151
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Schreiber A, Liedmann S, Brunotte L, Anhlan D, Ehrhardt C, Ludwig S. Type I interferon antagonistic properties of influenza B virus polymerase proteins. Cell Microbiol 2019; 22:e13143. [PMID: 31711273 DOI: 10.1111/cmi.13143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/24/2022]
Abstract
The innate immune system, in particular the type I interferon (IFN) response, is a powerful defence against virus infections. In turn, many if not all viruses have evolved various means to circumvent, resist, or counteract this host response to ensure efficient replication and propagation. Influenza viruses are no exception to this rule, and several viral proteins have been described to possess IFN-antagonistic functions. Although the viral nonstructural protein 1 appears to be a major antagonist in influenza A and B viruses (IAV and IBV), we have previously shown that a specific motif in the IAV polymerase proteins exerts an IFN-suppressive function very early in infection. The question remained whether a similar function would also exist in IBV polymerases. Here, we show that indeed a specific amino acid position (A523) of the PB1 protein in the IBV polymerase complex confers IFN-antagonistic properties. Mutation of this position leads to enhanced activation of the IFN-mediated signalling pathway after infection and subsequent reduction of virus titres. This indicates that inhibition of innate immune responses is a conserved activity shared by polymerase proteins of IAV and IBV.
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Affiliation(s)
- André Schreiber
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
| | - Swantje Liedmann
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
| | - Linda Brunotte
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
| | - Darisuren Anhlan
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
| | - Christina Ehrhardt
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster (IVM), Centre for Molecular Biology of Inflammation (ZMBE), Westfälische Wilhelms-Universität, Muenster, Germany
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152
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Suttie A, Deng YM, Greenhill AR, Dussart P, Horwood PF, Karlsson EA. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019; 55:739-768. [PMID: 31428925 PMCID: PMC6831541 DOI: 10.1007/s11262-019-01700-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
- School of Health and Life Sciences, Federation University, Churchill, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yi-Mo Deng
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew R Greenhill
- School of Health and Life Sciences, Federation University, Churchill, Australia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Erik A Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia.
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153
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Gao S, Zhang W, Lu C, Cao M, Cen S, Peng Y, Deng T. Identification of a Type-Specific Promoter Element That Differentiates between Influenza A and B Viruses. J Virol 2019; 93:e01164-19. [PMID: 31534045 PMCID: PMC6854497 DOI: 10.1128/jvi.01164-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/05/2019] [Indexed: 11/20/2022] Open
Abstract
Type A and type B influenza viruses (FluA and FluB viruses) are two major human pathogens that share common structural and functional features. FluA and FluB viruses can reassort within each type but never between the types. Here, we bioinformatically analyzed all promoter sequences of FluA and FluB viruses and confirmed the presence of the type-specific promoter elements. We then studied the promoter elements with cell-based in vivo assays and an in vitro replication initiation assay. Our results identified, for the first time, a type-specific promoter element-the nucleotide at position 5 in the 3' end of the viral RNA (vRNA)-that plays a key role(s) in modulating polymerase activity in a type-specific manner. Interestingly, swapping the promoter element between FluA and FluB recombinant viruses showed different tolerances: the replacement of FluA virus-specific U5 with FluB virus-specific C5 in influenza virus A/WSN/33 (H1N1) could be reverted to U5 after 2 to 3 passages, while the replacement of FluB virus-specific C5 with FluA virus-specific U5 in influenza virus B/Yamagata/88 could be maintained, but with significantly reduced replication efficiency. Therefore, our findings indicate that the nucleotide variation at position 5 in the 3' end of the vRNA promoter between FluA and FluB viruses contributes to their RNP incompatibility, which may shed new light on the mechanisms of intertypic exclusion of reassortment between FluA and FluB viruses.IMPORTANCE Genetic reassortment of influenza virus plays a key role in virus evolution and the emergence of pandemic strains. The reassortment occurs extensively within either FluA or FluB viruses but never between them. Here, we bioinformatically compared available promoter sequences of FluA and FluB viruses and confirmed the presence of the type-specific promoter elements. Our in vivo and in vitro mutagenesis studies showed that a type-specific promoter element-the nucleotide at position 5 in the 3' end of vRNA promoters-plays key roles in modulating polymerase activity. Interestingly, FluA and FluB viruses showed different tolerances upon key promoter element swapping in the context of virus infections. We concluded that the nucleotide at position 5 in the 3' end of the vRNA promoters of FluA and FluB viruses is a critical type-specific determinant. This work has implications for further elucidating the mechanisms of the intertypic exclusion of reassortment between FluA and FluB viruses.
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Affiliation(s)
- Shuman Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Wenyu Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Congyu Lu
- College of Biology, Hunan University, Changsha, People's Republic of China
| | - Mengmeng Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, People's Republic of China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, People's Republic of China
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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154
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Baker SF, Ledwith MP, Mehle A. Differential Splicing of ANP32A in Birds Alters Its Ability to Stimulate RNA Synthesis by Restricted Influenza Polymerase. Cell Rep 2019; 24:2581-2588.e4. [PMID: 30184493 DOI: 10.1016/j.celrep.2018.08.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 05/15/2018] [Accepted: 08/06/2018] [Indexed: 12/21/2022] Open
Abstract
Adaptation of viruses to their hosts can result in specialization and a restricted host range. Species-specific polymorphisms in the influenza virus polymerase restrict its host range during transmission from birds to mammals. ANP32A was recently identified as a cellular co-factor affecting polymerase adaption and activity. Avian influenza polymerases require ANP32A containing an insertion resulting from an exon duplication uniquely encoded in birds. Here we find that natural splice variants surrounding this exon create avian ANP32A proteins with distinct effects on polymerase activity. We demonstrate species-independent direct interactions between all ANP32A variants and the PB2 polymerase subunit. This interaction is enhanced in the presence of viral genomic RNA. In contrast, only avian ANP32A restored ribonucleoprotein complex assembly for a restricted polymerase by enhancing RNA synthesis. Our data suggest that ANP32A splicing variation among birds differentially affects viral replication, polymerase adaption, and the potential of avian hosts to be reservoirs.
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Affiliation(s)
- Steven F Baker
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell P Ledwith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
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155
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Förster A, Schulze-Briese C. A shared vision for macromolecular crystallography over the next five years. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064302. [PMID: 31832486 PMCID: PMC6892709 DOI: 10.1063/1.5131017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.
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156
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Rodriguez P, Marcos-Villar L, Zamarreño N, Yángüez E, Nieto A. Mutations of the segment-specific nucleotides at the 3' end of influenza virus NS segment control viral replication. Virology 2019; 539:104-113. [PMID: 31706162 DOI: 10.1016/j.virol.2019.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
The vRNAs of influenza A viruses contain 12 and 13 nucleotide-long sequences at their 3' and 5' termini respectively that are highly conserved and constitute the vRNA promoter. These sequences and the next three segment-specific nucleotides show inverted partial complementarity and are followed by several unpaired nucleotides of poorly characterized function at the 3' end. We have performed systematic point-mutations at the segment-specific nucleotides 15-18 of the 3'-end of a NS-like vRNA segment. All NS-like vRNAs containing mutations at position 15, and some at positions 16-18 showed reduced transcription/replication efficiency in a transfection/infection system. In addition, the replication of recombinant viruses containing mutations at position 15 was impaired both in single and multi-cycle experiments. This reduction was the consequence of a decreased expression of the NS segment. The data indicate that NS1 plays a role in the transcription/replication of its own segment, which elicits a global defect on virus replication.
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Affiliation(s)
- Paloma Rodriguez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Laura Marcos-Villar
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Noelia Zamarreño
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Emilio Yángüez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Amelia Nieto
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain.
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157
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Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. J Virol 2019; 93:JVI.00834-19. [PMID: 31462570 DOI: 10.1128/jvi.00834-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/19/2019] [Indexed: 01/16/2023] Open
Abstract
In various positive-sense single-stranded RNA viruses, a low-fidelity viral RNA-dependent RNA polymerase (RdRp) confers attenuated phenotypes by increasing the mutation frequency. We report a negative-sense single-stranded RNA virus RdRp mutant strain with a mutator phenotype. Based on structural data of RdRp, rational targeting of key residues, and screening of fidelity variants, we isolated a novel low-fidelity mutator strain of influenza virus that harbors a Tyr82-to-Cys (Y82C) single-amino-acid substitution in the PB1 polymerase subunit. The purified PB1-Y82C polymerase indeed showed an increased frequency of misincorporation compared with the wild-type PB1 in an in vitro biochemical assay. To further investigate the effects of position 82 on PB1 polymerase fidelity, we substituted various amino acids at this position. As a result, we isolated various novel mutators other than PB1-Y82C with higher mutation frequencies. The structural model of influenza virus polymerase complex suggested that the Tyr82 residue, which is located at the nucleoside triphosphate entrance tunnel, may influence a fidelity checkpoint. Interestingly, although the PB1-Y82C variant replicated with wild-type PB1-like kinetics in tissue culture, the 50% lethal dose of the PB1-Y82C mutant was 10 times lower than that of wild-type PB1 in embryonated chicken eggs. In conclusion, our data indicate that the Tyr82 residue of PB1 has a crucial role in regulating polymerase fidelity of influenza virus and is closely related to attenuated pathogenic phenotypes in vivo IMPORTANCE Influenza A virus rapidly acquires antigenic changes and antiviral drug resistance, which limit the effectiveness of vaccines and drug treatments, primarily owing to its high rate of evolution. Virus populations formed by quasispecies can contain resistance mutations even before a selective pressure is applied. To study the effects of the viral mutation spectrum and quasispecies, high- and low-fidelity variants have been isolated for several RNA viruses. Here, we report the discovery of a low-fidelity RdRp variant of influenza A virus that contains a substitution at Tyr82 in PB1. Viruses containing the PB1-Y82C substitution showed growth kinetics and viral RNA synthesis levels similar to those of the wild-type virus in cell culture; however, they had significantly attenuated phenotypes in a chicken egg infection experiment. These data demonstrated that decreased RdRp fidelity attenuates influenza A virus in vivo, which is a desirable feature for the development of safer live attenuated vaccine candidates.
