1
|
Tong Jia Ming S, Tan Yi Jun K, Carissimo G. Pathogenicity and virulence of O'nyong-nyong virus: A less studied Togaviridae with pandemic potential. Virulence 2024; 15:2355201. [PMID: 38797948 PMCID: PMC11135837 DOI: 10.1080/21505594.2024.2355201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
O'nyong-nyong virus (ONNV) is a neglected mosquito-borne alphavirus belonging to the Togaviridae family. ONNV is known to be responsible for sporadic outbreaks of acute febrile disease and polyarthralgia in Africa. As climate change increases the geographical range of known and potential new vectors, recent data indicate a possibility for ONNV to spread outside of the African continent and grow into a greater public health concern. In this review, we summarise the current knowledge on ONNV epidemiology, host-pathogen interactions, vector-virus responses, and insights into possible avenues to control risk of further epidemics. In this review, the limited ONNV literature is compared and correlated to other findings on mainly Old World alphaviruses. We highlight and discuss studies that investigate viral and host factors that determine viral-vector specificity, along with important mechanisms that determine severity and disease outcome of ONNV infection.
Collapse
Affiliation(s)
- Samuel Tong Jia Ming
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Katrina Tan Yi Jun
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technical University, Singapore, Singapore
| |
Collapse
|
2
|
Omler A, Mutso M, Vaher M, Freitas JR, Taylor A, David CT, Moseley GW, Liu X, Merits A, Mahalingam S. Exploring Barmah Forest virus pathogenesis: molecular tools to investigate non-structural protein 3 nuclear localization and viral genomic determinants of replication. mBio 2024; 15:e0099324. [PMID: 38953633 PMCID: PMC11323547 DOI: 10.1128/mbio.00993-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/03/2024] [Indexed: 07/04/2024] Open
Abstract
Barmah Forest virus (BFV) is a mosquito-borne virus that causes arthralgia with accompanying rash, fever, and myalgia in humans. The virus is mainly found in Australia and has caused outbreaks associated with significant health concerns. As the sole representative of the Barmah Forest complex within the genus Alphavirus, BFV is not closely related genetically to other alphaviruses. Notably, basic knowledge of BFV molecular virology has not been well studied due to a lack of critical investigative tools such as an infectious clone. Here we describe the construction of an infectious BFV cDNA clone based on Genbank sequence and demonstrate that the clone-derived virus has in vitro and in vivo properties similar to naturally occurring virus, BFV field isolate 2193 (BFV2193-FI). A substitution in nsP4, V1911D, which was identified in the Genbank reference sequence, was found to inhibit virus rescue and replication. T1325P substitution in nsP2 selected during virus passaging was shown to be an adaptive mutation, compensating for the inhibitory effect of nsP4-V1911D. The two mutations were associated with changes in viral non-structural polyprotein processing and type I interferon (IFN) induction. Interestingly, a nuclear localization signal, active in mammalian but not mosquito cells, was identified in nsP3. A point mutation abolishing nsP3 nuclear localization attenuated BFV replication. This effect was more prominent in the presence of type I interferon signaling, suggesting nsP3 nuclear localization might be associated with IFN antagonism. Furthermore, abolishing nsP3 nuclear localization reduced virus replication in mice but did not significantly affect disease.IMPORTANCEBarmah Forest virus (BFV) is Australia's second most prevalent arbovirus, with approximately 1,000 cases reported annually. The clinical symptoms of BFV infection include rash, polyarthritis, arthralgia, and myalgia. As BFV is not closely related to other pathogenic alphaviruses or well-studied model viruses, our understanding of its molecular virology and mechanisms of pathogenesis is limited. There is also a lack of molecular tools essential for corresponding studies. Here we describe the construction of an infectious clone of BFV, variants harboring point mutations, and sequences encoding marker protein. In infected mammalian cells, nsP3 of BFV was located in the nuclei. This finding extends our understanding of the diverse mechanisms used by alphavirus replicase proteins to interact with host cells. Our novel observations highlight the complex synergy through which the viral replication machinery evolves to correct mutation errors within the viral genome.
Collapse
Affiliation(s)
- Ailar Omler
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Institute of Bioengineering, University of Tartu, Tartu, Estonia
| | - Margit Mutso
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mihkel Vaher
- The Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Joseph R. Freitas
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Global Virus Network (GVN) Centre for Excellence in Arboviruses, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Adam Taylor
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Global Virus Network (GVN) Centre for Excellence in Arboviruses, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Cassandra T. David
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Gregory W. Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Xiang Liu
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Global Virus Network (GVN) Centre for Excellence in Arboviruses, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Andres Merits
- Institute of Bioengineering, University of Tartu, Tartu, Estonia
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Global Virus Network (GVN) Centre for Excellence in Arboviruses, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| |
Collapse
|
3
|
Shahini E, Argentiero A, Andriano A, Losito F, Maida M, Facciorusso A, Cozzolongo R, Villa E. Hepatitis E Virus: What More Do We Need to Know? MEDICINA (KAUNAS, LITHUANIA) 2024; 60:998. [PMID: 38929615 PMCID: PMC11205503 DOI: 10.3390/medicina60060998] [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: 05/10/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Hepatitis E virus (HEV) infection is typically a self-limiting, acute illness that spreads through the gastrointestinal tract but replicates in the liver. However, chronic infections are possible in immunocompromised individuals. The HEV virion has two shapes: exosome-like membrane-associated quasi-enveloped virions (eHEV) found in circulating blood or in the supernatant of infected cell cultures and non-enveloped virions ("naked") found in infected hosts' feces and bile to mediate inter-host transmission. Although HEV is mainly spread via enteric routes, it is unclear how it penetrates the gut wall to reach the portal bloodstream. Both virion types are infectious, but they infect cells in different ways. To develop personalized treatment/prevention strategies and reduce HEV impact on public health, it is necessary to decipher the entry mechanism for both virion types using robust cell culture and animal models. The contemporary knowledge of the cell entry mechanism for these two HEV virions as possible therapeutic target candidates is summarized in this narrative review.
Collapse
Affiliation(s)
- Endrit Shahini
- Gastroenterology Unit, National Institute of Gastroenterology-IRCCS “Saverio de Bellis”, Castellana Grotte, 70013 Bari, Italy; (F.L.); (R.C.)
| | | | - Alessandro Andriano
- Department of Precision and Regenerative Medicine and Ionian Area, University of Bari Aldo Moro Medical School, 70124 Bari, Italy;
| | - Francesco Losito
- Gastroenterology Unit, National Institute of Gastroenterology-IRCCS “Saverio de Bellis”, Castellana Grotte, 70013 Bari, Italy; (F.L.); (R.C.)
| | - Marcello Maida
- Gastroenterology and Endoscopy Unit, S. Elia-Raimondi Hospital, 93100 Caltanissetta, Italy;
| | - Antonio Facciorusso
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy;
| | - Raffaele Cozzolongo
- Gastroenterology Unit, National Institute of Gastroenterology-IRCCS “Saverio de Bellis”, Castellana Grotte, 70013 Bari, Italy; (F.L.); (R.C.)
| | - Erica Villa
- Gastroenterology Unit, CHIMOMO Department, University of Modena & Reggio Emilia, Via del Pozzo 71, 41121 Modena, Italy
| |
Collapse
|
4
|
Zeng Q, Jiang T. The role of FHL1 in tumors. Gene 2024; 911:148347. [PMID: 38458365 DOI: 10.1016/j.gene.2024.148347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Affiliation(s)
- Qun Zeng
- Department of Biochemistry and Molecular Biology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Tingting Jiang
- Department of Clinical Laboratory, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| |
Collapse
|
5
|
Wang N, Merits A, Veit M, Lello LS, Kong S, Jiao H, Chen J, Wang Y, Dobrikov G, Rey FA, Su S. LDL receptor in alphavirus entry: structural analysis and implications for antiviral therapy. Nat Commun 2024; 15:4906. [PMID: 38851803 PMCID: PMC11162471 DOI: 10.1038/s41467-024-49301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
Various low-density lipoprotein receptors (LPRs) have been identified as entry factors for alphaviruses, and structures of the corresponding virion-receptor complexes have been determined. Here, we analyze the similarities and differences in the receptor binding modes of multiple alphaviruses to understand their ability to infect a wide range of hosts. We further discuss the challenges associated with the development of broad-spectrum treatment strategies against a diverse range of alphaviruses.
