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Gonzales J, Kim I, Hwang W, Cho JH. Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of influenza A virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595776. [PMID: 38826371 PMCID: PMC11142230 DOI: 10.1101/2024.05.24.595776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Viral proteins frequently mutate to evade or antagonize host innate immune responses, yet the impact of these mutations on the molecular energy landscape remains unclear. Epistasis, the intramolecular communications between mutations, often renders the combined mutational effects unpredictable. Nonstructural protein 1 (NS1) is a major virulence factor of the influenza A virus (IAV) that activates host PI3K by binding to its p85β subunit. Here, we present the deep analysis for the impact of evolutionary mutations in NS1 that emerged between the 1918 pandemic IAV strain and its descendant PR8 strain. Our analysis reveal how the mutations rewired inter-residue communications which underlies long-range allosteric and epistatic networks in NS1. Our findings show that PR8 NS1 binds to p85β with approximately 10-fold greater affinity than 1918 NS1 due to allosteric mutational effects. Notably, these mutations also exhibited long-range epistatic effects. NMR chemical shift perturbation and methyl-axis order parameter analyses revealed that the mutations induced long-range structural and dynamic changes in PR8 NS1, enhancing its affinity to p85β. Complementary MD simulations and graph-based network analysis uncover how these mutations rewire dynamic residue interaction networks, which underlies the long-range epistasis and allosteric effects on p85β-binding affinity. Significantly, we find that conformational dynamics of residues with high betweenness centrality play a crucial role in communications between network communities and are highly conserved across influenza A virus evolution. These findings advance our mechanistic understanding of the allosteric and epistatic communications between distant residues and provides insight into their role in the molecular evolution of NS1.
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2
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Blake ME, Kleinpeter AB, Jureka AS, Petit CM. Structural Investigations of Interactions between the Influenza a Virus NS1 and Host Cellular Proteins. Viruses 2023; 15:2063. [PMID: 37896840 PMCID: PMC10612106 DOI: 10.3390/v15102063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The Influenza A virus is a continuous threat to public health that causes yearly epidemics with the ever-present threat of the virus becoming the next pandemic. Due to increasing levels of resistance, several of our previously used antivirals have been rendered useless. There is a strong need for new antivirals that are less likely to be susceptible to mutations. One strategy to achieve this goal is structure-based drug development. By understanding the minute details of protein structure, we can develop antivirals that target the most conserved, crucial regions to yield the highest chances of long-lasting success. One promising IAV target is the virulence protein non-structural protein 1 (NS1). NS1 contributes to pathogenicity through interactions with numerous host proteins, and many of the resulting complexes have been shown to be crucial for virulence. In this review, we cover the NS1-host protein complexes that have been structurally characterized to date. By bringing these structures together in one place, we aim to highlight the strength of this field for drug discovery along with the gaps that remain to be filled.
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Affiliation(s)
| | | | | | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.E.B.)
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3
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Wu W, Ye Y, Zhong Y, Yan X, Lin J, Qiu J, Liu S, Fang Z. Pterostilbene effectively inhibits influenza A virus infection by promoting the type I interferon production. Microbes Infect 2023; 25:105062. [PMID: 36280208 DOI: 10.1016/j.micinf.2022.105062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
With the prevalence of novel strains and drug-resistant influenza viruses, there is an urgent need to develop effective and low-toxicity anti-influenza therapeutics. Regulation of the type I interferon antiviral response is considered an attractive therapeutic strategy for viral infection. Pterostilbene, a 3,5-dimethoxy analog of resveratrol, is known for its remarkable pharmacological activity. Here, we found that pterostilbene effectively inhibited influenza A virus infection and mainly affected the late stages of viral replication. A mechanistic study showed that the antiviral activity of pterostilbene might promote the induction of antiviral type I interferon and expression of its downstream interferon-stimulated genes during viral infection. The same effect of pterostilbene was also observed in the condition of polyinosinic-polycytidylic acid (poly I:C) transfection. Further study showed that pterostilbene interacted with influenza non-structural 1 (NS1) protein, inhibited ubiquitination mediated degradation of RIG-I and activated the downstream antiviral pathway, orchestrating an antiviral state against influenza virus in the cell. Taken together, pterostilbene could be a promising anti-influenza agent for future antiviral drug exploitation and compounds with similar structures may provide new options for the development of novel inhibitors against influenza A virus (IAV).
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Affiliation(s)
- Wenjiao Wu
- Department of Pharmacy, Guangdong Second Provincial General Hospital, No.466 Middle Xingang Road, Guangzhou, 510317, China
| | - Yilu Ye
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, No. 1838 Shatai South Road, Baiyun District, Guangzhou, 510515, China
| | - Yingyuan Zhong
- Department of Pharmacy, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, No.23 Haipang Street, North Street, Jiangmen, 529030, China
| | - Xiukui Yan
- Department of Pharmacy, Guangdong Second Provincial General Hospital, No.466 Middle Xingang Road, Guangzhou, 510317, China
| | - Jianguo Lin
- Department of Pharmacy, Guangdong Second Provincial General Hospital, No.466 Middle Xingang Road, Guangzhou, 510317, China
| | - Jianxiang Qiu
- Department of Pharmacy, Guangdong Second Provincial General Hospital, No.466 Middle Xingang Road, Guangzhou, 510317, China.
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, No. 1838 Shatai South Road, Baiyun District, Guangzhou, 510515, China.
| | - Zhixin Fang
- Department of Pharmacy, Guangdong Second Provincial General Hospital, No.466 Middle Xingang Road, Guangzhou, 510317, China.
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Cunha AES, Loureiro RJS, Simões CJV, Brito RMM. Unveiling New Druggable Pockets in Influenza Non-Structural Protein 1: NS1-Host Interactions as Antiviral Targets for Flu. Int J Mol Sci 2023; 24:ijms24032977. [PMID: 36769298 PMCID: PMC9918223 DOI: 10.3390/ijms24032977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Influenza viruses are responsible for significant morbidity and mortality worldwide in winter seasonal outbreaks and in flu pandemics. Influenza viruses have a high rate of evolution, requiring annual vaccine updates and severely diminishing the effectiveness of the available antivirals. Identifying novel viral targets and developing new effective antivirals is an urgent need. One of the most promising new targets for influenza antiviral therapy is non-structural protein 1 (NS1), a highly conserved protein exclusively expressed in virus-infected cells that mediates essential functions in virus replication and pathogenesis. Interaction of NS1 with the host proteins PI3K and TRIM25 is paramount for NS1's role in infection and pathogenesis by promoting viral replication through the inhibition of apoptosis and suppressing interferon production, respectively. We, therefore, conducted an analysis of the druggability of this viral protein by performing molecular dynamics simulations on full-length NS1 coupled with ligand pocket detection. We identified several druggable pockets that are partially conserved throughout most of the simulation time. Moreover, we found out that some of these druggable pockets co-localize with the most stable binding regions of the protein-protein interaction (PPI) sites of NS1 with PI3K and TRIM25, which suggests that these NS1 druggable pockets are promising new targets for antiviral development.
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Affiliation(s)
- Andreia E. S. Cunha
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui J. S. Loureiro
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
| | - Carlos J. V. Simões
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Rui M. M. Brito
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
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5
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Matsubayashi H, Mountain J, Yao T, Peterson A, Roy AD, Inoue T. Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP-2-mediated endocytosis. RESEARCH SQUARE 2023:rs.3.rs-2432041. [PMID: 36712095 PMCID: PMC9882665 DOI: 10.21203/rs.3.rs-2432041/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Class IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable multifaceted roles, the catalytic subunit p110 utilizes a multi-domain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, their product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and its relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains previously uncharacterized AP-2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP-2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and upregulate both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.
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Matsubayashi HT, Mountain J, Yao T, Peterson AF, Deb Roy A, Inoue T. Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP-2-mediated endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522383. [PMID: 36712134 PMCID: PMC9881872 DOI: 10.1101/2022.12.31.522383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Class IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable multifaceted roles, the catalytic subunit p110 utilizes a multidomain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, their product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and its relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains previously uncharacterized AP-2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP-2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and upregulate both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.
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Affiliation(s)
- Hideaki T. Matsubayashi
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
| | - Jack Mountain
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
| | - Tony Yao
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
| | - Amy F. Peterson
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
| | - Abhijit Deb Roy
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
| | - Takanari Inoue
- Department of Cell Biology, School of Medicine, Johns Hopkins University
- Center for Cell Dynamics, Institute of Basic Biomedical Sciences, Johns Hopkins University
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7
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Kim I, Dubrow A, Zuniga B, Zhao B, Sherer N, Bastiray A, Li P, Cho JH. Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus. Nat Commun 2022; 13:5775. [PMID: 36182933 PMCID: PMC9526705 DOI: 10.1038/s41467-022-33554-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how individual mutations affect the protein energy landscape is crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis—the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of influenza A viruses (IAVs). We integrate structural, kinetic, thermodynamic, and conformational dynamics analyses of four NS1s of influenza strains that emerged between 1918 and 2004. Although functionally near-neutral, strain-specific NS1 mutations exhibit long-range epistatic interactions with residues at the p85β-binding interface. We reveal that strain-specific mutations reshaped the NS1 energy landscape during evolution. Using NMR spin dynamics, we find that the strain-specific mutations altered the conformational dynamics of the hidden network of tightly packed residues, underlying the evolution of long-range epistasis. This work shows how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution. Influenza A virus (IAV) nonstructural protein 1 (NS1) is a multifunctional virulence factor that interacts with several host factors such as phosphatidylinositol-3-kinase (PI3K). NS1 binds specifically to the p85β regulatory subunit of PI3K and subsequently activates PI3K signaling. Here, Kim et al. show that functionally near-neutral, strain-specific NS1 mutations lead to variations in binding kinetics to p85β exhibit long-range epistatic interactions. Applying NMR they provide evidence that the structural dynamics of the NS1 hydrophobic core have evolved over time and contributed to epistasis.
