1
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Merritt TN, Pei J, Leung DW. Pathogenicity and virulence of human respiratory syncytial virus: Multifunctional nonstructural proteins NS1 and NS2. Virulence 2023:2283897. [PMID: 37964591 DOI: 10.1080/21505594.2023.2283897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is a major cause of acute lower respiratory tract infections in children under the age of two as well as in the elderly and immunocompromised worldwide. Despite its discovery over 60 years ago and the global impact on human health, limited specific and effective prophylactic or therapeutic options have been available for hRSV infections. Part of the lack of treatment options is attributed to the legacy of vaccine failure in the 1960s using a formalin-inactivated RSV (FI-RSV), which led to enhancement of disease post exposure to hRSV infection and hampered subsequent development of vaccine candidates. Recent FDA approval of a vaccine for older adults and impending approval for a maternal vaccine are major advancements but leaves children between 6 months and 5 years of age unprotected. Part of this limitation can be attributed to a lack of complete understanding of the factors that contribute to hRSV pathogenesis. The nonstructural proteins NS1 and NS2 are multifunctional virulence factors that are unique to hRSV and that play critical roles during hRSV infection, including antagonizing interferon (IFN) signalling to modulate host responses to hRSV infection. However, the molecular mechanisms by which the nonstructural proteins mediate their IFN inhibitory functions have not been completely defined. Current progress on the characterization of NS1 and NS2 during infection provides deeper insight into their roles. Furthermore, reverse genetics systems for hRSV provide a viable strategy to generate attenuated viruses by introduction of select mutations while maintaining immunogenicity required to elicit a long-term protective response. Here we will review the current state of knowledge of the nonstructural proteins, their contributions to RSV pathogenesis, and their potential as targets for therapeutic development.
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Affiliation(s)
- Trudy N Merritt
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jingjing Pei
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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2
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Attaianese F, Guiducci S, Trapani S, Barbati F, Lodi L, Indolfi G, Azzari C, Ricci S. Reshaping Our Knowledge: Advancements in Understanding the Immune Response to Human Respiratory Syncytial Virus. Pathogens 2023; 12:1118. [PMID: 37764926 PMCID: PMC10536346 DOI: 10.3390/pathogens12091118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is a significant cause of respiratory tract infections, particularly in young children and older adults. In this review, we aimed to comprehensively summarize what is known about the immune response to hRSV infection. We described the innate and adaptive immune components involved, including the recognition of RSV, the inflammatory response, the role of natural killer (NK) cells, antigen presentation, T cell response, and antibody production. Understanding the complex immune response to hRSV infection is crucial for developing effective interventions against this significant respiratory pathogen. Further investigations into the immune memory generated by hRSV infection and the development of strategies to enhance immune responses may hold promise for the prevention and management of hRSV-associated diseases.
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Affiliation(s)
- Federica Attaianese
- Postgraduate School of Pediatrics, University of Florence, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy;
| | - Sara Guiducci
- Postgraduate School of Immunology, University of Florence, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy;
| | - Sandra Trapani
- Pediatric Unit, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (S.T.); (G.I.)
- Department of Health Sciences, University of Florence, 50139 Florence, Italy; (L.L.); (C.A.)
| | - Federica Barbati
- Postgraduate School of Pediatrics, University of Florence, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy;
| | - Lorenzo Lodi
- Department of Health Sciences, University of Florence, 50139 Florence, Italy; (L.L.); (C.A.)
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy
| | - Giuseppe Indolfi
- Pediatric Unit, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (S.T.); (G.I.)
- NEUROFARBA Department, University of Florence, 50139 Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, University of Florence, 50139 Florence, Italy; (L.L.); (C.A.)
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy
| | - Silvia Ricci
- Department of Health Sciences, University of Florence, 50139 Florence, Italy; (L.L.); (C.A.)
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy
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3
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García-Dorival I, Cuesta-Geijo MÁ, Galindo I, Del Puerto A, Barrado-Gil L, Urquiza J, Alonso C. Elucidation of the Cellular Interactome of African Swine Fever Virus Fusion Proteins and Identification of Potential Therapeutic Targets. Viruses 2023; 15:v15051098. [PMID: 37243184 DOI: 10.3390/v15051098] [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: 04/04/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
African swine fever virus (ASFV) encodes more than 150 proteins, most of them of unknown function. We used a high-throughput proteomic analysis to elucidate the interactome of four ASFV proteins, which potentially mediate a critical step of the infection cycle, the fusion and endosomal exit of the virions. Using affinity purification and mass spectrometry, we were able to identify potential interacting partners for those ASFV proteins P34, E199L, MGF360-15R and E248R. Representative molecular pathways for these proteins were intracellular and Golgi vesicle transport, endoplasmic reticulum organization, lipid biosynthesis, and cholesterol metabolism. Rab geranyl geranylation emerged as a significant hit, and also Rab proteins, which are crucial regulators of the endocytic pathway and interactors of both p34 and E199L. Rab proteins co-ordinate a tight regulation of the endocytic pathway that is necessary for ASFV infection. Moreover, several interactors were proteins involved in the molecular exchange at ER membrane contacts. These ASFV fusion proteins shared interacting partners, suggesting potential common functions. Membrane trafficking and lipid metabolism were important categories, as we found significant interactions with several enzymes of the lipid metabolism. These targets were confirmed using specific inhibitors with antiviral effect in cell lines and macrophages.
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Affiliation(s)
- Isabel García-Dorival
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Inmaculada Galindo
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Ana Del Puerto
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Jesús Urquiza
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Covadonga Alonso
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
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Ottenio de Lourenço I, Toscano Pedroso Quintino E, Henrique Pereira M, Sprengel Lima C, Campos Araújo G, Octávio Regasini L, Alves de Melo F, Pereira de Souza F, Andres Fossey M, Putinhon Caruso Í. Biophysical studies of the interaction of hRSV Non-Structural 1 protein with natural flavonoids and their acetylated derivatives by spectroscopic techniques and computational simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121751. [PMID: 35973382 DOI: 10.1016/j.saa.2022.121751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/14/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Human respiratory syncytial virus (hRSV) infections are one of the most causes of acute lower respiratory tract infections in children and elderly. The development of effective antiviral therapies or preventive vaccines against hRSV is not available yet. Thus, it is necessary to search for protein targets to combat this viral infection, as well as potential ways to block them. Non-Structural 1 (NS1) protein is an important factor for viral replication success since reduces the immune response by interacting with proteins in the type I interferon pathway. The influence of NS1 on the cell's immune response denotes the potential of its inhibition, being a possible target of treatment against hRSV infection. Here, it was studied the interaction of hRSV NS1 with natural flavonoids chrysin, morin, kaempferol, and myricetin and their mono-acetylated chrysin and penta-acetylated morin derivatives using spectroscopic techniques and computational simulations. The fluorescence data indicate that the binding affinities are on the order of 105 M-1, which are directly related to the partition coefficient of each flavonoid with Pearson's correlation coefficients of 0.76-0.80. The thermodynamic analysis suggests that hydrophobic interactions play a key role in the formation of the NS1/flavonoid complexes, with positive values of enthalpy and entropy changes. The computational approach proposes that flavonoids bind in a region of NS1 formed between the C-terminal α3-helix and the protein core, important for its biological function, and corroborate with experimental data revealing that hydrophobic contacts are important for the binding. Therefore, the present study provides relevant molecular details for the development of a possible new strategy to fight infections caused by hRSV.
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Affiliation(s)
- Isabella Ottenio de Lourenço
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Evelyn Toscano Pedroso Quintino
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Matheus Henrique Pereira
- Department of Chemistry and Environmental Sciences, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Caroline Sprengel Lima
- Department of Chemistry and Environmental Sciences, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Gabriela Campos Araújo
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Luis Octávio Regasini
- Department of Chemistry and Environmental Sciences, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando Alves de Melo
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Marcelo Andres Fossey
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil.
| | - Ícaro Putinhon Caruso
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP 15054-000, Brazil; Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
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5
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An Unexpected Encounter: Respiratory Syncytial Virus Nonstructural Protein 1 Interacts with Mediator Subunit MED25. J Virol 2022; 96:e0129722. [PMID: 36102648 PMCID: PMC9555202 DOI: 10.1128/jvi.01297-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Innate immune responses, including the production of type I and III interferons, play a crucial role in the first line of defense against RSV infection. However, only a poor induction of type I IFNs is observed during RSV infection, suggesting that RSV has evolved mechanisms to prevent type I IFN expression by the infected host cell.
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6
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Respiratory Syncytial virus NS1 protein targets the transactivator binding domain of MED25. J Mol Biol 2022; 434:167763. [PMID: 35907573 DOI: 10.1016/j.jmb.2022.167763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/28/2022] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
Abstract
Human RSV is the leading cause of infantile bronchiolitis in the world and one of the major causes of childhood deaths in resource-poor settings. It is a major unmet target for vaccines and anti-viral drugs. Respiratory syncytial virus has evolved a unique strategy to evade host immune response by coding for two non-structural proteins NS1 and NS2. Recently it was shown that in infected cells, nuclear NS1 could be involved in transcription regulation of host genes linked to innate immune response, via interactions with chromatin and the Mediator complex. Here we identified the MED25 Mediator subunit as an NS1 interactor in a yeast two-hybrid screen. We demonstrate that NS1 directly interacts with MED25 in vitro and in cellula, and that this interaction involves the MED25 transactivator binding ACID domain on the one hand, and the C-terminal α3 helix of NS1, with an additional contribution of the globular domain of NS1, on the other hand. By NMR we show that the NS1 α3 sequence primarily binds to the MED25 ACID H2 face, similarly to the α-helical transactivation domains (TADs) of transcription regulators such as Herpex simplex VP16 and ATF6α, a master regulator of ER stress response activated upon viral infection. Moreover, we found out that the NS1 could compete with ATF6α TAD for binding to MED25. These findings point to a mechanism of NS1 interfering with innate immune response by impairing recruitment by cellular TADs of the Mediator via MED25 and hence transcription of specific genes by RNA polymerase II.
