1
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Zhang X, Zhang Y, Wei F. Research progress on the nonstructural protein 1 (NS1) of influenza a virus. Virulence 2024; 15:2359470. [PMID: 38918890 PMCID: PMC11210920 DOI: 10.1080/21505594.2024.2359470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Influenza A virus (IAV) is the leading cause of highly contagious respiratory infections, which poses a serious threat to public health. The non-structural protein 1 (NS1) is encoded by segment 8 of IAV genome and is expressed in high levels in host cells upon IAV infection. It is the determinant of virulence and has multiple functions by targeting type Ι interferon (IFN-I) and type III interferon (IFN-III) production, disrupting cell apoptosis and autophagy in IAV-infected cells, and regulating the host fitness of influenza viruses. This review will summarize the current research on the NS1 including the structure and related biological functions of the NS1 as well as the interaction between the NS1 and host cells. It is hoped that this will provide some scientific basis for the prevention and control of the influenza virus.
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Affiliation(s)
- Xiaoyan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yuying Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Fanhua Wei
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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2
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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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3
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Pagano L, Simonetti L, Pennacchietti V, Toto A, Malagrinò F, Ivarsson Y, Gianni S. Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD. Biochem Biophys Res Commun 2024; 703:149658. [PMID: 38387229 DOI: 10.1016/j.bbrc.2024.149658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Adaptor proteins play a pivotal role in cellular signaling mediating a multitude of protein-protein interaction critical for cellular homeostasis. Dysregulation of these interactions has been linked to the onset of various cancer pathologies and exploited by viral pathogens during host cell takeover. CrkL is an adaptor protein composed of an N-terminal SH2 domain followed by two SH3 domains that mediate interactions with diverse partners through the recognition of specific binding motifs. In this study, we employed proteomic peptide-phage display (ProP-PD) to comprehensively explore the short linear motif (SLiM)-based interactions of CrkL. Furthermore, we scrutinized how the binding affinity for selected peptides was influenced in the context of the full-length CrkL versus the isolated N-SH3 domain. Importantly, our results provided insights into SLiM-binding sites within previously reported interactors, as well as revealing novel human and viral ligands, expanding our understanding of the interactions mediated by CrkL and highlighting the significance of SLiM-based interactions in mediating adaptor protein function, with implications for cancer and viral pathologies.
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Affiliation(s)
- L Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - L Simonetti
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden
| | - V Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - A Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - F Malagrinò
- Dipartimento di Medicina clinica, sanità pubblica, scienze della vita e dell'ambiente, Università dell'Aquila, Piazzale Salvatore Tommasi 1, L'Aquila, Coppito, 67010, Italy
| | - Y Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden.
| | - S Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy.
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4
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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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5
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Meseko C, Milani A, Inuwa B, Chinyere C, Shittu I, Ahmed J, Giussani E, Palumbo E, Zecchin B, Bonfante F, Maniero S, Angot A, Niang M, Fusaro A, Gobbo F, Terregino C, Olasoju T, Monne I, Muhammad M. The Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021-2022. Viruses 2023; 15:1387. [PMID: 37376688 DOI: 10.3390/v15061387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative regions in Nigeria. In this study, we characterized the genomes of 97 influenza A viruses of the subtypes H5N1, H5N2, and H5N8, which were identified in different agro-ecological zones and farms during the 2021-2022 epidemic. The phylogenetic analysis of the HA genes showed a widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses that have been detected in Europe since late 2020. The topology of the phylogenetic trees indicated the occurrence of several independent introductions of the virus into the country, followed by a regional evolution of the virus that was most probably linked to its persistent circulation in West African territories. Additional evidence of the evolutionary potential of the HPAI viruses circulating in this region is the identification in this study of a putative H5N1/H9N2 reassortant virus in a mixed-species commercial poultry farm. Our data confirm Nigeria as a crucial hotspot for HPAI virus introduction from the Eurasian territories and reveal a dynamic pattern of avian influenza virus evolution within the Nigerian poultry population.
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Affiliation(s)
- Clement Meseko
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Bitrus Inuwa
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Chinonyerem Chinyere
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - James Ahmed
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Edoardo Giussani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Elisa Palumbo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Silvia Maniero
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Angélique Angot
- Animal Health Service (NSAH), Food and Agriculture Organization of the United Nations (FAO-UN), 00198 Rome, Italy
| | - Mamadou Niang
- Regional Office for Africa (RAF), Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO-UN), Accra 00233, Ghana
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Federica Gobbo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Taiwo Olasoju
- Federal Department of Veterinary and Pest Control Services (FDV&PCS), Federal Ministry of Agriculture and Rural Development (FMARD), Abuja 900108, Nigeria
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Maryam Muhammad
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
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6
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Jiang L, Chen H, Li C. Advances in deciphering the interactions between viral proteins of influenza A virus and host cellular proteins. CELL INSIGHT 2023; 2:100079. [PMID: 37193064 PMCID: PMC10134199 DOI: 10.1016/j.cellin.2023.100079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 05/18/2023]
Abstract
Influenza A virus (IAV) poses a severe threat to the health of animals and humans. The genome of IAV consists of eight single-stranded negative-sense RNA segments, encoding ten essential proteins as well as certain accessory proteins. In the process of virus replication, amino acid substitutions continuously accumulate, and genetic reassortment between virus strains readily occurs. Due to this high genetic variability, new viruses that threaten animal and human health can emerge at any time. Therefore, the study on IAV has always been a focus of veterinary medicine and public health. The replication, pathogenesis, and transmission of IAV involve intricate interplay between the virus and host. On one hand, the entire replication cycle of IAV relies on numerous proviral host proteins that effectively allow the virus to adapt to its host and support its replication. On the other hand, some host proteins play restricting roles at different stages of the viral replication cycle. The mechanisms of interaction between viral proteins and host cellular proteins are currently receiving particular interest in IAV research. In this review, we briefly summarize the current advances in our understanding of the mechanisms by which host proteins affect virus replication, pathogenesis, or transmission by interacting with viral proteins. Such information about the interplay between IAV and host proteins could provide insights into how IAV causes disease and spreads, and might help support the development of antiviral drugs or therapeutic approaches.
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Affiliation(s)
- Li Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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7
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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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8
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Tossavainen H, Uğurlu H, Karjalainen M, Hellman M, Antenucci L, Fagerlund R, Saksela K, Permi P. Structure of SNX9 SH3 in complex with a viral ligand reveals the molecular basis of its unique specificity for alanine-containing class I SH3 motifs. Structure 2022; 30:828-839.e6. [PMID: 35390274 DOI: 10.1016/j.str.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/22/2021] [Accepted: 03/04/2022] [Indexed: 11/26/2022]
Abstract
Class I SH3 domain-binding motifs generally comply with the consensus sequence [R/K]xØPxxP, the hydrophobic residue Ø being proline or leucine. We have studied the unusual Ø = Ala-specificity of SNX9 SH3 by determining its complex structure with a peptide present in eastern equine encephalitis virus (EEEV) nsP3. The structure revealed the length and composition of the n-Src loop as important factors determining specificity. We also compared the affinities of EEEV nsP3 peptide, its mutants, and cellular ligands to SNX9 SH3. These data suggest that nsP3 has evolved to minimize reduction of conformational entropy upon binding, hence acquiring stronger affinity, enabling takeover of SNX9. The RxAPxxP motif was also found in human T cell leukemia virus-1 (HTLV-1) Gag polyprotein. We found that this motif was required for efficient HTLV-1 infection, and that the specificity of SNX9 SH3 for the RxAPxxP core binding motif was importantly involved in this process.
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Affiliation(s)
- Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Hasan Uğurlu
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Lina Antenucci
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland; Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Riku Fagerlund
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland; Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland.