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Affiliation(s)
- Iktae Kim
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Alyssa Dubrow
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Bryan Zuniga
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Noah Sherer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Abhishek Bastiray
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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8
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Lubna S, Chinta S, Burra P, Vedantham K, Ray S, Bandyopadhyay D. New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020. Health Sci Rep 2022; 5:e626. [PMID: 35509388 PMCID: PMC9059196 DOI: 10.1002/hsr2.626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Syeda Lubna
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Suma Chinta
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Prakruthi Burra
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Kiranmayi Vedantham
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | | | - Debashree Bandyopadhyay
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
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9
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Dubrow A, Zuniga B, Topo E, Cho JH. Suppressing Nonspecific Binding in Biolayer Interferometry Experiments for Weak Ligand-Analyte Interactions. ACS OMEGA 2022; 7:9206-9211. [PMID: 35350330 PMCID: PMC8945191 DOI: 10.1021/acsomega.1c05659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Quantitative analysis of protein-protein interactions (PPIs) using biolayer interferometry (BLI) requires effective suppression of nonspecific binding (NSB) between analytes and biosensors. In particular, the study of weak interactions (i.e., K D > 1 μM) requires high concentrations of analytes, which substantially increases NSB. However, there are only a few so-called NSB blockers compatible with biomolecules, which limits the use of BLI in the accurate analysis of weak interactions. The present study aims to identify a new NSB blocker for the quantitative analysis of weak PPIs using BLI. We find that saccharides, especially sucrose, are potent NSB blockers and demonstrate their compatibility with other blocking additives. We also demonstrate the effects of the new NSB blocker by characterizing the binding between nonstructural protein 1 of the influenza A virus and human phosphoinositide 3-kinase. We anticipate that the new NSB-blocking admixture will find broad applications in studying weak interactions using BLI.
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10
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Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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11
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Trigueiro-Louro J, Santos LA, Almeida F, Correia V, Brito RMM, Rebelo-de-Andrade H. NS1 protein as a novel anti-influenza target: Map-and-mutate antiviral rationale reveals new putative druggable hot spots with an important role on viral replication. Virology 2022; 565:106-116. [PMID: 34773868 DOI: 10.1016/j.virol.2021.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 01/28/2023]
Abstract
Influenza NS1 is a promising anti-influenza target, considering its conserved and druggable structure, and key function in influenza replication and pathogenesis. Notwithstanding, target identification and validation, strengthened by experimental data, are lacking. Here, we further explored our previously designed structure-based antiviral rationale directed to highly conserved druggable NS1 regions across a broad spectrum of influenza A viruses. We aimed to identify NS1-mutated viruses exhibiting a reduced growth phenotype and/or an altered cell apoptosis profile. We found that NS1 mutations Y171A, K175A (consensus druggable pocket 1), W102A (consensus druggable pocket 3), Q121A and G184P (multiple consensus druggable pockets) - located at hot spots amenable for pharmacological modulation - significantly impaired A(H1N1)pdm09 virus replication, in vitro. This is the first time that NS1-K175A, -W102A, and -Q121A mutations are characterized. Our map-and-mutate strategy provides the basis to establish the NS1 as a promising target using a rationale with a higher resilience to resistance development.
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Affiliation(s)
- João Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Luís A Santos
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Filipe Almeida
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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12
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How Influenza A Virus NS1 Deals with the Ubiquitin System to Evade Innate Immunity. Viruses 2021; 13:v13112309. [PMID: 34835115 PMCID: PMC8619935 DOI: 10.3390/v13112309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitination is a post-translational modification regulating critical cellular processes such as protein degradation, trafficking and signaling pathways, including activation of the innate immune response. Therefore, viruses, and particularly influenza A virus (IAV), have evolved different mechanisms to counteract this system to perform proper infection. Among IAV proteins, the non-structural protein NS1 is shown to be one of the main virulence factors involved in these viral hijackings. NS1 is notably able to inhibit the host's antiviral response through the perturbation of ubiquitination in different ways, as discussed in this review.
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13
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Tam EH, Liu YC, Woung CH, Liu HM, Wu GH, Wu CC, Kuo RL. Role of the Chaperone Protein 14-3-3ε in the Regulation of Influenza A Virus-Activated Beta Interferon. J Virol 2021; 95:e0023121. [PMID: 34379499 PMCID: PMC8475545 DOI: 10.1128/jvi.00231-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
The NS1 protein of the influenza A virus plays a critical role in regulating several biological processes in cells, including the type I interferon (IFN) response. We previously profiled the cellular factors that interact with the NS1 protein of influenza A virus and found that the NS1 protein interacts with proteins involved in RNA splicing/processing, cell cycle regulation, and protein targeting processes, including 14-3-3ε. Since 14-3-3ε plays an important role in retinoic acid-inducible gene I (RIG-I) translocation to mitochondrial antiviral-signaling protein (MAVS) to activate type I IFN expression, the interaction of the NS1 and 14-3-3ε proteins may prevent the RIG-I-mediated IFN response. In this study, we confirmed that the 14-3-3ε protein interacts with the N-terminal domain of the NS1 protein and that the NS1 protein inhibits RIG-I-mediated IFN-β promoter activation in 14-3-3ε-overexpressing cells. In addition, our results showed that knocking down 14-3-3ε can reduce IFN-β expression elicited by influenza A virus and enhance viral replication. Furthermore, we found that threonine in the 49th amino acid position of the NS1 protein plays a role in the interaction with 14-3-3ε. Influenza A virus expressing C terminus-truncated NS1 with a T49A mutation dramatically increases IFN-β mRNA in infected cells and causes slower replication than that of virus without the T-to-A mutation. Collectively, this study demonstrates that 14-3-3ε is involved in influenza A virus-initiated IFN-β expression and that the interaction of the NS1 protein and 14-3-3ε may be one of the mechanisms for inhibiting type I IFN activation during influenza A virus infection. IMPORTANCE Influenza A virus is an important human pathogen causing severe respiratory disease. The virus has evolved several strategies to dysregulate the innate immune response and facilitate its replication. We demonstrate that the NS1 protein of influenza A virus interacts with the cellular chaperone protein 14-3-3ε, which plays a critical role in retinoic acid-inducible gene I (RIG-I) translocation that induces type I interferon (IFN) expression, and that NS1 protein prevents RIG-I translocation to the mitochondrial membrane. The interaction site for 14-3-3ε is the RNA-binding domain (RBD) of the NS1 protein. Therefore, this research elucidates a novel mechanism by which the NS1 RBD mediates IFN-β suppression to facilitate influenza A viral replication. Additionally, the findings reveal the antiviral role of 14-3-3ε during influenza A virus infection.
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Affiliation(s)
- Ee-Hong Tam
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yen-Chin Liu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chian-Huey Woung
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Helene Minyi Liu
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Guan-Hong Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Rei-Lin Kuo
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
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14
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Salazar C, Galaz M, Ojeda N, Marshall SH. Expression of ssa-miR-155 during ISAV infection in vitro: Putative role as a modulator of the immune response in Salmo salar. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104109. [PMID: 33930457 DOI: 10.1016/j.dci.2021.104109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Multiple cellular components are involved in pathogen-host interaction during viral infection; in this context, the role of miRNAs have become highly relevant. We assessed the expression of selected miRNAs during an in vitro infection of a Salmo salar cell line with Infectious Salmon Anemia Virus (ISAV), the causative agent of a severe disease by the same name. Salmon orthologs for miRNAs that regulate antiviral responses were measured using RT-qPCR in an in vitro time-course assay. We observed a modulation of specific miRNAs expression, where ssa-miR-155-5p was differentially over-expressed. Using in silico analysis, we identified the putative mRNA targets for ssa-miR-155-5p, finding a high prevalence of hosts immune response-related genes; moreover, several mRNAs involved in the viral infective process were also identified as targets for this miRNA. Our results suggest a relevant role for miR-155-5p in Salmo salar during an ISAV infection as a regulator of the immune response to the virus.
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Affiliation(s)
- Carolina Salazar
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Martín Galaz
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Nicolás Ojeda
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Sergio H Marshall
- Instituto de Biologia, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile.
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15
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Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Front Mol Biosci 2021; 8:716477. [PMID: 34307465 PMCID: PMC8296144 DOI: 10.3389/fmolb.2021.716477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/28/2021] [Indexed: 11/24/2022] Open
Abstract
Biomolecular recognition often involves conformational changes as a prerequisite for binding (i.e., conformational selection) or concurrently with binding (i.e., induced-fit). Recent advances in structural and kinetic approaches have enabled the detailed characterization of protein motions at atomic resolution. However, to fully understand the role of the conformational dynamics in molecular recognition, studies on the binding transition state are needed. Here, we investigate the binding transition state between nonstructural protein 1 (NS1) of the pandemic 1918 influenza A virus and the human p85β subunit of PI3K. 1918 NS1 binds to p85β via conformational selection. We present the free-energy mapping of the transition and bound states of the 1918 NS1:p85β interaction using linear free energy relationship and ϕ-value analyses. We find that the binding transition state of 1918 NS1 and p85β is structurally similar to the bound state with well-defined binding orientation and hydrophobic interactions. Our finding provides a detailed view of how protein motion contributes to the development of intermolecular interactions along the binding reaction coordinate.
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Affiliation(s)
- Alyssa Dubrow
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Iktae Kim
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Elias Topo
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
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16
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Ludwig S, Hrincius ER, Boergeling Y. The Two Sides of the Same Coin-Influenza Virus and Intracellular Signal Transduction. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038513. [PMID: 31871235 PMCID: PMC7778220 DOI: 10.1101/cshperspect.a038513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cells respond to extracellular agents by activation of intracellular signaling pathways. Viruses can be regarded as such agents, leading to a firework of signaling inside the cell, primarily induced by pathogen-associated molecular patterns (PAMPs) that provoke safeguard mechanisms to defend from the invader. In the constant arms race between pathogen and cellular defense, viruses not only have evolved mechanisms to suppress or misuse supposedly antiviral signaling processes for their own benefit but also actively induce signaling to promote replication. This creates viral dependencies that may be exploited for novel strategies of antiviral intervention. Here, we will summarize the current knowledge of activation and function of influenza virus-induced signaling pathways with a focus on nuclear factor (NF)-κB signaling, mitogen-activated protein kinase cascades, and the phosphatidylinositol-3-kinase pathway. We will discuss the opportunities and drawbacks of targeting these signaling pathways for antiviral intervention.