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7
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Qin S, Huang X, Qu S. Baicalin Induces a Potent Innate Immune Response to Inhibit Respiratory Syncytial Virus Replication via Regulating Viral Non-Structural 1 and Matrix RNA. Front Immunol 2022; 13:907047. [PMID: 35812414 PMCID: PMC9259847 DOI: 10.3389/fimmu.2022.907047] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection is the most frequent cause of hospitalization in pediatric patients. Current systemic treatment and vaccines are not curative and re-infection is often associated with a more drastic incidence of the disease. Baicalin is a flavonoid isolated from Scutellaria baicalensis with potent anti-viral characteristics, namely against RSV. However, its precise mechanism of action remains unclear. Here, using in vitro methods and an in vivo murine model of RSV infection, we showed that baicalin inhibits RSV replication induces translational upregulation of type I interferons (IFNs), IFN-α and IFN-β, and reverses epithelial thickening in lung tissues. Moreover, baicalin inhibits transcription of the RSV non-structural proteins NS1 and NS2. Molecular docking and surface plasmon resonance-based affinity analysis showed that baicalin also binds to the α3 helix of the NS1 protein with an affinity constant of 1.119 × 10−5 M. Polysome profiling showed that baicalin inhibits translation of the RSV matrix protein (M) RNA. Baicalin mediates increased release of the ribosomal protein L13a from the large ribosomal subunit, where the extra ribosomal subunit L13a inhibits M RNA translation. These results comprehensively establish the multiple mechanisms by which baicalin induces a potent innate immune response against RSV infection.
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Affiliation(s)
- Sheng Qin
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, China
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Shaogang Qu, ; Xianzhang Huang,
| | - Shaogang Qu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, China
- *Correspondence: Shaogang Qu, ; Xianzhang Huang,
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8
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Van Royen T, Rossey I, Sedeyn K, Schepens B, Saelens X. How RSV Proteins Join Forces to Overcome the Host Innate Immune Response. Viruses 2022; 14:v14020419. [PMID: 35216012 PMCID: PMC8874859 DOI: 10.3390/v14020419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/10/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of severe acute lower respiratory tract infections in infants worldwide. Although several pattern recognition receptors (PRRs) can sense RSV-derived pathogen-associated molecular patterns (PAMPs), infection with RSV is typically associated with low to undetectable levels of type I interferons (IFNs). Multiple RSV proteins can hinder the host’s innate immune response. The main players are NS1 and NS2 which suppress type I IFN production and signalling in multiple ways. The recruitment of innate immune cells and the production of several cytokines are reduced by RSV G. Next, RSV N can sequester immunostimulatory proteins to inclusion bodies (IBs). N might also facilitate the assembly of a multiprotein complex that is responsible for the negative regulation of innate immune pathways. Furthermore, RSV M modulates the host’s innate immune response. The nuclear accumulation of RSV M has been linked to an impaired host gene transcription, in particular for nuclear-encoded mitochondrial proteins. In addition, RSV M might also directly target mitochondrial proteins which results in a reduced mitochondrion-mediated innate immune recognition of RSV. Lastly, RSV SH might prolong the viral replication in infected cells and influence cytokine production.
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Affiliation(s)
- Tessa Van Royen
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; (T.V.R.); (I.R.); (K.S.); (B.S.)
- Department for Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Iebe Rossey
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; (T.V.R.); (I.R.); (K.S.); (B.S.)
- Department for Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; (T.V.R.); (I.R.); (K.S.); (B.S.)
- Department for Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; (T.V.R.); (I.R.); (K.S.); (B.S.)
- Department for Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; (T.V.R.); (I.R.); (K.S.); (B.S.)
- Department for Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
- Correspondence:
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9
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Pei J, Beri NR, Zou AJ, Hubel P, Dorando HK, Bergant V, Andrews RD, Pan J, Andrews JM, Sheehan KCF, Pichlmair A, Amarasinghe GK, Brody SL, Payton JE, Leung DW. Nuclear-localized human respiratory syncytial virus NS1 protein modulates host gene transcription. Cell Rep 2021; 37:109803. [PMID: 34644581 PMCID: PMC8609347 DOI: 10.1016/j.celrep.2021.109803] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/28/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections in the pediatric, elderly, and immunocompromised individuals. RSV non-structural protein NS1 is a known cytosolic immune antagonist, but how NS1 modulates host responses remains poorly defined. Here, we observe NS1 partitioning into the nucleus of RSV-infected cells, including the human airway epithelium. Nuclear NS1 coimmunoprecipitates with Mediator complex and is chromatin associated. Chromatin-immunoprecipitation demonstrates enrichment of NS1 that overlaps Mediator and transcription factor binding within the promoters and enhancers of differentially expressed genes during RSV infection. Mutation of the NS1 C-terminal helix reduces NS1 impact on host gene expression. These data suggest that nuclear NS1 alters host responses to RSV infection by binding at regulatory elements of immune response genes and modulating host gene transcription. Our study identifies another layer of regulation by virally encoded proteins that shapes host response and impacts immunity to RSV.
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Affiliation(s)
- Jingjing Pei
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nina R Beri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Angela J Zou
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philipp Hubel
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried/Munich 82152, Germany
| | - Hannah K Dorando
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Valter Bergant
- Institute for Virology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Rebecca D Andrews
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiehong Pan
- Department of Medicine, Division of Pulmonary and Critical Care, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jared M Andrews
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andreas Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried/Munich 82152, Germany; Institute for Virology, Technical University of Munich, School of Medicine, 81675 Munich, Germany
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven L Brody
- Department of Medicine, Division of Pulmonary and Critical Care, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Daisy W Leung
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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10
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Pei J, Wagner ND, Zou AJ, Chatterjee S, Borek D, Cole AR, Kim PJ, Basler CF, Otwinowski Z, Gross ML, Amarasinghe GK, Leung DW. Structural basis for IFN antagonism by human respiratory syncytial virus nonstructural protein 2. Proc Natl Acad Sci U S A 2021; 118:e2020587118. [PMID: 33649232 PMCID: PMC7958447 DOI: 10.1073/pnas.2020587118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human respiratory syncytial virus (RSV) nonstructural protein 2 (NS2) inhibits host interferon (IFN) responses stimulated by RSV infection by targeting early steps in the IFN-signaling pathway. But the molecular mechanisms related to how NS2 regulates these processes remain incompletely understood. To address this gap, here we solved the X-ray crystal structure of NS2. This structure revealed a unique fold that is distinct from other known viral IFN antagonists, including RSV NS1. We also show that NS2 directly interacts with an inactive conformation of the RIG-I-like receptors (RLRs) RIG-I and MDA5. NS2 binding prevents RLR ubiquitination, a process critical for prolonged activation of downstream signaling. Structural analysis, including by hydrogen-deuterium exchange coupled to mass spectrometry, revealed that the N terminus of NS2 is essential for binding to the RIG-I caspase activation and recruitment domains. N-terminal mutations significantly diminish RIG-I interactions and result in increased IFNβ messenger RNA levels. Collectively, our studies uncover a previously unappreciated regulatory mechanism by which NS2 further modulates host responses and define an approach for targeting host responses.
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Affiliation(s)
- Jingjing Pei
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Angela J Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Srirupa Chatterjee
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Preston J Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Daisy W Leung
- John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110;
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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11
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Romano A, Casazza M, Gonella F. Addressing Non-linear System Dynamics of Single-Strand RNA Virus-Host Interaction. Front Microbiol 2021; 11:600254. [PMID: 33519741 PMCID: PMC7843927 DOI: 10.3389/fmicb.2020.600254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
Positive single-strand ribonucleic acid [(+)ssRNA] viruses can cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are tightly connected, generating a complex dynamics that conveys in virion assembly to ensure virus spread in the body. Starting from the knowledge of relevant processes in (+ss)RNA virus replication, transcription, translation, virions budding and shedding, and their respective energy costs, we built up a systems thinking (ST)-based diagram of the virus-host interaction, comprehensive of stocks, flows, and processes as well-described in literature. In ST approach, stocks and flows are expressed by a proxy of the energy embedded and transmitted, respectively, whereas processes are referred to the energy required for the system functioning. In this perspective, healthiness is just a particular configuration, in which stocks relevant for the system (equivalent but not limited to proteins, RNA, DNA, and all metabolites required for the survival) are constant, and the system behavior is stationary. At time of infection, the presence of additional stocks (e.g., viral protein and RNA and all metabolites required for virion assembly and spread) confers a complex network of feedbacks leading to new configurations, which can evolve to maximize the virions stock, thus changing the system structure, output, and purpose. The dynamic trajectories will evolve to achieve a new stationary status, a phenomenon described in microbiology as integration and symbiosis when the system is resilient enough to the changes, or the system may stop functioning and die. Application of external driving forces, acting on processes, can affect the dynamic trajectories adding a further degree of complexity, which can be captured by ST approach, used to address these new configurations. Investigation of system configurations in response to external driving forces acting is developed by computational analysis based on ST diagrams, with the aim at designing novel therapeutic approaches.