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9
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Zeng Y, Wang R, Wang F, Zhang M, Zhang L, Zhu C, Zhao J, Liu H. Interaction of influenza A virus NS1 and cytoskeleton scaffolding protein α-actinin 4. Virus Genes 2021; 58:15-22. [PMID: 34727338 DOI: 10.1007/s11262-021-01876-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/18/2021] [Indexed: 11/28/2022]
Abstract
NS1 (Non-structural protein 1) is a non-structural protein that can highly express when the avian influenza virus infects the host cells. NS1 can interact with various proteins to alter the intracellular distribution of host proteins and regulate the virulence and pathogenicity of the avian influenza virus. To further study the role of NS1 protein in replication and pathogenesis of avian influenza virus, Glutathione S-transferase (GST) Pull-down was used for screening more proteins interacting with NS1 in human lung adenocarcinoma cell line A549. By mass spectrometry, a potential interacted protein is identified as α-actinin 4 and its interaction with NS1 has not been reported yet. The interaction between NS1 and α-actinin 4 in vitro was confirmed by enzyme-linked immunosorbent assay experiments, and the results showed that the absorbance value of OD450nm in the experimental group was positively correlated with the concentration of NS1-GST protein compared to the negative control group. The co-immunoprecipitation and immunofluorescence results further confirmed the interaction between NS1 and α-actinin 4 at the cellular level. The interaction between NS1 and α-actinin 4 provided a new target for pathogenic mechanism studying and drug screening.
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Affiliation(s)
- Yingyue Zeng
- School of Life Sciences, Liaoning University, Shenyang, 110036, China.,Engineering Laboratory of Molecular Modeling and Design for Drug of Liaoning Province, Shenyang, 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning, Shenyang, 110036, China.,Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Shenyang, 110036, China
| | - Rui Wang
- School of Life Sciences, Liaoning University, Shenyang, 110036, China
| | - Fengchao Wang
- School of Life Sciences, Liaoning University, Shenyang, 110036, China
| | - Man Zhang
- School of Life Sciences, Liaoning University, Shenyang, 110036, China
| | - Li Zhang
- School of Life Sciences, Liaoning University, Shenyang, 110036, China.,Engineering Laboratory of Molecular Modeling and Design for Drug of Liaoning Province, Shenyang, 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning, Shenyang, 110036, China.,Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Shenyang, 110036, China
| | - Chunyu Zhu
- School of Life Sciences, Liaoning University, Shenyang, 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning, Shenyang, 110036, China
| | - Jian Zhao
- School of Life Sciences, Liaoning University, Shenyang, 110036, China.,Engineering Laboratory of Molecular Modeling and Design for Drug of Liaoning Province, Shenyang, 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning, Shenyang, 110036, China.,Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Shenyang, 110036, China
| | - Hongsheng Liu
- School of Pharmacy, Liaoning University, Shenyang, 110036, China. .,Engineering Laboratory of Molecular Modeling and Design for Drug of Liaoning Province, Shenyang, 110036, China. .,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning, Shenyang, 110036, China. .,Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Shenyang, 110036, China.
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10
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Structure and Activities of the NS1 Influenza Protein and Progress in the Development of Small-Molecule Drugs. Int J Mol Sci 2021; 22:ijms22084242. [PMID: 33921888 PMCID: PMC8074201 DOI: 10.3390/ijms22084242] [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: 03/18/2021] [Revised: 04/18/2021] [Accepted: 04/18/2021] [Indexed: 11/30/2022] Open
Abstract
The influenza virus causes human disease on a global scale and significant morbidity and mortality. The existing vaccination regime remains vulnerable to antigenic drift, and more seriously, a small number of viral mutations could lead to drug resistance. Therefore, the development of a new additional therapeutic small molecule-based anti-influenza virus is urgently required. The NS1 influenza gene plays a pivotal role in the suppression of host antiviral responses, especially by inhibiting interferon (IFN) production and the activities of antiviral proteins, such as dsRNA-dependent serine/threonine-protein kinase R (PKR) and 2′-5′-oligoadenylate synthetase (OAS)/RNase L. NS1 also modulates important aspects of viral RNA replication, viral protein synthesis, and virus replication cycle. Taken together, small molecules that target NS1 are believed to offer a means of developing new anti-influenza drugs.
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11
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HIV-1 Nef-Induced Secretion of the Proinflammatory Protease TACE into Extracellular Vesicles Is Mediated by Raf-1 and Can Be Suppressed by Clinical Protein Kinase Inhibitors. J Virol 2021; 95:JVI.00180-21. [PMID: 33597213 DOI: 10.1128/jvi.00180-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Chronic immune activation is an important driver of human immunodeficiency virus type 1 (HIV-1) pathogenesis and has been associated with the presence of tumor necrosis factor-α converting enzyme (TACE) in extracellular vesicles (EVs) circulating in infected individuals. We have recently shown that activation of the Src-family tyrosine kinase hematopoietic cell kinase (Hck) by HIV-1 Nef can trigger the packaging of TACE into EVs via an unconventional protein secretion pathway. Using a panel of HIV-1 Nef mutants and natural HIV-2 and simian immunodeficiency virus (SIV) Nef alleles, we now show that the capacity to promote TACE secretion depends on the superior ability of HIV-1-like Nef alleles to induce Hck kinase activity, whereas other Nef effector functions are dispensable. Strikingly, among the numerous Src-family downstream effectors, serine/threonine kinase Raf-1 was found to be necessary and alone sufficient to trigger the secretion of TACE into EVs. These data reveal the involvement of Raf-1 in regulation of unconventional protein secretion and highlight the importance of Raf-1 as a cellular effector of Nef, thereby suggesting a novel rationale for testing pharmacological inhibitors of the Raf-MAPK pathway to treat HIV-associated immune activation.IMPORTANCE Chronic immune activation contributes to the immunopathogenesis of human immunodeficiency virus type 1 (HIV-1) infection and is associated with poor recovery of the immune system despite potent antiretroviral therapy, which is observed in 10% to 40% drug-treated patients depending on the definition of immune reconstitution. We have previously shown that the HIV pathogenicity factor Nef can promote loading of the proinflammatory protease TACE into extracellular vesicles (EVs), and the levels of such TACE-containing EVs circulating in the blood correlate with low CD4 lymphocyte counts in HIV patients receiving antiretroviral therapy. Here, we show that Nef promotes uploading of TACE into EVs by triggering unconventional secretion via activation of the Hck/Raf/mitogen-activated protein kinase (MAPK) cascade. We find that several pharmaceutical inhibitors of these kinases that are currently in clinical use for other diseases can potently suppress this pathogenic deregulation and could thus provide a novel strategy for treating HIV-associated immune activation.
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12
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Roles of the Non-Structural Proteins of Influenza A Virus. Pathogens 2020; 9:pathogens9100812. [PMID: 33023047 PMCID: PMC7600879 DOI: 10.3390/pathogens9100812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Influenza A virus (IAV) is a segmented, negative single-stranded RNA virus that causes seasonal epidemics and has a potential for pandemics. Several viral proteins are not packed in the IAV viral particle and only expressed in the infected host cells. These proteins are named non-structural proteins (NSPs), including NS1, PB1-F2 and PA-X. They play a versatile role in the viral life cycle by modulating viral replication and transcription. More importantly, they also play a critical role in the evasion of the surveillance of host defense and viral pathogenicity by inducing apoptosis, perturbing innate immunity, and exacerbating inflammation. Here, we review the recent advances of these NSPs and how the new findings deepen our understanding of IAV–host interactions and viral pathogenesis.
