622521 PMCID: PMC5021334 DOI: 10.1371/journal.ppat.1005886] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/22/2016] [Indexed: 11/24/2022] Open
Abstract
Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18) alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα), allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization. DENV NS5 is critical for virus RNA replication and an important drug target based on its high sequence conservation across serotypes, and the successful development of potent drugs that target the homologous NS5B of hepatitis C virus. NS5 also mediates other functions that are important for innate and adaptive immune responses by the infected host. Extensive gene swapping and functional analyses between NS5 of DENV serotypes 1 and 2, that are the two most disparate in terms of nuclear vs cytoplasmic localization of NS5 identified the last 18 amino acid residues of the ~900 amino-acid residues long protein to be responsible for subcellular localization. Because this region is very flexible and not easily seen in crystal structures of DENV NS5, co-crystals of the newly discovered peptide region with importin α were obtained. Structure-based mutations introduced into a DENV2 infectious clone showed that the proline to threonine at position 884 resulted in NS5 being mostly cytoplasmic without affecting virus replication. However mutation of arginine 888, which is conserved in all flaviviruses, to alanine resulted in a completely non-viable virus, suggesting that the C-terminal region is essential for NS5 function irrespective of its role in subcellular location.
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Affiliation(s)
- Moon Y. F. Tay
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Ivan H. W. Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Kitti W. K. Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yongqian Zhao
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore
- UPMC UMRS CR7—CNRS ERL 8255-INSERM U1135 Centre d’Immunologie et des Maladies Infectieuses. Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine Pierre et Marie Curie, Paris, France
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - David A. Jans
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- * E-mail:
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87
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Sironi M, Forni D, Clerici M, Cagliani R. Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses. PLoS Negl Trop Dis 2016; 10:e0004978. [PMID: 27588756 PMCID: PMC5010288 DOI: 10.1371/journal.pntd.0004978] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/14/2016] [Indexed: 11/18/2022] Open
Abstract
The Flavivirus genus comprises several human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV). Although ZIKV usually causes mild symptoms, growing evidence is linking it to congenital birth defects and to increased risk of Guillain-Barré syndrome. ZIKV encodes a polyprotein that is processed to produce three structural and seven nonstructural (NS) proteins. We investigated the evolution of the viral polyprotein in ZIKV and in related flaviviruses (DENV, Spondweni virus, and Kedougou virus). After accounting for saturation issues, alignment uncertainties, and recombination, we found evidence of episodic positive selection on the branch that separates DENV from the other flaviviruses. NS1 emerged as the major selection target, and selected sites were located in immune epitopes or in functionally important protein regions. Three of these sites are located in an NS1 region that interacts with structural proteins and is essential for virion biogenesis. Analysis of the more recent evolutionary history of ZIKV lineages indicated that positive selection acted on NS5 and NS4B, this latter representing the preferential target. All selected sites were located in the N-terminal portion of NS4B, which inhibits interferon response. One of the positively selected sites (26M/I/T/V) in ZIKV also represents a selection target in sylvatic DENV2 isolates, and a nearby residue evolves adaptively in JEV. Two additional positively selected sites are within a protein region that interacts with host (e.g. STING) and viral (i.e. NS1, NS4A) proteins. Notably, mutations in the NS4B region of other flaviviruses modulate neurovirulence and/or neuroinvasiveness. These results suggest that the positively selected sites we identified modulate viral replication and contribute to immune evasion. These sites should be prioritized in future experimental studies. However, analyses herein detected no selective events associated to the spread of the Asian/American ZIKV lineage.
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Affiliation(s)
- Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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88
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Kumar A, Balakrishna AM, Nartey W, Manimekalai MSS, Grüber G. Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol. Free Radic Biol Med 2016; 97:588-601. [PMID: 27417938 DOI: 10.1016/j.freeradbiomed.2016.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/07/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has the ability to persist within the human host for a long time in a dormant stage and re-merges when the immune system is compromised. The pathogenic bacterium employs an elaborate antioxidant defence machinery composed of the mycothiol- and thioredoxin system in addition to a superoxide dismutase, a catalase, and peroxiredoxins (Prxs). Among the family of Peroxiredoxins, Mtb expresses a 1-cysteine peroxiredoxin, known as alkylhydroperoxide reductase E (MtAhpE), and defined as a potential tuberculosis drug target. The reduced MtAhpE (MtAhpE-SH) scavenges peroxides to become converted to MtAhpE-SOH. To provide continuous availability of MtAhpE-SH, MtAhpE-SOH has to become reduced. Here, we used NMR spectroscopy to delineate the reduced (MtAhpE-SH), sulphenic (MtAhpE-SOH) and sulphinic (MtAhpE-SO2H) states of MtAhpE through cysteinyl-labelling, and provide for the first time evidence of a mycothiol-dependent mechanism of MtAhpE reduction. This is confirmed by crystallographic studies, wherein MtAhpE was crystallized in the presence of mycothiol and the structure was solved at 2.43Å resolution. Combined with NMR-studies, the crystallographic structures reveal conformational changes of important residues during the catalytic cycle of MtAhpE. In addition, alterations of the overall protein in solution due to redox modulation are observed by small angle X-ray scattering (SAXS) studies. Finally, by employing SAXS and dynamic light scattering, insight is provided into the most probable physiological oligomeric state of MtAhpE necessary for activity, being also discussed in the context of concerted substrate binding inside the dimeric MtAhpE.