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158
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Shafiuddin M, Boon ACM. RNA Sequence Features Are at the Core of Influenza A Virus Genome Packaging. J Mol Biol 2019; 431:4217-4228. [PMID: 30914291 PMCID: PMC6756997 DOI: 10.1016/j.jmb.2019.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/18/2019] [Accepted: 03/11/2019] [Indexed: 11/23/2022]
Abstract
The influenza A virus (IAV), a respiratory pathogen for humans, poses serious medical and economic challenges to global healthcare systems. The IAV genome, consisting of eight single-stranded viral RNA segments, is incorporated into virions by a complex process known as genome packaging. Specific RNA sequences within the viral RNA segments serve as signals that are necessary for genome packaging. Although efficient packaging is a prerequisite for viral infectivity, many of the mechanistic details about this process are still missing. In this review, we discuss the recent advances toward the understanding of IAV genome packaging and focus on the RNA features that play a role in this process.
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Affiliation(s)
- Md Shafiuddin
- Department of Internal Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Adrianus C M Boon
- Department of Internal Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA.
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159
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Chen KY, Santos Afonso ED, Enouf V, Isel C, Naffakh N. Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. PLoS Pathog 2019; 15:e1008034. [PMID: 31581279 PMCID: PMC6776259 DOI: 10.1371/journal.ppat.1008034] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022] Open
Abstract
The influenza A virus RNA-dependent RNA polymerase complex consists in three subunits, PB2, PB1 and PA, that perform transcription and replication of the viral genome through very distinct mechanisms. Biochemical and structural studies have revealed that the polymerase can adopt multiple conformations and form oligomers. However so far it remained unclear whether the available oligomeric crystal structures represent a functional state of the polymerase. Here we gained new insights into this question, by investigating the incompatibility between non-cognate subunits of influenza polymerase brought together through genetic reassortment. We observed that a 7:1 reassortant virus whose PB2 segment derives from the A/WSN/33 (WSN) virus in an otherwise A/PR/8/34 (PR8) backbone is attenuated, despite a 97% identity between the PR8-PB2 and WSN-PB2 proteins. Independent serial passages led to the selection of phenotypic revertants bearing distinct second-site mutations on PA, PB1 and/or PB2. The constellation of mutations present on one revertant virus was studied extensively using reverse genetics and cell-based reconstitution of the viral polymerase. The PA-E349K mutation appeared to play a major role in correcting the initial defect in replication (cRNA -> vRNA) of the PR8xWSN-PB2 reassortant. Strikingly the PA-E349K mutation, and also the PB2-G74R and PB1-K577G mutations present on other revertants, are located at a dimerization interface of the polymerase. All three restore wild-type-like polymerase activity in a minigenome assay while decreasing the level of polymerase dimerization. Overall, our data show that the polymerase subunits co-evolve to ensure not only optimal inter-subunit interactions within the heterotrimer, but also proper levels of dimerization of the heterotrimer which appears to be essential for efficient viral RNA replication. Our findings point to influenza polymerase dimerization as a feature that is controlled by a complex interplay of genetic determinants, can restrict genetic reassortment, and could become a target for antiviral drug development.
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Affiliation(s)
- Kuang-Yu Chen
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Vincent Enouf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Centre National de Référence des Virus des Infections Respiratoires, Institut Pasteur, Paris, France
- Pasteur International Bioresources network (PIBnet), Plateforme de Microbiologie Mutualisée (P2M), Institut Pasteur, Paris, France
| | - Catherine Isel
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail:
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160
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Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans. Pathogens 2019; 8:pathogens8040168. [PMID: 31574965 PMCID: PMC6963926 DOI: 10.3390/pathogens8040168] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 12/14/2022] Open
Abstract
A large number of human genes associated with viral infections contain single nucleotide polymorphisms (SNPs), which represent a genetic variation caused by the change of a single nucleotide in the DNA sequence. SNPs are located in coding or non-coding genomic regions and can affect gene expression or protein function by different mechanisms. Furthermore, they have been linked to multiple human diseases, highlighting their medical relevance. Therefore, the identification and analysis of this kind of polymorphisms in the human genome has gained high importance in the research community, and an increasing number of studies have been published during the last years. As a consequence of this exhaustive exploration, an association between the presence of some specific SNPs and the susceptibility or severity of many infectious diseases in some risk population groups has been found. In this review, we discuss the relevance of SNPs that are important to understand the pathology derived from influenza A virus (IAV) infections in humans and the susceptibility of some individuals to suffer more severe symptoms. We also discuss the importance of SNPs for IAV vaccine effectiveness.
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161
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Abstract
RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.
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Affiliation(s)
- Mark A Boerneke
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
| | - Jeffrey E Ehrhardt
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
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162
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Sato Y, Aiba Y, Yajima S, Tanabe T, Higuchi K, Nishizawa S. Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region. Chembiochem 2019; 20:2752-2756. [DOI: 10.1002/cbic.201900331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuri Aiba
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Sayaka Yajima
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaaki Tanabe
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Kei Higuchi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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163
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Ghorbani A, Ngunjiri JM, Lee CW. Influenza A Virus Subpopulations and Their Implication in Pathogenesis and Vaccine Development. Annu Rev Anim Biosci 2019; 8:247-267. [PMID: 31479617 DOI: 10.1146/annurev-animal-021419-083756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The concept of influenza A virus (IAV) subpopulations emerged approximately 75 years ago, when Preben von Magnus described "incomplete" virus particles that interfere with the replication of infectious virus. It is now widely accepted that infectious particles constitute only a minor portion of biologically active IAV subpopulations. The IAV quasispecies is an extremely diverse swarm of biologically and genetically heterogeneous particle subpopulations that collectively influence the evolutionary fitness of the virus. This review summarizes the current knowledge of IAV subpopulations, focusing on their biologic and genomic diversity. It also discusses the potential roles IAV subpopulations play in virus pathogenesis and live attenuated influenza vaccine development.
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Affiliation(s)
- Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , ,
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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164
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Staller E, Sheppard CM, Neasham PJ, Mistry B, Peacock TP, Goldhill DH, Long JS, Barclay WS. ANP32 Proteins Are Essential for Influenza Virus Replication in Human Cells. J Virol 2019; 93:e00217-19. [PMID: 31217244 PMCID: PMC6694824 DOI: 10.1128/jvi.00217-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
ANP32 proteins have been implicated in supporting influenza virus replication, but most of the work to date has focused on the ability of avian Anp32 proteins to overcome restriction of avian influenza polymerases in human cells. Using a CRISPR approach, we show that the human acidic nuclear phosphoproteins (ANPs) ANP32A and ANP32B are functionally redundant but essential host factors for mammalian-adapted influenza A virus (IAV) and influenza B virus (IBV) replication in human cells. When both proteins are absent from human cells, influenza polymerases are unable to replicate the viral genome, and infectious virus cannot propagate. Provision of exogenous ANP32A or ANP32B recovers polymerase activity and virus growth. We demonstrate that this redundancy is absent in the murine Anp32 orthologues; murine Anp32A is incapable of recovering IAV polymerase activity, while murine Anp32B can do so. Intriguingly, IBV polymerase is able to use murine Anp32A. We show, using a domain swap and point mutations, that the leucine-rich repeat (LRR) 5 region comprises an important functional domain for mammalian ANP32 proteins. Our approach has identified a pair of essential host factors for influenza virus replication and can be harnessed to inform future interventions.IMPORTANCE Influenza virus is the etiological agent behind some of the most devastating infectious disease pandemics to date, and influenza outbreaks still pose a major threat to public health. Influenza virus polymerase, the molecule that copies the viral RNA genome, hijacks cellular proteins to support its replication. Current anti-influenza drugs are aimed against viral proteins, including the polymerase, but RNA viruses like influenza tend to become resistant to such drugs very rapidly. An alternative strategy is to design therapeutics that target the host proteins that are necessary for virus propagation. Here, we show that the human proteins ANP32A and ANP32B are essential for influenza A and B virus replication, such that in their absence cells become impervious to the virus. We map the proviral activity of ANP32 proteins to one region in particular, which could inform future intervention.