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17
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Molecular Dynamics Simulations of Influenza A Virus NS1 Reveal a Remarkably Stable RNA-Binding Domain Harboring Promising Druggable Pockets. Viruses 2020; 12:v12050537. [PMID: 32422922 PMCID: PMC7290946 DOI: 10.3390/v12050537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is considered to be the major antagonist of the interferon system and antiviral defenses of the cell. It could therefore represent a suitable target for novel antiviral strategies. As a first step towards the identification of small compounds targeting NS1, we here investigated the druggable potential of its RNA-binding domain since this domain is essential to the biological activities of NS1. We explored the flexibility of the full-length protein by running molecular dynamics simulations on one of its published crystal structures. While the RNA-binding domain structure was remarkably stable along the simulations, we identified a flexible site at the two extremities of the “groove” that is delimited by the antiparallel α-helices that make up its RNA-binding interface. This groove region is able to form potential binding pockets, which, in 60% of the conformations, meet the druggability criteria. We characterized these pockets and identified the residues that contribute to their druggability. All the residues involved in the druggable pockets are essential at the same time to the stability of the RNA-binding domain and to the biological activities of NS1. They are also strictly conserved across the large sequence diversity of NS1, emphasizing the robustness of this search towards the identification of broadly active NS1-targeting compounds.
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18
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Molecular Basis of the Ternary Interaction between NS1 of the 1918 Influenza A Virus, PI3K, and CRK. Viruses 2020; 12:v12030338. [PMID: 32244879 PMCID: PMC7150778 DOI: 10.3390/v12030338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 01/10/2023] Open
Abstract
The 1918 influenza A virus (IAV) caused the worst flu pandemic in human history. Non-structural protein 1 (NS1) is an important virulence factor of the 1918 IAV and antagonizes host antiviral immune responses. NS1 increases virulence by activating phosphoinositide 3-kinase (PI3K) via binding to the p85β subunit of PI3K. Intriguingly, unlike the NS1 of other human IAV strains, 1918 NS1 hijacks another host protein, CRK, to form a ternary complex with p85β, resulting in hyperactivation of PI3K. However, the molecular basis of the ternary interaction between 1918 NS1, CRK, and PI3K remains elusive. Here, we report the structural and thermodynamic bases of the ternary interaction. We find that the C-terminal tail (CTT) of 1918 NS1 remains highly flexible in the complex with p85β. Thus, the CTT of 1918 NS1 in the complex with PI3K can efficiently hijack CRK. Notably, our study indicates that 1918 NS1 enhances its affinity to p85β in the presence of CRK, which might result in enhanced activation of PI3K. Our results provide structural insight into how 1918 NS1 hijacks two host proteins simultaneously.
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19
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Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses. Proc Natl Acad Sci U S A 2020; 117:6550-6558. [PMID: 32152123 DOI: 10.1073/pnas.1920582117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 1918 influenza A virus (IAV) caused the most severe flu pandemic in recorded human history. Nonstructural protein 1 (NS1) is an important virulence factor of the 1918 IAV. NS1 antagonizes host defense mechanisms through interactions with multiple host factors. One pathway by which NS1 increases virulence is through the activation of phosphoinositide 3-kinase (PI3K) by binding to its p85β subunit. Here we present the mechanism underlying the molecular recognition of the p85β subunit by 1918 NS1. Using X-ray crystallography, we determine the structure of 1918 NS1 complexed with p85β of human PI3K. We find that the 1918 NS1 effector domain (1918 NS1ED) undergoes a conformational change to bind p85β. Using NMR relaxation dispersion and molecular dynamics simulation, we identify that free 1918 NS1ED exists in a dynamic equilibrium between p85β-binding-competent and -incompetent conformations in the submillisecond timescale. Moreover, we discover that NS1ED proteins of 1918 (H1N1) and Udorn (H3N2) strains exhibit drastically different conformational dynamics and binding kinetics to p85β. These results provide evidence of strain-dependent conformational dynamics of NS1. Using kinetic modeling based on the experimental data, we demonstrate that 1918 NS1ED can result in the faster hijacking of p85β compared to Ud NS1ED, although the former has a lower affinity to p85β than the latter. Our results suggest that the difference in binding kinetics may impact the competition with cellular antiviral responses for the activation of PI3K. We anticipate that our findings will increase the understanding of the strain-dependent behaviors of influenza NS1 proteins.
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20
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Rosário-Ferreira N, Preto AJ, Melo R, Moreira IS, Brito RMM. The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection. Int J Mol Sci 2020; 21:E1511. [PMID: 32098424 PMCID: PMC7073157 DOI: 10.3390/ijms21041511] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/07/2023] Open
Abstract
Influenza (flu) is a contagious viral disease, which targets the human respiratory tract and spreads throughout the world each year. Every year, influenza infects around 10% of the world population and between 290,000 and 650,000 people die from it according to the World Health Organization (WHO). Influenza viruses belong to the Orthomyxoviridae family and have a negative sense eight-segment single-stranded RNA genome that encodes 11 different proteins. The only control over influenza seasonal epidemic outbreaks around the world are vaccines, annually updated according to viral strains in circulation, but, because of high rates of mutation and recurrent genetic assortment, new viral strains of influenza are constantly emerging, increasing the likelihood of pandemics. Vaccination effectiveness is limited, calling for new preventive and therapeutic approaches and a better understanding of the virus-host interactions. In particular, grasping the role of influenza non-structural protein 1 (NS1) and related known interactions in the host cell is pivotal to better understand the mechanisms of virus infection and replication, and thus propose more effective antiviral approaches. In this review, we assess the structure of NS1, its dynamics, and multiple functions and interactions, to highlight the central role of this protein in viral biology and its potential use as an effective therapeutic target to tackle seasonal and pandemic influenza.
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Affiliation(s)
- Nícia Rosário-Ferreira
- Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
| | - António J. Preto
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
| | - Rita Melo
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
- Centro de Ciências e Tecnologias Nucleares and Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Irina S. Moreira
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Rui M. M. Brito
- Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
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21
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Differential Modulation of Innate Immune Responses in Human Primary Cells by Influenza A Viruses Carrying Human or Avian Nonstructural Protein 1. J Virol 2019; 94:JVI.00999-19. [PMID: 31597767 PMCID: PMC6912104 DOI: 10.1128/jvi.00999-19] [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: 07/10/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) cause seasonal epidemics which result in an important health and economic burden. Wild aquatic birds are the natural host of IAV. However, IAV can infect diverse hosts, including humans, domestic poultry, pigs, and others. IAVs circulating in animals occasionally cross the species barrier, infecting humans, which results in mild to very severe disease. In some cases, these viruses can acquire the ability to be transmitted among humans and initiate a pandemic. The nonstructural 1 (NS1) protein of IAV is an important antagonist of the innate immune response. In this study, using recombinant viruses and primary human cells, we show that NS1 proteins from human and avian hosts show intrinsic differences in the modulation of the innate immunity in human dendritic cells and epithelial cells, as well as different cellular localization dynamics in infected cells. The influenza A virus (IAV) nonstructural protein 1 (NS1) contributes to disease pathogenesis through the inhibition of host innate immune responses. Dendritic cells (DCs) release interferons (IFNs) and proinflammatory cytokines and promote adaptive immunity upon viral infection. In order to characterize the strain-specific effects of IAV NS1 on human DC activation, we infected human DCs with a panel of recombinant viruses with the same backbone (A/Puerto Rico/08/1934) expressing different NS1 proteins from human and avian origin. We found that these viruses induced a clearly distinct phenotype in DCs. Specifically, viruses expressing NS1 from human IAV (either H1N1 or H3N2) induced higher levels of expression of type I (IFN-α and IFN-β) and type III (IFN-λ1 to IFNλ3) IFNs than viruses expressing avian IAV NS1 proteins (H5N1, H7N9, and H7N2), but the differences observed in the expression levels of proinflammatory cytokines like tumor necrosis factor alpha (TNF-α) or interleukin-6 (IL-6) were not significant. In addition, using imaging flow cytometry, we found that human and avian NS1 proteins segregate based on their subcellular trafficking dynamics, which might be associated with the different innate immune profile induced in DCs by viruses expressing those NS1 proteins. Innate immune responses induced by our panel of IAV recombinant viruses were also characterized in normal human bronchial epithelial cells, and the results were consistent with those in DCs. Altogether, our results reveal an increased ability of NS1 from avian viruses to antagonize innate immune responses in human primary cells compared to the ability of NS1 from human viruses, which could contribute to the severe disease induced by avian IAV in humans. IMPORTANCE Influenza A viruses (IAVs) cause seasonal epidemics which result in an important health and economic burden. Wild aquatic birds are the natural host of IAV. However, IAV can infect diverse hosts, including humans, domestic poultry, pigs, and others. IAVs circulating in animals occasionally cross the species barrier, infecting humans, which results in mild to very severe disease. In some cases, these viruses can acquire the ability to be transmitted among humans and initiate a pandemic. The nonstructural 1 (NS1) protein of IAV is an important antagonist of the innate immune response. In this study, using recombinant viruses and primary human cells, we show that NS1 proteins from human and avian hosts show intrinsic differences in the modulation of the innate immunity in human dendritic cells and epithelial cells, as well as different cellular localization dynamics in infected cells.