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Affiliation(s)
- Alessandra Romano
- Sezione di Ematologia, Dipartimento di Chirurgia Generale e Specialità Medico Chirurgiche (CHIRMED), Università degli Studi di Catania, Catania, Italy
- Division of Hematology, U.O.C di Ematologia, Azienda Ospedaliero Universitaria Policlinico “G.Rodolico - San Marco”, Catania, Italy
| | - Marco Casazza
- Division of Hematology, U.O.C di Ematologia, Azienda Ospedaliero Universitaria Policlinico “G.Rodolico - San Marco”, Catania, Italy
| | - Francesco Gonella
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Venezia, Italy
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12
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Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol 2021; 17:e8792. [PMID: 33434350 PMCID: PMC7803364 DOI: 10.15252/msb.20188792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
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13
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Elawar F, Oraby AK, Kieser Q, Jensen LD, Culp T, West FG, Marchant DJ. Pharmacological targets and emerging treatments for respiratory syncytial virus bronchiolitis. Pharmacol Ther 2020; 220:107712. [PMID: 33121940 DOI: 10.1016/j.pharmthera.2020.107712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022]
Abstract
RSV infection of the lower respiratory tract in infants is the leading cause of pediatric hospitalizations and second to malaria in causing infant deaths worldwide. RSV also causes substantial morbidity in immunocompromised and elderly populations. The only available therapeutic is a prophylactic drug called Palivizumab that is a humanized monoclonal antibody, given to high-risk infants. However, this intervention is expensive and has a limited impact on annual hospitalization rates caused by RSV. No vaccine is available, nor are efficacious antivirals to treat an active infection, and there is still no consensus on how infants with bronchiolitis should be treated during hospital admission. In this comprehensive review, we briefly outline the function of the RSV proteins and their suitability as therapeutic targets. We then discuss the most promising drug candidates, their inhibitory mechanisms, and whether they are in the process of clinical trials. We also briefly discuss the reasons for some of the failures in RSV therapeutics and vaccines. In summary, we provide insight into current antiviral development and the considerations toward producing licensed antivirals and therapeutics.
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Affiliation(s)
- Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Ahmed K Oraby
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Misr University for Science &Technology, Al-Motamayez District, 6th of October City, P.O. Box 77, Egypt
| | - Quinten Kieser
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Lionel D Jensen
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tyce Culp
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - David J Marchant
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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14
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Thornhill EM, Verhoeven D. Respiratory Syncytial Virus's Non-structural Proteins: Masters of Interference. Front Cell Infect Microbiol 2020; 10:225. [PMID: 32509597 PMCID: PMC7248305 DOI: 10.3389/fcimb.2020.00225] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/22/2020] [Indexed: 01/12/2023] Open
Abstract
Respiratory Syncytial Virus (RSV) is a highly prevalent virus that affects the majority of the population. The virus can cause severe disease in vulnerable populations leading to high hospitalization rates from bronchiolitis or secondary bacterial infections leading to pneumonia. Two early and non-structural proteins (Ns1 and Ns2), strongly over-ride the antiviral innate system but also diminish the adaptive response as well. This review will cover interactions of Ns1 and Ns2 with the host antiviral response with a focus on alterations to signaling pathways, cytokine gene expression, and effects of the Ns proteins on mitochondria.
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Affiliation(s)
| | - David Verhoeven
- Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
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15
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Nathan KG, Lal SK. The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication. Viruses 2020; 12:E436. [PMID: 32294919 PMCID: PMC7232403 DOI: 10.3390/v12040436] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023] Open
Abstract
The 14-3-3 proteins are a family of ubiquitous and exclusively eukaryotic proteins with an astoundingly significant number of binding partners. Their binding alters the activity, stability, localization, and phosphorylation state of a target protein. The association of 14-3-3 proteins with the regulation of a wide range of general and specific signaling pathways suggests their crucial role in health and disease. Recent studies have linked 14-3-3 to several RNA and DNA viruses that may contribute to the pathogenesis and progression of infections. Therefore, comprehensive knowledge of host-virus interactions is vital for understanding the viral life cycle and developing effective therapeutic strategies. Moreover, pharmaceutical research is already moving towards targeting host proteins in the control of virus pathogenesis. As such, targeting the right host protein to interrupt host-virus interactions could be an effective therapeutic strategy. In this review, we generated a 14-3-3 protein interactions roadmap in viruses, using the freely available Virusmentha network, an online virus-virus or virus-host interaction tool. Furthermore, we summarize the role of the 14-3-3 family in RNA and DNA viruses. The participation of 14-3-3 in viral infections underlines its significance as a key regulator for the expression of host and viral proteins.
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Affiliation(s)
- Kavitha Ganesan Nathan
- School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia;
| | - Sunil K. Lal
- School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia;
- Tropical Medicine & Biology Platform, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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16
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Hu M, Bogoyevitch MA, Jans DA. Impact of Respiratory Syncytial Virus Infection on Host Functions: Implications for Antiviral Strategies. Physiol Rev 2020; 100:1527-1594. [PMID: 32216549 DOI: 10.1152/physrev.00030.2019] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the leading causes of viral respiratory tract infection in infants, the elderly, and the immunocompromised worldwide, causing more deaths each year than influenza. Years of research into RSV since its discovery over 60 yr ago have elucidated detailed mechanisms of the host-pathogen interface. RSV infection elicits widespread transcriptomic and proteomic changes, which both mediate the host innate and adaptive immune responses to infection, and reflect RSV's ability to circumvent the host stress responses, including stress granule formation, endoplasmic reticulum stress, oxidative stress, and programmed cell death. The combination of these events can severely impact on human lungs, resulting in airway remodeling and pathophysiology. The RSV membrane envelope glycoproteins (fusion F and attachment G), matrix (M) and nonstructural (NS) 1 and 2 proteins play key roles in modulating host cell functions to promote the infectious cycle. This review presents a comprehensive overview of how RSV impacts the host response to infection and how detailed knowledge of the mechanisms thereof can inform the development of new approaches to develop RSV vaccines and therapeutics.
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Affiliation(s)
- MengJie Hu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Marie A Bogoyevitch
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - David A Jans
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia; and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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17
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Very-long-chain fatty acid metabolic capacity of 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12) promotes replication of hepatitis C virus and related flaviviruses. Sci Rep 2020; 10:4040. [PMID: 32132633 PMCID: PMC7055353 DOI: 10.1038/s41598-020-61051-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Flaviviridae infections represent a major global health burden. By deciphering mechanistic aspects of hepatitis C virus (HCV)-host interactions, one could discover common strategy for inhibiting the replication of related flaviviruses. By elucidating the HCV interactome, we identified the 17-beta-hydroxysteroid dehydrogenase type 12 (HSD17B12) as a human hub of the very-long-chain fatty acid (VLCFA) synthesis pathway and core interactor. Here we show that HSD17B12 knockdown (KD) impairs HCV replication and reduces virion production. Mechanistically, depletion of HSD17B12 induces alterations in VLCFA-containing lipid species and a drastic reduction of lipid droplets (LDs) that play a critical role in virus assembly. Oleic acid supplementation rescues viral RNA replication and production of infectious particles in HSD17B12 depleted cells, supporting a specific role of VLCFA in HCV life cycle. Furthermore, the small-molecule HSD17B12 inhibitor, INH-12, significantly reduces replication and infectious particle production of HCV as well as dengue virus and Zika virus revealing a conserved requirement across Flaviviridae virus family. Overall, the data provide a strong rationale for the advanced evaluation of HSD17B12 inhibition as a promising broad-spectrum antiviral strategy for the treatment of Flaviviridae infections.
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18
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Aljabr W, Armstrong S, Rickett NY, Pollakis G, Touzelet O, Cloutman-Green E, Matthews DA, Hiscox JA. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses 2019; 11:v11100926. [PMID: 31658630 PMCID: PMC6832471 DOI: 10.3390/v11100926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.
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Affiliation(s)
- Waleed Aljabr
- King Fahad Medical City, Research Center, 59046 Riyadh 11525, Saudi Arabia.