Collapse
Affiliation(s)
- Ningning Wang
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Andres Merits
- Institute of Bioengineering, University of Tartu, Nooruse Street 1, Tartu, Estonia
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany
| | - Laura Sandra Lello
- Institute of Bioengineering, University of Tartu, Nooruse Street 1, Tartu, Estonia
| | - Shuhan Kong
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Houqi Jiao
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Jie Chen
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yu Wang
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Georgi Dobrikov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Bl. 9, Sofia, Bulgaria
| | - Félix A Rey
- Institut Pasteur, Unité de Virologie Structurale, Department Virologie, CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| | - Shuo Su
- Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China.
| |
Collapse
|
6
|
Xie Y, Cao J, Gan S, Xu L, Zhang D, Qian S, Xu F, Ding Q, Schoggins JW, Fan W. TRIM32 inhibits Venezuelan Equine Encephalitis Virus Infection by targeting a late step in viral entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597282. [PMID: 38895352 PMCID: PMC11185716 DOI: 10.1101/2024.06.04.597282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alphaviruses are mosquito borne RNA viruses that are a reemerging public health threat. Alphaviruses have a broad host range, and can cause diverse disease outcomes like arthritis, and encephalitis. The host ubiquitin proteasome system (UPS) plays critical roles in regulating cellular processes to control the infections with various viruses, including alphaviruses. Previous studies suggest alphaviruses hijack UPS for virus infection, but the molecular mechanisms remain poorly characterized. In addition, whether certain E3 ubiquitin ligases or deubiquitinases act as alphavirus restriction factors remains poorly understood. Here, we employed a cDNA expression screen to identify E3 ubiquitin ligase TRIM32 as a novel intrinsic restriction factor against alphavirus infection, including VEEV-TC83, SINV, and ONNV. Ectopic expression of TRIM32 reduces alphavirus infection, whereas depletion of TRIM32 with CRISPR-Cas9 increases infection. We demonstrate that TRIM32 inhibits alphaviruses through a mechanism that is independent of the TRIM32-STING-IFN axis. Combining reverse genetics and biochemical assays, we found that TRIM32 interferes with genome translation after membrane fusion, prior to replication of the incoming viral genome. Furthermore, our data indicate that the monoubiquitination of TRIM32 is important for its antiviral activity. Notably, we also show two TRIM32 pathogenic mutants R394H and D487N, related to Limb-girdle muscular dystrophy (LGMD), have a loss of antiviral activity against VEEV-TC83. Collectively, these results reveal that TRIM32 acts as a novel intrinsic restriction factor suppressing alphavirus infection and provides insights into the interaction between alphaviruses and the host UPS.
Collapse
Affiliation(s)
- Yifan Xie
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jie Cao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shuyi Gan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lingdong Xu
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Dongjie Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Suhong Qian
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, China
| | - Qiang Ding
- School of Medical Sciences, Tsinghua University, Beijing, China
| | - John W. Schoggins
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenchun Fan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| |
Collapse
|
7
|
de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fiuza TS, Viana VAF, Melo MEL, Ferraz CPM, Silva DB, Duarte LMF, Barbosa PP, Amorim MR, Judice CC, Toledo-Teixeira DA, Ramundo MS, Aguilar PV, Araújo ELL, Costa FTM, Cerqueira-Silva T, Khouri R, Boaventura VS, Figueiredo LTM, Fang R, Moreno B, López-Vergès S, Mello LP, Skaf MS, Catharino RR, Granja F, Martins-de-Souza D, Plante JA, Plante KS, Sabino EC, Diamond MS, Eugenin E, Proença-Módena JL, Faria NR, Weaver SC. Pathophysiology of chikungunya virus infection associated with fatal outcomes. Cell Host Microbe 2024; 32:606-622.e8. [PMID: 38479396 PMCID: PMC11018361 DOI: 10.1016/j.chom.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
Collapse
Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA.
| | - Marcilio J Fumagalli
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Deyse C M Carvalho
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Laboratory of Immunobiotechnology, Biotechnology Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Cristian Hernandez
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Victor C Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Yamilka Díaz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Rodrigo B Kato
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Clauber H S Costa
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Tayna S Fiuza
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Programa de Pós Graduação em Bioinformática, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Vânia A F Viana
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | | | - Débora B Silva
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Emerson L L Araújo
- Coordenação Geral de Atenção às Doenças Transmissíveis na Atenção Primária, Departamento de Gestão ao cuidado Integral, Secretaria de Atenção Primária à Saúde, Ministério da Saúde, Brasília, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thiago Cerqueira-Silva
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Viviane S Boaventura
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil; Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Serviço de Otorrinolaringologia, Salvador, Bahia, Brazil
| | - Luiz Tadeu M Figueiredo
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rong Fang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama; Sistema Nacional de Investigación from SENACYT, Panama, Panama
| | | | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Roraima, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; D'Or Institute for Research and Education, São Paulo, São Paulo, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, São Paulo, Brazil
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| |
Collapse
|
8
|
Jaquet M, Bengue M, Lambert K, Carnac G, Missé D, Bisbal C. Human muscle cells sensitivity to chikungunya virus infection relies on their glycolysis activity and differentiation stage. Biochimie 2024; 218:85-95. [PMID: 37716499 DOI: 10.1016/j.biochi.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/22/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023]
Abstract
Changes to our environment have led to the emergence of human pathogens such as chikungunya virus. Chikungunya virus infection is today a major public health concern. It is a debilitating chronic disease impeding patients' mobility, affecting millions of people. Disease development relies on skeletal muscle infection. The importance of skeletal muscle in chikungunya virus infection led to the hypothesis that it could serve as a viral reservoir and could participate to virus persistence. Here we questioned the interconnection between skeletal muscle cells metabolism, their differentiation stage and the infectivity of the chikungunya virus. We infected human skeletal muscle stem cells at different stages of differentiation with chikungunya virus to study the impact of their metabolism on virus production and inversely the impact of virus on cell metabolism. We observed that chikungunya virus infectivity is cell differentiation and metabolism-dependent. Chikungunya virus interferes with the cellular metabolism in quiescent undifferentiated and proliferative muscle cells. Moreover, activation of chikungunya infected quiescent muscle stem cells, induces their proliferation, increases glycolysis and amplifies virus production. Therefore, our results showed that Chikungunya virus infectivity and the antiviral response of skeletal muscle cells relies on their energetic metabolism and their differentiation stage. Then, muscle stem cells could serve as viral reservoir producing virus after their activation.
Collapse
Affiliation(s)
- M Jaquet
- PhyMedExp, Univ. Montpellier, INSERM U1046, CNRS UMR 9214, 34295, Montpellier Cedex 5, France; MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394, Montpellier, France
| | - M Bengue
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394, Montpellier, France
| | - K Lambert
- PhyMedExp, Univ. Montpellier, INSERM U1046, CNRS UMR 9214, 34295, Montpellier Cedex 5, France
| | - G Carnac
- PhyMedExp, Univ. Montpellier, INSERM U1046, CNRS UMR 9214, 34295, Montpellier Cedex 5, France
| | - D Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394, Montpellier, France.
| | - C Bisbal
- PhyMedExp, Univ. Montpellier, INSERM U1046, CNRS UMR 9214, 34295, Montpellier Cedex 5, France.
| |
Collapse
|
9
|
Tapescu I, Taschuk F, Pokharel SM, Zginnyk O, Ferretti M, Bailer PF, Whig K, Madden EA, Heise MT, Schultz DC, Cherry S. The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection. Mol Cell 2023; 83:4174-4189.e7. [PMID: 37949067 PMCID: PMC10722560 DOI: 10.1016/j.molcel.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Alphaviruses are a large group of re-emerging arthropod-borne RNA viruses. The compact viral RNA genomes harbor diverse structures that facilitate replication. These structures can be recognized by antiviral cellular RNA-binding proteins, including DExD-box (DDX) helicases, that bind viral RNAs to control infection. The full spectrum of antiviral DDXs and the structures that are recognized remain unclear. Genetic screening identified DDX39A as antiviral against the alphavirus chikungunya virus (CHIKV) and other medically relevant alphaviruses. Upon infection, the predominantly nuclear DDX39A accumulates in the cytoplasm inhibiting alphavirus replication, independent of the canonical interferon pathway. Biochemically, DDX39A binds to CHIKV genomic RNA, interacting with the 5' conserved sequence element (5'CSE), which is essential for the antiviral activity of DDX39A. Altogether, DDX39A relocalization and binding to a conserved structural element in the alphavirus genomic RNA attenuates infection, revealing a previously unknown layer to the cellular control of infection.