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22
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Ramos I, Smith G, Ruf-Zamojski F, Martínez-Romero C, Fribourg M, Carbajal EA, Hartmann BM, Nair VD, Marjanovic N, Monteagudo PL, DeJesus VA, Mutetwa T, Zamojski M, Tan GS, Jayaprakash C, Zaslavsky E, Albrecht RA, Sealfon SC, García-Sastre A, Fernandez-Sesma A. Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1. J Virol 2019; 93:e00559-19. [PMID: 31375585 PMCID: PMC6798124 DOI: 10.1128/jvi.00559-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Early interactions of influenza A virus (IAV) with respiratory epithelium might determine the outcome of infection. The study of global cellular innate immune responses often masks multiple aspects of the mechanisms by which populations of cells work as organized and heterogeneous systems to defeat virus infection, and how the virus counteracts these systems. In this study, we experimentally dissected the dynamics of IAV and human epithelial respiratory cell interaction during early infection at the single-cell level. We found that the number of viruses infecting a cell (multiplicity of infection [MOI]) influences the magnitude of virus antagonism of the host innate antiviral response. Infections performed at high MOIs resulted in increased viral gene expression per cell and stronger antagonist effect than infections at low MOIs. In addition, single-cell patterns of expression of interferons (IFN) and IFN-stimulated genes (ISGs) provided important insights into the contributions of the infected and bystander cells to the innate immune responses during infection. Specifically, the expression of multiple ISGs was lower in infected than in bystander cells. In contrast with other IFNs, IFN lambda 1 (IFNL1) showed a widespread pattern of expression, suggesting a different cell-to-cell propagation mechanism more reliant on paracrine signaling. Finally, we measured the dynamics of the antiviral response in primary human epithelial cells, which highlighted the importance of early innate immune responses at inhibiting virus spread.IMPORTANCE Influenza A virus (IAV) is a respiratory pathogen of high importance to public health. Annual epidemics of seasonal IAV infections in humans are a significant public health and economic burden. IAV also causes sporadic pandemics, which can have devastating effects. The main target cells for IAV replication are epithelial cells in the respiratory epithelium. The cellular innate immune responses induced in these cells upon infection are critical for defense against the virus, and therefore, it is important to understand the complex interactions between the virus and the host cells. In this study, we investigated the innate immune response to IAV in the respiratory epithelium at the single-cell level, providing a better understanding on how a population of epithelial cells functions as a complex system to orchestrate the response to virus infection and how the virus counteracts this system.
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Affiliation(s)
- Irene Ramos
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gregory Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miguel Fribourg
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Edwin A Carbajal
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Boris M Hartmann
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nada Marjanovic
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paula L Monteagudo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Veronica A DeJesus
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tinaye Mutetwa
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gene S Tan
- Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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23
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Shen Q, Cho JH. The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. Biochem Biophys Res Commun 2019; 518:178-182. [PMID: 31420169 DOI: 10.1016/j.bbrc.2019.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 12/25/2022]
Abstract
Nonstructural protein 1 (NS1) is a multifunctional virulence factor of influenza virus. The effector domain (ED) of influenza viruses is capable of binding to a variety of host factors, however, the molecular basis of the interactions remains to be investigated. The isolated NS1-ED exists in equilibrium between the monomer and homodimer. Although the structural diversity of the dimer interface has been well-characterized, limited information is available regarding the internal conformational heterogeneity of the monomeric NS1-ED. Here, we present the solution NMR structure of the NS1-ED W187R of the 1918 influenza A virus, which caused the "Spanish flu." Structural plasticity is an essential property to understand the molecular mechanism by which NS1-ED interacts with multiple host proteins. Structural comparison with the NS1-ED from influenza A/Udorn/1972 (Ud) strain revealed a similar overall structure but a distinct conformational variation and flexibility. Our results suggest that conformational flexibility of the NS1-ED might differ depending on the influenza strain.
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Affiliation(s)
- Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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24
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Trigueiro-Louro JM, Correia V, Santos LA, Guedes RC, Brito RMM, Rebelo-de-Andrade H. To hit or not to hit: Large-scale sequence analysis and structure characterization of influenza A NS1 unlocks new antiviral target potential. Virology 2019; 535:297-307. [PMID: 31104825 DOI: 10.1016/j.virol.2019.04.009] [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: 02/19/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Abstract
Influenza NS1 protein is among the most promising novel druggable anti-influenza target, based on its structure; multiple interactions; and global function in influenza replication and pathogenesis. Notwithstanding, drug development guidance based on NS1 structural biology is lacking. Here, we design a promising strategy directed to highly conserved druggable regions as a result of an exhaustive large-scale sequence analysis and structure characterization of NS1 protein across human-infecting influenza A subtypes, over the past 100 years. We have identified 3 druggable pockets and 8 new potential hot spot residues in the NS1 protein, not described before, additionally to other 16 sites previously identified, which represent attractive targets for pharmacological modulation. This study provides a rationale towards structure-function studies of NS1 druggable sites, which have the potential to accelerate the NS1 target validation. This research also contributes to a deeper comprehension and insight into the evolutionary dynamics of influenza A NS1 protein.
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Affiliation(s)
- João M Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Luís A Santos
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rita C Guedes
- Medicinal Chemistry Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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25
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The Nonstructural NS1 Protein of Influenza Viruses Modulates TP53 Splicing through Host Factor CPSF4. J Virol 2019; 93:JVI.02168-18. [PMID: 30651364 DOI: 10.1128/jvi.02168-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) are known to modulate and "hijack" several cellular host mechanisms, including gene splicing and RNA maturation machineries. These modulations alter host cellular responses and enable an optimal expression of viral products throughout infection. The interplay between the host protein p53 and IAV, in particular through the viral nonstructural protein NS1, has been shown to be supportive for IAV replication. However, it remains unknown whether alternatively spliced isoforms of p53, known to modulate p53 transcriptional activity, are affected by IAV infection and contribute to IAV replication. Using a TP53 minigene, which mimics intron 9 alternative splicing, we have shown here that the NS1 protein of IAV changes the expression pattern of p53 isoforms. Our results demonstrate that CPSF4 (cellular protein cleavage and polyadenylation specificity factor 4) independently and the interaction between NS1 and CPSF4 modulate the alternative splicing of TP53 transcripts, which may result in the differential activation of p53-responsive genes. Finally, we report that CPSF4 and most likely beta and gamma spliced p53 isoforms affect both viral replication and IAV-associated type I interferon secretion. All together, our data show that cellular p53 and CPSF4 factors, both interacting with viral NS1, have a crucial role during IAV replication that allows IAV to interact with and alter the expression of alternatively spliced p53 isoforms in order to regulate the cellular innate response, especially via type I interferon secretion, and perform efficient viral replication.IMPORTANCE Influenza A viruses (IAV) constitute a major public health issue, causing illness and death in high-risk populations during seasonal epidemics or pandemics. IAV are known to modulate cellular pathways to promote their replication and avoid immune restriction via the targeting of several cellular proteins. One of these proteins, p53, is a master regulator involved in a large panel of biological processes, including cell cycle arrest, apoptosis, or senescence. This "cellular gatekeeper" is also involved in the control of viral infections, and viruses have developed a wide diversity of mechanisms to modulate/hijack p53 functions to achieve an optimal replication in their hosts. Our group and others have previously shown that p53 activity is finely modulated by different multilevel mechanisms during IAV infection. Here, we characterized IAV nonstructural protein NS1 and the cellular factor CPSF4 as major partners involved in the IAV-induced modulation of the TP53 alternative splicing that was associated with a strong modulation of p53 activity and notably the p53-mediated antiviral response.
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Teo SHC, Wu JP, Mok CK, Tan YJ. A NS1-binding monoclonal antibody interacts with two residues that are highly conserved in seasonal as well as newly emerged influenza A virus. Pathog Dis 2019; 77:5370084. [PMID: 30839053 PMCID: PMC7273928 DOI: 10.1093/femspd/ftz012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/05/2019] [Indexed: 11/22/2022] Open
Abstract
The non-structural protein 1 (NS1) of influenza A virus (IAV) is a multifunctional protein that antagonizes host antiviral responses, modulating virus pathogenesis. As such, it serves as a good target for research and diagnostic assay development. In this study, we have generated a novel monoclonal antibody (mAb) 19H9 and epitope mapping revealed that two residues, P85 and Y89, of NS1 are essential for interacting with this mAb. Furthermore, residues P85 and Y89 are found to be highly conserved across different IAV subtypes, namely seasonal H1N1 and H3N2, as well as the highly pathogenic H5N1 and H5N6 avian strains. Indeed, mAb 19H9 exhibits broad cross-reactivity with IAV strains of different subtypes. The binding of mAb 19H9 to residue Y89 was further confirmed by the abrogation of interaction between NS1 and p85β. Additionally, mAb 19H9 also detected NS1 proteins expressed in IAV-infected cells, showing NS1 intracellular localization in the cytoplasm and nucleolus. To our knowledge, mAb 19H9 is the first murine mAb to bind at the juxtaposition between the N-terminal RNA-binding domain and C-terminal effector domain of NS1. It could serve as a useful research tool for studying the conformational plasticity and dynamic changes in NS1.