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Affiliation(s)
- Arvind Kumar
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | | | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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89
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Structure of the NS3 helicase from Zika virus. Nat Struct Mol Biol 2016; 23:752-4. [PMID: 27399257 PMCID: PMC5085289 DOI: 10.1038/nsmb.3258] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 12/27/2022]
Abstract
Zika virus has emerged as a pathogen of major health concern. Here, we present a high-resolution (1.62-Å) crystal structure of the RNA helicase from the French Polynesia strain. The structure is similar to that of the RNA helicase from Dengue virus, with variability in the conformations of loops typically involved in binding ATP and RNA. We identify druggable 'hotspots' that are well suited for in silico and/or fragment-based high-throughput drug discovery.
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90
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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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91
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Subramanian Manimekalai MS, Saw WG, Pan A, Grüber A, Grüber G. Identification of the critical linker residues conferring differences in the compactness of NS5 from Dengue virus serotype 4 and NS5 from Dengue virus serotypes 1-3. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:795-807. [PMID: 27303800 DOI: 10.1107/s2059798316006665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/19/2016] [Indexed: 11/10/2022]
Abstract
Dengue virus (DENV) nonstructural protein 5 (NS5) consists of a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. The cross-talk between these domains occurs via a ten-residue linker. Recent solution studies of DENV NS5 from all four serotypes (DENV-1 to DENV-4) showed that NS5 adopts multiple conformations owing to its flexible linker and that DENV-4 NS5 is more compact and less flexible compared with NS5 from DENV-1 to DENV-3 [Saw et al. (2015), Acta Cryst. D71, 2309-2327]. Here, using a variety of single, double, triple and quadruple mutants of DENV-4 NS5 combined with solution X-ray scattering studies, insight into the critical residues responsible for the differential flexibility of DENV-4 NS5 is presented. The DENV-4 NS5 mutants K271T and S266N/T267A as well as the deletion mutant ΔS266T267 showed enlarged dimensions and flexibility similar to those of DENV-3 NS5. The data indicate that the residues Lys271, Ser266 and Thr267 are important for the compactness of DENV-4 NS5 and therefore may be critical for the regulation of virus replication. Furthermore, quantitative characterization of the flexibility of these DENV-4 NS5 linker mutants using the ensemble-optimization method revealed that these mutants possess a similar conformational distribution to DENV-3 NS5, confirming that these residues in the linker region cause the higher compactness of DENV-4 NS5.
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Affiliation(s)
| | - Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ankita Pan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ardina Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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92
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A Proline-Rich N-Terminal Region of the Dengue Virus NS3 Is Crucial for Infectious Particle Production. J Virol 2016; 90:5451-61. [PMID: 27009958 DOI: 10.1128/jvi.00206-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/17/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Dengue virus is currently the most important insect-borne viral human pathogen. Viral nonstructural protein 3 (NS3) is a key component of the viral replication machinery that performs multiple functions during viral replication and participates in antiviral evasion. Using dengue virus infectious clones and reporter systems to dissect each step of the viral life cycle, we examined the requirements of different domains of NS3 on viral particle assembly. A thorough site-directed mutagenesis study based on solvent-accessible surface areas of NS3 revealed that, in addition to being essential for RNA replication, different domains of dengue virus NS3 are critically required for production of infectious viral particles. Unexpectedly, point mutations in the protease, interdomain linker, or helicase domain were sufficient to abolish infectious particle formation without affecting translation, polyprotein processing, or RNA replication. In particular, we identified a novel proline-rich N-terminal unstructured region of NS3 that contains several amino acid residues involved in infectious particle formation. We also showed a new role for the interdomain linker of NS3 in virion assembly. In conclusion, we present a comprehensive genetic map of novel NS3 determinants for viral particle assembly. Importantly, our results provide evidence of a central role of NS3 in the coordination of both dengue virus RNA replication and particle formation. IMPORTANCE Dengue virus is an important human pathogen, and its prominence is expanding globally; however, basic aspects of its biology are still unclear, hindering the development of effective therapeutic and prophylactic treatments. Little is known about the initial steps of dengue and other flavivirus particle assembly. This process involves a complex interplay between viral and cellular components, making it an attractive antiviral target. Unpredictably, we identified spatially separated regions of the large NS3 viral protein as determinants for dengue virus particle assembly. NS3 is a multifunctional enzyme that participates in different steps of the viral life cycle. Using reporter systems to dissect different viral processes, we identified a novel N-terminal unstructured region of the NS3 protein as crucial for production of viral particles. Based on our findings, we propose new ideas that include NS3 as a possible scaffold for the viral assembly process.