Collapse
Affiliation(s)
- Iulia Tapescu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Frances Taschuk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Swechha M Pokharel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oleksandr Zginnyk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter F Bailer
- Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanupryia Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
10
|
Ng WH, Liu X, Ling ZL, Santos CNO, Magalhães LS, Kueh AJ, Herold MJ, Taylor A, Freitas JR, Koit S, Wang S, Lloyd AR, Teixeira MM, Merits A, Almeida RP, King NJC, Mahalingam S. FHL1 promotes chikungunya and o'nyong-nyong virus infection and pathogenesis with implications for alphavirus vaccine design. Nat Commun 2023; 14:6605. [PMID: 37884534 PMCID: PMC10603155 DOI: 10.1038/s41467-023-42330-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Arthritogenic alphaviruses are positive-strand RNA viruses that cause debilitating musculoskeletal diseases affecting millions worldwide. A recent discovery identified the four-and-a-half-LIM domain protein 1 splice variant A (FHL1A) as a crucial host factor interacting with the hypervariable domain (HVD) of chikungunya virus (CHIKV) nonstructural protein 3 (nsP3). Here, we show that acute and chronic chikungunya disease in humans correlates with elevated levels of FHL1. We generated FHL1-/- mice, which when infected with CHIKV or o'nyong-nyong virus (ONNV) displayed reduced arthritis and myositis, fewer immune infiltrates, and reduced proinflammatory cytokine/chemokine outputs, compared to infected wild-type (WT) mice. Interestingly, disease signs were comparable in FHL1-/- and WT mice infected with arthritogenic alphaviruses Ross River virus (RRV) or Mayaro virus (MAYV). This aligns with pull-down assay data, which showed the ability of CHIKV and ONNV nsP3 to interact with FHL1, while RRV and MAYV nsP3s did not. We engineered a CHIKV mutant unable to bind FHL1 (CHIKV-ΔFHL1), which was avirulent in vivo. Following inoculation with CHIKV-ΔFHL1, mice were protected from disease upon challenge with CHIKV and ONNV, and viraemia was significantly reduced in RRV- and MAYV-challenged mice. Targeting FHL1-binding as an approach to vaccine design could lead to breakthroughs in mitigating alphaviral disease.
Collapse
Affiliation(s)
- Wern Hann Ng
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Xiang Liu
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Zheng L Ling
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Camilla N O Santos
- Division of Immunology and Molecular Biology Laboratory, University Hospital/EBSERH, Federal University of Sergipe (UFS), Aracaju, Brazil
| | - Lucas S Magalhães
- Division of Immunology and Molecular Biology Laboratory, University Hospital/EBSERH, Federal University of Sergipe (UFS), Aracaju, Brazil
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3050, Australia
| | - Adam Taylor
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Joseph R Freitas
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Sandra Koit
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Andrew R Lloyd
- Viral Immunology Systems Program, Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Mauro M Teixeira
- Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Roque P Almeida
- Division of Immunology and Molecular Biology Laboratory, University Hospital/EBSERH, Federal University of Sergipe (UFS), Aracaju, Brazil
| | - Nicholas J C King
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
- Global Virus Network (GVN) Centre of Excellence in Arboviruses, Griffith University, Gold Coast, QLD, Australia.
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia.
| |
Collapse
|
11
|
Paiva IM, Damasceno S, Cunha TM. CRISPR Libraries and Whole-Genome Screening to Identify Essential Factors for Viral Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:157-172. [PMID: 37486521 DOI: 10.1007/978-3-031-33325-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The CRISPR-Cas9 system has revolutionized genetics and offers a simple and inexpensive way of generating perturbation that results in gene repression, activation, or editing. The advances in this technique make possible the development of CRISPR libraries which consist of a set of sgRNAs to cause perturbations in several genes in the same cell population. The use of libraries raised the CRISPR-Cas9 technique to a genomic scale and provides a powerful approach for identifying previously unknown molecular mechanisms and pathways involved in a specific phenotype or biological process. More specifically, the CRISPRko libraries (set of sgRNAs for gene knockout) and their high-throughput screenings are widely used in research with viral agents, and it was enlarged even more with the COVID-19 pandemic. With this chapter, we aim to point out how this tool helps in understanding virus-host relationships, such as the mechanisms of virus entry into the cell, the essential factors for its replication, and the cellular pathways involved in the response against the pathogen. The chapter also provided some practical considerations for each step of an experimentation using these tools that include choosing the library and screening type, the target cell, the viral strain, the library amplification and guaranteeing its coverage, the strategies for the gene screening pipeline by bioinformatics, and finally, target validation. To conclude, it was presented a table reviewing the last updates in the research for antiviral therapies using CRISPR libraries.
Collapse
Affiliation(s)
- Isadora Marques Paiva
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Thiago Mattar Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil.
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
12
|
Basavappa MG, Ferretti M, Dittmar M, Stoute J, Sullivan MC, Whig K, Shen H, Liu KF, Schultz DC, Beiting DP, Lynch KW, Henao-Mejia J, Cherry S. The lncRNA ALPHA specifically targets chikungunya virus to control infection. Mol Cell 2022; 82:3729-3744.e10. [PMID: 36167073 PMCID: PMC10464526 DOI: 10.1016/j.molcel.2022.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/06/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022]
Abstract
Arthropod-borne viruses, including the alphavirus chikungunya virus (CHIKV), cause acute disease in millions of people and utilize potent mechanisms to antagonize and circumvent innate immune pathways including the type I interferon (IFN) pathway. In response, hosts have evolved antiviral counterdefense strategies that remain incompletely understood. Recent studies have found that long noncoding RNAs (lncRNAs) regulate classical innate immune pathways; how lncRNAs contribute to additional antiviral counterdefenses remains unclear. Using high-throughput genetic screening, we identified a cytoplasmic antiviral lncRNA that we named antiviral lncRNA prohibiting human alphaviruses (ALPHA), which is transcriptionally induced by alphaviruses and functions independently of IFN to inhibit the replication of CHIKV and its closest relative, O'nyong'nyong virus (ONNV), but not other viruses. Furthermore, we showed that ALPHA interacts with CHIKV genomic RNA and restrains viral RNA replication. Together, our findings reveal that ALPHA and potentially other lncRNAs can mediate non-canonical antiviral immune responses against specific viruses.