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Natasha Y Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
| | - Olivier Touzelet
- School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
| | | | - David A Matthews
- School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
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19
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Conci J, Alvarez-Paggi D, de Oliveira GAP, Pagani TD, Esperante SA, Borkosky SS, Aran M, Alonso LG, Mohana-Borges R, Prat-Gay GD. Conformational Isomerization Involving Conserved Proline Residues Modulates Oligomerization of the NS1 Interferon Response Inhibitor from the Syncytial Respiratory Virus. Biochemistry 2019; 58:2883-2892. [PMID: 31243994 DOI: 10.1021/acs.biochem.8b01288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Interferon response suppression by the respiratory syncytial virus relies on two unique nonstructural proteins, NS1 and NS2, that interact with cellular partners through high-order complexes. We hypothesized that two conserved proline residues, P81 and P67, participate in the conformational change leading to oligomerization. We found that the molecular dynamics of NS1 show a highly mobile C-terminal helix, which becomes rigid upon in silico replacement of P81. A soluble oligomerization pathway into regular spherical structures at low ionic strengths competes with an aggregation pathway at high ionic strengths with an increase in temperature. P81A requires higher temperatures to oligomerize and has a small positive effect on aggregation, while P67A is largely prone to aggregation. Chemical denaturation shows a first transition, involving a high fluorescence and ellipticity change corresponding to both a conformational change and substantial effects on the environment of its single tryptophan, that is strongly destabilized by P67A but stabilized by P81A. The subsequent global cooperative unfolding corresponding to the main β-sheet core is not affected by the proline mutations. Thus, a clear link exists between the effect of P81 and P67 on the stability of the first transition and oligomerization/aggregation. Interestingly, both P67 and P81 are located far away in space and sequence from the C-terminal helix, indicating a marked global structural dynamics. This provides a mechanism for modulating the oligomerization of NS1 by unfolding of a weak helix that exposes hydrophobic surfaces, linked to the participation of NS1 in multiprotein complexes.
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Affiliation(s)
- Julieta Conci
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Damian Alvarez-Paggi
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas , Universidade Federal do Rio de Janeiro , 21941-902 Rio de Janeiro , Brazil
| | - Talita D Pagani
- Instituto de Biofísica Carlos Chagas Filho , Universidade Federal do Rio de Janeiro , 21941-902 Rio de Janeiro , Brazil
| | - Sebastian A Esperante
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Silvina S Borkosky
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Martin Aran
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Leonardo G Alonso
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
| | - Ronaldo Mohana-Borges
- Instituto de Biofísica Carlos Chagas Filho , Universidade Federal do Rio de Janeiro , 21941-902 Rio de Janeiro , Brazil
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory , Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435 , 1405 Buenos Aires , Argentina
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20
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Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein. Viruses 2019; 11:v11040382. [PMID: 31022991 PMCID: PMC6521123 DOI: 10.3390/v11040382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The accessory protein ORF3 of porcine epidemic diarrhea virus (PEDV) has been proposed to play a key role in virus replication. However, our understanding of its function regarding virus and host interaction is still limited. In this study, we employed immunoprecipitation and mass spectrometry to screen for cellular interacting partners of ORF3. Gene ontology analysis of the host interactome highlighted the involvement of ORF3 in endosomal and immune signaling pathways. Among the identified ORF3-interacting proteins, the vacuolar protein-sorting-associated protein 36 (VPS36) was assessed for its role in PEDV replication. VPS36 was found to interact with ORF3 regardless of its GLUE domain. As a result of VPS36-ORF3 interaction, PEDV replication was substantially suppressed in cells overexpressing VPS36. Interestingly, the ORF3 protein expression was diminished in VPS36-overexpressing cells, an effect that could not be restored by treatment of lysosomal inhibitors. In addition, disruption of endogenously-expressed VPS36 by siRNA could partially augment PEDV replication. Taken together, our study provides mechanistic insights into the contribution of ORF3 in PEDV replication.
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21
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Andrew RJ, Fisher K, Heesom KJ, Kellett KAB, Hooper NM. Quantitative interaction proteomics reveals differences in the interactomes of amyloid precursor protein isoforms. J Neurochem 2019; 149:399-412. [PMID: 30664241 DOI: 10.1111/jnc.14666] [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: 02/28/2018] [Revised: 06/21/2018] [Accepted: 01/16/2019] [Indexed: 02/04/2023]
Abstract
The generation of the amyloid-β (Aβ) peptides from the amyloid precursor protein (APP) through sequential proteolysis by β- and γ-secretases is a key pathological event in the initiation and propagation of Alzheimer's disease. Aβ and the transcriptionally active APP intracellular domain are generated preferentially from the APP695 isoform compared to the longer APP751 isoform. As the Aβ and amyloid precursor protein intracellular domain produced from cleavage of APP695 and APP751 are identical we hypothesised that the two isoforms have differences within their interactomes which mediate the differential processing of the two isoforms. To investigate this, we applied a proteomics-based approach to identify differences in the interactomes of the APP695 and APP751 isoforms. Using stable isotope labelling of amino acids in cell culture and quantitative proteomics, we compared the interactomes of APP695 and APP751 expressed in human SH-SY5Y cells. Through this approach, we identified enrichment of proteins involved in mitochondrial function, the nuclear pore and nuclear transport specifically in the APP695 interactome. Further interrogation of the APP interactome and subsequent experimental validation (co-immunoprecipitation and siRNA knockdown) revealed GAP43 as a specific modulator of APP751 proteolysis, altering Aβ generation. Our data indicate that interrogation of the APP interactome can be exploited to identify proteins which influence APP proteolysis and Aβ production in an isoform dependent-manner. Cover Image for this issue: doi: 10.1111/jnc.14504.
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Affiliation(s)
- Robert J Andrew
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Kate Fisher
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Kate J Heesom
- Proteomics Facility, Faculty of Medical and Veterinary Sciences, University of Bristol, Bristol, UK
| | - Katherine A B Kellett
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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22
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Chaperoning the Mononegavirales: Current Knowledge and Future Directions. Viruses 2018; 10:v10120699. [PMID: 30544818 PMCID: PMC6315898 DOI: 10.3390/v10120699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
The order Mononegavirales harbors numerous viruses of significant relevance to human health, including both established and emerging infections. Currently, vaccines are only available for a small subset of these viruses, and antiviral therapies remain limited. Being obligate cellular parasites, viruses must utilize the cellular machinery for their replication and spread. Therefore, targeting cellular pathways used by viruses can provide novel therapeutic approaches. One of the key challenges confronted by both hosts and viruses alike is the successful folding and maturation of proteins. In cells, this task is faced by cellular molecular chaperones, a group of conserved and abundant proteins that oversee protein folding and help maintain protein homeostasis. In this review, we summarize the current knowledge of how the Mononegavirales interact with cellular chaperones, highlight key gaps in our knowledge, and discuss the potential of chaperone inhibitors as antivirals.
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23
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Abstract
Viruses utilize a number of host factors in order to carry out their replication cycles. Influenza A virus (IAV) and human respiratory syncytial virus (RSV) both infect the tissues of the respiratory tract, and as such we hypothesize that they might require similar host factors. Several published genome-wide screens have identified putative IAV host factors; however, there is significant discordance between their hits. In order to build on this work, we integrated a variety of "OMICS" data sources using two complementary network analyses, yielding 51 genes enriched for both IAV and RSV replication. We designed a targeted small interfering RNA (siRNA)-based assay to screen these genes against IAV under robust conditions and identified 13 genes supported by two IAV subtypes in both primary and transformed human lung cells. One of these hits, RNA binding motif 14 (RBM14), was validated as a required host factor and furthermore was shown to relocalize to the nucleolus upon IAV infection but not with other viruses. Additionally, the IAV NS1 protein is both necessary and sufficient for RBM14 relocalization, and relocalization also requires the double-stranded RNA (dsRNA) binding capacity of NS1. This work reports the discovery of a new host requirement for IAV replication and exposes a novel example of interplay between IAV NS1 and the host protein, RBM14.IMPORTANCE Influenza A virus (IAV) and respiratory syncytial virus (RSV) present major global disease burdens. There are high economic costs associated with morbidity as well as significant mortality rates, especially in developing countries, in children, and in the elderly. There are currently limited therapeutic options for these viruses, which underscores the need for novel research into virus biology that may lead to the discovery of new therapeutic approaches. This work extends existing research into host factors involved in virus replication and explores the interaction between IAV and one such host factor, RBM14. Further study to fully characterize this interaction may elucidate novel mechanisms used by the virus during its replication cycle and open new avenues for understanding virus biology.
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24
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Green C, Sande C, de Lara C, Thompson A, Silva-Reyes L, Napolitano F, Pierantoni A, Capone S, Vitelli A, Klenerman P, Pollard A. Humoral and cellular immunity to RSV in infants, children and adults. Vaccine 2018; 36:6183-6190. [DOI: 10.1016/j.vaccine.2018.08.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/08/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022]
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25
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Shahriari S, Wei KJ, Ghildyal R. Respiratory Syncytial Virus Matrix (M) Protein Interacts with Actin In Vitro and in Cell Culture. Viruses 2018; 10:v10100535. [PMID: 30274351 PMCID: PMC6213044 DOI: 10.3390/v10100535] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 01/26/2023] Open
Abstract
The virus–host protein interactions that underlie respiratory syncytial virus (RSV) assembly are still not completely defined, despite almost 60 years of research. RSV buds from the apical surface of infected cells, once virion components have been transported to the budding sites. Association of RSV matrix (M) protein with the actin cytoskeleton may play a role in facilitating this transport. We have investigated the interaction of M with actin in vitro and cell culture. Purified wildtype RSV M protein was found to bind directly to polymerized actin in vitro. Vero cells were transfected to express full-length M (1–256) as a green fluorescent protein-(GFP) tagged protein, followed by treatment with the microfilament destabilizer, cytochalasin D. Destabilization of the microfilament network resulted in mislocalization of full-length M, from mostly cytoplasmic to diffused across both cytoplasm and nucleus, suggesting that M interacts with microfilaments in this system. Importantly, treatment of RSV-infected cells with cytochalasin D results in lower infectious virus titers, as well as mislocalization of M to the nucleus. Finally, using deletion mutants of M in a transfected cell system, we show that both the N- and C-terminus of the protein are required for the interaction. Together, our data suggest a possible role for M–actin interaction in transporting virion components in the infected cell.