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Affiliation(s)
- Su Hui Catherine Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, MD4, 5 Science Drive 2, Singapore 117545
| | - Jian-Ping Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, MD4, 5 Science Drive 2, Singapore 117545
| | - Chee-Keng Mok
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, MD4, 5 Science Drive 2, Singapore 117545
| | - Yee-Joo Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, MD4, 5 Science Drive 2, Singapore 117545
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Dr, Singapore 138673
- Correspondence author: Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, MD4, 5 Science Drive 2, Singapore 117545. Tel: +65 65163692; E-mail:
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27
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Pereira CF, Wise HM, Kurian D, Pinto RM, Amorim MJ, Gill AC, Digard P. Effects of mutations in the effector domain of influenza A virus NS1 protein. BMC Res Notes 2018; 11:673. [PMID: 30227889 PMCID: PMC6145200 DOI: 10.1186/s13104-018-3779-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/12/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The multifunctional NS1 protein of influenza A virus has roles in antagonising cellular innate immune responses and promoting viral gene expression. To better understand the interplay between these functions, we tested the effects of NS1 effector domain mutations known to affect homo-dimerisation or interactions with cellular PI3 kinase or Trim25 on NS1 ability to promote nuclear export of viral mRNAs. RESULTS The NS1 dimerisation mutant W187R retained the functions of binding cellular NXF1 as well as stabilising NXF1 interaction with viral segment 7 mRNAs and promoting their nuclear export. Two PI3K-binding mutants, NS1 Y89F and Y89A still bound NXF1 but no longer promoted NXF1 interactions with segment 7 mRNA or its nuclear export. The Trim25-binding mutant NS1 E96A/E97A bound NXF1 and supported NXF1 interactions with segment 7 mRNA but no longer supported mRNA nuclear export. Analysis of WT and mutant NS1 interaction partners identified hsp70 as specifically binding to NS1 E96A/E97A. Whilst these data suggest the possibility of functional links between NS1's effects on intracellular signalling and its role in viral mRNA nuclear export, they also indicate potential pleiotropic effects of the NS1 mutations; in the case of E96A/E97A possibly via disrupted protein folding leading to chaperone recruitment.
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Affiliation(s)
- Carina F Pereira
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,European Commission, Place Rogier 16, 1210, Brussels, Belgium
| | - Helen M Wise
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Department of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Dominic Kurian
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Rute M Pinto
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Maria J Amorim
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,Cell Biology of Viral Infection, Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Andrew C Gill
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Green Lane, Lincoln, Lincolnshire, LN6 7DL, UK
| | - Paul Digard
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. .,The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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28
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Koliopoulos MG, Lethier M, van der Veen AG, Haubrich K, Hennig J, Kowalinski E, Stevens RV, Martin SR, Reis e Sousa C, Cusack S, Rittinger K. Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nat Commun 2018; 9:1820. [PMID: 29739942 PMCID: PMC5940772 DOI: 10.1038/s41467-018-04214-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 04/13/2018] [Indexed: 02/04/2023] Open
Abstract
RIG-I is a viral RNA sensor that induces the production of type I interferon (IFN) in response to infection with a variety of viruses. Modification of RIG-I with K63-linked poly-ubiquitin chains, synthesised by TRIM25, is crucial for activation of the RIG-I/MAVS signalling pathway. TRIM25 activity is targeted by influenza A virus non-structural protein 1 (NS1) to suppress IFN production and prevent an efficient host immune response. Here we present structures of the human TRIM25 coiled-coil-PRYSPRY module and of complexes between the TRIM25 coiled-coil domain and NS1. These structures show that binding of NS1 interferes with the correct positioning of the PRYSPRY domain of TRIM25 required for substrate ubiquitination and provide a mechanistic explanation for how NS1 suppresses RIG-I ubiquitination and hence downstream signalling. In contrast, the formation of unanchored K63-linked poly-ubiquitin chains is unchanged by NS1 binding, indicating that RING dimerisation of TRIM25 is not affected by NS1.
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Affiliation(s)
- Marios G Koliopoulos
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mathilde Lethier
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | | | - Kevin Haubrich
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Eva Kowalinski
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Rebecca V Stevens
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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29
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Unexpected Functional Divergence of Bat Influenza Virus NS1 Proteins. J Virol 2018; 92:JVI.02097-17. [PMID: 29237829 PMCID: PMC5809727 DOI: 10.1128/jvi.02097-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/19/2022] Open
Abstract
Recently, two influenza A virus (FLUAV) genomes were identified in Central and South American bats. These sequences exhibit notable divergence from classical FLUAV counterparts, and functionally, bat FLUAV glycoproteins lack canonical receptor binding and destroying activity. Nevertheless, other features that distinguish these viruses from classical FLUAVs have yet to be explored. Here, we studied the viral nonstructural protein NS1, a virulence factor that modulates host signaling to promote efficient propagation. Like all FLUAV NS1 proteins, bat FLUAV NS1s bind double-stranded RNA and act as interferon antagonists. Unexpectedly, we found that bat FLUAV NS1s are unique in being unable to bind host p85β, a regulatory subunit of the cellular metabolism-regulating enzyme, phosphoinositide 3-kinase (PI3K). Furthermore, neither bat FLUAV NS1 alone nor infection with a chimeric bat FLUAV efficiently activates Akt, a PI3K effector. Structure-guided mutagenesis revealed that the bat FLUAV NS1-p85β interaction can be reengineered (in a strain-specific manner) by changing two to four NS1 residues (96L, 99M, 100I, and 145T), thereby creating a hydrophobic patch. Notably, ameliorated p85β-binding is insufficient for bat FLUAV NS1 to activate PI3K, and a chimeric bat FLUAV expressing NS1 with engineered hydrophobic patch mutations exhibits cell-type-dependent, but species-independent, propagation phenotypes. We hypothesize that bat FLUAV hijacking of PI3K in the natural bat host has been selected against, perhaps because genes in this metabolic pathway were differentially shaped by evolution to suit the unique energy use strategies of this flying mammal. These data expand our understanding of the enigmatic functional divergence between bat FLUAVs and classical mammalian and avian FLUAVs. IMPORTANCE The potential for novel influenza A viruses to establish infections in humans from animals is a source of continuous concern due to possible severe outbreaks or pandemics. The recent discovery of influenza A-like viruses in bats has raised questions over whether these entities could be a threat to humans. Understanding unique properties of the newly described bat influenza A-like viruses, such as their mechanisms to infect cells or how they manipulate host functions, is critical to assess their likelihood of causing disease. Here, we characterized the bat influenza A-like virus NS1 protein, a key virulence factor, and found unexpected functional divergence of this protein from counterparts in other influenza A viruses. Our study dissects the molecular changes required by bat influenza A-like virus NS1 to adopt classical influenza A virus properties and suggests consequences of bat influenza A-like virus infection, potential future evolutionary trajectories, and intriguing virus-host biology in bat species.
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Vasin AV, Petrova-Brodskaya AV, Plotnikova MA, Tsvetkov VB, Klotchenko SA. EVOLUTIONARY DYNAMICS OF STRUCTURAL AND FUNCTIONAL DOMAINS OF INFLUENZA A VIRUS NS1 PROTEIN. Vopr Virusol 2017; 62:246-258. [PMID: 36494956 DOI: 10.18821/0507-4088-2017-62-6-246-258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022]
Abstract
Influenza A virus (IAV) NS1 protein is one of the key viral factors responsible for virus-host interactions. NS1 counteracts host antiviral defense, participates in the processing and export of cellular mRNAs, regulates the activity of viral RNA polymerase and the expression of viral genes, and influences the cellular signaling systems. Multiple NS1 functions are carried out due to the interactions with cellular factors, the number of which exceeds one hundred. It is noteworthy that only two segments of IAV genome - NS and NP - did not undergo reassortment and evolved in the course of genetic drift, beginning with the pandemic of 1918 to the present. This fact may indicate the importance of NS1 and its numerous interactions with cellular factors in the interspecific adaptation of the virus. The review presents data on the evolution of the human IAV NS1 protein and analysis of the amino acid substitutions in the main structural and functional domains of NS1 protein during evolution.
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Affiliation(s)
- A V Vasin
- Research Institute of Influenza.,Peter the Great St. Petersburg Polytechnic University
| | - A V Petrova-Brodskaya
- Research Institute of Influenza.,Peter the Great St. Petersburg Polytechnic University
| | | | - V B Tsvetkov
- Research Institute of Influenza.,A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences.,Federal Research and Clinical Center of Physical-Chemical Medicine
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31
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Structure-Guided Functional Annotation of the Influenza A Virus NS1 Protein Reveals Dynamic Evolution of the p85β-Binding Site during Circulation in Humans. J Virol 2017; 91:JVI.01081-17. [PMID: 28814525 PMCID: PMC5640874 DOI: 10.1128/jvi.01081-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/13/2017] [Indexed: 01/28/2023] Open
Abstract
Rational characterization of virulence and host-adaptive markers in the multifunctional influenza A virus NS1 protein is hindered by a lack of comprehensive knowledge about NS1-host protein protein interfaces. Here, we surveyed the impact of amino acid variation in NS1 at its structurally defined binding site for host p85β, a regulator of phosphoinositide 3-kinase (PI3K) signaling. Structure-guided alanine scanning of all viral residues at this interface defined 10 positions contributing to the interaction, with residues 89, 95, 98, 133, 145, and 162 being the most important. A bioinformatic study of >24,000 publicly available NS1 sequences derived from viruses infecting different hosts highlighted several prevalent amino acid variants at the p85β interface that either enhanced (I95) or weakened (N135, T145, L161, Y161, S164) p85β binding. Interestingly, analysis of viruses circulating in humans since the 1918 pandemic revealed the temporal acquisition of functionally relevant variants at this interface. I95 (which enhanced p85β binding) quickly became prevalent in the 1940s and experimentally conferred a fitness advantage to a recombinant 1930s-based H1N1 virus in human lung epithelial cells. Surprisingly, H1N1 and H3N2 viruses recently acquired T145 or N135, respectively, which diminished p85β binding but apparently not the overall fitness in the human population. Evolutionary analyses revealed covariation of the NS1-p85β binding phenotype in humans with functional changes at multiple residues in other viral proteins, suggesting an unexplored compensatory or synergistic interplay between phenotypes in vivo. Overall, our data provide a resource to understand the consequences of the NS1-p85β binding spectrum of different influenza viruses and highlight the dynamic evolution of this property in viruses circulating in humans. IMPORTANCE In humans, influenza A viruses are responsible for causing seasonal epidemics and occasional pandemics. These viruses also circulate and evolve in other animal species, creating a reservoir from which novel viruses with distinct properties can emerge. The viral nonstructural protein NS1 is an important host range determinant and virulence factor that exhibits strain-specific interactions with several host factors, although few have been characterized extensively. In the study described here, we comprehensively surveyed the impact of natural and unnatural NS1 variations on the binding of NS1 to host p85β, a subunit of phosphoinositide 3-kinase that regulates intracellular metabolism and contributes to virus replication and virulence. We define the p85β-binding site on NS1 and provide a predictive resource to assess this ability of NS1 in viruses from different hosts. Strikingly, we uncover a spectrum of p85β binding by different NS1 proteins and reveal that viruses evolving in humans have undergone dynamic changes in this NS1 function over the last century.