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13
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Carvalho GC, Sábio RM, de Cássia Ribeiro T, Monteiro AS, Pereira DV, Ribeiro SJL, Chorilli M. Highlights in Mesoporous Silica Nanoparticles as a Multifunctional Controlled Drug Delivery Nanoplatform for Infectious Diseases Treatment. Pharm Res 2020; 37:191. [PMID: 32895867 PMCID: PMC7476752 DOI: 10.1007/s11095-020-02917-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022]
Abstract
Infectious diseases are a major global concern being responsible for high morbidity and mortality mainly due to the development and enhancement of multidrug-resistant microorganisms exposing the fragility of medicines and vaccines commonly used to these treatments. Taking into account the scarcity of effective formulation to treat infectious diseases, nanotechnology offers a vast possibility of ground-breaking platforms to design new treatment through smart nanostructures for drug delivery purposes. Among the available nanosystems, mesoporous silica nanoparticles (MSNs) stand out due their multifunctionality, biocompatibility and tunable properties make them emerging and actual nanocarriers for specific and controlled drug release. Considering the high demand for diseases prevention and treatment, this review exploits the MSNs fabrication and their behavior in biological media besides highlighting the most of strategies to explore the wide MSNs functionality as engineered, smart and effective controlled drug release nanovehicles for infectious diseases treatment. Graphical Abstract Schematic representation of multifunctional MSNs-based nanoplatforms for infectious diseases treatment.
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Affiliation(s)
- Gabriela Corrêa Carvalho
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, 14800-903, Brazil
| | - Rafael Miguel Sábio
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, 14800-903, Brazil.
| | - Tais de Cássia Ribeiro
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, 14800-903, Brazil
| | - Andreia Sofia Monteiro
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, 14800-060, Brazil
| | | | | | - Marlus Chorilli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, 14800-903, Brazil
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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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15
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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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16
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Influenza A Virus Protein NS1 Exhibits Strain-Independent Conformational Plasticity. J Virol 2019; 93:JVI.00917-19. [PMID: 31375595 DOI: 10.1128/jvi.00917-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Influenza A virus (IAV) nonstructural protein 1 (NS1), a potent antagonist of the host immune response, is capable of interacting with RNA and a wide range of cellular proteins. NS1 consists of an RNA-binding domain (RBD) and an effector domain (ED) separated by a flexible linker region (LR). H5N1-NS1 has a characteristic 5-residue deletion in the LR, with either G (minor group) or E (major group) at the 71st position, and non-H5N1-NS1 contains E71 with an intact linker. Based on the orientation of the ED with respect to the RBD, previous crystallographic studies have shown that minor group H5N1-NS1(G71), a non-H5N1-NS1 [H6N6-NS1(E71)], and the LR deletion mutant H6N6-NS1(Δ80-84/E71) mimicking the major group H5N1-NS1 exhibit "open," "semiopen," and "closed" conformations, respectively, suggesting that NS1 exhibits a strain-dependent conformational preference. Here we report the first crystal structure of a naturally occurring H5N1-NS1(E71) and show that it adopts an open conformation similar to that of the minor group of H5N1-NS1 [H5N1-NS1(G71)]. We also show that H6N6-NS1(Δ80-84/E71) under a different crystallization condition and H6N6-NS1(Δ80-84/G71) also exhibit open conformations, suggesting that NS1 can adopt an open conformation irrespective of E or G at the 71st position. Our single-molecule fluorescence resonance energy transfer (FRET) analysis to investigate the conformational preference of NS1 in solution showed that all NS1 constructs predominantly exist in an open conformation. Further, our coimmunoprecipitation and binding studies showed that they all bind to cellular factors with similar affinities. Taken together, our studies suggest that NS1 exhibits strain-independent structural plasticity that allows it to interact with a wide variety of cellular ligands during viral infection.IMPORTANCE IAV is responsible for several pandemics over the last century and continues to infect millions annually. The frequent rise in drug-resistant strains necessitates exploring novel targets for developing antiviral drugs that can reduce the global burden of influenza infection. Because of its critical role in the replication and pathogenesis of IAV, nonstructural protein 1 (NS1) is a potential target for developing antivirals. Previous studies suggested that NS1 adopts strain-dependent "open," "semiopen," and "closed" conformations. Here we show, based on three crystal structures, that NS1 irrespective of strain differences can adopt an open conformation. We further show that NS1 from different strains primarily exists in an open conformation in solution and binds to cellular proteins with a similar affinity. Together, our findings suggest that conformational polymorphism facilitated by a flexible linker is intrinsic to NS1, and this may be the underlying factor allowing NS1 to bind several cellular factors during IAV replication.
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17
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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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18
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MC159 of Molluscum Contagiosum Virus Suppresses Autophagy by Recruiting Cellular SH3BP4 via an SH3 Domain-Mediated Interaction. J Virol 2019; 93:JVI.01613-18. [PMID: 30842330 DOI: 10.1128/jvi.01613-18] [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: 09/12/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
MC159 is a viral FLIP (FLICE inhibitory protein) encoded by the molluscum contagiosum virus (MCV) enabling MCV to evade antiviral immunity and to establish persistent infections in humans. Here, we show that MC159 contains a functional SH3 binding motif, which mediates avid and selective binding to SH3BP4, a signaling protein known to regulate endocytic trafficking and suppress cellular autophagy. The capacity to bind SH3BP4 was dispensable for regulation of NF-κB-mediated transcription and suppression of proapoptotic caspase activation but contributed to inhibition of amino acid starvation-induced autophagy by MC159. These results provide new insights into the cellular functions of MC159 and reveal SH3BP4 as a novel host cell factor targeted by a viral immune evasion protein.IMPORTANCE After the eradication of smallpox, molluscum contagiosum virus (MCV) is the only poxvirus restricted to infecting humans. MCV infection is common and causes benign skin lesions that usually resolve spontaneously but may persist for years and grow large, especially in immunocompromised individuals. While not life threatening, MCV infections pose a significant global health burden. No vaccine or specific anti-MCV therapy is available. MCV encodes several proteins that enable it to evade antiviral immunity, a notable example of which is the MC159 protein. In this study, we describe a novel mechanism of action for MC159 involving hijacking of a host cell protein called SH3BP4 to suppress autophagy, a cellular recycling mechanism important for antiviral immunity. This study contributes to our understanding of the host cell interactions of MCV and the molecular function of MC159.
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19
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Shen Q, Shi J, Zeng D, Zhao B, Li P, Hwang W, Cho JH. Molecular Mechanisms of Tight Binding through Fuzzy Interactions. Biophys J 2019; 114:1313-1320. [PMID: 29590589 DOI: 10.1016/j.bpj.2018.01.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) form fuzzy complexes upon binding to their targets. Although many IDPs are weakly bound in fuzzy complexes, some IDPs form high-affinity complexes. One example is the nonstructural protein 1 (NS1) of the 1918 Spanish influenza A virus, which hijacks cellular CRKII through the strong binding affinity (Kd ∼10 nM) of its proline-rich motif (PRMNS1) to the N-terminal Src-homology 3 domain of CRKII. However, its molecular mechanism remains elusive. Here, we examine the interplay between structural disorder of a bound PRMNS1 and its long-range electrostatic interactions. Using x-ray crystallography and NMR spectroscopy, we found that PRMNS1 retains substantial conformational flexibility in the bound state. Moreover, molecular dynamics simulations showed that structural disorder of the bound PRMNS1 increases the number of electrostatic interactions and decreases the mean distances between the positively charged residues in PRMNS1 and the acidic residues in the N-terminal Src-homology 3 domain. These results are analyzed using a polyelectrostatic model. Our results provide an insight into the molecular recognition mechanism for a high-affinity fuzzy complex.
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Affiliation(s)
- Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jie Shi
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science and Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea.