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Affiliation(s)
- Ecco Staller
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Carol M Sheppard
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Peter J Neasham
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Bhakti Mistry
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Thomas P Peacock
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Daniel H Goldhill
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Jason S Long
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Wendy S Barclay
- Section of Molecular Virology, Imperial College London, St Mary's Campus, London, United Kingdom
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165
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Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E. Structures of influenza A virus RNA polymerase offer insight into viral genome replication. Nature 2019; 573:287-290. [PMID: 31485076 PMCID: PMC6795553 DOI: 10.1038/s41586-019-1530-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022]
Abstract
Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans1,2. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPolA) composed of PB1, PB2 and PA subunits3-5. Although the high-resolution crystal structure of FluPolA of bat influenza A virus has previously been reported6, there are no complete structures available for human and avian FluPolA. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase7-10-remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPolA from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPolA forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPolA bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPolA dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPolA dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPolA, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPolA that could be targeted in the development of antiviral drugs.
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Affiliation(s)
- Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Itziar Serna Martin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Narin Hengrung
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Didcot, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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166
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mSphere of Influence: Resolution of the Structure of an Influenza Virus Polymerase Is a Game Changer. mSphere 2019; 4:4/4/e00473-19. [PMID: 31434746 PMCID: PMC6706468 DOI: 10.1128/msphere.00473-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mathilde Richard works in the field of virology, more specifically on the evolution and pathogenesis of influenza viruses. In this mSphere of Influence article, she reflects on how the two articles “Structure of Influenza A Polymerase Bound to the Viral RNA Promoter” by A. Pflug, D. Guilligay, S. Reich, and S. Cusack (Nature 516:355–360, 2014, https://doi.org/10.1038/nature14008) and “Structural Insight into Cap-Snatching and RNA Synthesis by Influenza Polymerase” by S. Reich, D. Guilligay, A. Pflug, H. Malet, I. Berger, et al. (Nature 516:361–366, 2014, https://doi.org/10.1038/nature14009) made an impact on her by providing new grounds to study the influenza virus polymerase and its role in virus biology and evolution. Mathilde Richard works in the field of virology, more specifically on the evolution and pathogenesis of influenza viruses. In this mSphere of Influence article, she reflects on how the two articles “Structure of Influenza A Polymerase Bound to the Viral RNA Promoter” by A. Pflug, D. Guilligay, S. Reich, and S. Cusack (Nature 516:355–360, 2014, https://doi.org/10.1038/nature14008) and “Structural Insight into Cap-Snatching and RNA Synthesis by Influenza Polymerase” by S. Reich, D. Guilligay, A. Pflug, H. Malet, I. Berger, et al. (Nature 516:361–366, 2014, https://doi.org/10.1038/nature14009) made an impact on her by providing new grounds to study the influenza virus polymerase and its role in virus biology and evolution.
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167
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De Vlugt C, Sikora D, Rocheleau L, Pelchat M. Priming and realignment by the influenza a virus RdRp is dependent on the length of the host primers and the extent of base pairing to viral RNA. Virology 2019; 536:91-100. [PMID: 31404845 DOI: 10.1016/j.virol.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 11/25/2022]
Abstract
Initiation of influenza A virus (IAV) transcription depends on RNA primers derived from host RNAs. During this process, some primers are elongated by a few nucleotides, realigned on the viral RNA templates (vRNA), and then used to initiate another round of transcription. Here, we used information on the host primers used by four IAV strains and four mini-replicons to investigate the characteristics of primer undergoing priming and realignment. We report that primers are biased towards this mechanism on the basis of length and RNA duplex stability with the vRNA templates. Priming and realignment results in primers three nucleotides longer, ending in a nucleotide sequence able to base pair with the 3' end of the vRNA template. By acting on primers based on length and sequence compatibility with the 3' end of the vRNA, priming and realignment rescues suboptimal primers, converting them into ones that can efficiently initiate transcription.
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Affiliation(s)
- Corey De Vlugt
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Dorota Sikora
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Lynda Rocheleau
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.
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168
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Di Giorgio A, Duca M. Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. MEDCHEMCOMM 2019; 10:1242-1255. [PMID: 31534649 PMCID: PMC6748380 DOI: 10.1039/c9md00195f] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in many pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified. Among the most important ones, one can mention prokaryotic ribosomal RNA which is the target of several marketed antibiotics, viral RNAs or oncogenic microRNAs that are tightly involved in the development and progression of various cancers. Oligonucleotides are efficient and specific RNA targeting agents but suffer from poor pharmacodynamic and pharmacokinetic properties. For this reason, a number of synthetic small-molecule ligands have been identified and studied upon screening of chemical libraries or focused design of RNA binders. In this review, we report the most relevant examples of synthetic compounds bearing sufficient selectivity to envisage clinical studies and future therapeutic applications with a particular attention for the main strategies that can be undertaken toward the improvement of selectivity and biological activity.
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Affiliation(s)
- A Di Giorgio
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
| | - M Duca
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
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169
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Zhang J, Hu Y, Musharrafieh R, Yin H, Wang J. Focusing on the Influenza Virus Polymerase Complex: Recent Progress in Drug Discovery and Assay Development. Curr Med Chem 2019; 26:2243-2263. [PMID: 29984646 DOI: 10.2174/0929867325666180706112940] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 03/27/2018] [Accepted: 05/06/2018] [Indexed: 12/17/2022]
Abstract
Influenza viruses are severe human pathogens that pose persistent threat to public health. Each year more people die of influenza virus infection than that of breast cancer. Due to the limited efficacy associated with current influenza vaccines, as well as emerging drug resistance from small molecule antiviral drugs, there is a clear need to develop new antivirals with novel mechanisms of action. The influenza virus polymerase complex has become a promising target for the development of the next-generation of antivirals for several reasons. Firstly, the influenza virus polymerase, which forms a heterotrimeric complex that consists of PA, PB1, and PB2 subunits, is highly conserved. Secondly, both individual polymerase subunit (PA, PB1, and PB2) and inter-subunit interactions (PA-PB1, PB1- PB2) represent promising drug targets. Lastly, growing insight into the structure and function of the polymerase complex has spearheaded the structure-guided design of new polymerase inhibitors. In this review, we highlight recent progress in drug discovery and assay development targeting the influenza virus polymerase complex and discuss their therapeutic potentials.
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Affiliation(s)
- Jiantao Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Rami Musharrafieh
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Hang Yin
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States.,BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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170
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Pflug A, Gaudon S, Resa-Infante P, Lethier M, Reich S, Schulze WM, Cusack S. Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors. Nucleic Acids Res 2019; 46:956-971. [PMID: 29202182 PMCID: PMC5778463 DOI: 10.1093/nar/gkx1210] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/22/2017] [Indexed: 12/24/2022] Open
Abstract
Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation (’priming state’) and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA. In particular, mutation of PB2 Arg264, which interacts with the triphosphate linkage in the cap, significantly and specifically decreases cap-dependent transcription. We also compare the configuration of the midlink and cap-binding domains in the priming state with their very different relative arrangement (called the ‘apo’ state) in structures where the potent cap-binding inhibitor VX-787, or a close analogue, is bound. In the ‘apo’ state the inhibitor makes additional interactions to the midlink domain that increases its affinity beyond that to the cap-binding domain alone. The comparison suggests that the mechanism of resistance of certain mutations that allow virus to escape from VX-787, notably PB2 N510T, can only be rationalized if VX-787 has a dual mode of action, direct inhibition of capped RNA binding as well as stabilization of the transcriptionally inactive ‘apo’ state.
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Affiliation(s)
- Alexander Pflug
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stephanie Gaudon
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Patricia Resa-Infante
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Mathilde Lethier
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stefan Reich
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Wiebke M Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
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171
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Ren X, Yu Y, Li H, Huang J, Zhou A, Liu S, Hu P, Li B, Qi W, Liao M. Avian Influenza A Virus Polymerase Recruits Cellular RNA Helicase eIF4A3 to Promote Viral mRNA Splicing and Spliced mRNA Nuclear Export. Front Microbiol 2019; 10:1625. [PMID: 31379779 PMCID: PMC6646474 DOI: 10.3389/fmicb.2019.01625] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/01/2019] [Indexed: 01/16/2023] Open
Abstract
The influenza A virus replicates in a broad range of avian and mammalian species by hijacking cellular factors and processes. Avian influenza A viruses (AIVs) generally propagated poorly in mammalian cells, but some mutants of virus-encoded RNA polymerase components, especially PB2 subunit, can overcome host restriction. Host factors associated with PB2 may be essential for efficient AIV replication in mammalian cells. Here, we infected human cells with the PB2 Flag-tagged replication-competent recombinant AIV and identified cellular proteins that coprecipitate with PB2 protein by mass spectrometry. We confirmed one of the coprecipitating host factors, DEAD-box protein eIF4A3, that interacts with viral PB2, PB1, and NP proteins. Depletion of endogenous eIF4A3 significantly reduced virus replication. Later studies showed that eIF4A3 is essential for viral RNA polymerase activity and viral RNAs synthesis. Upon systematic dissection of the influenza virus progeny mRNA generation, from pre-mRNA processing to nuclear export, we found that the depletion of eIF4A3 resulted in significant defects in the ratio of M2 to M1 and NS2 to NS1, and the proportion of viral spliced mRNA in the nucleus increased, indicating that eIF4A3 plays a significant function in viral nascent intron mRNA splicing and spliced mRNA (M2 and NS2) nuclear export. Additionally, we confirmed that in specific deletion of eIF4A3, the synthesis of reduced NS2 can significantly impair neo-synthetized viral ribonucleoprotein (vRNP) nuclear export. Taken together, our findings revealed that eIF4A3 is a key mediator of AIV polymerase activity, mRNA splicing, and spliced mRNA nuclear export.