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32
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Mok BWY, Liu H, Chen P, Liu S, Lau SY, Huang X, Liu YC, Wang P, Yuen KY, Chen H. The role of nuclear NS1 protein in highly pathogenic H5N1 influenza viruses. Microbes Infect 2017; 19:587-596. [PMID: 28903072 DOI: 10.1016/j.micinf.2017.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 11/28/2022]
Abstract
The non-structural protein (NS1) of influenza A viruses (IAV) performs multiple functions during viral infection. NS1 contains two nuclear localization signals (NLS): NLS1 and NLS2. The NS1 protein is located predominantly in the nucleus during the early stages of infection and subsequently exported to the cytoplasm. A nonsense mutation that results in a large deletion in the carboxy-terminal region of the NS1 protein that contains the NLS2 domain was found in some IAV subtypes, including highly pathogenic avian influenza (HPAI) H7N9 and H5N1 viruses. We introduced different mutations into the NLS domains of NS1 proteins in various strains of IAV, and demonstrated that mutation of the NLS2 region in the NS1 protein of HPAI H5N1 viruses severely affects its nuclear localization pattern. H5N1 viruses expressing NS1 protein that is unable to localize to the nucleus are less potent in antagonizing cellular antiviral responses than viruses expressing wild-type NS1. However, no significant difference was observed with respect to viral replication and pathogenesis. In contrast, the replication and antiviral defenses of H1N1 viruses are greatly attenuated when nuclear localization of the NS1 protein is blocked. Our data reveals a novel functional plasticity for NS1 proteins among different IAV subtypes.
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Affiliation(s)
- Bobo Wing-Yee Mok
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Honglian Liu
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Pin Chen
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Siwen Liu
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Siu-Ying Lau
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Xiaofeng Huang
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yen-Chin Liu
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Pui Wang
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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Hamidi A, Song J, Thakur N, Itoh S, Marcusson A, Bergh A, Heldin CH, Landström M. TGF-β promotes PI3K-AKT signaling and prostate cancer cell migration through the TRAF6-mediated ubiquitylation of p85α. Sci Signal 2017; 10:10/486/eaal4186. [PMID: 28676490 DOI: 10.1126/scisignal.aal4186] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transforming growth factor-β (TGF-β) is a pluripotent cytokine that regulates cell fate and plasticity in normal tissues and tumors. The multifunctional cellular responses evoked by TGF-β are mediated by the canonical SMAD pathway and by noncanonical pathways, including mitogen-activated protein kinase (MAPK) pathways and the phosphatidylinositol 3'-kinase (PI3K)-protein kinase B (AKT) pathway. We found that TGF-β activated PI3K in a manner dependent on the activity of the E3 ubiquitin ligase tumor necrosis factor receptor-associated factor 6 (TRAF6). TRAF6 polyubiquitylated the PI3K regulatory subunit p85α and promoted the formation of a complex between the TGF-β type I receptor (TβRI) and p85α, which led to the activation of PI3K and AKT. Lys63-linked polyubiquitylation of p85α on Lys513 and Lys519 in the iSH2 (inter-Src homology 2) domain was required for TGF-β-induced activation of PI3K-AKT signaling and cell motility in prostate cancer cells and activated macrophages. Unlike the activation of SMAD pathways, the TRAF6-mediated activation of PI3K and AKT was not dependent on the kinase activity of TβRI. In situ proximity ligation assays revealed that polyubiquitylation of p85α was evident in aggressive prostate cancer tissues. Thus, our data reveal a molecular mechanism by which TGF-β activates the PI3K-AKT pathway to drive cell migration.
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Affiliation(s)
- Anahita Hamidi
- Ludwig Institute for Cancer Research and Science for Life Laboratory, Uppsala University, Uppsala SE 751 24, Sweden
| | - Jie Song
- Unit of Pathology, Department of Medical Biosciences, Umeå University, Umeå SE 901 85, Sweden
| | - Noopur Thakur
- Ludwig Institute for Cancer Research and Science for Life Laboratory, Uppsala University, Uppsala SE 751 24, Sweden
| | - Susumu Itoh
- Laboratory of Biochemistry, Showa Pharmaceutical University, Tokyo 194-8543, Japan
| | - Anders Marcusson
- Ludwig Institute for Cancer Research and Science for Life Laboratory, Uppsala University, Uppsala SE 751 24, Sweden
| | - Anders Bergh
- Unit of Pathology, Department of Medical Biosciences, Umeå University, Umeå SE 901 85, Sweden
| | - Carl-Henrik Heldin
- Ludwig Institute for Cancer Research and Science for Life Laboratory, Uppsala University, Uppsala SE 751 24, Sweden.
| | - Maréne Landström
- Ludwig Institute for Cancer Research and Science for Life Laboratory, Uppsala University, Uppsala SE 751 24, Sweden. .,Unit of Pathology, Department of Medical Biosciences, Umeå University, Umeå SE 901 85, Sweden
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Yin Y, Dang W, Zhou X, Xu L, Wang W, Cao W, Chen S, Su J, Cai X, Xiao S, Peppelenbosch MP, Pan Q. PI3K-Akt-mTOR axis sustains rotavirus infection via the 4E-BP1 mediated autophagy pathway and represents an antiviral target. Virulence 2017; 9:83-98. [PMID: 28475412 PMCID: PMC5955461 DOI: 10.1080/21505594.2017.1326443] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rotavirus infection is a major cause of severe dehydrating diarrhea in infants younger than 5 y old and in particular cases of immunocompromised patients irrespective to the age of the patients. Although vaccines have been developed, antiviral therapy is an important complement that cannot be substituted. Because of the lack of specific approved treatment, it is urgent to facilitate the cascade of further understanding of the infection biology, identification of druggable targets and the final development of effective antiviral therapies. PI3K-Akt-mTOR signaling pathway plays a vital role in regulating the infection course of many viruses. In this study, we have dissected the effects of PI3K-Akt-mTOR signaling pathway on rotavirus infection using both conventional cell culture models and a 3D model of human primary intestinal organoids. We found that PI3K-Akt-mTOR signaling is essential in sustaining rotavirus infection. Thus, blocking the key elements of this pathway, including PI3K, mTOR and 4E-BP1, has resulted in potent anti-rotavirus activity. Importantly, a clinically used mTOR inhibitor, rapamycin, potently inhibited both experimental and patient-derived rotavirus strains. This effect involves 4E-BP1 mediated induction of autophagy, which in turn exerts anti-rotavirus effects. These results revealed new insights on rotavirus-host interactions and provided new avenues for antiviral drug development.
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Affiliation(s)
- Yuebang Yin
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Wen Dang
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Xinying Zhou
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Lei Xu
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Wenshi Wang
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Wanlu Cao
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Sunrui Chen
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Junhong Su
- b Medical Faculty, Kunming University of Science and Technology , Kunming , P. R. China
| | - Xuepeng Cai
- c State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Lanzhou , P. R. China
| | - Shaobo Xiao
- d State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University , Wuhan , P. R. China
| | - Maikel P Peppelenbosch
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
| | - Qiuwei Pan
- a Department of Gastroenterology and Hepatology , Erasmus MC-University Medical Center , Rotterdam , The Netherlands
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35
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Wang BX, Brown EG, Fish EN. Residues F103 and M106 within the influenza A virus NS1 CPSF4-binding region regulate interferon-stimulated gene translation initiation. Virology 2017; 508:170-179. [PMID: 28554059 DOI: 10.1016/j.virol.2017.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 11/25/2022]
Abstract
Influenza A virus (IAV) non-structural protein 1 (NS1) suppresses host innate immune responses by inhibiting type I interferon (IFN) production. We provide evidence that residues F103 and M106 in the CPSF4-binding domain of A/HK/1/68 [H3N2] NS1 contribute to post-transcriptional inhibition of antiviral IFN-stimulated genes (ISGs), thereby suppressing an antiviral type I IFN response. Recombinant (r) IAVs encoding F103L and M106I mutations in NS1 replicate to significantly lower viral titers in human A549 lung epithelial cells and primary type II alveolar cells. In A549 cells, rIAVs encoding these mutant NS1s induce higher levels of IFN-β production and are more sensitive to the antiviral effects of IFN-β treatment. qPCR characterization of polysomal mRNA, in the presence or absence of IFN-β treatment, identified a greater proportion of heavy polysome-associated ISGs including EIF2AK2, OAS1, and MxA in A549 cells infected with rIAVs encoding these CPSF4-binding mutant NS1s, in contrast to rIAV encoding wildtype NS1.
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Affiliation(s)
- Ben X Wang
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8; Toronto General Hospital Research Institute, University Health Network, 67 College Street, Room 424, Toronto, Ontario, Canada M5G 2M1
| | - Earl G Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Eleanor N Fish
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8; Toronto General Hospital Research Institute, University Health Network, 67 College Street, Room 424, Toronto, Ontario, Canada M5G 2M1.