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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20
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Zhao Z, Kesti T, Uğurlu H, Baur AS, Fagerlund R, Saksela K. Tyrosine phosphorylation directs TACE into extracellular vesicles via unconventional secretion. Traffic 2019; 20:202-212. [PMID: 30569492 DOI: 10.1111/tra.12630] [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: 07/18/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023]
Abstract
When studying how HIV-1 Nef can promote packaging of the proinflammatory transmembrane protease TACE (tumor necrosis factor-α converting enzyme) into extracellular vesicles (EVs) we have revealed a novel tyrosine kinase-regulated unconventional protein secretion (UPS) pathway for TACE. When TACE was expressed without its trafficking cofactor iRhom allosteric Hck activation by Nef triggered translocation of TACE into EVs. This process was insensitive to blocking of classical secretion by inhibiting endoplasmic reticulum (ER) to Golgi transport, and involved a distinct form of TACE devoid of normal glycosylation and incompletely processed for prodomain removal. Like most other examples of UPS this process was Golgi reassembly stacking protein (GRASP)-dependent but was not associated with ER stress. These data indicate that Hck-activated UPS provides an alternative pathway for TACE secretion that can bypass iRhom-dependent ER to Golgi transfer, and suggest that tyrosine phosphorylation might have a more general role in regulating UPS.
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Affiliation(s)
- Zhe Zhao
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tapio Kesti
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hasan Uğurlu
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Andreas S Baur
- Department of Dermatology, Translational Research Center, University Hospital Erlangen, Erlangen, Germany
| | - Riku Fagerlund
- 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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21
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Belser JA, Maines TR, Tumpey TM. Importance of 1918 virus reconstruction to current assessments of pandemic risk. Virology 2018; 524:45-55. [DOI: 10.1016/j.virol.2018.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/25/2018] [Accepted: 08/09/2018] [Indexed: 01/13/2023]
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22
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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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23
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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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24
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Zhao M, Wang L, Li S. Influenza A Virus-Host Protein Interactions Control Viral Pathogenesis. Int J Mol Sci 2017; 18:ijms18081673. [PMID: 28763020 PMCID: PMC5578063 DOI: 10.3390/ijms18081673] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/20/2022] Open
Abstract
The influenza A virus (IAV), a member of the Orthomyxoviridae family, is a highly transmissible respiratory pathogen and represents a continued threat to global health with considerable economic and social impact. IAV is a zoonotic virus that comprises a plethora of strains with different pathogenic profiles. The different outcomes of viral pathogenesis are dependent on the engagement between the virus and the host cellular protein interaction network. The interactions may facilitate virus hijacking of host molecular machinery to fulfill the viral life cycle or trigger host immune defense to eliminate the virus. In recent years, much effort has been made to discover the virus–host protein interactions and understand the underlying mechanisms. In this paper, we review the recent advances in our understanding of IAV–host interactions and how these interactions contribute to host defense and viral pathogenesis.
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Affiliation(s)
- Mengmeng Zhao
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Lingyan Wang
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Shitao Li
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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25
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Shen Q, Zeng D, Zhao B, Bhatt VS, Li P, Cho JH. The Molecular Mechanisms Underlying the Hijack of Host Proteins by the 1918 Spanish Influenza Virus. ACS Chem Biol 2017; 12:1199-1203. [PMID: 28368102 DOI: 10.1021/acschembio.7b00168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The 1918 Spanish influenza A virus (IAV) caused one of the most serious pandemics in history. The nonstructural protein 1 (NS1) of the 1918 IAV hijacks the interaction between human CrkII and JNK1. Little is, however, known about its molecular mechanism. Here, we performed X-ray crystallography, NMR relaxation dispersion experiment, and fluorescence spectroscopy to determine the structural, kinetic, and thermodynamic mechanisms underlying the hijacking of CrkII by 1918 IAV NS1. We observed that the interaction between a proline-rich motif in NS1 and the N-terminal SH3 domain of CrkII displays strikingly rapid kinetics and exceptionally high affinity with 100-fold faster kon and 3300-fold lower Kd compared to those for the CrkII-JNK1 interaction. These results provide molecular insight into the mechanism by which 1918 IAV NS1 hijacks CrkII and disrupts its interactions with critical cellular signaling proteins.
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Affiliation(s)
- Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Veer S. Bhatt
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
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26
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Cysteine 893 is a target of regulatory thiol modifications of GluA1 AMPA receptors. PLoS One 2017; 12:e0171489. [PMID: 28152104 PMCID: PMC5289633 DOI: 10.1371/journal.pone.0171489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/21/2017] [Indexed: 11/19/2022] Open
Abstract
Recent studies indicate that glutamatergic signaling involves, and is regulated by, thiol modifying and redox-active compounds. In this study, we examined the role of a reactive cysteine residue, Cys-893, in the cytosolic C-terminal tail of GluA1 AMPA receptor as a potential regulatory target. Elimination of the thiol function by substitution of serine for Cys-893 led to increased steady-state expression level and strongly reduced interaction with SAP97, a major cytosolic interaction partner of GluA1 C-terminus. Moreover, we found that of the three cysteine residues in GluA1 C-terminal tail, Cys-893 is the predominant target for S-nitrosylation induced by exogenous nitric oxide donors in cultured cells and lysates. Co-precipitation experiments provided evidence for native association of SAP97 with neuronal nitric oxide synthase (nNOS) and for the potential coupling of Ca2+-permeable GluA1 receptors with nNOS via SAP97. Our results show that Cys-893 can serve as a molecular target for regulatory thiol modifications of GluA1 receptors, including the effects of nitric oxide.
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27
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Sadewasser A, Saenger S, Paki K, Schwecke T, Wolff T. Disruption of Src homology 3-binding motif within non-structural protein 1 of influenza B virus unexpectedly enhances viral replication in human cells. J Gen Virol 2016; 97:2856-2867. [PMID: 27654951 DOI: 10.1099/jgv.0.000604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The influenza virus non-structural protein 1 (NS1) is a multifunctional virulence factor that plays a crucial role during infection by blocking the innate antiviral immune response of infected cells. In contrast to the well-studied NS1 protein of influenza A virus, knowledge about structure and functions of the influenza B virus homologue B/NS1, which shares less than 25 % sequence identity, is still limited. Here, we report on a reverse genetic analysis to study the role of a highly conserved class II Src homology 3 domain-binding motif matching the consensus PxxPx(K/R) that we identified at positions 122-127 of the B/NS1 protein. Surprisingly, glycine substitutions in the Src homology 3 domain-binding motif increased virus replication up to three orders of magnitude in human lung cells. Enhanced mutant virus propagation was accompanied by increased gene expression and apoptosis induction linking this motif to the control of programmed cell death. A MS-based interactome study revealed that the glycine substitutions facilitate binding of B/NS1 to heat shock protein 90-beta (HSP90β). Moreover, recruitment of the viral polymerase basic protein 2 to the B/NS1-HSP90β complex was observed. Pharmacological inhibition of HSP90 reduced mutant virus propagation suggesting that the mutation-induced involvement of HSP90β enhanced viral replication. This study not only functionally characterizes a conserved motif within the B/NS1 protein, but also illustrates a rare example in which mutation of a highly conserved sequence within a viral protein does not result in high fitness costs, but rather increases viral replication via recruitment of a host factor.