Collapse
Affiliation(s)
- Megha G Basavappa
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julian Stoute
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kanupriya Whig
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Shen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C Schultz
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Pennsylvania, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
13
|
Bonaventure B, Rebendenne A, Chaves Valadão AL, Arnaud‐Arnould M, Gracias S, Garcia de Gracia F, McKellar J, Labaronne E, Tauziet M, Vivet‐Boudou V, Bernard E, Briant L, Gros N, Djilli W, Courgnaud V, Parrinello H, Rialle S, Blaise M, Lacroix L, Lavigne M, Paillart J, Ricci EP, Schulz R, Jouvenet N, Moncorgé O, Goujon C. The
DEAD
box
RNA
helicase
DDX42
is an intrinsic inhibitor of positive‐strand
RNA
viruses. EMBO Rep 2022; 23:e54061. [PMID: 36161446 PMCID: PMC9638865 DOI: 10.15252/embr.202154061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Genome‐wide screens are powerful approaches to unravel regulators of viral infections. Here, a CRISPR screen identifies the RNA helicase DDX42 as an intrinsic antiviral inhibitor of HIV‐1. Depletion of endogenous DDX42 increases HIV‐1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibits HIV‐1 infection, whereas expression of a dominant‐negative mutant increases infection. Importantly, DDX42 also restricts LINE‐1 retrotransposition and infection with other retroviruses and positive‐strand RNA viruses, including CHIKV and SARS‐CoV‐2. However, DDX42 does not impact the replication of several negative‐strand RNA viruses, arguing against an unspecific effect on target cells, which is confirmed by RNA‐seq analysis. Proximity ligation assays show DDX42 in the vicinity of viral elements, and cross‐linking RNA immunoprecipitation confirms a specific interaction of DDX42 with RNAs from sensitive viruses. Moreover, recombinant DDX42 inhibits HIV‐1 reverse transcription in vitro. Together, our data strongly suggest a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Our results identify DDX42 as an intrinsic viral inhibitor, opening new perspectives to target the life cycle of numerous RNA viruses.
Collapse
Affiliation(s)
| | | | | | | | - Ségolène Gracias
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
| | | | | | | | | | - Valérie Vivet‐Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002 Strasbourg France
| | | | | | - Nathalie Gros
- CEMIPAI, CNRS Université de Montpellier Montpellier France
| | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | - Stéphanie Rialle
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | | | - Laurent Lacroix
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL Paris France
| | - Marc Lavigne
- Department of Virology Institut Pasteur Paris France
| | | | | | - Reiner Schulz
- Department of Medical & Molecular Genetics King's College London London UK
| | - Nolwenn Jouvenet
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
| | | | | |
Collapse
|
14
|
Liu Z, Meng M, Ding S, Zhou X, Feng K, Huang T, Cai YD. Identification of methylation signatures and rules for predicting the severity of SARS-CoV-2 infection with machine learning methods. Front Microbiol 2022; 13:1007295. [PMID: 36212830 PMCID: PMC9537378 DOI: 10.3389/fmicb.2022.1007295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Patients infected with SARS-CoV-2 at various severities have different clinical manifestations and treatments. Mild or moderate patients usually recover with conventional medical treatment, but severe patients require prompt professional treatment. Thus, stratifying infected patients for targeted treatment is meaningful. A computational workflow was designed in this study to identify key blood methylation features and rules that can distinguish the severity of SARS-CoV-2 infection. First, the methylation features in the expression profile were deeply analyzed by a Monte Carlo feature selection method. A feature list was generated. Next, this ranked feature list was fed into the incremental feature selection method to determine the optimal features for different classification algorithms, thereby further building optimal classifiers. These selected key features were analyzed by functional enrichment to detect their biofunctional information. Furthermore, a set of rules were set up by a white-box algorithm, decision tree, to uncover different methylation patterns on various severity of SARS-CoV-2 infection. Some genes (PARP9, MX1, IRF7), corresponding to essential methylation sites, and rules were validated by published academic literature. Overall, this study contributes to revealing potential expression features and provides a reference for patient stratification. The physicians can prioritize and allocate health and medical resources for COVID-19 patients based on their predicted severe clinical outcomes.
Collapse
Affiliation(s)
- Zhiyang Liu
- School of Life Sciences, Changchun Sci-Tech University, Changchun, China
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - XiaoChao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
| |
Collapse
|
15
|
Neyret A, Bernard E, Aïqui-Reboul-Paviet O, Bakhache W, Eldin P, Chaloin L, Briant L. Identification of a non-canonical G3BP-binding sequence in a Mayaro virus nsP3 hypervariable domain. Front Cell Infect Microbiol 2022; 12:958176. [PMID: 36034716 PMCID: PMC9403187 DOI: 10.3389/fcimb.2022.958176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Ras-GTPase-activating SH3 domain-binding-proteins 1 (G3BP1) and 2 (G3BP2) are multifunctional RNA-binding proteins involved in stress granule nucleation, previously identified as essential cofactors of Old World alphaviruses. They are recruited to viral replication complexes formed by the Chikungunya virus (CHIKV), Semliki Forest virus (SFV), and Sindbis virus (SINV) via an interaction with a duplicated FGxF motif conserved in the hypervariable domain (HVD) of virus-encoded nsP3. According to mutagenesis studies, this FGxF duplication is strictly required for G3BP binding and optimal viral growth. Contrasting with this scenario, nsP3 encoded by Mayaro virus (MAYV), an arthritogenic virus grouped with Old World alphaviruses, contains a single canonical FGxF sequence. In light of this unusual feature, we questioned MAYV nsP3/G3BPs relationships. We report that G3BP1 and G3BP2 are both required for MAYV growth in human cells and bind nsP3 protein. In infected cells, they are recruited to nsP3-containing cytosolic foci and active replication complexes. Unexpectedly, deletion of the single FGxF sequence in MAYV nsP3 did not abolish these phenotypes. Using mutagenesis and in silico modeling, we identify an upstream FGAP amino acid sequence as an additional MAYV nsP3/G3BP interaction motif required for optimal viral infectivity. These results, therefore, highlight a non-conventional G3BP binding sequence in MAYV nsP3.
Collapse
|
16
|
The Tetraspanin CD81 Is a Host Factor for Chikungunya Virus Replication. mBio 2022; 13:e0073122. [PMID: 35612284 PMCID: PMC9239085 DOI: 10.1128/mbio.00731-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is an arthritogenic reemerging virus replicating in plasma membrane-derived compartments termed "spherules." Here, we identify the human transmembrane protein CD81 as host factor required for CHIKV replication. Ablation of CD81 results in decreased CHIKV permissiveness, while overexpression enhances infection. CD81 is dispensable for virus uptake but critically required for viral genome replication. Likewise, murine CD81 is crucial for CHIKV permissiveness and is expressed in target cells such as dermal fibroblasts, muscle and liver cells. Whereas related alphaviruses, including Ross River virus (RRV), Semliki Forest virus (SFV), Sindbis virus (SINV) and Venezuelan equine encephalitis virus (VEEV), also depend on CD81 for infection, RNA viruses from other families, such as coronaviruses, replicate independently of CD81. Strikingly, the replication-enhancing function of CD81 is linked to cholesterol binding. These results define a mechanism exploited by alphaviruses to hijack the membrane microdomain-modeling protein CD81 for virus replication through interaction with cholesterol. IMPORTANCE In this study, we discover the tetraspanin CD81 as a host factor for the globally emerging chikungunya virus and related alphaviruses. We show that CD81 promotes replication of viral genomes in human and mouse cells, while virus entry into cells is independent of CD81. This provides novel insights into how alphaviruses hijack host proteins to complete their life cycle. Alphaviruses replicate at distinct sites of the plasma membrane, which are enriched in cholesterol. We found that the cholesterol-binding ability of CD81 is important for its function as an alphavirus host factor. This discovery thus broadens our understanding of the alphavirus replication process and the use of host factors to reprogram cells into virus replication factories.
Collapse
|
17
|
Javaid A, Ijaz A, Ashfaq UA, Arshad M, Irshad S, Saif S. An overview of chikungunya virus molecular biology, epidemiology, pathogenesis, treatment and prevention strategies. Future Virol 2022. [DOI: 10.2217/fvl-2019-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chikungunya virus (CHIKV) causes a devastating musculoskeletal inflammatory disease with symptoms of headache, rash, polyarthralgia, fever and myalgia. CHIKV has appeared intermittently around the world and in different ecological zones of Pakistan. Aedes mosquito species are the main vectors of CHIKV transmission and cause high disease rates in the urban transmission cycle. Even though the CHIKV is responsible for many cases of disease, no authorized antibodies or antiviral treatments are available, and prevention is the primary countermeasure. This review describes an update on CHIKV molecular biology, replication cycle, epidemiology, ecological factors, clinical manifestations and treatment and suggests a way forward to control and prevent this infection strategically in the future.