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Affiliation(s)
- Xingxing Ren
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuandi Yu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Huanan Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinyu Huang
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Aobaixue Zhou
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shukai Liu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Pingsheng Hu
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bo Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory (Guangzhou), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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172
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Ogino T, Green TJ. RNA Synthesis and Capping by Non-segmented Negative Strand RNA Viral Polymerases: Lessons From a Prototypic Virus. Front Microbiol 2019; 10:1490. [PMID: 31354644 PMCID: PMC6636387 DOI: 10.3389/fmicb.2019.01490] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022] Open
Abstract
Non-segmented negative strand (NNS) RNA viruses belonging to the order Mononegavirales are highly diversified eukaryotic viruses including significant human pathogens, such as rabies, measles, Nipah, and Ebola. Elucidation of their unique strategies to replicate in eukaryotic cells is crucial to aid in developing anti-NNS RNA viral agents. Over the past 40 years, vesicular stomatitis virus (VSV), closely related to rabies virus, has served as a paradigm to study the fundamental molecular mechanisms of transcription and replication of NNS RNA viruses. These studies provided insights into how NNS RNA viruses synthesize 5'-capped mRNAs using their RNA-dependent RNA polymerase L proteins equipped with an unconventional mRNA capping enzyme, namely GDP polyribonucleotidyltransferase (PRNTase), domain. PRNTase or PRNTase-like domains are evolutionally conserved among L proteins of all known NNS RNA viruses and their related viruses belonging to Jingchuvirales, a newly established order, in the class Monjiviricetes, suggesting that they may have evolved from a common ancestor that acquired the unique capping system to replicate in a primitive eukaryotic host. This article reviews what has been learned from biochemical and structural studies on the VSV RNA biosynthesis machinery, and then focuses on recent advances in our understanding of regulatory and catalytic roles of the PRNTase domain in RNA synthesis and capping.
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Affiliation(s)
- Tomoaki Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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173
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Discovery of 5-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrazin-2(1H)-one derivatives as new potent PB2 inhibitors. Bioorg Med Chem Lett 2019; 29:1609-1613. [DOI: 10.1016/j.bmcl.2019.04.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 11/22/2022]
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174
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Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. mBio 2019; 10:mBio.01162-19. [PMID: 31213560 PMCID: PMC6581862 DOI: 10.1128/mbio.01162-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The emergence of the PB2 E627K substitution is critical in the mammalian adaptation and pathogenesis of AIV. H7N9 AIVs that emerged in 2013 possess a prominent ability in gaining the PB2 E627K mutation in humans. Here, we demonstrate that the acquisition of the H7N9 PB2 E627K mutation is driven by the low polymerase activity conferred by the viral PA protein in human cells, and four PA residues are collectively involved in this process. Notably, the H7N9 PA protein leads to significant dependence of viral polymerase function on human ANP32A protein, and Anp32a knockout abolishes PB2 E627K acquisition in mice. These findings reveal that viral PA and host ANP32A are crucial for the emergence of PB2 E627K during adaptation of H7N9 AIVs to humans. Avian influenza viruses (AIVs) must acquire mammalian-adaptive mutations before they can efficiently replicate in and transmit among humans. The PB2 E627K mutation is known to play a prominent role in the mammalian adaptation of AIVs. The H7N9 AIVs that emerged in 2013 in China easily acquired the PB2 E627K mutation upon replication in humans. Here, we generate a series of reassortant or mutant H7N9 AIVs and test them in mice. We show that the low polymerase activity attributed to the viral PA protein is the intrinsic driving force behind the emergence of PB2 E627K during H7N9 AIV replication in mice. Four residues in the N-terminal region of PA are critical in mediating the PB2 E627K acquisition. Notably, due to the identity of viral PA protein, the polymerase activity and growth of H7N9 AIV are highly sensitive to changes in expression levels of human ANP32A protein. Furthermore, the impaired viral polymerase activity of H7N9 AIV caused by the depletion of ANP32A led to reduced virus replication in Anp32a−/− mice, abolishing the acquisition of the PB2 E627K mutation and instead driving the virus to acquire the alternative PB2 D701N mutation. Taken together, our findings show that the emergence of the PB2 E627K mutation of H7N9 AIV is driven by the intrinsic low polymerase activity conferred by the viral PA protein, which also involves the engagement of mammalian ANP32A.
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175
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Structural insight into RNA synthesis by influenza D polymerase. Nat Microbiol 2019; 4:1750-1759. [PMID: 31209309 DOI: 10.1038/s41564-019-0487-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/13/2019] [Indexed: 01/03/2023]
Abstract
The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design.
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176
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Kouba T, Drncová P, Cusack S. Structural snapshots of actively transcribing influenza polymerase. Nat Struct Mol Biol 2019; 26:460-470. [PMID: 31160782 PMCID: PMC7610713 DOI: 10.1038/s41594-019-0232-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 12/15/2022]
Abstract
Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.
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Affiliation(s)
- Tomas Kouba
- European Molecular Biology Laboratory, Grenoble, France
| | - Petra Drncová
- European Molecular Biology Laboratory, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France.
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177
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Abstract
Atomic structures of the polymerase–endonuclease complex of the orthomyxovirus influenza and the orthobunyavirus La Crosse—two distinct segmented negative-sense (SNS) RNA viruses—demonstrate that binding of the genomic 5′ RNA rearranges the catalytic residues of the RNA-dependent RNA-polymerase (RdRP). Working with the arenavirus, Machupo, we demonstrate that 5′ RNAs from the genomic and antigenomic copies of both segments activate the RdRP in conjunction with a specific promoter. This study builds upon structural studies with two different SNS RNA viruses to reveal a previously unappreciated mechanism of RNA-guided promoter-specific polymerase regulation in SNS RNA viruses. The conservation of activating RNA elements among the polymerase–endonuclease complexes of SNS RNA viruses suggests new avenues for developing antiviral therapeutics. Segmented negative-sense (SNS) RNA viruses initiate infection by delivering into cells a suite of genomic RNA segments, each sheathed by the viral nucleocapsid protein and bound by the RNA-dependent RNA-polymerase (RdRP). For the orthomyxovirus influenza and the bunyavirus La Crosse, the 5′ end of the genomic RNA binds as a hook-like structure proximal to the active site of the RdRP. Using an in vitro assay for the RNA-dependent RNA-polymerase (RdRP) of the arenavirus Machupo (MACV), we demonstrate that the 5′ genomic and antigenomic RNAs of both small and large genome segments stimulate activity in a promoter-specific manner. Functional probing of the activating RNAs identifies intramolecular base-pairing between positions +1 and +7 and a pseudotemplated 5′ terminal guanine residue as key for activation. Binding of structured 5′ RNAs is a conserved feature of all SNS RNA virus polymerases, implying that promoter-specific RdRP activation extends beyond the arenaviruses. The 5′ RNAs and the RNA binding pocket itself represent targets for therapeutic intervention.
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178
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In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors. Sci Rep 2019; 9:6809. [PMID: 31048746 PMCID: PMC6497722 DOI: 10.1038/s41598-019-43129-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 04/17/2019] [Indexed: 01/05/2023] Open
Abstract
The Crimean-Congo Hemorrhagic Fever virus (CCHFV) is a segmented negative single-stranded RNA virus (-ssRNA) which causes severe hemorrhagic fever in humans with a mortality rate of ~50%. To date, no vaccine has been approved. Treatment is limited to supportive care with few investigational drugs in practice. Previous studies have identified viral RNA dependent RNA Polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Since no crystal structure is available yet, we report the structural elucidation of CCHFV-RdRp by in-depth homology modeling. Even with low sequence identity, the generated model suggests a similar overall structure as previously reported RdRps. More specifically, the model suggests the presence of structural/functional conserved RdRp motifs for polymerase function, the configuration of uniform spatial arrangement of core RdRp sub-domains, and predicted positively charged entry/exit tunnels, as seen in sNSV polymerases. Extensive pharmacophore modeling based on per-residue energy contribution with investigational drugs allowed the concise mapping of pharmacophoric features and identified potential hits. The combination of pharmacophoric features with interaction energy analysis revealed functionally important residues in the conserved motifs together with in silico predicted common inhibitory binding modes with highly potent reference compounds.