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Affiliation(s)
- Anne Sadewasser
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Sandra Saenger
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Katharina Paki
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Torsten Schwecke
- ZBS 6 - Proteomics and Spectroscopy, Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Thorsten Wolff
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
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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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Kazlauskas A, Schmotz C, Kesti T, Hepojoki J, Kleino I, Kaneko T, Li SSC, Saksela K. Large-Scale Screening of Preferred Interactions of Human Src Homology-3 (SH3) Domains Using Native Target Proteins as Affinity Ligands. Mol Cell Proteomics 2016; 15:3270-3281. [PMID: 27440912 DOI: 10.1074/mcp.m116.060483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/17/2022] Open
Abstract
The Src Homology-3 (SH3) domains are ubiquitous protein modules that mediate important intracellular protein interactions via binding to short proline-rich consensus motifs in their target proteins. The affinity and specificity of such core SH3 - ligand contacts are typically modest, but additional binding interfaces can give rise to stronger and more specific SH3-mediated interactions. To understand how commonly such robust SH3 interactions occur in the human protein interactome, and to identify these in an unbiased manner we have expressed 324 predicted human SH3 ligands as full-length proteins in mammalian cells, and screened for their preferred SH3 partners using a phage display-based approach. This discovery platform contains an essentially complete repertoire of the ∼300 human SH3 domains, and involves an inherent binding threshold that ensures selective identification of only SH3 interactions with relatively high affinity. Such strong and selective SH3 partners could be identified for only 19 of these 324 predicted ligand proteins, suggesting that the majority of human SH3 interactions are relatively weak, and thereby have capacity for only modest inherent selectivity. The panel of exceptionally robust SH3 interactions identified here provides a rich source of leads and hypotheses for further studies. However, a truly comprehensive characterization of the human SH3 interactome will require novel high-throughput methods based on function instead of absolute binding affinity.
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Affiliation(s)
- Arunas Kazlauskas
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Constanze Schmotz
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tapio Kesti
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jussi Hepojoki
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Iivari Kleino
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tomonori Kaneko
- §Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Shawn S C Li
- §Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Kalle Saksela
- From the ‡Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland;
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Thulasi Raman SN, Zhou Y. Networks of Host Factors that Interact with NS1 Protein of Influenza A Virus. Front Microbiol 2016; 7:654. [PMID: 27199973 PMCID: PMC4855030 DOI: 10.3389/fmicb.2016.00654] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/19/2016] [Indexed: 11/13/2022] Open
Abstract
Pigs are an important host of influenza A viruses due to their ability to generate reassortant viruses with pandemic potential. NS1 protein of influenza A viruses is a key virulence factor and a major antagonist of innate immune responses. It is also involved in enhancing viral mRNA translation and regulation of virus replication. Being a protein with pleiotropic functions, NS1 has a variety of cellular interaction partners. Hence, studies on swine influenza viruses (SIV) and identification of swine influenza NS1-interacting host proteins is of great interest. Here, we constructed a recombinant SIV carrying a Strep-tag in the NS1 protein and infected primary swine respiratory epithelial cells (SRECs) with this virus. The Strep-tag sequence in the NS1 protein enabled us to purify intact, the NS1 protein and its interacting protein complex specifically. We identified cellular proteins present in the purified complex by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and generated a dataset of these proteins. 445 proteins were identified by LC-MS/MS and among them 192 proteins were selected by setting up a threshold based on MS parameters. The selected proteins were analyzed by bioinformatics and were categorized as belonging to different functional groups including translation, RNA processing, cytoskeleton, innate immunity, and apoptosis. Protein interaction networks were derived using these data and the NS1 interactions with some of the specific host factors were verified by immunoprecipitation. The novel proteins and the networks revealed in our study will be the potential candidates for targeted study of the molecular interaction of NS1 with host proteins, which will provide insights into the identification of new therapeutic targets to control influenza infection and disease pathogenesis.
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Affiliation(s)
- Sathya N Thulasi Raman
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
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31
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Ylösmäki L, Fagerlund R, Kuisma I, Julkunen I, Saksela K. Nuclear Translocation of Crk Adaptor Proteins by the Influenza A Virus NS1 Protein. Viruses 2016; 8:101. [PMID: 27092521 PMCID: PMC4848595 DOI: 10.3390/v8040101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/18/2022] Open
Abstract
The non-structural protein-1 (NS1) of many influenza A strains, especially those of avian origin, contains an SH3 ligand motif, which binds tightly to the cellular adaptor proteins Crk (Chicken tumor virus number 10 (CT10) regulator of kinase) and Crk-like adapter protein (CrkL). This interaction has been shown to potentiate NS1-induced activation of the phosphatidylinositol 3-kinase (PI3K), but additional effects on the host cell physiology may exist. Here we show that NS1 can induce an efficient translocation of Crk proteins from the cytoplasm into the nucleus, which results in an altered pattern of nuclear protein tyrosine phosphorylation. This was not observed using NS1 proteins deficient in SH3 binding or engineered to be exclusively cytoplasmic, indicating a physical role for NS1 as a carrier in the nuclear translocation of Crk. These data further emphasize the role of Crk proteins as host cell interaction partners of NS1, and highlight the potential for host cell manipulation gained by a viral protein simply via acquiring a short SH3 binding motif.
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Affiliation(s)
- Leena Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland.
| | - Riku Fagerlund
- Department of Virology, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland.
| | - Inka Kuisma
- Department of Virology, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland.
| | - Ilkka Julkunen
- Department of Virology, University of Turku, 20520 Turku, Finland and Virology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), 00300 Helsinki, Finland.
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland.
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Luo LY, Hahn WC. Oncogenic Signaling Adaptor Proteins. J Genet Genomics 2015; 42:521-529. [PMID: 26554907 PMCID: PMC4643408 DOI: 10.1016/j.jgg.2015.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 02/08/2023]
Abstract
Signal transduction pathways activated by receptor tyrosine kinases (RTK) play a critical role in many aspects of cell function. Adaptor proteins serve an important scaffolding function that facilitates key signaling transduction events downstream of RTKs. Recent work integrating both structural and functional genomic approaches has identified several adaptor proteins as new oncogenes. In this review, we focus on the discovery, structure and function, and therapeutic implication of three of these adaptor oncogenes, CRKL, GAB2, and FRS2. Each of the three genes is recurrently amplified in lung adenocarcinoma or ovarian cancer, and is essential to cancer cell lines that harbor such amplification. Overexpression of each gene is able to transform immortalized human cell lines in in vitro or in vivo models. These observations identify adaptor protein as a distinct class of oncogenes and potential therapeutic targets.
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Affiliation(s)
- Leo Y Luo
- Health Sciences and Technology Program, Harvard Medical School, Boston, MA 02115, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
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Khaliq Z, Leijon M, Belák S, Komorowski J. A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins. BMC Microbiol 2015; 15:128. [PMID: 26112351 PMCID: PMC4482282 DOI: 10.1186/s12866-015-0465-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/12/2015] [Indexed: 01/18/2023] Open
Abstract
Background Polybasic cleavage sites of the hemagglutinin (HA) proteins are considered to be the most important determinants indicating virulence of the avian influenza viruses (AIV). However, evidence is accumulating that these sites alone are not sufficient to establish high pathogenicity. There need to exist other sites located on the HA protein outside the cleavage site or on the other proteins expressed by AIV that contribute to the pathogenicity. Results We employed rule-based computational modeling to construct a map, with high statistical significance, of amino acid (AA) residues associated to pathogenicity in 11 proteins of the H5 type viruses. We found potential markers of pathogenicity in all of the 11 proteins expressed by the H5 type of AIV. AA mutations S-43HA1-D, D-83HA1-A in HA; S-269-D, E-41-H in NA; S-48-N, K-212-N in NS1; V-166-A in M1; G-14-E in M2; K-77-R, S-377-N in NP; and Q-48-P in PB1-F2 were identified as having a potential to shift the pathogenicity from low to high. Our results suggest that the low pathogenicity is common to most of the subtypes of the H5 AIV while the high pathogenicity is specific to each subtype. The models were developed using public data and validated on new, unseen sequences. Conclusions Our models explicitly define a viral genetic background required for the virus to be highly pathogenic and thus confirm the hypothesis of the presence of pathogenicity markers beyond the cleavage site. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0465-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zeeshan Khaliq
- Department of Cell and Molecular Biology, Computational and Systems Biology, 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 and Systems Biology, 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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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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Baltina LA, Zarubaev VV, Baltina LA, Orshanskaya IA, Fairushina AI, Kiselev OI, Yunusov MS. Glycyrrhizic acid derivatives as influenza A/H1N1 virus inhibitors. Bioorg Med Chem Lett 2015; 25:1742-1746. [PMID: 25801933 PMCID: PMC7127794 DOI: 10.1016/j.bmcl.2015.02.074] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/24/2022]
Abstract
This Letter describes the synthesis and antiviral activity study of some glycyrrhizic acid (GL) derivatives against influenza A/H1N1/pdm09 virus in MDCK cells. Conjugation of GL with l-amino acids or their methyl esters, and amino sugar (d-galactose amine) dramatically changed its activity. The most active compounds were GL conjugates with aromatic amino acids methyl esters (phenylalanine and tyrosine) (SI=61 and 38), and S-benzyl-cysteine (SI=71). Thus modification of GL is a perspective route in the search of new antivirals, and some of GL derivatives are potent as anti-influenza A/H1N1 agents.