Collapse
Affiliation(s)
- Anam Javaid
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Aroosa Ijaz
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Maham Arshad
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Shakeel Irshad
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saira Saif
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| |
Collapse
|
18
|
A Review on Chikungunya Virus Epidemiology, Pathogenesis and Current Vaccine Development. Viruses 2022; 14:v14050969. [PMID: 35632709 PMCID: PMC9147731 DOI: 10.3390/v14050969] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that recently re-emerged in many parts of the world causing large-scale outbreaks. CHIKV infection presents as a febrile illness known as chikungunya fever (CHIKF). Infection is self-limited and characterized mainly by severe joint pain and myalgia that can last for weeks or months; however, severe disease presentation can also occur in a minor proportion of infections. Among the atypical CHIKV manifestations that have been described, severe arthralgia and neurological complications, such as encephalitis, meningitis, and Guillain–Barré Syndrome, are now reported in many outbreaks. Moreover, death cases were also reported, placing CHIKV as a relevant public health disease. Virus evolution, globalization, and climate change may have contributed to CHIKV spread. In addition to this, the lack of preventive vaccines and approved antiviral treatments is turning CHIKV into a major global health threat. In this review, we discuss the current knowledge about CHIKV pathogenesis, with a focus on atypical disease manifestations, such as persistent arthralgia and neurologic disease presentation. We also bring an up-to-date review of the current CHIKV vaccine development. Altogether, these topics highlight some of the most recent advances in our understanding of CHIKV pathogenesis and also provide important insights into the current development and clinical trials of CHIKV potential vaccine candidates.
Collapse
|
19
|
Labeau A, Fery-Simonian L, Lefevre-Utile A, Pourcelot M, Bonnet-Madin L, Soumelis V, Lotteau V, Vidalain PO, Amara A, Meertens L. Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep 2022; 39:110744. [PMID: 35477000 PMCID: PMC9040432 DOI: 10.1016/j.celrep.2022.110744] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/28/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which has led to a devastating global health crisis. The emergence of variants that escape neutralizing responses emphasizes the urgent need to deepen our understanding of SARS-CoV-2 biology. Using a comprehensive identification of RNA-binding proteins (RBPs) by mass spectrometry (ChIRP-MS) approach, we identify 107 high-confidence cellular factors that interact with the SARS-CoV-2 genome during infection. By systematically knocking down their expression in human lung epithelial cells, we find that the majority of the identified RBPs are SARS-CoV-2 proviral factors. In particular, we show that HNRNPA2B1, ILF3, QKI, and SFPQ interact with the SARS-CoV-2 genome and promote viral RNA amplification. Our study provides valuable resources for future investigations into the mechanisms of SARS-CoV-2 replication and the identification of host-centered antiviral therapies.
Collapse
Affiliation(s)
- Athéna Labeau
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Luc Fery-Simonian
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Alain Lefevre-Utile
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Marie Pourcelot
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Lucie Bonnet-Madin
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vassili Soumelis
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Pierre-Olivier Vidalain
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Ali Amara
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
| | - Laurent Meertens
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
| |
Collapse
|
20
|
An E3 Ubiquitin Ligase Scaffolding Protein Is Proviral during Chikungunya Virus Infection in Aedes aegypti. Microbiol Spectr 2022; 10:e0059522. [PMID: 35435754 PMCID: PMC9241663 DOI: 10.1128/spectrum.00595-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chikungunya virus (CHIKV) is a reemerging alphavirus causing chikungunya disease (CHIKD) and is transmitted to humans by Aedes mosquitoes. The virus establishes an intricate balance of cellular interactions that ultimately helps in its replication and dodges cellular immune response. In an attempt to identify cellular host factors required during CHIKV replication in Aag2 cells, we performed global transcriptomics of CHIKV-infected Aag2 cells, and further, we compared this library with the Drosophila RNAi Screening Center (DRSC) database and identified transcripts that were regulated in Aedes aegypti during CHIKV infection. These analyses revealed specific pathways, such as ubiquitin-related pathways, proteolysis pathways, protein catabolic processes, protein modification, and cellular protein metabolic processes, involved during replication of the virus. Loss-of-function assays of selected candidates revealed their proviral or antiviral characteristics upon CHIKV infection in A. aegypti-derived Aag2 cells. Further validations identified that the ubiquitin proteasomal pathway is required for CHIKV infection in A. aegypti and that an important member of this family of proteins, namely, AeCullin-3 (Aedes ortholog of human cullin-3), is a proviral host factor of CHIKV replication in Aag2 cells. IMPORTANCE Arboviruses cause several diseases in humans and livestock. Vector control is the main strategy for controlling diseases transmitted by mosquitoes. In this context, it becomes paramount to understand how the viruses replicate in the vector for designing better transmission blocking strategies. We obtained the global transcriptome signature of A. aegypti cells during CHIKV infection, and in order to obtain the maximum information from these data sets, we further utilized the well-characterized Drosophila system and arrived upon a set of transcripts and their pathways that affect A. aegypti cells during CHIKV infection. These analyses and further validations reveal that important pathways related to protein degradation are actively involved during CHIKV infection in A. aegypti and are mainly proviral. Targeting these molecules may provide novel approaches for blocking CHIKV replication in A. aegypti.
Collapse
|
21
|
Tanaka A, Suzuki Y. Genome-Wide Approaches to Unravel the Host Factors Involved in Chikungunya Virus Replication. Front Microbiol 2022; 13:866271. [PMID: 35401487 PMCID: PMC8988064 DOI: 10.3389/fmicb.2022.866271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/26/2022] [Indexed: 01/05/2023] Open
Abstract
Chikungunya virus (CHIKV), the causative agent of Chikungunya fever (CHIKVF) that is often characterized by fever, headache, rash, and arthralgia, is transmitted to humans by Aedes mosquito bites. Although the mortality rate associated with CHIKV infection is not very high, CHIKVF has been confirmed in more than 40 countries, not only in tropical but also in temperate areas. Therefore, CHIKV is a growing major threat to the public health of the world. However, a specific drug is not available for CHIKV infection. As demonstrated by many studies, the processes completing the replication of CHIKV are assisted by many host factors, whereas it has become clear that the host cell possesses some factors limiting the virus replication. This evidence will provide us with an important clue for the development of pharmacological treatment against CHIKVF. In this review, we briefly summarize cellular molecules participating in the CHIKV infection, particularly focusing on introducing recent genome-wide screen studies that enabled illuminating the virus-host interactions.
Collapse
Affiliation(s)
- Atsushi Tanaka
- Division of Research Animal Laboratory and Translational Medicine, Research and Development Center, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
- *Correspondence: Atsushi Tanaka,
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
- Youichi Suzuki,
| |
Collapse
|
22
|
RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication. J Virol 2022; 96:e0196221. [PMID: 35266803 DOI: 10.1128/jvi.01962-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.