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93
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Kato F, Ishida Y, Oishi S, Fujii N, Watanabe S, Vasudevan SG, Tajima S, Takasaki T, Suzuki Y, Ichiyama K, Yamamoto N, Yoshii K, Takashima I, Kobayashi T, Miura T, Igarashi T, Hishiki T. Novel antiviral activity of bromocriptine against dengue virus replication. Antiviral Res 2016; 131:141-7. [PMID: 27181378 DOI: 10.1016/j.antiviral.2016.04.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/25/2016] [Accepted: 04/28/2016] [Indexed: 11/28/2022]
Abstract
Dengue virus (DENV) infectious disease is a major public health problem worldwide; however, licensed vaccines or specific antiviral drugs against this infection are not available. To identify novel anti-DENV compounds, we screened 1280 pharmacologically active compounds using focus reduction assay. Bromocriptine (BRC) was found to have potent anti-DENV activity and low cytotoxicity (half maximal effective concentration [EC50], 0.8-1.6 μM; and half maximal cytotoxicity concentration [CC50], 53.6 μM). Time-of-drug-addition and time-of-drug-elimination assays suggested that BRC inhibits translation and/or replication steps in the DENV life cycle. A subgenomic replicon system was used to verify that BRC restricts RNA replication step. Furthermore, a single amino acid substitution (N374H) was detected in the NS3 protein that conferred resistance to BRC. In summary, BRC was found to be a novel DENV inhibitor and a potential candidate for the treatment of DENV infectious disease.
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Affiliation(s)
- Fumihiro Kato
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan; Department of Virology 1, National Institute of Infectious Diseases, Japan
| | - Yuki Ishida
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Shigeru Tajima
- Department of Virology 1, National Institute of Infectious Diseases, Japan
| | - Tomohiko Takasaki
- Department of Virology 1, National Institute of Infectious Diseases, Japan
| | - Youichi Suzuki
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Koji Ichiyama
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Naoki Yamamoto
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kentaro Yoshii
- Laboratry of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Ikuo Takashima
- Laboratry of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takeshi Kobayashi
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Tomoyuki Miura
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Tatsuhiko Igarashi
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Takayuki Hishiki
- Laboratory of Primate Model, Institute for Virus Research, Kyoto University, Kyoto, Japan; Viral Infectious Diseases Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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94
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Liu W, Zhang J, Fan JS, Tria G, Grüber G, Yang D. A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein. Biophys J 2016; 110:1943-56. [PMID: 27166803 PMCID: PMC4939551 DOI: 10.1016/j.bpj.2016.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 10/21/2022] Open
Abstract
Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein.
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Affiliation(s)
- Wei Liu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jingfeng Zhang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Giancarlo Tria
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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95
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Saw WG, Tria G, Grüber A, Subramanian Manimekalai MS, Zhao Y, Chandramohan A, Srinivasan Anand G, Matsui T, Weiss TM, Vasudevan SG, Grüber G. Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2309-27. [PMID: 26527147 PMCID: PMC4631481 DOI: 10.1107/s1399004715017721] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/21/2015] [Indexed: 01/22/2023]
Abstract
Infection by the four serotypes of Dengue virus (DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all four Dengue virus serotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain. The DENV-1 to DENV-4 NS5 forms are elongated and flexible in solution, with DENV-4 NS5 being more compact relative to NS5 from DENV-1, DENV-2 and DENV-3. Solution studies of the individual MTase and RdRp domains show the compactness of the RdRp domain as well as the contribution of the MTase domain and the ten-residue linker region to the flexibility of the entire NS5. Swapping the ten-residue linker between DENV-4 NS5FL and DENV-3 NS5FL demonstrated its importance in MTase-RdRp communication and in concerted interaction with viral and host proteins, as probed by amide hydrogen/deuterium mass spectrometry. Conformational alterations owing to RNA binding are presented.