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A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Viruses 2017; 9:v9050107. [PMID: 28498306 PMCID: PMC5454420 DOI: 10.3390/v9050107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 01/24/2023] Open
Abstract
The non-structural protein, NS1, is a virulence factor encoded by influenza A viruses (IAVs). In this report, we provide evidence that the conserved residue, tyrosine (Y) 84, in a conserved putative SH2-binding domain in A/Duck/Hubei/2004/L-1 [H5N1] NS1 is critical for limiting an interferon (IFN) response to infection. A phenylalanine (F) substitution of this Y84 residue abolishes NS1-mediated downregulation of IFN-inducible STAT phosphorylation, and surface IFNAR1 expression. Recombinant IAV (rIAV) [H1N1] expressing A/Grey Heron/Hong Kong/837/2004 [H5N1] NS1-Y84F (rWSN-GH-NS1-Y84F) replicates to lower titers in human lung epithelial cells and is more susceptible to the antiviral effects of IFN-β treatment compared with rIAV expressing the intact H5N1 NS1 (rWSN-GH-NS1-wt). Cells infected with rWSN-GH-NS1-Y84F express higher levels of IFN stimulated genes (ISGs) associated with an antiviral response compared with cells infected with rWSN-GH-NS1-wt. In mice, intranasal infection with rWSN-GH-NS1-Y84F resulted in a delay in onset of weight loss, reduced lung pathology, lower lung viral titers and higher ISG expression, compared with mice infected with rWSN-GH-NS1-wt. IFN-β treatment of mice infected with rWSN-GH-NS1-Y84F reduced lung viral titers and increased lung ISG expression, but did not alter viral titers and ISG expression in mice infected with rWSN-GH-NS1-wt. Viewed altogether, these data suggest that the virulence associated with this conserved Y84 residue in NS1 is, in part, due to its role in regulating the host IFN response.
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Khaliq Z, Leijon M, Belák S, Komorowski J. Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes. BMC Genomics 2016; 17:529. [PMID: 27473048 PMCID: PMC4966792 DOI: 10.1186/s12864-016-2919-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 07/07/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts. RESULTS We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among all proteins, including the newly discovered PA-X protein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. M1, M2, PB1-F2, PB1 and PB2 of H1N1 subtype, in addition to H1N1 signatures, also carry H3N2 signatures. Similarly M1, M2, NP, NS1, NEP and PB2 of H3N2 subtype were shown to carry both H3N2 and H1N1 host-specific signatures (HSSs). CONCLUSIONS To sum it up, we computationally constructed simple IF-THEN rule-based models that could distinguish between aa sequences of avian and human IAVs. From the rules we identified HSSs having a potential to affect the adaptation to specific hosts. The identification of combinatorial HSSs suggests that the process of adaptation of IAVs to a new host is more complex than previously suggested. The present study provides a basis for further detailed studies with the aim to elucidate the molecular mechanisms providing the foundation for the adaptation process.
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Affiliation(s)
- Zeeshan Khaliq
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Mikael Leijon
- Department of Virology, Parasitology and Immunobiology (VIP), National Veterinary Institute (SVA), Uppsala, Sweden.,OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden
| | - Sándor Belák
- OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden. .,Institute of Computer Science, Polish Academy of Sciences, 01-248, Warszawa, Poland.
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Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture. PLoS One 2016; 11:e0156906. [PMID: 27272307 PMCID: PMC4896458 DOI: 10.1371/journal.pone.0156906] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/20/2016] [Indexed: 12/01/2022] Open
Abstract
Influenza A virus is a significant public health threat, but little is understood about the viral RNA structure and function. Current vaccines and therapeutic options to control influenza A virus infections are mostly protein-centric and of limited effectiveness. Here, we report using an ensemble defect approach to design mutations to misfold regions of conserved mRNA structures in influenza A virus segments 7 and 8. Influenza A mutant viruses inhibit pre-mRNA splicing and attenuate viral replication in cell culture, thus providing evidence for functions of the targeted regions. Targeting these influenza A viral RNA regions provides new possibilities for designing vaccines and therapeutics against this important human respiratory pathogen. The results also demonstrate that the ensemble defect approach is an efficient way to test for function of RNA sequences.
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Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase. Comput Biol Chem 2016; 61:210-20. [PMID: 26908254 DOI: 10.1016/j.compbiolchem.2016.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 01/07/2016] [Accepted: 01/21/2016] [Indexed: 12/20/2022]
Abstract
Angiopoietin-like protein 8 (ANGPTL8) (also known as betatrophin) is a newly identified secretory protein with a potential role in autophagy, lipid metabolism and pancreatic beta-cell proliferation. Its structural characterization is required to enhance our current understanding of its mechanism of action which could help in identifying its receptor and/or other binding partners. Based on the physiological significance and necessity of exploring structural features of ANGPTL8, the present study is conducted with a specific aim to model the structure of ANGPTL8 and study its possible interactions with Lipoprotein Lipase (LPL). To the best of our knowledge, this is the first attempt to predict 3-dimensional (3D) structure of ANGPTL8. Three different approaches were used for modeling of ANGPTL8 including homology modeling, de-novo structure prediction and their amalgam which is then proceeded by structure verification using ERRATT, PROSA, Qmean and Ramachandran plot scores. The selected models of ANGPTL8 were further evaluated for protein-protein interaction (PPI) analysis with LPL using CPORT and HADDOCK server. Our results have shown that the crystal structure of iSH2 domain of Phosphatidylinositol 3-kinase (PI3K) p85β subunit (PDB entry: 3mtt) is a good candidate for homology modeling of ANGPTL8. Analysis of inter-molecular interactions between the structure of ANGPTL8 and LPL revealed existence of several non-covalent interactions. The residues of LPL involved in these interactions belong from its lid region, thrombospondin (TSP) region and heparin binding site which is suggestive of a possible role of ANGPTL8 in regulating the proteolysis, motility and localization of LPL. Besides, the conserved residues of SE1 region of ANGPTL8 formed interactions with the residues around the hinge region of LPL. Overall, our results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab studies in future.
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40
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Shen Z, Lou K, Wang W. New small-molecule drug design strategies for fighting resistant influenza A. Acta Pharm Sin B 2015; 5:419-30. [PMID: 26579472 PMCID: PMC4629447 DOI: 10.1016/j.apsb.2015.07.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/05/2015] [Indexed: 11/24/2022] Open
Abstract
Influenza A virus is the major cause of seasonal or pandemic flu worldwide. Two main treatment strategies-vaccination and small molecule anti-influenza drugs are currently available. As an effective vaccine usually takes at least 6 months to develop, anti-influenza small molecule drugs are more effective for the first line of protection against the virus during an epidemic outbreak, especially in the early stage. Two major classes of anti-influenza drugs currently available are admantane-based M2 protein blockers (amantadine and rimantadine) and neuraminidase (NA) inhibitors (oseltamivir, zanamivir, and peramivir). However, the continuous evolvement of influenza A virus and the rapid emergence of resistance to current drugs, particularly to amantadine, rimantadine, and oseltamivir, have raised an urgent need for developing new anti-influenza drugs against resistant forms of influenza A virus. In this review, we first give a brief introduction of the molecular mechanisms behind resistance, and then discuss new strategies in small-molecule drug development to overcome influenza A virus resistance targeting mutant M2 proteins and neuraminidases, and other viral proteins not associated with current drugs.
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Affiliation(s)
- Zuyuan Shen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
| | - Kaiyan Lou
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
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41
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Ylösmäki L, Schmotz C, Ylösmäki E, Saksela K. Reorganization of the host cell Crk(L)-PI3 kinase signaling complex by the influenza A virus NS1 protein. Virology 2015; 484:146-152. [PMID: 26099693 DOI: 10.1016/j.virol.2015.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 11/26/2022]
Abstract
The non-structural protein-1 (NS1) of influenza A virus binds the p85β subunit of phosphoinositide 3-kinase (PI3K) to induce PI3K activity in the infected cells. Some virus strains encode NS1 containing a motif that binds tightly to the SH3 domain of the cellular adapter proteins Crk and CrkL to potentiate NS1-induced PI3K activation. Here we show that this potentiation involves reorganization of the natural CrkL-p85β complex into a novel trimeric complex where NS1 serves as a bridging factor. Of note, NS1 proteins that lack the SH3 binding capacity can also associate with CrkL, but in a less stable trimeric complex mediated by p85β. The data presented here establish Crk proteins as general host cell cofactors of NS1, and show that the enhanced PI3K activation by SH3 binding-competent NS1 variants is mediated by a more efficient tethering of Crk proteins to the NS1-PI3K complex.
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Affiliation(s)
- Leena Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Constanze Schmotz
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Erkko Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
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Santos LA, Solá S, Rodrigues CMP, Rebelo-de-Andrade H. Distinct kinetics and pathways of apoptosis in influenza A and B virus infection. Virus Res 2015; 205:33-40. [PMID: 26002021 DOI: 10.1016/j.virusres.2015.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/10/2015] [Accepted: 05/11/2015] [Indexed: 11/30/2022]
Abstract
Annual influenza epidemics are associated with high incidence and mortality rates, and are an important cause of work absenteeism and productivity losses. For successful replication, influenza viruses have evolved as to counteract and/or take a part on host defense mechanisms. Manipulation of apoptosis is one of such mechanisms that have been subject of attention, particularly in relation to influenza type A viruses over the past years. However, this knowledge has not been extended to include influenza type B viruses. In this study, MDCK-SIAT1 cells were infected with influenza A and B strains and the kinetics and pathways of apoptosis post infection were studied, through LDH measurements, Hoechst dye staining, caspase activity assays and protein expression analysis. The resulting data points to a difference in induction of apoptosis profiles between influenza A and B strains. While influenza A strain induced apoptosis later in the course of infection and mainly by the intrinsic pathway, influenza B strain induced apoptosis early in infection by both intrinsic and extrinsic pathways. Also, data revealed the IκB/NF-κB pathway as the major contributor for the observed differences. The study of the virus-host interactions, particularly those that could have an impact on viral replication, are essential in both influenza A and B viruses, as they will allow the identification of viral/host targets common to both influenza types, which could affect viral replication. This information may prove useful for vaccine and antiviral research.