Collapse
|
23
|
Pott F, Postmus D, Brown RJP, Wyler E, Neumann E, Landthaler M, Goffinet C. Single-cell analysis of arthritogenic alphavirus-infected human synovial fibroblasts links low abundance of viral RNA to induction of innate immunity and arthralgia-associated gene expression. Emerg Microbes Infect 2021; 10:2151-2168. [PMID: 34723780 PMCID: PMC8604527 DOI: 10.1080/22221751.2021.2000891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/25/2022]
Abstract
Infection by (re-)emerging RNA arboviruses including Chikungunya virus (CHIKV) and Mayaro virus primarily cause acute febrile disease and transient polyarthralgia. However, in a significant subset of infected individuals, debilitating arthralgia persists for weeks over months up to years. The underlying immunopathogenesis of chronification of arthralgia upon primary RNA-viral infection remains unclear. Here, we analysed cell-intrinsic responses to ex vivo arthritogenic alphaviral infection of primary human synovial fibroblasts isolated from knee joints, one the most affected joint types during acute and chronic CHIKV disease. Synovial fibroblasts were susceptible and permissive to alphaviral infection. Base-line and exogenously added type I interferon (IFN) partially and potently restricted infection, respectively. RNA-seq revealed a CHIKV infection-induced transcriptional profile that comprised upregulation of expression of several hundred IFN-stimulated and arthralgia-mediating genes. Single-cell virus-inclusive RNA-seq uncovered a fine-tuned switch from induction to repression of cell-intrinsic immune responses depending on the abundance of viral RNA in an individual cell. Specifically, responses were most pronounced in cells displaying low-to-intermediate amounts of viral RNA and absence of virus-encoded, fluorescent reporter protein expression, arguing for efficient counteraction of innate immunity in cells expressing viral antagonists at sufficient quantities. In summary, cell-intrinsic sensing of viral RNA that potentially persists or replicates at low levels in synovial fibroblasts and other target cell types in vivo may contribute to the chronic arthralgia induced by alphaviral infections. Our findings might advance our understanding of the immunopathophysiology of long-term pathogenesis of RNA-viral infections.
Collapse
Affiliation(s)
- Fabian Pott
- Institute of Virology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Dylan Postmus
- Institute of Virology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Emanuel Wyler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Elena Neumann
- Internal Medicine and Rheumatology, Justus-Liebig-University Giessen, Bad Nauheim, Germany
| | - Markus Landthaler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- IRI Life Sciences, Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
24
|
Mei H, Zha Z, Wang W, Xie Y, Huang Y, Li W, Wei D, Zhang X, Qu J, Liu J. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Genome Biol 2021; 22:297. [PMID: 34686207 PMCID: PMC8532573 DOI: 10.1186/s13059-021-02513-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02513-w.
Collapse
Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Yusang Xie
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuege Huang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Shanghai Clinical Research and Trial Center, 201210, Shanghai, People's Republic of China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510182, Guangdong Province, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, People's Republic of China. .,Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou Interntional Bio Island, Guangdong Province, 510005, Guangzhou, China.
| |
Collapse
|
25
|
Abstract
Alphaviruses are positive-strand RNA viruses, typically transmitted by mosquitoes between vertebrate hosts. They encode four essential replication proteins, the non-structural proteins nsP1-4, which possess the enzymatic activities of RNA capping, RNA helicase, site-specific protease, ADP-ribosyl removal and RNA polymerase. Alphaviruses have been key models in the study of membrane-associated RNA replication, which is a conserved feature among the positive-strand RNA viruses of animals and plants. We review new structural and functional information on the nsPs and their interaction with host proteins and membranes, as well as with viral RNA sequences. The dodecameric ring structure of nsP1 is likely to be one of the evolutionary innovations that facilitated the success of the progenitors of current positive-strand RNA viruses.
Collapse
Affiliation(s)
- Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia.
| |
Collapse
|
26
|
Teppor M, Žusinaite E, Karo-Astover L, Omler A, Rausalu K, Lulla V, Lulla A, Merits A. Semliki Forest Virus Chimeras with Functional Replicase Modules from Related Alphaviruses Survive by Adaptive Mutations in Functionally Important Hot Spots. J Virol 2021; 95:e0097321. [PMID: 34319778 PMCID: PMC8475518 DOI: 10.1128/jvi.00973-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Alphaviruses (family Togaviridae) include both human pathogens such as chikungunya virus (CHIKV) and Sindbis virus (SINV) and model viruses such as Semliki Forest virus (SFV). The alphavirus positive-strand RNA genome is translated into nonstructural (ns) polyprotein(s) that are precursors for four nonstructural proteins (nsPs). The three-dimensional structures of nsP2 and the N-terminal 2/3 of nsP3 reveal that these proteins consist of several domains. Cleavage of the ns-polyprotein is performed by the strictly regulated protease activity of the nsP2 region. Processing results in the formation of a replicase complex that can be considered a network of functional modules. These modules work cooperatively and should perform the same task for each alphavirus. To investigate functional interactions between replicase components, we generated chimeras using the SFV genome as a backbone. The functional modules corresponding to different parts of nsP2 and nsP3 were swapped with their counterparts from CHIKV and SINV. Although some chimeras were nonfunctional, viruses harboring the CHIKV N-terminal domain of nsP2 or any domain of nsP3 were viable. Viruses harboring the protease part of nsP2, the full-length nsP2 of CHIKV, or the nsP3 macrodomain of SINV required adaptive mutations for functionality. Seven mutations that considerably improved the infectivity of the corresponding chimeric genomes affected functionally important hot spots recurrently highlighted in previous alphavirus studies. These data indicate that alphaviruses utilize a rather limited set of strategies to survive and adapt. Furthermore, functional analysis revealed that the disturbance of processing was the main defect resulting from chimeric alterations within the ns-polyprotein. IMPORTANCE Alphaviruses cause debilitating symptoms and have caused massive outbreaks. There are currently no approved antivirals or vaccines for treating these infections. Understanding the functions of alphavirus replicase proteins (nsPs) provides valuable information for both antiviral drug and vaccine development. The nsPs of all alphaviruses consist of similar functional modules; however, to what extent these are independent in functionality and thus interchangeable among homologous viruses is largely unknown. Homologous domain swapping was used to study the functioning of modules from nsP2 and nsP3 of other alphaviruses in the context of Semliki Forest virus. Most of the introduced substitutions resulted in defects in the processing of replicase precursors that were typically compensated by adaptive mutations that mapped to determinants of polyprotein processing. Understanding the principles of virus survival strategies and identifying hot spot mutations that permit virus adaptation highlight a route to the rapid development of attenuated viruses as potential live vaccine candidates.
Collapse
Affiliation(s)
- Mona Teppor
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Eva Žusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Ailar Omler
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kai Rausalu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Valeria Lulla
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Aleksei Lulla
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| |
Collapse
|
27
|
Kril V, Aïqui-Reboul-Paviet O, Briant L, Amara A. New Insights into Chikungunya Virus Infection and Pathogenesis. Annu Rev Virol 2021; 8:327-347. [PMID: 34255544 DOI: 10.1146/annurev-virology-091919-102021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus responsible for major outbreaks of disease since 2004 in the Indian Ocean islands, South east Asia, and the Americas. CHIKV causes debilitating musculoskeletal disorders in humans that are characterized by fever, rash, polyarthralgia, and myalgia. The disease is often self-limiting and nonlethal; however, some patients experience atypical or severe clinical manifestations, as well as a chronic rheumatic syndrome. Unfortunately, no efficient antivirals against CHIKV infection are available so far, highlighting the importance of deepening our knowledge of CHIKV host cell interactions and viral replication strategies. In this review, we discuss recent breakthroughs in the molecular mechanisms that regulate CHIKV infection and lay down the foundations to understand viral pathogenesis. We describe the role of the recently identified host factors co-opted by the virus for infection and pathogenesis, and emphasize the importance of CHIKV nonstructural proteins in both replication complex assembly and host immune response evasion. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Vasiliya Kril
- Biology of Emerging Virus Team, INSERM U944, CNRS UMR 7212, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, 75010 Paris, France;
| | - Olivier Aïqui-Reboul-Paviet
- RNA Viruses and Metabolism Team, CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, 34293 Montpellier, France;
| | - Laurence Briant
- RNA Viruses and Metabolism Team, CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, 34293 Montpellier, France;
| | - Ali Amara
- Biology of Emerging Virus Team, INSERM U944, CNRS UMR 7212, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, 75010 Paris, France;
| |
Collapse
|
28
|
Franz S, Pott F, Zillinger T, Schüler C, Dapa S, Fischer C, Passos V, Stenzel S, Chen F, Döhner K, Hartmann G, Sodeik B, Pessler F, Simmons G, Drexler JF, Goffinet C. Human IFITM3 restricts chikungunya virus and Mayaro virus infection and is susceptible to virus-mediated counteraction. Life Sci Alliance 2021; 4:e202000909. [PMID: 34078739 PMCID: PMC8200292 DOI: 10.26508/lsa.202000909] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/29/2022] Open
Abstract
Interferon-induced transmembrane (IFITM) proteins restrict membrane fusion and virion internalization of several enveloped viruses. The role of IFITM proteins during alphaviral infection of human cells and viral counteraction strategies are insufficiently understood. Here, we characterized the impact of human IFITMs on the entry and spread of chikungunya virus and Mayaro virus and provide first evidence for a CHIKV-mediated antagonism of IFITMs. IFITM1, 2, and 3 restricted infection at the level of alphavirus glycoprotein-mediated entry, both in the context of direct infection and cell-to-cell transmission. Relocalization of normally endosomal IFITM3 to the plasma membrane resulted in loss of antiviral activity. rs12252-C, a naturally occurring variant of IFITM3 that may associate with severe influenza in humans, restricted CHIKV, MAYV, and influenza A virus infection as efficiently as wild-type IFITM3 Antivirally active IFITM variants displayed reduced cell surface levels in CHIKV-infected cells involving a posttranscriptional process mediated by one or several nonstructural protein(s) of CHIKV. Finally, IFITM3-imposed reduction of specific infectivity of nascent particles provides a rationale for the necessity of a virus-encoded counteraction strategy against this restriction factor.