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Affiliation(s)
- Lidia A Baltina
- Institute of Organic Chemistry Ufa Research Centre of Russian Academy of Sciences, 71, prospect Oktyabrya, Ufa 450054, Russian Federation.
| | - Vladimir V Zarubaev
- Influenza Research Institute, Ministry of Health of Russia, 15/17, prof. Popov str., St. Peterburg 197376, Russian Federation
| | - Lia A Baltina
- Institute of Organic Chemistry Ufa Research Centre of Russian Academy of Sciences, 71, prospect Oktyabrya, Ufa 450054, Russian Federation
| | - Iana A Orshanskaya
- Influenza Research Institute, Ministry of Health of Russia, 15/17, prof. Popov str., St. Peterburg 197376, Russian Federation
| | - Alina I Fairushina
- Institute of Organic Chemistry Ufa Research Centre of Russian Academy of Sciences, 71, prospect Oktyabrya, Ufa 450054, Russian Federation
| | - Oleg I Kiselev
- Influenza Research Institute, Ministry of Health of Russia, 15/17, prof. Popov str., St. Peterburg 197376, Russian Federation
| | - Marat S Yunusov
- Institute of Organic Chemistry Ufa Research Centre of Russian Academy of Sciences, 71, prospect Oktyabrya, Ufa 450054, Russian Federation
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Hrincius ER, Liedmann S, Finkelstein D, Vogel P, Gansebom S, Ehrhardt C, Ludwig S, Hains DS, Webby R, McCullers JA. Nonstructural protein 1 (NS1)-mediated inhibition of c-Abl results in acute lung injury and priming for bacterial co-infections: insights into 1918 H1N1 pandemic? J Infect Dis 2014; 211:1418-28. [PMID: 25367299 DOI: 10.1093/infdis/jiu609] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/17/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Nonstructural protein 1 (NS1) proteins from avian influenza viruses like the 1918 pandemic NS1 are capable of inhibiting the key signaling integrator c-Abl (Abl1), resulting in massive cytopathic cell alterations. METHODS In the current study, we addressed the consequences of NS1-mediated alteration of c-Abl on acute lung injury and pathogenicity in an in vivo mouse model. RESULTS Comparing isogenic strains that differ only in their ability to inhibit c-Abl, we observed elevated pathogenicity for the c-Abl-inhibiting virus. NS1-mediated blockade of c-Abl resulted in severe lung pathology and massive edema formation and facilitated secondary bacterial pneumonia. This phenotype was independent of differences in replication and immune responses, defining it as an NS1 virulence mechanism distinct from its canonical functions. Microarray analysis revealed extensive downregulation of genes involved in cell integrity and vascular endothelial regulation. CONCLUSIONS NS1 protein-mediated blockade of c-Abl signaling drives acute lung injury and primes for bacterial coinfections revealing potential insights into the pathogenicity of the 1918 pandemic virus.
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Affiliation(s)
| | - Swantje Liedmann
- Institute of Molecular Virology, University of Muenster, Germany
| | | | - Peter Vogel
- Department of Veterinary Pathology, St Jude Children's Research Hospital
| | | | | | - Stephan Ludwig
- Institute of Molecular Virology, University of Muenster, Germany
| | - David S Hains
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis
| | | | - Jonathan A McCullers
- Department of Infectious Diseases Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis
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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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Wei K, Chen Y, Lin Y, Pan Y. Genetic dynamic analysis of the influenza A H5N1 NS1 gene in China. PLoS One 2014; 9:e101384. [PMID: 25003973 PMCID: PMC4086889 DOI: 10.1371/journal.pone.0101384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/06/2014] [Indexed: 12/03/2022] Open
Abstract
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996–2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1–RNA and NS1–protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
| | - Yanhui Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yina Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yutian Pan
- The Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
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40
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Forbes N, Selman M, Pelchat M, Jia JJ, Stintzi A, Brown EG. Identification of adaptive mutations in the influenza A virus non-structural 1 gene that increase cytoplasmic localization and differentially regulate host gene expression. PLoS One 2013; 8:e84673. [PMID: 24391972 PMCID: PMC3877356 DOI: 10.1371/journal.pone.0084673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 11/18/2013] [Indexed: 12/22/2022] Open
Abstract
The NS1 protein of influenza A virus (IAV) is a multifunctional virulence factor. We have previously characterized gain-of-function mutations in the NS1 protein arising from the experimental adaptation of the human isolate A/Hong Kong/1/1968(H3N2) (HK) to the mouse. The majority of these mouse adapted NS1 mutations were demonstrated to increase virulence, viral fitness, and interferon antagonism, but differ in binding to the post-transcriptional processing factor cleavage and polyadenylation specificity factor 30 (CPSF30). Because nuclear trafficking is a major genetic determinant of influenza virus host adaptation, we assessed subcellular localization and host gene expression of NS1 adaptive mutations. Recombinant HK viruses with adaptive mutations in the NS1 gene were assessed for NS1 protein subcellular localization in mouse and human cells using confocal microscopy and cellular fractionation. In human cells the HK wild-type (HK-wt) virus NS1 protein partitioned equivalently between the cytoplasm and nucleus but was defective in cytoplasmic localization in mouse cells. Several adaptive mutations increased the proportion of NS1 in the cytoplasm of mouse cells with the greatest effects for mutations M106I and D125G. The host gene expression profile of the adaptive mutants was determined by microarray analysis of infected mouse cells to show either high or low extents of host-gene regulation (HGR or LGR) phenotypes. While host genes were predominantly down regulated for the HGR group of mutants (D2N, V23A, F103L, M106I+L98S, L98S, M106V, and M106V+M124I), the LGR phenotype mutants (D125G, M106I, V180A, V226I, and R227K) were characterized by a predominant up regulation of host genes. CPSF30 binding affinity of NS1 mutants did not predict effects on host gene expression. To our knowledge this is the first report of roles of adaptive NS1 mutations that impact intracellular localization and regulation of host gene expression.