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Affiliation(s)
- Shadi Shahriari
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra ACT 2617, Australia.
| | - Ke-Jun Wei
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra ACT 2617, Australia.
| | - Reena Ghildyal
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra ACT 2617, Australia.
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26
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Abstract
Pathogen-host interactions (PHIs) underlie the process of infection. The systems biology view of the whole PHI system is superior to the investigation of the pathogen or host separately in understanding the infection mechanisms. Especially, the identification of host-oriented drug targets for the next-generation anti-infection therapeutics requires the properties of the host factors targeted by pathogens. Here, we provide an outline of computational analysis of PHI networks, focusing on the properties of the pathogen-targeted host proteins. We also provide information about the available PHI data and the related Web-based resources.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
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27
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Ribaudo M, Barik S. The nonstructural proteins of Pneumoviruses are remarkably distinct in substrate diversity and specificity. Virol J 2017; 14:215. [PMID: 29110727 PMCID: PMC5674761 DOI: 10.1186/s12985-017-0881-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
Background Interferon (IFN) inhibits viruses by inducing several hundred cellular genes, aptly named ‘interferon (IFN)-stimulated genes’ (ISGs). The only two RNA viruses of the Pneumovirus genus of the Paramyxoviridae family, namely Respiratory Syncytial Virus (RSV) and Pneumonia Virus of Mice (PVM), each encode two nonstructural (NS) proteins that share no sequence similarity but yet suppress IFN. Since suppression of IFN underlies the ability of these viruses to replicate in the host cells, the mechanism of such suppression has become an important area of research. This Short Report is an important extension of our previous efforts in defining this mechanism. Results We show that, like their PVM counterparts, the RSV NS proteins also target multiple members of the ISG family. While significantly extending the substrate repertoire of the RSV NS proteins, these results, unexpectedly, also reveal that the target preferences of the NS proteins of the two viruses are entirely different. This is surprising since the two Pneumoviruses are phylogenetically close with similar genome organization and gene function, and the NS proteins of both also serve as suppressors of host IFN response. Conclusion The finding that the NS proteins of the two highly similar viruses suppress entirely different members of the ISG family raises intriguing questions of pneumoviral NS evolution and mechanism of action.
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Affiliation(s)
- Michael Ribaudo
- Department of Biological, Geological and Environmental Sciences, and Center for Gene Regulation in Health and Disease, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
| | - Sailen Barik
- Department of Biological, Geological and Environmental Sciences, and Center for Gene Regulation in Health and Disease, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA. .,3780 Pelham Drive, Mobile, AL, 36619, USA.
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28
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Chatterjee S, Luthra P, Esaulova E, Agapov E, Yen BC, Borek DM, Edwards MR, Mittal A, Jordan DS, Ramanan P, Moore ML, Pappu RV, Holtzman MJ, Artyomov MN, Basler CF, Amarasinghe GK, Leung DW. Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses. Nat Microbiol 2017; 2:17101. [PMID: 28665409 DOI: 10.1038/nmicrobiol.2017.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Human respiratory syncytial virus (hRSV) is a major cause of morbidity and mortality in the paediatric, elderly and immune-compromised populations1,2. A gap in our understanding of hRSV disease pathology is the interplay between virally encoded immune antagonists and host components that limit hRSV replication. hRSV encodes for non-structural (NS) proteins that are important immune antagonists3-6; however, the role of these proteins in viral pathogenesis is incompletely understood. Here, we report the crystal structure of hRSV NS1 protein, which suggests that NS1 is a structural paralogue of hRSV matrix (M) protein. Comparative analysis of the shared structural fold with M revealed regions unique to NS1. Studies on NS1 wild type or mutant alone or in recombinant RSVs demonstrate that structural regions unique to NS1 contribute to modulation of host responses, including inhibition of type I interferon responses, suppression of dendritic cell maturation and promotion of inflammatory responses. Transcriptional profiles of A549 cells infected with recombinant RSVs show significant differences in multiple host pathways, suggesting that NS1 may have a greater role in regulating host responses than previously appreciated. These results provide a framework to target NS1 for therapeutic development to limit hRSV-associated morbidity and mortality.
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Affiliation(s)
- Srirupa Chatterjee
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.,Computer Technologies Department, ITMO University, Saint Petersburg 197101, Russia
| | - Eugene Agapov
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Benjamin C Yen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dominika M Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Texas 75390, USA
| | - Megan R Edwards
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - David S Jordan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Parameshwar Ramanan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Martin L Moore
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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29
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Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol 2017; 13:922. [PMID: 28348067 PMCID: PMC5371729 DOI: 10.15252/msb.20167062] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.
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Affiliation(s)
- Pierre M Jean Beltran
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
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30
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Rey-Jurado E, Kalergis AM. Immunological Features of Respiratory Syncytial Virus-Caused Pneumonia-Implications for Vaccine Design. Int J Mol Sci 2017; 18:E556. [PMID: 28273842 PMCID: PMC5372572 DOI: 10.3390/ijms18030556] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 01/05/2023] Open
Abstract
The human respiratory syncytial virus (hRSV) is the causative agent for high rates of hospitalizations due to viral bronchiolitis and pneumonia worldwide. Such a disease is characterized by an infection of epithelial cells of the distal airways that leads to inflammation and subsequently to respiratory failure. Upon infection, different pattern recognition receptors recognize the virus and trigger the innate immune response against the hRSV. Further, T cell immunity plays an important role for virus clearance. Based on animal studies, it is thought that the host immune response to hRSV is based on a biased T helper (Th)-2 and Th17 T cell responses with the recruitment of T cells, neutrophils and eosinophils to the lung, causing inflammation and tissue damage. In contrast, human immunity against RSV has been shown to be more complex with no definitive T cell polarization profile. Nowadays, only a humanized monoclonal antibody, known as palivizumab, is available to protect against hRSV infection in high-risk infants. However, such treatment involves several injections at a significantly high cost. For these reasons, intense research has been focused on finding novel vaccines or therapies to prevent hRSV infection in the population. Here, we comprehensively review the recent literature relative to the immunological features during hRSV infection, as well as the new insights into preventing the disease caused by this virus.
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Affiliation(s)
- Emma Rey-Jurado
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330644, Chile.
| | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330644, Chile.
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330644, Chile.
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31
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García-Dorival I, Wu W, Armstrong SD, Barr JN, Carroll MW, Hewson R, Hiscox JA. Elucidation of the Cellular Interactome of Ebola Virus Nucleoprotein and Identification of Therapeutic Targets. J Proteome Res 2016; 15:4290-4303. [PMID: 27786485 DOI: 10.1021/acs.jproteome.6b00337] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ebola virus (EBOV) infection results in severe disease and in some cases lethal hemorrhagic fever. The infection is directed by seven viral genes that encode nine viral proteins. By definition, viruses are obligate intracellular parasites and require aspects of host cell biology in order to replicate their genetic material, assemble new virus particles, and subvert host cell antiviral responses. Currently licensed antivirals are targeted against viral proteins to inhibit their function. However, experience with treating HIV and influenza virus demonstrates that resistant viruses are soon selected. An emerging area in virology is to transiently target host cell proteins that play critical proviral roles in virus biology, especially for acute infections. This has the advantage that the protein being targeted is evolutionary removed from the genome of the virus. Proteomics can aid in discovery biology and identify cellular proteins that may be utilized by the virus to facilitate infection. This work focused on defining the interactome of the EBOV nucleoprotein and identified that cellular chaperones, including HSP70, associate with this protein to promote stability. Utilization of a mini-genome replication system based on a recent Makona isolate demonstrated that disrupting the stability of NP had an adverse effect on viral RNA synthesis.
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Affiliation(s)
- Isabel García-Dorival
- Institute of Infection and Global Health, University of Liverpool , Liverpool L3 5RF, U.K.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections , Liverpool L69 3GL, U.K
| | - Weining Wu
- Institute of Infection and Global Health, University of Liverpool , Liverpool L3 5RF, U.K
| | - Stuart D Armstrong
- Institute of Infection and Global Health, University of Liverpool , Liverpool L3 5RF, U.K.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections , Liverpool L69 3GL, U.K
| | - John N Barr
- School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds , Leeds LS2 9JT, U.K
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections , Liverpool L69 3GL, U.K.,Public Health England , Porton Down, Salisbury SP4 0JG, U.K
| | - Roger Hewson
- Public Health England , Porton Down, Salisbury SP4 0JG, U.K
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool , Liverpool L3 5RF, U.K.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections , Liverpool L69 3GL, U.K
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32
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Shahriari S, Gordon J, Ghildyal R. Host cytoskeleton in respiratory syncytial virus assembly and budding. Virol J 2016; 13:161. [PMID: 27670781 PMCID: PMC5037899 DOI: 10.1186/s12985-016-0618-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/17/2016] [Indexed: 12/02/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the major pathogens responsible for lower respiratory tract infections (LRTI) in young children, the elderly, and the immunosuppressed. Currently, there are no antiviral drugs or vaccines available that effectively target RSV infections, proving a significant challenge in regards to prevention and treatment. An in-depth understanding of the host-virus interactions that underlie assembly and budding would inform new targets for antiviral development.Current research suggests that the polymerised form of actin, the filamentous or F-actin, plays a role in RSV assembly and budding. Treatment with cytochalasin D, which disrupts F-actin, has been shown to inhibit virus release. In addition, the actin cytoskeleton has been shown to interact with the RSV matrix (M) protein, which plays a central role in RSV assembly. For this reason, the interaction between these two components is hypothesised to facilitate the movement of viral components in the cytoplasm and to the budding site. Despite increases in our knowledge of RSV assembly and budding, M-actin interactions are not well understood. In this review, we discuss the current literature on the role of actin cytoskeleton during assembly and budding of RSV with the aim to integrate disparate studies to build a hypothetical model of the various molecular interactions between actin and RSV M protein that facilitate RSV assembly and budding.