Collapse
Affiliation(s)
- Sergej Franz
- Institute of Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Vitalant Research Institute, San Francisco, CA, USA
| | - Fabian Pott
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, Venusberg-Campus 1, Bonn, Germany
| | - Christiane Schüler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra Dapa
- Institute of Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Carlo Fischer
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Vânia Passos
- Institute of Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Saskia Stenzel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Fangfang Chen
- Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hanover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hanover, Germany
| | - Katinka Döhner
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Gunther Hartmann
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hanover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hanover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hanover, Germany
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Christine Goffinet
- Institute of Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
29
|
Abdullah N, Ahemad N, Aliazis K, Khairat JE, Lee TC, Abdul Ahmad SA, Adnan NAA, Macha NO, Hassan SS. The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence. Viruses 2021; 13:v13061021. [PMID: 34071712 PMCID: PMC8228767 DOI: 10.3390/v13061021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.
Collapse
Affiliation(s)
- Nurshariza Abdullah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia;
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
| | - Konstantinos Aliazis
- Institute of Immunology and Immunotherapy, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Jasmine Elanie Khairat
- Institute of Biological Sciences, Faculty of Science, University Malaya, Kuala Lumpur 50603, Malaysia;
| | - Thong Chuan Lee
- Faculty of Industrial Sciences & Technology, University Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan 26300, Pahang, Malaysia;
| | - Siti Aisyah Abdul Ahmad
- Immunogenetic Unit, Allergy and Immunology Research Center, Institute for Medical Research, Ministry of Health Malaysia, Shah Alam 40170, Selangor, Malaysia;
| | - Nur Amelia Azreen Adnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nur Omar Macha
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
- Correspondence: ; Tel.: +60-3-5514-6340
| |
Collapse
|
30
|
Dutt M, Ng YK, Molendijk J, Karimkhanloo H, Liao L, Blazev R, Montgomery MK, Watt MJ, Parker BL. Western Diet Induced Remodelling of the Tongue Proteome. Proteomes 2021; 9:proteomes9020022. [PMID: 34066295 PMCID: PMC8163156 DOI: 10.3390/proteomes9020022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 12/14/2022] Open
Abstract
The tongue is a heavily innervated and vascularized striated muscle that plays an important role in vocalization, swallowing and digestion. The surface of the tongue is lined with papillae which contain gustatory cells expressing various taste receptors. There is growing evidence to suggest that our perceptions of taste and food preference are remodelled following chronic consumption of Western diets rich in carbohydrate and fats. Our sensitivity to taste and also to metabolising Western diets may be a key factor in the rising prevalence of obesity; however, a systems-wide analysis of the tongue is lacking. Here, we defined the proteomic landscape of the mouse tongue and quantified changes following chronic consumption of a chow or Western diet enriched in lipid, fructose and cholesterol for 7 months. We observed a dramatic remodelling of the tongue proteome including proteins that regulate fatty acid and mitochondrial metabolism. Furthermore, the expressions of several receptors, metabolic enzymes and hormones were differentially regulated, and are likely to provide novel therapeutic targets to alter taste perception and food preference to combat obesity.
Collapse
|
31
|
Phosphorylation Sites in the Hypervariable Domain in Chikungunya Virus nsP3 Are Crucial for Viral Replication. J Virol 2021; 95:JVI.02276-20. [PMID: 33568506 DOI: 10.1128/jvi.02276-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/30/2021] [Indexed: 01/26/2023] Open
Abstract
Chikungunya virus (CHIKV, family Togaviridae) is a mosquito-transmitted alphavirus. The positive-sense RNA genome of CHIKV encodes four nonstructural proteins (nsP1 to nsP4) that are virus-specific subunits of the RNA replicase. Among nsP functions, those of nsP3 are the least understood. The C-terminal hypervariable domain (HVD) in nsP3 is disordered and serves as a platform for interactions with multiple host proteins. For Sindbis virus (SINV) and Semliki Forest virus (SFV), the nsP3 HVD has been shown to be phosphorylated. Deletion of phosphorylated regions has a mild effect on the growth of SFV and SINV in vertebrate cells. Using radiolabeling, we demonstrated that nsP3 in CHIKV and o'nyong-nyong virus is also phosphorylated. We showed that the phosphorylated residues in CHIKV nsP3 are not clustered at the beginning of the HVD. The substitution of 20 Ser/Thr residues located in the N-terminal half of the HVD or 26 Ser/Thr residues located in its C-terminal half with Ala residues reduced the activity of the CHIKV replicase and the infectivity of CHIKV in mammalian cells. Furthermore, the substitution of all 46 potentially phosphorylated residues resulted in the complete loss of viral RNA synthesis and infectivity. The mutations did not affect the interaction of the HVD in nsP3 with the host G3BP1 protein; interactions with CD2AP, BIN1, and FHL1 proteins were significantly reduced but not abolished. Thus, CHIKV differs from SFV and SINV both in the location of the phosphorylated residues in the HVD in nsP3 and, significantly, in their effect on replicase activity and virus infectivity.IMPORTANCE CHIKV outbreaks have affected millions of people, creating a need for the development of antiviral approaches. nsP3 is a component of the CHIKV RNA replicase and is involved in interactions with host proteins and signaling cascades. Phosphorylation of the HVD in nsP3 is important for the virulent alphavirus phenotype. Here, we demonstrate that nsP3 in CHIKV is phosphorylated and that the phosphorylation sites in the HVD are distributed in a unique pattern. Furthermore, the abrogation of some of the phosphorylation sites results in the attenuation of CHIKV, while abolishing all the phosphorylation sites completely blocked its replicase activity. Thus, the phosphorylation of nsP3 and/or the phosphorylation sites in nsP3 have a major impact on CHIKV infectivity. Therefore, they represent promising targets for antiviral compounds and CHIKV attenuation. In addition, this new information offers valuable insight into the vast network of virus-host interactions.