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179
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Walker AP, Fodor E. Interplay between Influenza Virus and the Host RNA Polymerase II Transcriptional Machinery. Trends Microbiol 2019; 27:398-407. [PMID: 30642766 PMCID: PMC6467242 DOI: 10.1016/j.tim.2018.12.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/30/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022]
Abstract
The influenza virus RNA-dependent RNA polymerase (RdRP) cleaves the 5' end of nascent capped host RNAs and uses the capped RNA fragment to prime viral transcription in a mechanism called 'cap snatching'. Cap snatching requires an intimate association between influenza RdRP and cellular RNA polymerase II (Pol II), which is the source of nascent capped host RNAs targeted by influenza virus. Recent structural studies have revealed how influenza RdRP binds to Pol II and how this binding promotes the initiation of viral transcription by influenza RdRP. In this review we focus on these recent insights into the mechanism of cap snatching by influenza virus and the impact of cap snatching on host gene expression during influenza virus infection.
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Affiliation(s)
- Alexander P Walker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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180
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Klingen TR, Loers J, Stanelle-Bertram S, Gabriel G, McHardy AC. Structures and functions linked to genome-wide adaptation of human influenza A viruses. Sci Rep 2019; 9:6267. [PMID: 31000776 PMCID: PMC6472403 DOI: 10.1038/s41598-019-42614-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/27/2019] [Indexed: 11/12/2022] Open
Abstract
Human influenza A viruses elicit short-term respiratory infections with considerable mortality and morbidity. While H3N2 viruses circulate for more than 50 years, the recent introduction of pH1N1 viruses presents an excellent opportunity for a comparative analysis of the genome-wide evolutionary forces acting on both subtypes. Here, we inferred patches of sites relevant for adaptation, i.e. being under positive selection, on eleven viral protein structures, from all available data since 1968 and correlated these with known functional properties. Overall, pH1N1 have more patches than H3N2 viruses, especially in the viral polymerase complex, while antigenic evolution is more apparent for H3N2 viruses. In both subtypes, NS1 has the highest patch and patch site frequency, indicating that NS1-mediated viral attenuation of host inflammatory responses is a continuously intensifying process, elevated even in the longtime-circulating subtype H3N2. We confirmed the resistance-causing effects of two pH1N1 changes against oseltamivir in NA activity assays, demonstrating the value of the resource for discovering functionally relevant changes. Our results represent an atlas of protein regions and sites with links to host adaptation, antiviral drug resistance and immune evasion for both subtypes for further study.
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MESH Headings
- Drug Resistance, Viral/genetics
- Evolution, Molecular
- Genome, Viral/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza, Human/genetics
- Influenza, Human/pathology
- Influenza, Human/virology
- Oseltamivir/therapeutic use
- Respiratory Tract Infections/genetics
- Respiratory Tract Infections/virology
- Viral Nonstructural Proteins/genetics
- Virus Replication/genetics
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Affiliation(s)
- Thorsten R Klingen
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Jens Loers
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | | | - Gülsah Gabriel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- University of Veterinary Medicine, Hannover, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.
- German Center for Infection Research (DZIF), Braunschweig, Germany.
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181
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Reply to Holmes and Duchêne, "Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?": Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless. mBio 2019; 10:mBio.00542-19. [PMID: 30992352 PMCID: PMC6469970 DOI: 10.1128/mbio.00542-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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182
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Liu G, Zhou Y. Cytoplasm and Beyond: Dynamic Innate Immune Sensing of Influenza A Virus by RIG-I. J Virol 2019; 93:e02299-18. [PMID: 30760567 PMCID: PMC6450113 DOI: 10.1128/jvi.02299-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/05/2019] [Indexed: 12/24/2022] Open
Abstract
Innate immune sensing of influenza A virus (IAV) requires retinoic acid-inducible gene I (RIG-I), a fundamental cytoplasmic RNA sensor. How RIG-I's cytoplasmic localization reconciles with the nuclear replication nature of IAV is poorly understood. Recent findings provide advanced insights into the spatiotemporal RIG-I sensing of IAV and highlight the contribution of various RNA ligands to RIG-I activation. Understanding a compartment-specific RIG-I-sensing paradigm would facilitate the identification of the full spectrum of physiological RIG-I ligands produced during IAV infection.
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Affiliation(s)
- GuanQun Liu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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183
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Imai H, Dinis JM, Zhong G, Moncla LH, Lopes TJS, McBride R, Thompson AJ, Peng W, Le MTQ, Hanson A, Lauck M, Sakai-Tagawa Y, Yamada S, Eggenberger J, O'Connor DH, Suzuki Y, Hatta M, Paulson JC, Neumann G, Friedrich TC, Kawaoka Y. Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004-2010. Emerg Infect Dis 2019; 24:1128-1238. [PMID: 29912683 PMCID: PMC6038741 DOI: 10.3201/eid2407.171441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Influenza viruses exist in each host as a collection of genetically diverse variants, which might enhance their adaptive potential. To assess the genetic and functional diversity of highly pathogenic avian influenza A(H5N1) viruses within infected humans, we used deep-sequencing methods to characterize samples obtained from infected patients in northern Vietnam during 2004–2010 on different days after infection, from different anatomic sites, or both. We detected changes in virus genes that affected receptor binding, polymerase activity, or interferon antagonism, suggesting that these factors could play roles in influenza virus adaptation to humans. However, the frequency of most of these mutations remained low in the samples tested, implying that they were not efficiently selected within these hosts. Our data suggest that adaptation of influenza A(H5N1) viruses is probably stepwise and depends on accumulating combinations of mutations that alter function while maintaining fitness.
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184
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Vogel D, Rosenthal M, Gogrefe N, Reindl S, Günther S. Biochemical characterization of the Lassa virus L protein. J Biol Chem 2019; 294:8088-8100. [PMID: 30926610 PMCID: PMC6527160 DOI: 10.1074/jbc.ra118.006973] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
The L protein of arena- and bunyaviruses is structurally and functionally related to the orthomyxovirus polymerase complex. It plays a central role in the viral life cycle, as it replicates the virus genome and generates viral mRNA via a cap-snatching mechanism. Here, we aimed to biochemically characterize the L protein of Lassa virus, a human-pathogenic arenavirus endemic in West Africa. Full-length 250-kDa L protein was expressed using a baculovirus expression system. A low-resolution structure calculated from small-angle X-ray scattering data revealed a conformation similar to that in the crystal structure of the orthomyxovirus polymerase complex. Although the L protein did not exhibit cap-snatching endonuclease activity, it synthesized RNA in vitro. RNA polymerization required manganese rather than magnesium ions, was independent of nucleotide primers, and was inhibited by viral Z protein. Maximum activity was mediated by double-stranded promoter sequences with a minimum length of 17 nucleotides, containing a nontemplated 5′-G overhang, as in the natural genome context, as well as the naturally occurring base mismatches between the complementary promoter strands. Experiments with various short primers revealed the presence of two replication initiation sites at the template strand and evidence for primer translocation as proposed by the prime-and-realign hypothesis. Overall, our findings provide the foundation for a detailed understanding of the mechanistic differences and communalities in the polymerase proteins of segmented negative-strand RNA viruses and for the search for antiviral compounds targeting the RNA polymerase of Lassa virus.
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Affiliation(s)
- Dominik Vogel
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, Hamburg 20359, Germany
| | - Maria Rosenthal
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, Hamburg 20359, Germany
| | - Nadja Gogrefe
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, Hamburg 20359, Germany
| | - Sophia Reindl
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, Hamburg 20359, Germany.
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, Hamburg 20359, Germany; German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg 20359, Germany.
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185
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Liu G, Lu Y, Liu Q, Zhou Y. Inhibition of Ongoing Influenza A Virus Replication Reveals Different Mechanisms of RIG-I Activation. J Virol 2019; 93:e02066-18. [PMID: 30602605 PMCID: PMC6401434 DOI: 10.1128/jvi.02066-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022] Open
Abstract
Pattern recognition receptors provide essential nonself immune surveillance within distinct cellular compartments. Retinoic acid-inducible gene I (RIG-I) is one of the primary cytosolic RNA sensors, with an emerging role in the nucleus. It is involved in the spatiotemporal sensing of influenza A virus (IAV) replication, leading to the induction of type I interferons (IFNs). Nonetheless, the physiological viral ligands activating RIG-I during IAV infection remain underexplored. Other than full-length viral genomes, cellular constraints that impede ongoing viral replication likely potentiate an erroneous viral polymerase generating aberrant viral RNA species with RIG-I-activating potential. Here, we investigate the origins of RIG-I-activating viral RNA under two such constraints. Using chemical inhibitors that inhibit continuous viral protein synthesis, we identify the incoming, but not de novo-synthesized, viral defective interfering (DI) genomes contributing to RIG-I activation. In comparison, deprivation of viral nucleoprotein (NP), the key RNA chain elongation factor for the viral polymerase, leads to the production of aberrant viral RNA species activating RIG-I; however, their nature is likely to be distinct from that of DI RNA. Moreover, RIG-I activation in response to NP deprivation is not adversely affected by expression of the nuclear export protein (NEP), which diminishes the generation of a major subset of aberrant viral RNA but facilitates the accumulation of small viral RNA (svRNA). Overall, our results indicate the existence of fundamentally different mechanisms of RIG-I activation under cellular constraints that impede ongoing IAV replication.IMPORTANCE The induction of an IFN response by IAV is mainly mediated by the RNA sensor RIG-I. The physiological RIG-I ligands produced during IAV infection are not fully elucidated. Cellular constraints leading to the inhibition of ongoing viral replication likely potentiate an erroneous viral polymerase producing aberrant viral RNA species activating RIG-I. Here, we demonstrate that RIG-I activation during chemical inhibition of continuous viral protein synthesis is attributable to the incoming DI genomes. Erroneous viral replication driven by NP deprivation promotes the generation of RIG-I-activating aberrant viral RNA, but their nature is likely to be distinct from that of DI RNA. Our results thus reveal distinct mechanisms of RIG-I activation by IAV under cellular constraints impeding ongoing viral replication. A better understanding of RIG-I sensing of IAV infection provides insight into the development of novel interventions to combat influenza virus infection.