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Affiliation(s)
- Shadi Shahriari
- Respiratory Virology Group, Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, 2617, Australia
| | - James Gordon
- Respiratory Virology Group, Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, 2617, Australia
| | - Reena Ghildyal
- Respiratory Virology Group, Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, 2617, Australia.
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33
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Bohmwald K, Espinoza JA, Rey-Jurado E, Gómez RS, González PA, Bueno SM, Riedel CA, Kalergis AM. Human Respiratory Syncytial Virus: Infection and Pathology. Semin Respir Crit Care Med 2016; 37:522-37. [PMID: 27486734 PMCID: PMC7171722 DOI: 10.1055/s-0036-1584799] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human respiratory syncytial virus (hRSV) is by far the major cause of acute lower respiratory tract infections (ALRTIs) worldwide in infants and children younger than 2 years. The overwhelming number of hospitalizations due to hRSV-induced ALRTI each year is due, at least in part, to the lack of licensed vaccines against this virus. Thus, hRSV infection is considered a major public health problem and economic burden in most countries. The lung pathology developed in hRSV-infected individuals is characterized by an exacerbated proinflammatory and unbalanced Th2-type immune response. In addition to the adverse effects in airway tissues, hRSV infection can also cause neurologic manifestations in the host, such as seizures and encephalopathy. Although the origins of these extrapulmonary symptoms remain unclear, studies with patients suffering from neurological alterations suggest an involvement of the inflammatory response against hRSV. Furthermore, hRSV has evolved numerous mechanisms to modulate and evade the immune response in the host. Several studies have focused on elucidating the interactions between hRSV virulence factors and the host immune system, to rationally design new vaccines and therapies against this virus. Here, we discuss about the infection, pathology, and immune response triggered by hRSV in the host.
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Affiliation(s)
- Karen Bohmwald
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Janyra A Espinoza
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Emma Rey-Jurado
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roberto S Gómez
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A González
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A Riedel
- Departamento de Ciencias Biológicas y Facultad de Medicina, Millennium Institute on Immunology and Immunotherapy, Universidad Andrés Bello, Santiago, Chile
| | - Alexis M Kalergis
- Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
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34
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Bakre A, Wu W, Hiscox J, Spann K, Teng MN, Tripp RA. Human respiratory syncytial virus non-structural protein NS1 modifies miR-24 expression via transforming growth factor-β. J Gen Virol 2016; 96:3179-3191. [PMID: 26253191 DOI: 10.1099/jgv.0.000261] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major health challenge in the young and elderly owing to the lack of a safe and effective vaccine and proven antiviral drugs. Understanding the mechanisms by which viral genes and proteins modulate the host response to infection is critical for identifying novel disease intervention strategies. In this study, the RSV non-structural protein NS1 was shown to suppress miR-24 expression during infection. Lack of NS1 was linked to increased expression of miR-24, whilst NS1 overexpression suppressed miR-24 expression. NS1 was found to induce Kruppel-like factor 6 (KLF6), a transcription factor that positively regulates the transforming growth factor (TGF)-b pathway to induce cell cycle arrest. Silencing of KLF6 led to increased miR-24 expression via downregulation of TGF-β. Treatment with exogenous TGF-β suppressed miR-24 expression and induced KLF6. Confocal microscopy showed co-localization of KLF6 and RSV NS1. These findings indicated that RSV NS1 interacts with KLF6 and modulates miR-24 expression and TGF-β, which facilitates RSV replication.
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Affiliation(s)
- Abhijeet Bakre
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Weining Wu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Julian Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Kirsten Spann
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Michael N Teng
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ralph A Tripp
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
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35
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Song T, Fang L, Wang D, Zhang R, Zeng S, An K, Chen H, Xiao S. Quantitative interactome reveals that porcine reproductive and respiratory syndrome virus nonstructural protein 2 forms a complex with viral nucleocapsid protein and cellular vimentin. J Proteomics 2016; 142:70-81. [PMID: 27180283 DOI: 10.1016/j.jprot.2016.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/17/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Porcine reproductive and respiratory syndrome virus (PRRSV) is an Arterivirus that has heavily impacted the global swine industry. The PRRSV nonstructural protein 2 (nsp2) plays crucial roles in viral replication and host immune regulation, most likely by interacting with viral or cellular proteins that have not yet been identified. In this study, a quantitative interactome approach based on immunoprecipitation and stable isotope labeling with amino acids in cell culture (SILAC) was performed to identify nsp2-interacting proteins in PRRSV-infected cells with an nsp2-specific monoclonal antibody. Nine viral proteins and 62 cellular proteins were identified as potential nsp2-interacting partners. Our data demonstrate that the PRRSV nsp1α, nsp1β, and nucleocapsid proteins all interact directly with nsp2. Nsp2-interacting cellular proteins were classified into different functional groups and an interactome network of nsp2 was generated. Interestingly, cellular vimentin, a known receptor for PRRSV, forms a complex with nsp2 by using viral nucleocapsid protein as an intermediate. Taken together, the nsp2 interactome under the condition of virus infection clarifies a role of nsp2 in PRRSV replication and immune evasion. BIOLOGICAL SIGNIFICANCE Viral proteins must interact with other virus-encoded proteins and/or host cellular proteins to function, and interactome analysis is an ideal approach for identifying such interacting proteins. In this study, we used the quantitative interactome methodology to identify the viral and cellular proteins that potentially interact with the nonstructural protein 2 (nsp2) of porcine reproductive and respiratory syndrome virus (PRRSV) under virus infection conditions, thus providing a rich source of potential viral and cellular interaction partners for PRRSV nsp2. Based on the interactome data, we further demonstrated that PRRSV nsp2 and nucleocapsid protein together with cellular vimentin, form a complex that may be essential for viral attachment and replication, which partly explains the role of nsp2 in PRRSV replication and immune evasion.
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Affiliation(s)
- Tao Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, PR China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Ruoxi Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Songlin Zeng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Kang An
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, PR China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, PR China.
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Lorente E, Barriga A, Barnea E, Mir C, Gebe JA, Admon A, López D. Structural and Nonstructural Viral Proteins Are Targets of T-Helper Immune Response against Human Respiratory Syncytial Virus. Mol Cell Proteomics 2016; 15:2141-51. [PMID: 27090790 DOI: 10.1074/mcp.m115.057356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 11/06/2022] Open
Abstract
Proper antiviral humoral and cellular immune responses require previous recognition of viral antigenic peptides that are bound to HLA class II molecules, which are exposed on the surface of antigen-presenting cells. The helper immune response is critical for the control and the clearance of human respiratory syncytial virus (HRSV) infection, a virus with severe health risk in infected pediatric, immunocompromised, and elderly populations. In this study, using a mass spectrometry analysis of complex HLA class II-bound peptide pools that were isolated from large amounts of HRSV-infected cells, 19 naturally processed HLA-DR ligands, most of them included in a complex nested set of peptides, were identified. Both the immunoprevalence and the immunodominance of the HLA class II response to HRSV were focused on one nonstructural (NS1) and two structural (matrix and mainly fusion) proteins of the infective virus. These findings have clear implications for analysis of the helper immune response as well as for antiviral vaccine design.