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Affiliation(s)
- Luis A Santos
- Unidade de Investigação e Desenvolvimento, Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal; Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Instituto de Medicina Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Susana Solá
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Cecilia M P Rodrigues
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Helena Rebelo-de-Andrade
- Unidade de Investigação e Desenvolvimento, Departamento de Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal; Centro de Patogénese Molecular, Unidade dos Retrovírus e Infecções Associadas, Instituto de Medicina Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
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43
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Sasaki K, Hayashi K, Lee JB, Kurosaki F, Hayashi T. Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. PLoS One 2015; 10:e0121205. [PMID: 25793397 PMCID: PMC4368802 DOI: 10.1371/journal.pone.0121205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/28/2015] [Indexed: 12/31/2022] Open
Abstract
It is generally accepted that live attenuated influenza vaccine (LAIV) has the potential for use as a vaccination against flu. In this study, we demonstrated the nature of an influenza A virus (IAV) mutant induced by treating the IAV with a stable furan derivative, (1R,2R)-1-(5’-methylfur-3’-yl)propane-1,2,3-triol (MFPT), which had been isolated from Streptomyces sp. strain FV60 with the objective of it being an LAIV candidate. The resulting MFPT-resistant (MFPTr) IAVs possessed attenuated pathogenicity in vitro and in vivo when compared with that of the parent virus (H1N1 subtype, NWS strain). Sequencing analysis revealed that a novel mutation, C490U in ns gene (P164S in NS1), was detected in all MFPTr virus clones tested. Therefore, NS1 might be a main target of MFPT, and it was suggested that the P164S mutation contributed to the attenuated pathogenicity of the mutants. Although the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway is one of the targets of NS1, the MFPTr virus suppressed the phosphorylation of Akt when compared with the wild-type (WT) virus. It was suggested that this might lead to the subsequent inhibition of the cleavage of PARP-1 and caspase-3, which is important for the progression of apoptosis. At the same time, nucleoprotein (NP) was found to be retained in the nuclei in MFPTr virus-infected cells while nuclear export of NP was detected in WT virus-infected cells. In addition, the expression levels of interferon-β transcripts were significantly decreased in MFPTr virus-infected cells. From these results it can be shown that the mutation, NS1P164S, might be one of the key residues to control NS1 function concerning the induction of apoptosis. In conclusion, MFPT induced favorable mutation in the ns gene for the attenuation of IAV, and therefore might provide the novel methodology for preparing LAIVs.
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Affiliation(s)
- Kohei Sasaki
- Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Toyama, Toyama, 930–0194, Japan
| | - Kyoko Hayashi
- Research Institute of Life and Health Sciences, Chubu University, Kasugai, Aichi, 487–8501, Japan
| | - Jung-Bum Lee
- Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Toyama, Toyama, 930–0194, Japan
- * E-mail:
| | - Fumiya Kurosaki
- Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Toyama, Toyama, 930–0194, Japan
| | - Toshimitsu Hayashi
- Research Institute of Life and Health Sciences, Chubu University, Kasugai, Aichi, 487–8501, Japan
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Burke JE, Williams RL. Synergy in activating class I PI3Ks. Trends Biochem Sci 2015; 40:88-100. [PMID: 25573003 DOI: 10.1016/j.tibs.2014.12.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
The class I phosphoinositide 3-kinases (PI3Ks) are lipid kinases that transduce a host of cellular signals and regulate a broad range of essential functions including growth, proliferation, and migration. As such, PI3Ks have pivotal roles in diseases such as cancer, diabetes, primary immune disorders, and inflammation. These enzymes are activated downstream of numerous activating stimuli including receptor tyrosine kinases, G protein-coupled receptors (GPCRs), and the Ras superfamily of small G proteins. A major challenge is to decipher how each PI3K isoform is able to successfully synergize these inputs into their intended signaling function. This article highlights recent progress in characterizing the molecular mechanisms of PI3K isoform-specific activation pathways, as well as novel roles for PI3Ks in human diseases, specifically cancer and immune diseases.
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Affiliation(s)
- John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Drive, Victoria BC, V8P 5C2, Canada.
| | - Roger L Williams
- Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
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45
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Abstract
The non-structural protein 1 of influenza virus (NS1) is a relatively small polypeptide with an outstanding number of ascribed functions. NS1 is the main viral antagonist of the innate immune response during influenza virus infection, chiefly by inhibiting the type I interferon system at multiple steps. As such, its role is critical to overcome the first barrier the host presents to halt the viral infection. However, the pro-viral activities of this well-studied protein go far beyond and include regulation of viral RNA and protein synthesis, and disruption of the host cell homeostasis by dramatically affecting general gene expression while tweaking the PI3K signaling network. Because of all of this, NS1 is a key virulence factor that impacts influenza pathogenesis, and adaptation to new hosts, making it an attractive target for control strategies. Here, we will overview the many roles that have been ascribed to the NS1 protein, and give insights into the sequence features and structural properties that make them possible, highlighting the need to understand how NS1 can actually perform all of these functions during viral infection.
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Affiliation(s)
- Juan Ayllon
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG, Wu G. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses. Sci Rep 2014; 4:7455. [PMID: 25503687 PMCID: PMC4264002 DOI: 10.1038/srep07455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 11/09/2022] Open
Abstract
Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.
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Affiliation(s)
- Zeynep A Koçer
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - John Obenauer
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Richard J Webby
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert G Webster
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
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Hutchinson EC, Charles PD, Hester SS, Thomas B, Trudgian D, Martínez-Alonso M, Fodor E. Conserved and host-specific features of influenza virion architecture. Nat Commun 2014; 5:4816. [PMID: 25226414 PMCID: PMC4167602 DOI: 10.1038/ncomms5816] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/28/2014] [Indexed: 01/11/2023] Open
Abstract
Viruses use virions to spread between hosts, and virion composition is therefore the primary determinant of viral transmissibility and immunogenicity. However, the virions of many viruses are complex and pleomorphic, making them difficult to analyse in detail. Here we address this by identifying and quantifying virion proteins with mass spectrometry, producing a complete and quantified model of the hundreds of viral and host-encoded proteins that make up the pleomorphic virions of influenza viruses. We show that a conserved influenza virion architecture is maintained across diverse combinations of virus and host. This ‘core’ architecture, which includes substantial quantities of host proteins as well as the viral protein NS1, is elaborated with abundant host-dependent features. As a result, influenza virions produced by mammalian and avian hosts have distinct protein compositions. Finally we note that influenza virions share an underlying protein composition with exosomes, suggesting that influenza virions form by subverting microvesicle production.
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Affiliation(s)
- Edward C Hutchinson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Philip D Charles
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Svenja S Hester
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Benjamin Thomas
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - David Trudgian
- 1] Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK [2]
| | - Mónica Martínez-Alonso
- 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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48
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Appearance of L90I and N205S Mutations in Effector Domain of NS1 Gene of pdm (09) H1N1 Virus from India during 2009-2013. Adv Virol 2014; 2014:861709. [PMID: 25309598 PMCID: PMC4181907 DOI: 10.1155/2014/861709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022] Open
Abstract
In the present study, full length sequencing of NS gene was done in 91 samples which were obtained from patients over the time period of five years from 2009 to 2013. The sequencing of NS gene was undertaken in order to determine the changes/mutations taking place in the NS gene of A H1N1 pdm (09) since its emergence in 2009. Analysis has shown that the majority of samples belong to New York (G1 type) strain with valine at position 123. Effector domain of NS1 protein displays the appearance of three mutations L90I, I123V, and N205S in almost all the samples from 2010 onwards. Phylogenetic analysis of available NS1 sequences from India has grouped all the sequences into four clusters with mean genetic distance ranging from 12% to 24% between the clusters. Variability in length of NS1 protein was seen in sequences from these clusters, 230-amino-acid-residue NS1 for all strains from year 2007 to 2008 and for 21 strains from year 2009 and 219-residue products for 37 strains from year 2009 and all strains from year 2010 to 2013. Mutations like K62R, K131Q, L147R, and A202P were observed for the first time in NS1 protein and their function remains to be determined.
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49
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Marc D. Influenza virus non-structural protein NS1: interferon antagonism and beyond. J Gen Virol 2014; 95:2594-2611. [PMID: 25182164 DOI: 10.1099/vir.0.069542-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1.
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Affiliation(s)
- Daniel Marc
- Université François Rabelais, UMR1282 Infectiologie et Santé Publique, 37000 Tours, France.,Pathologie et Immunologie Aviaire, INRA, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
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50
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Hrincius ER, Liedmann S, Anhlan D, Wolff T, Ludwig S, Ehrhardt C. Avian influenza viruses inhibit the major cellular signalling integrator c-Abl. Cell Microbiol 2014; 16:1854-74. [PMID: 25052580 DOI: 10.1111/cmi.12332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 11/27/2022]
Abstract
The non-structural protein 1 (NS1) of influenza A viruses (IAV) encodes several src homology (SH) binding motifs (bm) (one SH2bm, up to two SH3bm), which mediate interactions with host cell proteins. In contrast to NS1 of human IAV, NS1 of avian strains possess the second SH3bm (SH3(II)bm) consensus sequence. Since our former studies demonstrated an NS1-CRK interaction, mediated by this motif, here, we addressed the regulatory properties of this SH3bm for cellular signalling. Initially, we observed a reduced basal CRK phosphorylation upon infection with avian IAV harbouring an NS1 with an SH3(II)bm in contrast to human IAV. Reduced activity of the tyrosine kinase c-Abl was identified to be responsible for reduced CRK phosphorylation. Further, binding of NS1 to c-Abl was determined, and mutational manipulation of the SH3(II)bm illustrated the necessity of this motif for c-Abl inhibition. Interestingly, Abl kinase inhibition resulted in impaired avian IAV propagation and pathogenicity and mutational analysis linked the pronounced inhibition of c-Abl to cytopathogenic cell alterations upon avian IAV infections. Taken together, NS1 proteins of avian IAV interfere with the kinase activity of c-Abl, a major cellular signalling integrator that controls multiple signalling processes and cell fate regulations apparently including IAV infections.
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Affiliation(s)
- Eike R Hrincius
- Institute of Molecular Virology (IMV), Center of Molecular Biology of Inflammation (ZMBE), University of Muenster, Von Esmarch-Str. 56, D-48149, Muenster, Germany; Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
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