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Affiliation(s)
- GuanQun Liu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yao Lu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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186
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Nannetti G, Massari S, Mercorelli B, Bertagnin C, Desantis J, Palù G, Tabarrini O, Loregian A. Potent and broad-spectrum cycloheptathiophene-3-carboxamide compounds that target the PA-PB1 interaction of influenza virus RNA polymerase and possess a high barrier to drug resistance. Antiviral Res 2019; 165:55-64. [PMID: 30885750 DOI: 10.1016/j.antiviral.2019.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022]
Abstract
Influenza viruses are major respiratory pathogens responsible for both seasonal epidemics and occasional pandemics worldwide. The current available treatment options have limited efficacy and thus the development of new antivirals is highly needed. We previously reported the identification of a series of cycloheptathiophene-3-carboxamide compounds as influenza A virus inhibitors that act by targeting the protein-protein interactions between the PA-PB1 subunits of the viral polymerase. In this study, we characterized the antiviral properties of the most promising compounds as well as investigated their propensity to induce drug resistance. Our results show that some of the selected compounds possess potent, broad-spectrum anti-influenza activity as they efficiently inhibited the replication of several strains of influenza A and B viruses, including an oseltamivir-resistant clinical isolate, with nanomolar or low-micromolar potency. The most promising compounds specifically inhibited the PA-PB1 binding in vitro and interfered with the influenza A virus polymerase activity in a cellular context, without showing cytotoxicity. The most active PA-PB1 inhibitors showed to possess a drug resistance barrier higher than that of oseltamivir. Indeed, no viral variants with reduced susceptibility to the selected compounds emerged after serial passages of influenza A virus under drug selective pressure. Overall, our studies identified potent PA-PB1 inhibitors as promising candidates for the development of new anti-influenza drugs.
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Affiliation(s)
- Giulio Nannetti
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
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187
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Ben Ouirane K, Boulard Y, Bressanelli S. The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif. J Biol Chem 2019; 294:7573-7587. [PMID: 30867194 DOI: 10.1074/jbc.ra118.005209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
RNA viruses synthesize new genomes in the infected host thanks to dedicated, virally-encoded RNA-dependent RNA polymerases (RdRps). As such, these enzymes are prime targets for antiviral therapy, as has recently been demonstrated for hepatitis C virus (HCV). However, peculiarities in the architecture and dynamics of RdRps raise fundamental questions about access to their active site during RNA polymerization. Here, we used molecular modeling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp. Tracing the possible passage of incoming UTP or GTP through the RdRp-specific entry tunnel, we found two successive checkpoints that regulate nucleotide traffic to the active site. We observed that a magnesium-bound nucleotide first binds next to the tunnel entry, and interactions with the triphosphate moiety orient it such that its base moiety enters first. Dynamics of RdRp motifs F1 + F3 then allow the nucleotide to interrogate the RNA template base prior to nucleotide insertion into the active site. These dynamics are finely regulated by a second magnesium dication, thus coordinating the entry of a magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. The findings of our work suggest that at least some of these features are general to viral RdRps and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses.
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Affiliation(s)
- Kaouther Ben Ouirane
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Yves Boulard
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Stéphane Bressanelli
- From the Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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188
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A Minigenome Study of Hazara Nairovirus Genomic Promoters. J Virol 2019; 93:JVI.02118-18. [PMID: 30626667 DOI: 10.1128/jvi.02118-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Hazara nairovirus (HAZV) is a trisegmented RNA virus most closely related to Crimean-Congo hemorrhagic fever virus (CCHFV) in the order Bunyavirales The terminal roughly 20 nucleotides (nt) of its genome ends are highly complementary, similar to those of other segmented negative-strand RNA viruses (sNSV), and act as promoters for RNA synthesis. These promoters contain two elements: the extreme termini of both strands (promoter element 1 [PE1]) are conserved and virus specific and are found bound to separate sites on the polymerase surface in crystal structures of promoter-polymerase complexes. The following sequences (PE2) are segment specific, with the potential to form double-stranded RNA (dsRNA), and the latter aspect is also important for promoter activity. Nairovirus genome promoters differ from those of peribunyaviruses and arenaviruses in that they contain a short single-stranded region between the two regions of complementarity. Using a HAZV minigenome system, we found the single-stranded nature of this region, as well as the potential of the following sequence to form dsRNA, is essential for reporter gene expression. Most unexpectedly, the sequence of the PE2 dsRNA appears to be equally important for promoter activity. These differences in sNSV PE2 promoter elements are discussed in light of our current understanding of the initiation of RNA synthesis.IMPORTANCE A minigenome system for HAZV, closely related to CCHFV, was used to study its genome replication. HAZV genome ends, like those of other sNSV, such as peribunyaviruses and arenaviruses, are highly complementary and serve as promoters for genome synthesis. These promoters are composed of two elements: the extreme termini of both 3' and 5' strands that are initially bound to separate sites on the polymerase surface in a sequence-specific fashion and the following sequences with the potential to anneal but whose sequence is not important. Nairovirus promoters differ from the other sNSV cited in that they contain a short single-stranded RNA (ssRNA) region between the two elements. The single-stranded nature of this region is an essential element of the promoter, whereas its sequence is unimportant. The sequence of the following complementary region is unexpectedly also important, a possible rare example of sequence-specific dsRNA recognition.
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189
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Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DFK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. A Short Chemically Modified dsRNA-Binding PNA (dbPNA) Inhibits Influenza Viral Replication by Targeting Viral RNA Panhandle Structure. Bioconjug Chem 2019; 30:931-943. [PMID: 30721034 DOI: 10.1021/acs.bioconjchem.9b00039] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNAs play critical roles in diverse catalytic and regulatory biological processes and are emerging as important disease biomarkers and therapeutic targets. Thus, developing chemical compounds for targeting any desired RNA structures has great potential in biomedical applications. The viral and cellular RNA sequence and structure databases lay the groundwork for developing RNA-binding chemical ligands through the recognition of both RNA sequence and RNA structure. Influenza A virion consists of eight segments of negative-strand viral RNA (vRNA), all of which contain a highly conserved panhandle duplex structure formed between the first 13 nucleotides at the 5' end and the last 12 nucleotides at the 3' end. Here, we report our binding and cell culture anti-influenza assays of a short 10-mer chemically modified double-stranded RNA (dsRNA)-binding peptide nucleic acid (PNA) designed to bind to the panhandle duplex structure through novel major-groove PNA·RNA2 triplex formation. We demonstrated that incorporation of chemically modified PNA residues thio-pseudoisocytosine (L) and guanidine-modified 5-methyl cytosine (Q) previously developed by us facilitates the sequence-specific recognition of Watson-Crick G-C and C-G pairs, respectively, at physiologically relevant conditions. Significantly, the chemically modified dsRNA-binding PNA (dbPNA) shows selective binding to the dsRNA region in panhandle structure over a single-stranded RNA (ssRNA) and a dsDNA containing the same sequence. The panhandle structure is not accessible to traditional antisense DNA or RNA with a similar length. Conjugation of the dbPNA with an aminosugar neamine enhances the cellular uptake. We observed that 2-5 μM dbPNA-neamine conjugate results in a significant reduction of viral replication. In addition, the 10-mer dbPNA inhibits innate immune receptor RIG-I binding to panhandle structure and thus RIG-I ATPase activity. These findings would provide the foundation for developing novel dbPNAs for the detection of influenza viral RNAs and therapeutics with optimal antiviral and immunomodulatory activities.