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Affiliation(s)
- Elena Lorente
- From the ‡Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain
| | - Alejandro Barriga
- From the ‡Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain
| | - Eilon Barnea
- §Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Carmen Mir
- From the ‡Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain
| | - John A Gebe
- ¶Benaroya Research Institute, Seattle, WA 98101, USA
| | - Arie Admon
- §Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Daniel López
- From the ‡Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain,
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Xiao Y, Wu W, Gao J, Smith N, Burkard C, Xia D, Zhang M, Wang C, Archibald A, Digard P, Zhou EM, Hiscox JA. Characterization of the Interactome of the Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 2 Reveals the Hyper Variable Region as a Binding Platform for Association with 14–3–3 Proteins. J Proteome Res 2016; 15:1388-401. [DOI: 10.1021/acs.jproteome.5b00396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Yihong Xiao
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, U.K
- Department
of Basic Veterinary Medicine, College of Animal Science and Veterinary
Medicine, Shandong Agricultural University, Tai’an 271018, P.R. China
| | - Weining Wu
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, U.K
| | - Jiming Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, P.R. China
| | - Nikki Smith
- The
Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, U.K
| | - Christine Burkard
- The
Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, U.K
| | - Dong Xia
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, U.K
| | - Minxia Zhang
- Department
of Basic Veterinary Medicine, College of Animal Science and Veterinary
Medicine, Shandong Agricultural University, Tai’an 271018, P.R. China
| | - Chengbao Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, P.R. China
| | - Alan Archibald
- The
Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, U.K
| | - Paul Digard
- The
Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, U.K
| | - En-min Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, P.R. China
| | - Julian A. Hiscox
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, U.K
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, P.R. China
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38
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Gomes DE, Caruso ÍP, Araujo GCD, Lourenço IOD, Melo FAD, Cornélio ML, Fossey MA, Souza FPD. Experimental evidence and molecular modeling of the interaction between hRSV-NS1 and quercetin. Int J Biol Macromol 2016; 85:40-7. [DOI: 10.1016/j.ijbiomac.2015.12.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 11/29/2015] [Accepted: 12/14/2015] [Indexed: 12/28/2022]
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Serrano JB, da Cruz E Silva OAB, Rebelo S. Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. MEMBRANES 2016; 6:membranes6010008. [PMID: 26784240 PMCID: PMC4812414 DOI: 10.3390/membranes6010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
Lamina-associated polypeptide 1 (LAP1) is a type II transmembrane protein of the inner nuclear membrane encoded by the human gene TOR1AIP1. LAP1 is involved in maintaining the nuclear envelope structure and appears be involved in the positioning of lamins and chromatin. To date, LAP1’s precise function has not been fully elucidated but analysis of its interacting proteins will permit unraveling putative associations to specific cellular pathways and cellular processes. By assessing public databases it was possible to identify the LAP1 interactome, and this was curated. In total, 41 interactions were identified. Several functionally relevant proteins, such as TRF2, TERF2IP, RIF1, ATM, MAD2L1 and MAD2L1BP were identified and these support the putative functions proposed for LAP1. Furthermore, by making use of the Ingenuity Pathways Analysis tool and submitting the LAP1 interactors, the top two canonical pathways were “Telomerase signalling” and “Telomere Extension by Telomerase” and the top functions “Cell Morphology”, “Cellular Assembly and Organization” and “DNA Replication, Recombination, and Repair”. Once again, putative LAP1 functions are reinforced but novel functions are emerging.
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Affiliation(s)
- Joana B Serrano
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Odete A B da Cruz E Silva
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sandra Rebelo
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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40
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Hover S, King B, Hall B, Loundras EA, Taqi H, Daly J, Dallas M, Peers C, Schnettler E, McKimmie C, Kohl A, Barr JN, Mankouri J. Modulation of Potassium Channels Inhibits Bunyavirus Infection. J Biol Chem 2015; 291:3411-22. [PMID: 26677217 PMCID: PMC4751384 DOI: 10.1074/jbc.m115.692673] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/06/2022] Open
Abstract
Bunyaviruses are considered to be emerging pathogens facilitated by the segmented nature of their genome that allows reassortment between different species to generate novel viruses with altered pathogenicity. Bunyaviruses are transmitted via a diverse range of arthropod vectors, as well as rodents, and have established a global disease range with massive importance in healthcare, animal welfare, and economics. There are no vaccines or anti-viral therapies available to treat human bunyavirus infections and so development of new anti-viral strategies is urgently required. Bunyamwera virus (BUNV; genus Orthobunyavirus) is the model bunyavirus, sharing aspects of its molecular and cellular biology with all Bunyaviridae family members. Here, we show for the first time that BUNV activates and requires cellular potassium (K(+)) channels to infect cells. Time of addition assays using K(+) channel modulating agents demonstrated that K(+) channel function is critical to events shortly after virus entry but prior to viral RNA synthesis/replication. A similar K(+) channel dependence was identified for other bunyaviruses namely Schmallenberg virus (Orthobunyavirus) as well as the more distantly related Hazara virus (Nairovirus). Using a rational pharmacological screening regimen, two-pore domain K(+) channels (K2P) were identified as the K(+) channel family mediating BUNV K(+) channel dependence. As several K2P channel modulators are currently in clinical use, our work suggests they may represent a new and safe drug class for the treatment of potentially lethal bunyavirus disease.
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Affiliation(s)
- Samantha Hover
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Barnabas King
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH
| | - Bradley Hall
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Eleni-Anna Loundras
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Hussah Taqi
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Janet Daly
- Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2RD
| | - Mark Dallas
- School of Pharmacy, University of Reading, Reading RG6 6AP, and
| | - Chris Peers
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - Clive McKimmie
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - John N Barr
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT,
| | - Jamel Mankouri
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT,
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41
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Colpitts CC, El-Saghire H, Pochet N, Schuster C, Baumert TF. High-throughput approaches to unravel hepatitis C virus-host interactions. Virus Res 2015; 218:18-24. [PMID: 26410623 DOI: 10.1016/j.virusres.2015.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/18/2015] [Accepted: 09/22/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) remains a major global health burden, with more than 130 million individuals chronically infected and at risk for the development of hepatocellular carcinoma (HCC). The recent clinical licensing of direct-acting antivirals enables viral cure. However, limited access to therapy and treatment failure in patient subgroups warrants a continuing effort to develop complementary antiviral strategies. Furthermore, once fibrosis is established, curing HCV infection does not eliminate the risk for HCC. High-throughput approaches and screens have enabled the investigation of virus-host interactions on a genome-wide scale. Gain- and loss-of-function screens have identified essential host-dependency factors in the HCV viral life cycle, such as host cell entry factors or regulatory factors for viral replication and assembly. Network analyses of systems-scale data sets provided a comprehensive view of the cellular state following HCV infection, thus improving our understanding of the virus-induced responses of the target cell. Interactome, metabolomics and gene expression studies identified dysregulated cellular processes potentially contributing to HCV pathogenesis and HCC. Drug screens using chemical libraries led to the discovery of novel antivirals. Here, we review the contribution of high-throughput approaches for the investigation of virus-host interactions, viral pathogenesis and drug discovery.
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Affiliation(s)
- Che C Colpitts
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Hussein El-Saghire
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Nathalie Pochet
- Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Catherine Schuster
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France; Université de Strasbourg, 67000 Strasbourg, France; Institut Hospitalo-Universitaire, PôleHépato-digestif, HôpitauxUniversitaires de Strasbourg, 67000 Strasbourg, France.
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42
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Pretel E, Sánchez IE, Fassolari M, Chemes LB, de Prat-Gay G. Conformational Heterogeneity Determined by Folding and Oligomer Assembly Routes of the Interferon Response Inhibitor NS1 Protein, Unique to Human Respiratory Syncytial Virus. Biochemistry 2015; 54:5136-46. [DOI: 10.1021/acs.biochem.5b00615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Esteban Pretel
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Ignacio E. Sánchez
- Protein
Physiology Laboratory, Departamento de Química Biológica,
Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marisol Fassolari
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B. Chemes
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
- Ciência
Sem Fronteiras Senior Fellow, CNPq, Laboratório de Genômica
Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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43
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Espinoza JA, Bohmwald K, Céspedes PF, Riedel CA, Bueno SM, Kalergis AM. Modulation of host adaptive immunity by hRSV proteins. Virulence 2015; 5:740-51. [PMID: 25513775 PMCID: PMC4189880 DOI: 10.4161/viru.32225] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Globally, the human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infections (LRTIs) in infants and children younger than 2 years old. Furthermore, the number of hospitalizations due to LRTIs has shown a sustained increase every year due to the lack of effective vaccines against hRSV. Thus, this virus remains as a major public health and economic burden worldwide. The lung pathology developed in hRSV-infected humans is characterized by an exacerbated inflammatory and Th2 immune response. In order to rationally design new vaccines and therapies against this virus, several studies have focused in elucidating the interactions between hRSV virulence factors and the host immune system. Here, we discuss the main features of hRSV biology, the processes involved in virus recognition by the immune system and the most relevant mechanisms used by this pathogen to avoid the antiviral host response.
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Affiliation(s)
- Janyra A Espinoza
- a Millenium Institute on Immunology and Immunotherapy; Departamento de Genética Molecular y Microbiología; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago, Chile
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44
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Durmuş S, Çakır T, Özgür A, Guthke R. A review on computational systems biology of pathogen-host interactions. Front Microbiol 2015; 6:235. [PMID: 25914674 PMCID: PMC4391036 DOI: 10.3389/fmicb.2015.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 12/27/2022] Open
Abstract
Pathogens manipulate the cellular mechanisms of host organisms via pathogen-host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein-protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.
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Affiliation(s)
- Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boǧaziçi University, IstanbulTurkey
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knoell-Institute, JenaGermany
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45
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Liu L, Lear Z, Hughes DJ, Wu W, Zhou EM, Whitehouse A, Chen H, Hiscox JA. Resolution of the cellular proteome of the nucleocapsid protein from a highly pathogenic isolate of porcine reproductive and respiratory syndrome virus identifies PARP-1 as a cellular target whose interaction is critical for virus biology. Vet Microbiol 2014; 176:109-19. [PMID: 25614100 PMCID: PMC4414928 DOI: 10.1016/j.vetmic.2014.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 11/24/2014] [Accepted: 11/26/2014] [Indexed: 02/01/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to the swine industry and food security worldwide. The nucleocapsid (N) protein is a major structural protein of PRRSV. The primary function of this protein is to encapsidate the viral RNA genome, and it is also thought to participate in the modulation of host cell biology and recruitment of cellular factors to facilitate virus infection. In order to the better understand these latter roles the cellular interactome of PRRSV N protein was defined using label free quantitative proteomics. This identified several cellular factors that could interact with the N protein including poly [ADP-ribose] polymerase 1 (PARP-1), a cellular protein, which can add adenosine diphosphate ribose to a protein. Use of the PARP-1 small molecule inhibitor, 3-AB, in PRRSV infected cells demonstrated that PARP-1 was required and acted as an enhancer factor for virus biology. Serial growth of PRRSV in different concentrations of 3-AB did not yield viruses that were able to grow with wild type kinetics, suggesting that by targeting a cellular protein crucial for virus biology, resistant phenotypes did not emerge. This study provides further evidence that cellular proteins, which are critical for virus biology, can also be targeted to ablate virus growth and provide a high barrier for the emergence of drug resistance.