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Affiliation(s)
- Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Giancarlo Tria
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ardina Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Yongqian Zhao
- Program in Emerging Infectious Diseases, Duke–NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Arun Chandramohan
- Department of Biological Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laborator, Menlo Park, California, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Laborator, Menlo Park, California, USA
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke–NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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96
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Nartey W, Basak S, Kamariah N, Manimekalai MSS, Robson S, Wagner G, Eisenhaber B, Eisenhaber F, Grüber G. NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery. FEBS J 2015; 282:4620-38. [DOI: 10.1111/febs.13522] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/28/2015] [Accepted: 09/21/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Wilson Nartey
- School of Biological Sciences; Nanyang Technological University; Singapore City Singapore
| | - Sandip Basak
- School of Biological Sciences; Nanyang Technological University; Singapore City Singapore
| | - Neelagandan Kamariah
- Bioinformatics Institute; Agency for Science; Technology and Research (A*STAR); Singapore City Singapore
| | | | - Scott Robson
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston MA USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston MA USA
| | - Birgit Eisenhaber
- Bioinformatics Institute; Agency for Science; Technology and Research (A*STAR); Singapore City Singapore
| | - Frank Eisenhaber
- School of Biological Sciences; Nanyang Technological University; Singapore City Singapore
- School of Computer Engineering; Nanyang Technological University (NTU); Singapore City Singapore
- Department of Biological Sciences; National University of Singapore; Singapore
| | - Gerhard Grüber
- School of Biological Sciences; Nanyang Technological University; Singapore City Singapore
- Bioinformatics Institute; Agency for Science; Technology and Research (A*STAR); Singapore City Singapore
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97
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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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98
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Flexibility of NS5 Methyltransferase-Polymerase Linker Region Is Essential for Dengue Virus Replication. J Virol 2015; 89:10717-21. [PMID: 26269182 DOI: 10.1128/jvi.01239-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/03/2015] [Indexed: 11/20/2022] Open
Abstract
We examined the function of the conserved Val/Ile residue within the dengue virus NS5 interdomain linker (residues 263 to 272) by site-directed mutagenesis. Gly substitution or Gly/Pro insertion after the conserved residue increased the linker flexibility and created slightly attenuated viruses. In contrast, Pro substitution abolished virus replication by imposing rigidity in the linker and restricting NS5's conformational plasticity. Our biochemical and reverse genetics experiments demonstrate that NS5 utilizes conformational regulation to achieve optimum viral replication.
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99
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Lim SP, Noble CG, Shi PY. The dengue virus NS5 protein as a target for drug discovery. Antiviral Res 2015; 119:57-67. [DOI: 10.1016/j.antiviral.2015.04.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/19/2015] [Accepted: 04/11/2015] [Indexed: 12/25/2022]
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100
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Kamariah N, Manimekalai MSS, Nartey W, Eisenhaber F, Eisenhaber B, Grüber G. Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1139-52. [PMID: 26092085 DOI: 10.1016/j.bbabio.2015.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
Abstract
Redox homeostasis is significant for the survival of pro- and eukaryotic cells and is crucial for defense against reactive oxygen species like superoxide and hydrogen peroxide. In Escherichia coli, the reduction of peroxides occurs via the redox active disulfide center of the alkyl hydroperoxide reductase C subunit (AhpC), whose reduced state becomes restored by AhpF. The 57kDa EcAhpF contains an N-terminal domain (NTD), which catalyzes the electron transfer from NADH via an FAD of the C-terminal domain into EcAhpC. The NTD is connected to the C-terminal domain via a linker. Here, the first crystal structure of E. coli AhpF bound with NADH and NAD(+) has been determined at 2.5Å and 2.4Å resolution, respectively. The NADH-bound form of EcAhpF reveals that the NADH-binding domain is required to alter its conformation to bring a bound NADH to the re-face of the isoalloxazine ring of the flavin, and thereby render the NADH-domain dithiol center accessible to the NTD disulfide center for electron transfer. The NAD(+)-bound form of EcAhpF shows conformational differences for the nicotinamide end moieties and its interacting residue M467, which is proposed to represent an intermediate product-release conformation. In addition, the structural alterations in EcAhpF due to NADH- and NAD(+)-binding in solution are shown by small angle X-ray scattering studies. The EcAhpF is revealed to adopt many intermediate conformations in solution to facilitate the electron transfer from the substrate NADH to the C-terminal domain, and subsequently to the NTD of EcAhpF for the final step of AhpC reduction.
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Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | | | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore; Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore 117597, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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