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Affiliation(s)
- Nicole Forbes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Mohammed Selman
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jian Jun Jia
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Earl G. Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Park SJ, Lee EH, Choi EH, Pascua PNQ, Kwon HI, Kim EH, Lim GJ, Decano A, Kim SM, Choi YK. Avian-derived NS gene segments alter pathogenicity of the A/Puerto Rico/8/34 virus. Virus Res 2013; 179:64-72. [PMID: 24269912 DOI: 10.1016/j.virusres.2013.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 11/06/2013] [Accepted: 11/11/2013] [Indexed: 02/02/2023]
Abstract
While the effect of the influenza A virus non-structural protein (NS) on cytokine production during viral infection is well known, inconsistent results have been observed with some other influenza A virus backbone studied. In this study, in order to focus on the impact of the avian NS gene segments on viral virulence, the NS genes encoded by different strains of avian influenza A viruses were incorporated into an identical [A/Puerto Rico/8/1934(H1N1), PR8] virus background to generate various NS recombinant viruses. Thus, PR8NS, PR8×[A/Hong Kong/483/97(H5N1) 483NS, PR8×[A/Ck/Korea/150/03(H9N2) 150NS, and PR8×[A/EM/Korea/W149/06(H5N1) W149NS were constructed utilizing reverse genetics. Here, we show the effects of each of these recombinant viruses upon viral pathogenesis and cytokine production during viral replication in vivo. In this regard, we found that infection of mice with the PR8×150NS recombinant virus resulted in the lowest pathogenicity (6.0×10(4)MLD50), yet elicited the highest levels of TNF-α production in bronchoalveolar lavage (BAL) fluid compared to infection with the other recombinant influenza viruses. In contrast, infection with the PR8 virus showed the highest pathogenicity (1.0×10(2)MLD50) as well as relatively high cytokine levels (IL-1α, IL-1β, IL-17, and eotaxin) in mouse BAL fluid. In addition, the PR8 and PR8×483NS viruses induced severe and extensive inflammation in infected lungs compared with that of PR8×150 NS recombinant virus-infected mice. These results clearly demonstrate that the NS genes of diverse influenza A strains can variable impact pathogenicity, histopathology, and cytokine production in mice even when expressed in an identical genetic background.
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Affiliation(s)
- Su-Jin Park
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Eun Ho Lee
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Eun Hye Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Philippe Noriel Q Pascua
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Hyeok-Il Kwon
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Eun-Ha Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Gyo-Jin Lim
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Arun Decano
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Se Mi Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong Henugduk-Ku, Cheongju 361-763, Republic of Korea.
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42
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Abdelwhab EM, Veits J, Mettenleiter TC. Avian influenza virus NS1: A small protein with diverse and versatile functions. Virulence 2013; 4:583-8. [PMID: 24051601 PMCID: PMC3906290 DOI: 10.4161/viru.26360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- E M Abdelwhab
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Insel Riems, Germany
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43
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de Chassey B, Aublin-Gex A, Ruggieri A, Meyniel-Schicklin L, Pradezynski F, Davoust N, Chantier T, Tafforeau L, Mangeot PE, Ciancia C, Perrin-Cocon L, Bartenschlager R, André P, Lotteau V. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication. PLoS Pathog 2013; 9:e1003440. [PMID: 23853584 PMCID: PMC3701712 DOI: 10.1371/journal.ppat.1003440] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/06/2013] [Indexed: 12/24/2022] Open
Abstract
Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution. Viruses are obligate intracellular parasites that rely on cellular functions for efficient replication. As most biological processes are sustained by protein-protein interactions, the identification of interactions between viral and host proteins can provide a global overview about the cellular functions engaged during viral replication. Influenza viruses express 13 viral proteins, including NS1 and NS2, which are translated from an alternatively spliced RNA derived from the same genome segment. We present here a comprehensive overview of possible interactions of cellular proteins with NS1 and NS2 from 9 viral strains. Seventy nine cellular proteins were identified to interact with NS1, NS2 or both NS1 and NS2. These interacting host cell proteins are potentially involved in many steps of the virus life cycle and 7 can directly control the viral replication. Most of the cellular targets are shared by the majority of the virus strains, especially the double-stranded RNA binding domain protein family that is strikingly targeted by NS1. One of its members, ADAR1, is essential for influenza virus replication. ADAR1 colocalizes with NS1 in nuclear structures and its editing activity is enhanced by NS1 expressed on its own and during virus infection. A similar phenomenon is observed for dengue virus whose NS3 protein also interacts with ADAR1, suggesting a parallel virus-host co-evolution.
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Affiliation(s)
- Benoît de Chassey
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
| | - Anne Aublin-Gex
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Alessia Ruggieri
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Laurène Meyniel-Schicklin
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Fabrine Pradezynski
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Nathalie Davoust
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Thibault Chantier
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Lionel Tafforeau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Philippe-Emmanuel Mangeot
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Claire Ciancia
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Patrice André
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
- * E-mail:
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44
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Engel DA. The influenza virus NS1 protein as a therapeutic target. Antiviral Res 2013; 99:409-16. [PMID: 23796981 DOI: 10.1016/j.antiviral.2013.06.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/08/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
Abstract
Nonstructural protein 1 (NS1) of influenza A virus plays a central role in virus replication and blockade of the host innate immune response, and is therefore being considered as a potential therapeutic target. The primary function of NS1 is to dampen the host interferon (IFN) response through several distinct molecular mechanisms that are triggered by interactions with dsRNA or specific cellular proteins. Sequestration of dsRNA by NS1 results in inhibition of the 2'-5' oligoadenylate synthetase/RNase L antiviral pathway, and also inhibition of dsRNA-dependent signaling required for new IFN production. Binding of NS1 to the E3 ubiquitin ligase TRIM25 prevents activation of RIG-I signaling and subsequent IFN induction. Cellular RNA processing is also targeted by NS1, through recognition of cleavage and polyadenylation specificity factor 30 (CPSF30), leading to inhibition of IFN-β mRNA processing as well as that of other cellular mRNAs. In addition NS1 binds to and inhibits cellular protein kinase R (PKR), thus blocking an important arm of the IFN system. Many additional proteins have been reported to interact with NS1, either directly or indirectly, which may serve its anti-IFN and additional functions, including the regulation of viral and host gene expression, signaling pathways and viral pathogenesis. Many of these interactions are potential targets for small-molecule intervention. Structural, biochemical and functional studies have resulted in hypotheses for drug discovery approaches that are beginning to bear experimental fruit, such as targeting the dsRNA-NS1 interaction, which could lead to restoration of innate immune function and inhibition of virus replication. This review describes biochemical, cell-based and nucleic acid-based approaches to identifying NS1 antagonists.
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Affiliation(s)
- Daniel A Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, United States.
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45
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Sevilla-Reyes EE, Chavaro-Pérez DA, Piten-Isidro E, Gutiérrez-González LH, Santos-Mendoza T. Protein clustering and RNA phylogenetic reconstruction of the influenza A [corrected] virus NS1 protein allow an update in classification and identification of motif conservation. PLoS One 2013; 8:e63098. [PMID: 23667580 PMCID: PMC3646732 DOI: 10.1371/journal.pone.0063098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/28/2013] [Indexed: 12/30/2022] Open
Abstract
The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96.8% amino acid similarity produced 415 clusters that enhanced our capability to detect distinct subgroups and lineages, which were assigned a numerical nomenclature. Maximum likelihood phylogenetic reconstruction using RNA sequences indicated the previously identified deep branching separating group A from group B, with five distinct subgroups within A as well as two and five lineages within the A4 and A5 subgroups, respectively. Our classification model proposes that sequence patterns in thirteen amino acid positions are sufficient to fit >99.9% of all currently available NS1 sequences into the A subgroups/lineages or the B group. This classification reduces host and virus bias through the prioritization of NS1 RNA phylogenetics over host or virus phenetics. We found significant sequence conservation within the subgroups and lineages with characteristic patterns of functional motifs, such as the differential binding of CPSF30 and crk/crkL or the availability of a C-terminal PDZ-binding motif. To understand selection pressures and evolution acting on NS1, it is necessary to organize the available data. This updated classification may help to clarify and organize the study of NS1 interactions and pathogenic differences and allow the drawing of further functional inferences on sequences in each group, subgroup and lineage rather than on a strain-by-strain basis.