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Affiliation(s)
- Long Liu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Zoe Lear
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Hughes
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Weining Wu
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - En-min Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Hongying Chen
- College of Life Sciences, Northwest A&F University, Yangling, China.
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; College of Veterinary Medicine, Northwest A&F University, Yangling, China; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
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46
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Munday DC, Howell G, Barr JN, Hiscox JA. Proteomic analysis of mitochondria in respiratory epithelial cells infected with human respiratory syncytial virus and functional implications for virus and cell biology. ACTA ACUST UNITED AC 2014; 67:300-18. [PMID: 25533920 DOI: 10.1111/jphp.12349] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/12/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this study was to quantitatively characterise the mitochondrial proteome of airway epithelial cells infected with human respiratory syncytial virus (HRSV), a major cause of paediatric illness. METHODS Quantitative proteomics, underpinned by stable isotope labelling with amino acids in cell culture, coupled to LC-MS/MS, was applied to mitochondrial fractions prepared from HRSV-infected and mock-infected cells 12 and 24 h post-infection. Datasets were analysed using ingenuity pathway analysis, and the results were validated and characterised using bioimaging, targeted inhibition and gene depletion. KEY FINDINGS The data quantitatively indicated that antiviral signalling proteins converged on mitochondria during HRSV infection. The mitochondrial receptor protein Tom70 was found to act in an antiviral manner, while its chaperone, Hsp90, was confirmed to be a positive viral factor. Proteins associated with different organelles were also co-enriched in the mitochondrial fractions from HRSV-infected cells, suggesting that alterations in organelle dynamics and membrane associations occur during virus infection. CONCLUSIONS Protein and pathway-specific alterations occur to the mitochondrial proteome in a spatial and temporal manner during HRSV infection, suggesting that this organelle may have altered functions. These could be targeted as part of potential therapeutic strategies to disrupt virus biology.
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Affiliation(s)
- Diane C Munday
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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47
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de Chassey B, Meyniel-Schicklin L, Vonderscher J, André P, Lotteau V. Virus-host interactomics: new insights and opportunities for antiviral drug discovery. Genome Med 2014; 6:115. [PMID: 25593595 PMCID: PMC4295275 DOI: 10.1186/s13073-014-0115-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The current therapeutic arsenal against viral infections remains limited, with often poor efficacy and incomplete coverage, and appears inadequate to face the emergence of drug resistance. Our understanding of viral biology and pathophysiology and our ability to develop a more effective antiviral arsenal would greatly benefit from a more comprehensive picture of the events that lead to viral replication and associated symptoms. Towards this goal, the construction of virus-host interactomes is instrumental, mainly relying on the assumption that a viral infection at the cellular level can be viewed as a number of perturbations introduced into the host protein network when viral proteins make new connections and disrupt existing ones. Here, we review advances in interactomic approaches for viral infections, focusing on high-throughput screening (HTS) technologies and on the generation of high-quality datasets. We show how these are already beginning to offer intriguing perspectives in terms of virus-host cell biology and the control of cellular functions, and we conclude by offering a summary of the current situation regarding the potential development of host-oriented antiviral therapeutics.
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Affiliation(s)
| | | | | | - Patrice André
- />Hospices Civils de Lyon, Lyon, France
- />CIRI, Université de Lyon, Lyon, 69365 France
- />Inserm, U1111, Lyon, 69365 France
| | - Vincent Lotteau
- />CIRI, Université de Lyon, Lyon, 69365 France
- />Inserm, U1111, Lyon, 69365 France
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48
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Interactome analysis of the human respiratory syncytial virus RNA polymerase complex identifies protein chaperones as important cofactors that promote L-protein stability and RNA synthesis. J Virol 2014; 89:917-30. [PMID: 25355874 DOI: 10.1128/jvi.01783-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED The human respiratory syncytial virus (HRSV) core viral RNA polymerase comprises the large polymerase protein (L) and its cofactor, the phosphoprotein (P), which associate with the viral ribonucleoprotein complex to replicate the genome and, together with the M2-1 protein, transcribe viral mRNAs. While cellular proteins have long been proposed to be involved in the synthesis of HRSV RNA by associating with the polymerase complex, their characterization has been hindered by the difficulty of purifying the viral polymerase from mammalian cell culture. In this study, enhanced green fluorescent protein (EGFP)-tagged L- and P-protein expression was coupled with high-affinity anti-GFP antibody-based immunoprecipitation and quantitative proteomics to identify cellular proteins that interacted with either the L- or the P-proteins when expressed as part of a biologically active viral RNP. Several core groups of cellular proteins were identified that interacted with each viral protein including, in both cases, protein chaperones. Ablation of chaperone activity by using small-molecule inhibitors confirmed previously reported studies which suggested that this class of proteins acted as positive viral factors. Inhibition of HSP90 chaperone function in the current study showed that HSP90 is critical for L-protein function and stability, whether in the presence or absence of the P-protein. Inhibition studies suggested that HSP70 also disrupts virus biology and might help the polymerase remodel the nucleocapsid to allow RNA synthesis to occur efficiently. This indicated a proviral role for protein chaperones in HRSV replication and demonstrates that the function of cellular proteins can be targeted as potential therapeutics to disrupt virus replication. IMPORTANCE Human respiratory syncytial virus (HRSV) represents a major health care and economic burden, being the main cause of severe respiratory infections in infants worldwide. No vaccine or effective therapy is available. This study focused on identifying those cellular proteins that potentially interact specifically with the viral proteins that are central to virus replication and transcription, with a view to providing potential targets for the development of a specific, transient therapeutic which disrupts virus biology but prevents the emergence of resistance, while maintaining cell viability. In particular, protein chaperones (heat shock proteins 70 and 90), which aid protein folding and function, were identified. The mechanism by which these chaperones contribute to virus biology was tested, and this study demonstrates to the field that cellular protein chaperones may be required for maintaining the correct folding and therefore functionality of specific proteins within the virus replication complex.
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García-Dorival I, Wu W, Dowall S, Armstrong S, Touzelet O, Wastling J, Barr JN, Matthews D, Carroll M, Hewson R, Hiscox JA. Elucidation of the Ebola Virus VP24 Cellular Interactome and Disruption of Virus Biology through Targeted Inhibition of Host-Cell Protein Function. J Proteome Res 2014; 13:5120-35. [DOI: 10.1021/pr500556d] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Isabel García-Dorival
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Weining Wu
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Stuart Dowall
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Stuart Armstrong
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Olivier Touzelet
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Jonathan Wastling
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - John N. Barr
- School
of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David Matthews
- School
of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Miles Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Julian A. Hiscox
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
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Carpp LN, Rogers RS, Moritz RL, Aitchison JD. Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection. Mol Cell Proteomics 2014; 13:2836-54. [PMID: 24855065 DOI: 10.1074/mcp.m114.038984] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Dengue virus is considered to be the most important mosquito-borne virus worldwide and poses formidable economic and health care burdens on many tropical and subtropical countries. Dengue infection induces drastic rearrangement of host endoplasmic reticulum membranes into complex membranous structures housing replication complexes; the contribution(s) of host proteins and pathways to this process is poorly understood but is likely to be mediated by protein-protein interactions. We have developed an approach for obtaining high confidence protein-protein interaction data by employing affinity tags and quantitative proteomics, in the context of viral infection, followed by robust statistical analysis. Using this approach, we identified high confidence interactors of NS5, the viral polymerase, and NS3, the helicase/protease. Quantitative proteomics allowed us to exclude a large number of presumably nonspecific interactors from our data sets and imparted a high level of confidence to our resulting data sets. We identified 53 host proteins reproducibly associated with NS5 and 41 with NS3, with 13 of these candidates present in both data sets. The host factors identified have diverse functions, including retrograde Golgi-to-endoplasmic reticulum transport, biosynthesis of long-chain fatty-acyl-coenzyme As, and in the unfolded protein response. We selected GBF1, a guanine nucleotide exchange factor responsible for ARF activation, from the NS5 data set for follow up and functional validation. We show that GBF1 plays a critical role early in dengue infection that is independent of its role in the maintenance of Golgi structure. Importantly, the approach described here can be applied to virtually any organism/system as a tool for better understanding its molecular interactions.
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Affiliation(s)
- Lindsay N Carpp
- From the ‡Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109
| | - Richard S Rogers
- ‖Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109
| | - Robert L Moritz
- §Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington 98109
| | - John D Aitchison
- From the ‡Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109; §Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington 98109, ‖Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109.
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