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Affiliation(s)
- Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | | | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 636921 , Singapore
| | - Louis Zimmermann
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Jean-Luc Decout
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Dahai Luo
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link , National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
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190
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AZT acts as an anti-influenza nucleotide triphosphate targeting the catalytic site of A/PR/8/34/H1N1 RNA dependent RNA polymerase. J Comput Aided Mol Des 2019; 33:387-404. [PMID: 30739239 DOI: 10.1007/s10822-019-00189-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/02/2019] [Indexed: 10/27/2022]
Abstract
To develop potent drugs that inhibit the activity of influenza virus RNA dependent RNA polymerase (RdRp), a set of compounds favipiravir, T-705, T-1105 and T-1106, ribavirin, ribavirin triphosphate viramidine, 2FdGTP (2'-deoxy-2'-fluoroguanosine triphosphate) and AZT-TP (3'-Azido-3'-deoxy-thymidine-5'-triphosphate) were docked with a homology model of IAV RdRp from the A/PR/8/34/H1N1 strain. These compounds bind to four pockets A-D of the IAV RdRp with different mechanism of action. In addition, AZT-TP also binds to the PB1 catalytic site near to the tip of the priming loop with a highest ΔG of - 16.7 Kcal/mol exhibiting an IC50 of 1.12 µM in an in vitro enzyme transcription assay. This shows that AZT-TP mainly prevents the incorporation of incoming nucleotide involved in initiation of vRNA replication. Conversely, 2FdGTP used as a positive control binds to pocket-B at the end of tunnel-II with a highest ΔG of - 16.3 Kcal/mol inhibiting chain termination with a similar IC50 of 1.12 µM. Overall, our computational results in correlation with experimental studies gives information for the first time about the binding modes of the known influenza antiviral compounds in different models of vRNA replication by IAV RdRp. This in turn gives new structural insights for the development of new therapeutics exhibiting high specificity to the PB1 catalytic site of influenza A viruses.
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191
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In silico structure-based design of enhanced peptide inhibitors targeting RNA polymerase PA N-PB1 C interaction. Comput Biol Chem 2019; 78:273-281. [PMID: 30597438 DOI: 10.1016/j.compbiolchem.2018.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/05/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022]
Abstract
Developing antivirals for influenza A virus (FluA) has become more challenging due to high range of antigenic mutation and increasing numbers of drug-resistant viruses. Finding a selective inhibitor to target highly conserved region of protein-protein interactions interface, thereby increasing its efficiency against drug resistant virus could be highly beneficial. In this study, we used in silico approach to derive FluAPep1 from highly conserved region, PAN-PB1C interface and generated 121 FluAPep1 analogues. Interestingly, we found that the FluAPep1 interaction region in the PAN domain are highly conserved in many FluA subtypes. Especially, FluAPep1 targets two pandemic FluA strains, H1N1/avian/2009 and H3N2/Victoria/1975. All of these FluA subtypes PAN domain (H1N1/H3N2CAN/H3N2VIC/H7N1/H7N2) were superimposed with PAN domain from H17N10 and the calculated root mean standards deviations were less than 3 Å. FlexPepDock analysis revealed that FluAPep1 exhibited higher binding affinity (score -246.155) with the PAN domain. In addition, around 86% of non-hot spot mutated peptides (FluAPep28-122) showed enhanced binding affinity with PAN domain. ToxinPred analysis confirmed that designed peptides were non-toxic. Thus, FluAPep1 and its analogues has potential to be further developed into an antiviral treatment against FluA infection.
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192
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Shin WJ, Seong BL. Novel antiviral drug discovery strategies to tackle drug-resistant mutants of influenza virus strains. Expert Opin Drug Discov 2018; 14:153-168. [PMID: 30585088 DOI: 10.1080/17460441.2019.1560261] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION The emergence of drug-resistant influenza virus strains highlights the need for new antiviral therapeutics to combat future pandemic outbreaks as well as continuing seasonal cycles of influenza. Areas covered: This review summarizes the mechanisms of current FDA-approved anti-influenza drugs and patterns of resistance to those drugs. It also discusses potential novel targets for broad-spectrum antiviral drugs and recent progress in novel drug design to overcome drug resistance in influenza. Expert opinion: Using the available structural information about drug-binding pockets, research is currently underway to identify molecular interactions that can be exploited to generate new antiviral drugs. Despite continued efforts, antivirals targeting viral surface proteins like HA, NA, and M2, are all susceptible to developing resistance. Structural information on the internal viral polymerase complex (PB1, PB2, and PA) provides a new avenue for influenza drug discovery. Host factors, either at the initial step of viral infection or at the later step of nuclear trafficking of viral RNP complex, are being actively pursued to generate novel drugs with new modes of action, without resulting in drug resistance.
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Affiliation(s)
- Woo-Jin Shin
- a Department of Molecular Microbiology and Immunology, Keck School of Medicine , University of Southern California , Los Angeles , CA , USA
| | - Baik L Seong
- b Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,c Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
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193
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Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML. Modulation of Innate Immune Responses by the Influenza A NS1 and PA-X Proteins. Viruses 2018; 10:v10120708. [PMID: 30545063 PMCID: PMC6315843 DOI: 10.3390/v10120708] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) can infect a broad range of animal hosts, including humans. In humans, IAV causes seasonal annual epidemics and occasional pandemics, representing a serious public health and economic problem, which is most effectively prevented through vaccination. The defense mechanisms that the host innate immune system provides restrict IAV replication and infection. Consequently, to successfully replicate in interferon (IFN)-competent systems, IAV has to counteract host antiviral activities, mainly the production of IFN and the activities of IFN-induced host proteins that inhibit virus replication. The IAV multifunctional proteins PA-X and NS1 are virulence factors that modulate the innate immune response and virus pathogenicity. Notably, these two viral proteins have synergistic effects in the inhibition of host protein synthesis in infected cells, although using different mechanisms of action. Moreover, the control of innate immune responses by the IAV NS1 and PA-X proteins is subject to a balance that can determine virus pathogenesis and fitness, and recent evidence shows co-evolution of these proteins in seasonal viruses, indicating that they should be monitored for enhanced virulence. Importantly, inhibition of host gene expression by the influenza NS1 and/or PA-X proteins could be explored to develop improved live-attenuated influenza vaccines (LAIV) by modulating the ability of the virus to counteract antiviral host responses. Likewise, both viral proteins represent a reasonable target for the development of new antivirals for the control of IAV infections. In this review, we summarize the role of IAV NS1 and PA-X in controlling the antiviral response during viral infection.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Centro de Investigación en Sanidad Animal (CISA)-INIA, Valdeolmos, 28130 Madrid, Spain.
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Marta L DeDiego
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, New York, NY 14642, USA.
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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194
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Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV. Origins and Evolution of the Global RNA Virome. mBio 2018; 9:e02329-18. [PMID: 30482837 PMCID: PMC6282212 DOI: 10.1128/mbio.02329-18] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/31/2018] [Indexed: 01/12/2023] Open
Abstract
Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (-) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Adriana Lucía-Sanz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Centro Nacional de Biotecnología, Madrid, Spain
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Mart Krupovic
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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195
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Liu W, Shi X, Gong P. A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase. Nucleic Acids Res 2018; 46:10840-10854. [PMID: 30239956 PMCID: PMC6237809 DOI: 10.1093/nar/gky848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/11/2018] [Indexed: 01/07/2023] Open
Abstract
Typically not assisted by proofreading, the RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses may need to independently control its fidelity to fulfill virus viability and fitness. However, the precise mechanism by which the RdRP maintains its optimal fidelity level remains largely elusive. By solving 2.1-2.5 Å resolution crystal structures of the classical swine fever virus (CSFV) NS5B, an RdRP with a unique naturally fused N-terminal domain (NTD), we identified high-resolution intra-molecular interactions between the NTD and the RdRP palm domain. In order to dissect possible regulatory functions of NTD, we designed mutations at residues Y471 and E472 to perturb key interactions at the NTD-RdRP interface. When crystallized, some of these NS5B interface mutants maintained the interface, while the others adopted an 'open' conformation that no longer retained the intra-molecular interactions. Data from multiple in vitro RdRP assays indicated that the perturbation of the NTD-RdRP interactions clearly reduced the fidelity level of the RNA synthesis, while the processivity of the NS5B elongation complex was not affected. Collectively, our work demonstrates an explicit and unique mode of polymerase fidelity modulation and provides a vivid example of co-evolution in multi-domain enzymes.
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Affiliation(s)
- Weichi Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoling Shi
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,To whom correspondence should be addressed. Tel: +86 27 87197578;
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196
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De Vlugt C, Sikora D, Pelchat M. Insight into Influenza: A Virus Cap-Snatching. Viruses 2018; 10:v10110641. [PMID: 30453478 PMCID: PMC6266781 DOI: 10.3390/v10110641] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/12/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022] Open
Abstract
The influenza A virus (IAV) genome consists of eight single-stranded RNA segments. Each segment is associated with a protein complex, with the 3′ and 5′ ends bound to the RNA-dependent RNA polymerase (RdRp) and the remainder associated with the viral nucleoprotein. During transcription of viral mRNA, this ribonucleoprotein complex steals short, 5′-capped transcripts produced by the cellular DNA dependent RNA polymerase II (RNAPII) and uses them to prime transcription of viral mRNA. Here, we review the current knowledge on the process of IAV cap-snatching and suggest a requirement for RNAPII promoter-proximal pausing for efficient IAV mRNA transcription.