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Affiliation(s)
- Edgar E. Sevilla-Reyes
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- * E-mail: (TSM); (EESR)
| | - David A. Chavaro-Pérez
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Elvira Piten-Isidro
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Luis H. Gutiérrez-González
- Departmento de Virología y Micología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Teresa Santos-Mendoza
- Departmento de Inmunología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- * E-mail: (TSM); (EESR)
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46
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Tønnessen R, Hauge AG, Hansen EF, Rimstad E, Jonassen CM. Host restrictions of avian influenza viruses: in silico analysis of H13 and H16 specific signatures in the internal proteins. PLoS One 2013; 8:e63270. [PMID: 23646204 PMCID: PMC3639990 DOI: 10.1371/journal.pone.0063270] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 04/02/2013] [Indexed: 12/01/2022] Open
Abstract
Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific signatures are present only in the internal proteins of H13 and H16 AIVs, using a bioinformatics approach. Amino acids identified in an initial analysis performed on 15 selected sequences were checked against a comprehensive set of AIV sequences retrieved from Genbank to verify them as H13 and H16 specific signatures. Analysis of protein similarities and prediction of subcellular localization signals were performed to search for possible functions associated with the confirmed signatures. H13 and H16 AIV specific signatures were found in all the internal proteins examined, but most were found in the non-structural protein 1 (NS1) and in the nucleoprotein. A putative functional signature was predicted to be present in the nuclear export protein. Moreover, it was predicted that the NS1 of H13 and H16 AIVs lack one of the nuclear localization signals present in NS1 of other AIV subtypes. These findings suggest that the signatures found in the internal proteins of H13 and H16 viruses are possibly related to host restriction.
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Affiliation(s)
- Ragnhild Tønnessen
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, Oslo, Norway.
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47
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Han X, Li Z, Chen H, Wang H, Mei L, Wu S, Zhang T, Liu B, Lin X. Influenza virus A/Beijing/501/2009(H1N1) NS1 interacts with β-tubulin and induces disruption of the microtubule network and apoptosis on A549 cells. PLoS One 2012; 7:e48340. [PMID: 23139776 PMCID: PMC3491056 DOI: 10.1371/journal.pone.0048340] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022] Open
Abstract
NS1 of influenza A virus is a key multifunctional protein that plays various roles in regulating viral replication mechanisms, host innate/adaptive immune responses, and cellular signalling pathways. These functions rely on its ability to participate in a multitude of protein-protein and protein-RNA interactions. To gain further insight into the role of NS1, a tandem affinity purification (TAP) method was utilized to find unknown interaction partner of NS1. The protein complexes of NS1 and its interacting partner were purified from A549 cell using TAP-tagged NS1 as bait, and co-purified cellular factors were identified by mass spectrometry (MS). We identified cellular β-tubulin as a novel interaction partner of NS1. The RNA-binding domain of NS1 interacts with β-tubulin through its RNA-binding domain, as judged by a glutathione S-transferase (GST) pull-down assay with the GST-fused functional domains of NS1. Immunofluorescence analysis further revealed that NS1 with β-tubulin co-localized in the nucleus. In addition, the disruption of the microtubule network and apoptosis were also observed on NS1-transfected A549 cells. Our findings suggest that influenza A virus may utilize its NS1 protein to interact with cellular β-tubulin to further disrupt normal cell division and induce apoptosis. Future work will illustrate whether this interaction is uniquely specific to the 2009 pandemic H1N1 virus.
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Affiliation(s)
- Xueqing Han
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhihui Li
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Hongjun Chen
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Huiyu Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Lin Mei
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Shaoqiang Wu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Tianyi Zhang
- College of Veterinary Medicine, China Agricultural University, Bejing, China
| | - Bohua Liu
- State Key Laboratory of Pathogens and Bio-security, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (XL); (BL)
| | - Xiangmei Lin
- Chinese Academy of Inspection and Quarantine, Beijing, China
- * E-mail: (XL); (BL)
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48
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Melén K, Tynell J, Fagerlund R, Roussel P, Hernandez-Verdun D, Julkunen I. Influenza A H3N2 subtype virus NS1 protein targets into the nucleus and binds primarily via its C-terminal NLS2/NoLS to nucleolin and fibrillarin. Virol J 2012; 9:167. [PMID: 22909121 PMCID: PMC3493336 DOI: 10.1186/1743-422x-9-167] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/08/2012] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Influenza A virus non-structural protein 1 (NS1) is a virulence factor, which is targeted into the cell cytoplasm, nucleus and nucleolus. NS1 is a multi-functional protein that inhibits host cell pre-mRNA processing and counteracts host cell antiviral responses. Previously, we have shown that the NS1 protein of the H3N2 subtype influenza viruses possesses a C-terminal nuclear localization signal (NLS) that also functions as a nucleolar localization signal (NoLS) and targets the protein into the nucleolus. RESULTS Here, we show that the NS1 protein of the human H3N2 virus subtype interacts in vitro primarily via its C-terminal NLS2/NoLS and to a minor extent via its N-terminal NLS1 with the nucleolar proteins, nucleolin and fibrillarin. Using chimeric green fluorescence protein (GFP)-NS1 fusion constructs, we show that the nucleolar retention of the NS1 protein is determined by its C-terminal NLS2/NoLS in vivo. Confocal laser microscopy analysis shows that the NS1 protein colocalizes with nucleolin in nucleoplasm and nucleolus and with B23 and fibrillarin in the nucleolus of influenza A/Udorn/72 virus-infected A549 cells. Since some viral proteins contain NoLSs, it is likely that viruses have evolved specific nucleolar functions. CONCLUSION NS1 protein of the human H3N2 virus interacts primarily via the C-terminal NLS2/NoLS and to a minor extent via the N-terminal NLS1 with the main nucleolar proteins, nucleolin, B23 and fibrillarin.
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Affiliation(s)
- Krister Melén
- Virology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Mannerheimintie 166, FIN-00300, Helsinki, Finland
| | - Janne Tynell
- Virology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Mannerheimintie 166, FIN-00300, Helsinki, Finland
| | - Riku Fagerlund
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pascal Roussel
- Functional Organization of the Nucleolus, RNA Biology-FRE 3402 CNRS, Université Pierre et Marie Curie, 75252, Paris cedex 5, France
| | - Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, Institut Jacques Monod-UMR 7592 CNRS, Université Paris Diderot, 75205, Paris cedex 13, France
| | - Ilkka Julkunen
- Virology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Mannerheimintie 166, FIN-00300, Helsinki, Finland
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Arnold R, Boonen K, Sun MG, Kim PM. Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods 2012; 57:508-18. [PMID: 22750305 PMCID: PMC7128575 DOI: 10.1016/j.ymeth.2012.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 11/05/2022] Open
Abstract
Bacterial and viral pathogens affect their eukaryotic host partly by interacting with proteins of the host cell. Hence, to investigate infection from a systems' perspective we need to construct complete and accurate host-pathogen protein-protein interaction networks. Because of the paucity of available data and the cost associated with experimental approaches, any construction and analysis of such a network in the near future has to rely on computational predictions. Specifically, this challenge consists of a number of sub-problems: First, prediction of possible pathogen interactors (e.g. effector proteins) is necessary for bacteria and protozoa. Second, the prospective host binding partners have to be determined and finally, the impact on the host cell analyzed. This review gives an overview of current bioinformatics approaches to obtain and understand host-pathogen interactions. As an application example of the methods covered, we predict host-pathogen interactions of Salmonella and discuss the value of these predictions as a prospective for further research.
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Affiliation(s)
- Roland Arnold
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Kurt Boonen
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Mark G.F. Sun
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 3E1
- Department of Computer Science, University of Toronto, Toronto, ON, Canada M5S 3E1
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Hrincius ER, Hennecke AK, Gensler L, Nordhoff C, Anhlan D, Vogel P, McCullers JA, Ludwig S, Ehrhardt C. A Single Point Mutation (Y89F) within the Non-Structural Protein 1 of Influenza A Viruses Limits Epithelial Cell Tropism and Virulence in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:2361-74. [DOI: 10.1016/j.ajpath.2012.02.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/22/2012] [Accepted: 02/28/2012] [Indexed: 12/15/2022]
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