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Affiliation(s)
- Corey De Vlugt
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Dorota Sikora
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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197
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Abstract
Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections, in particular due to the apparent lack of emergence of resistance mutations against the drug in cell culture or animal studies. We demonstrate here that a mutation in a conserved region of the viral RNA polymerase confers resistance to favipiravir in vitro and in cell culture. The resistance mutation has a cost to viral fitness, but this can be restored by a compensatory mutation in the polymerase. Our findings support the development of favipiravir-resistance diagnostic and surveillance testing strategies and reinforce the importance of considering combinations of therapies to treat influenza infections. Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections. While emergence of resistance has been observed for many antiinfluenza drugs, to date, clinical trials and laboratory studies of favipiravir have not yielded resistant viruses. Here we show evolution of resistance to favipiravir in the pandemic H1N1 influenza A virus in a laboratory setting. We found that two mutations were required for robust resistance to favipiravir. We demonstrate that a K229R mutation in motif F of the PB1 subunit of the influenza virus RNA-dependent RNA polymerase (RdRP) confers resistance to favipiravir in vitro and in cell culture. This mutation has a cost to viral fitness, but fitness can be restored by a P653L mutation in the PA subunit of the polymerase. K229R also conferred favipiravir resistance to RNA polymerases of other influenza A virus strains, and its location within a highly conserved structural feature of the RdRP suggests that other RNA viruses might also acquire resistance through mutations in motif F. The mutations identified here could be used to screen influenza virus-infected patients treated with favipiravir for the emergence of resistance.
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198
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Martínez-Sobrido L, Peersen O, Nogales A. Temperature Sensitive Mutations in Influenza A Viral Ribonucleoprotein Complex Responsible for the Attenuation of the Live Attenuated Influenza Vaccine. Viruses 2018; 10:E560. [PMID: 30326610 PMCID: PMC6213772 DOI: 10.3390/v10100560] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/03/2018] [Accepted: 10/12/2018] [Indexed: 01/29/2023] Open
Abstract
Live attenuated influenza vaccines (LAIV) have prevented morbidity and mortality associated with influenza viral infections for many years and represent the best therapeutic option to protect against influenza viral infections in humans. However, the development of LAIV has traditionally relied on empirical methods, such as the adaptation of viruses to replicate at low temperatures. These approaches require an extensive investment of time and resources before identifying potential vaccine candidates that can be safely implemented as LAIV to protect humans. In addition, the mechanism of attenuation of these vaccines is poorly understood in some cases. Importantly, LAIV are more efficacious than inactivated vaccines because their ability to mount efficient innate and adaptive humoral and cellular immune responses. Therefore, the design of potential LAIV based on known properties of viral proteins appears to be a highly appropriate option for the treatment of influenza viral infections. For that, the viral RNA synthesis machinery has been a research focus to identify key amino acid substitutions that can lead to viral attenuation and their use in safe, immunogenic, and protective LAIV. In this review, we discuss the potential to manipulate the influenza viral RNA-dependent RNA polymerase (RdRp) complex to generate attenuated forms of the virus that can be used as LAIV for the treatment of influenza viral infections, one of the current and most effective prophylactic options for the control of influenza in humans.
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Affiliation(s)
- Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York, NY 14642, USA.
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, CO 80523, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York, NY 14642, USA.
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199
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Hayden FG, Sugaya N, Hirotsu N, Lee N, de Jong MD, Hurt AC, Ishida T, Sekino H, Yamada K, Portsmouth S, Kawaguchi K, Shishido T, Arai M, Tsuchiya K, Uehara T, Watanabe A. Baloxavir Marboxil for Uncomplicated Influenza in Adults and Adolescents. N Engl J Med 2018; 379:913-923. [PMID: 30184455 DOI: 10.1056/nejmoa1716197] [Citation(s) in RCA: 554] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Baloxavir marboxil is a selective inhibitor of influenza cap-dependent endonuclease. It has shown therapeutic activity in preclinical models of influenza A and B virus infections, including strains resistant to current antiviral agents. METHODS We conducted two randomized, double-blind, controlled trials involving otherwise healthy outpatients with acute uncomplicated influenza. After a dose-ranging (10 to 40 mg) placebo-controlled trial, we undertook a placebo- and oseltamivir-controlled trial of single, weight-based doses of baloxavir (40 or 80 mg) in patients 12 to 64 years of age during the 2016-2017 season. The dose of oseltamivir was 75 mg twice daily for 5 days. The primary efficacy end point was the time to alleviation of influenza symptoms in the intention-to-treat infected population. RESULTS In the phase 2 trial, the median time to alleviation of influenza symptoms was 23.4 to 28.2 hours shorter in the baloxavir groups than in the placebo group (P<0.05). In the phase 3 trial, the intention-to-treat infected population included 1064 patients; 84.8 to 88.1% of patients in each group had influenza A(H3N2) infection. The median time to alleviation of symptoms was 53.7 hours (95% confidence interval [CI], 49.5 to 58.5) with baloxavir, as compared with 80.2 hours (95% CI, 72.6 to 87.1) with placebo (P<0.001). The time to alleviation of symptoms was similar with baloxavir and oseltamivir. Baloxavir was associated with greater reductions in viral load 1 day after initiation of the regimen than placebo or oseltamivir. Adverse events were reported in 20.7% of baloxavir recipients, 24.6% of placebo recipients, and 24.8% of oseltamivir recipients. The emergence of polymerase acidic protein variants with I38T/M/F substitutions conferring reduced susceptibility to baloxavir occurred in 2.2% and 9.7% of baloxavir recipients in the phase 2 trial and phase 3 trial, respectively. CONCLUSIONS Single-dose baloxavir was without evident safety concerns, was superior to placebo in alleviating influenza symptoms, and was superior to both oseltamivir and placebo in reducing the viral load 1 day after initiation of the trial regimen in patients with uncomplicated influenza. Evidence for the development of decreased susceptibility to baloxavir after treatment was also observed. (Funded by Shionogi; JapicCTI number, 153090, and CAPSTONE-1 ClinicalTrials.gov number, NCT02954354 .).
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Affiliation(s)
- Frederick G Hayden
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Norio Sugaya
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Nobuo Hirotsu
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Nelson Lee
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Menno D de Jong
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Aeron C Hurt
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Tadashi Ishida
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Hisakuni Sekino
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Kota Yamada
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Simon Portsmouth
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Keiko Kawaguchi
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Takao Shishido
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Masatsugu Arai
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Kenji Tsuchiya
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Takeki Uehara
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
| | - Akira Watanabe
- From the Department of Medicine, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Pediatrics, Keiyu Hospital, Yokohama (N.S.), Hirotsu Clinic, Kawasaki (N.H.), the Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki (T.I.), Sekino Hospital, Tokyo (H.S.), Tsuchiura Beryl Clinic, Tsuchiura (K.Y.), Shionogi, Osaka (K.K., T.S., M.A., K.T., T.U.), and the Research Division for Development of Anti-Infective Agents, Institute of Development, Aging, and Cancer, Tohoku University, Sendai (A.W.) - all in Japan; the Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada (N.L.); the Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam (M.D.J.); the Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia (A.C.H.); and Shionogi, Florham Park, NJ (S.P.)
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Arai Y, Kawashita N, Hotta K, Hoang PVM, Nguyen HLK, Nguyen TC, Vuong CD, Le TT, Le MTQ, Soda K, Ibrahim MS, Daidoji T, Takagi T, Shioda T, Nakaya T, Ito T, Hasebe F, Watanabe Y. Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Sci Rep 2018; 8:13066. [PMID: 30166556 PMCID: PMC6117316 DOI: 10.1038/s41598-018-31397-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/15/2018] [Indexed: 12/31/2022] Open
Abstract
The role of the influenza virus polymerase complex in host range restriction has been well-studied and several host range determinants, such as the polymerase PB2-E627K and PB2-D701N mutations, have been identified. However, there may be additional, currently unknown, human adaptation polymerase mutations. Here, we used a database search of influenza virus H5N1 clade 1.1, clade 2.3.2.1 and clade 2.3.4 strains isolated from 2008-2012 in Southern China, Vietnam and Cambodia to identify polymerase adaptation mutations that had been selected in infected patients. Several of these mutations acted either alone or together to increase viral polymerase activity in human airway cells to levels similar to the PB2-D701N and PB2-E627K single mutations and to increase progeny virus yields in infected mouse lungs to levels similar to the PB2-D701N single mutation. In particular, specific mutations acted synergistically with the PB2-D701N mutation and showed synergistic effects on viral replication both in human airway cells and mice compared with the corresponding single mutations. Thus, H5N1 viruses in infected patients were able to acquire multiple polymerase mutations that acted cooperatively for human adaptation. Our findings give new insight into the human adaptation of AI viruses and help in avian influenza virus risk assessment.
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Affiliation(s)
- Yasuha Arai
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Norihito Kawashita
- Graduate School of Science and Engineering, Kindai University, Osaka, Japan.,Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Kozue Hotta
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Hanoi, Vietnam.,Laboratory of Veterinary Public Health, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Phuong Vu Mai Hoang
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hang Le Khanh Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thach Co Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Cuong Duc Vuong
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Thi Le
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Mai Thi Quynh Le
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Kosuke Soda
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Madiha S Ibrahim
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiro Ito
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Futoshi Hasebe
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Hanoi, Vietnam
| | - Yohei Watanabe
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan. .,Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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