Collapse
|
32
|
Bengue M, Ferraris P, Barthelemy J, Diagne CT, Hamel R, Liégeois F, Nougairède A, de Lamballerie X, Simonin Y, Pompon J, Salinas S, Missé D. Mayaro Virus Infects Human Brain Cells and Induces a Potent Antiviral Response in Human Astrocytes. Viruses 2021; 13:v13030465. [PMID: 33799906 PMCID: PMC8001792 DOI: 10.3390/v13030465] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Mayaro virus (MAYV) and chikungunya virus (CHIKV) are known for their arthrotropism, but accumulating evidence shows that CHIKV infections are occasionally associated with serious neurological complications. However, little is known about the capacity of MAYV to invade the central nervous system (CNS). We show that human neural progenitors (hNPCs), pericytes and astrocytes are susceptible to MAYV infection, resulting in the production of infectious viral particles. In primary astrocytes, MAYV, and to a lesser extent CHIKV, elicited a strong antiviral response, as demonstrated by an increased expression of several interferon-stimulated genes, including ISG15, MX1 and OAS2. Infection with either virus led to an enhanced expression of inflammatory chemokines, such as CCL5, CXCL10 and CXCL11, whereas MAYV induced higher levels of IL-6, IL-12 and IL-15 in these cells. Moreover, MAYV was more susceptible than CHIKV to the antiviral effects of both type I and type II interferons. Taken together, this study shows that although MAYV and CHIKV are phylogenetically related, they induce different types of antiviral responses in astrocytes. This work is the first to evaluate the potential neurotropism of MAYV and shows that brain cells and particularly astrocytes and hNPCs are permissive to MAYV, which, consequently, could lead to MAYV-induced neuropathology.
Collapse
Affiliation(s)
- Michèle Bengue
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Pauline Ferraris
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Jonathan Barthelemy
- Pathogenesis and Control of Chronic Infections, Inserm, Université de Montpellier, Etablissement Français du Sang, 34394 Montpellier, France; (J.B.); (Y.S.)
| | - Cheikh Tidiane Diagne
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Rodolphe Hamel
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Florian Liégeois
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Antoine Nougairède
- Unité Des Virus Emergents (UVE, Aix Marseille Université, IRD 190, Inserm 1207, IHU Méditerranée Infection), 13005 Marseille, France; (A.N.); (X.d.L.)
| | - Xavier de Lamballerie
- Unité Des Virus Emergents (UVE, Aix Marseille Université, IRD 190, Inserm 1207, IHU Méditerranée Infection), 13005 Marseille, France; (A.N.); (X.d.L.)
| | - Yannick Simonin
- Pathogenesis and Control of Chronic Infections, Inserm, Université de Montpellier, Etablissement Français du Sang, 34394 Montpellier, France; (J.B.); (Y.S.)
| | - Julien Pompon
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
| | - Sara Salinas
- Pathogenesis and Control of Chronic Infections, Inserm, Université de Montpellier, Etablissement Français du Sang, 34394 Montpellier, France; (J.B.); (Y.S.)
- Correspondence: (S.S.); (D.M.)
| | - Dorothée Missé
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (M.B.); (P.F.); (C.T.D.); (R.H.); (F.L.); (J.P.)
- Correspondence: (S.S.); (D.M.)
| |
Collapse
|
33
|
Lebedev M, McEligot HA, Mutua VN, Walsh P, Carvallo Chaigneau FR, Gershwin LJ. Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor. PLoS One 2021; 16:e0246695. [PMID: 33600498 PMCID: PMC7891793 DOI: 10.1371/journal.pone.0246695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Bovine Respiratory Syncytial virus (BRSV) is one of the major infectious agents in the etiology of the bovine respiratory disease complex. BRSV causes a respiratory syndrome in calves, which is associated with severe bronchiolitis. In this study we describe the effect of treatment with antiviral fusion protein inhibitor (FPI) and ibuprofen, on gene expression in lung tissue of calves infected with BRSV. Calves infected with BRSV are an excellent model of human RSV in infants: we hypothesized that FPI in combination with ibuprofen would provide the best therapeutic intervention for both species. The following experimental treatment groups of BRSV infected calves were used: 1) ibuprofen day 3-10, 2) ibuprofen day 5-10, 3) placebo, 4) FPI day 5-10, 5) FPI and ibuprofen day 5-10, 6) FPI and ibuprofen day 3-10. All calves were infected with BRSV on day 0. Daily clinical evaluation with monitoring of virus shedding by qRT-PCR was conducted. On day10 lung tissue with lesions (LL) and non-lesional (LN) was collected at necropsy, total RNA extracted, and RNA sequencing performed. Differential gene expression analysis was conducted with Gene ontology (GO) and KEGG pathway enrichment analysis. The most significant differential gene expression in BRSV infected lung tissues was observed in the comparison of LL with LN; oxidative stress and cell damage was especially noticeable. Innate and adaptive immune functions were reduced in LL. As expected, combined treatment with FPI and Ibuprofen, when started early, made the most difference in gene expression patterns in comparison with placebo, especially in pathways related to the innate and adaptive immune response in both LL and LN. Ibuprofen, when used alone, negatively affected the antiviral response and caused higher virus loads as shown by increased viral shedding. In contrast, when used with FPI Ibuprofen enhanced the specific antiviral effect of FPI, due to its ability to reduce the damaging effect of prostanoids and oxidative stress.
Collapse
Affiliation(s)
- Maxim Lebedev
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Heather A. McEligot
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Victoria N. Mutua
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Paul Walsh
- Pediatric Emergency Medicine, Sutter Medical Center Sacramento, Sacramento, California, United States of America
| | - Francisco R. Carvallo Chaigneau
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech., Blacksburg, VA, United States of America
| | - Laurel J. Gershwin
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| |
Collapse
|
34
|
Ghildiyal R, Gabrani R. Deciphering the human cellular interactors of alphavirus unique domain of chikungunya virus. Virus Res 2021; 295:198288. [PMID: 33418023 DOI: 10.1016/j.virusres.2020.198288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/07/2020] [Accepted: 12/25/2020] [Indexed: 01/10/2023]
Abstract
The life-threatening re-emerged chikungunya virus (CHIKV) can cause an epidemic outbreak and still has no vaccine available so far. Alphavirus unique domain (AUD) of CHIKV nsP3 is a multifunctional domain that remains conserved among alphaviruses and is critical for CHIKV replication. The understanding of AUD-host protein-protein interactions and their association with the cellular processes concerning CHIKV infection are not well studied. In the current study, the protein-protein interactions of AUD and its human host were elucidated by screening of universal human cDNA library using yeast two-hybrid system. The chosen interactions were further validated by GST pull-down assay, and their network mapping was analyzed. The study revealed that the identified interactors are linked with the vesicle trafficking and transcription corepressor activities. Further, the interfacial residues of interactions between viral and host proteins were predicted, which will further provide the new platform to develop novel antivirals.
Collapse
Affiliation(s)
- Ritu Ghildiyal
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP, 201309, India.
| | - Reema Gabrani
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP, 201309, India.
| |
Collapse
|
35
|
Structural and Functional Characterization of Host FHL1 Protein Interaction with Hypervariable Domain of Chikungunya Virus nsP3 Protein. J Virol 2020; 95:JVI.01672-20. [PMID: 33055253 DOI: 10.1128/jvi.01672-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/10/2020] [Indexed: 11/20/2022] Open
Abstract
Decades of insufficient control have resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe, and millions have suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with the hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a prerequisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has a detectable stimulatory effect(s) on CHIKV replication, and Fhl1 knockout (KO) cell lines demonstrate slower infection spread. Nuclear magnetic resonance (NMR)-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps that of another proviral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by the LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP-binding sites remain viable and develop spreading infection in multiple cell types. Our study also demonstrated that other members of the FHL family can bind to CHIKV HVD and thus may be involved in viral replication.IMPORTANCE Replication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of the cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and, subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive proviral functions. Elimination of the FHL1-binding site in the nsP3 HVD can be used for the development of stable, attenuated vaccine candidates.
Collapse
|
36
|
Abstract
Alphaviruses cause severe human illnesses including persistent arthritis and fatal encephalitis. As alphavirus entry into target cells is the first step in infection, intensive research efforts have focused on elucidating aspects of this pathway, including attachment, internalization, and fusion. Herein, we review recent developments in the molecular understanding of alphavirus entry both in vitro and in vivo and how these advances might enable the design of therapeutics targeting this critical step in the alphavirus life cycle.
Collapse
|
37
|
Akhbari P, Richardson SJ, Morgan NG. Type 1 Diabetes: Interferons and the Aftermath of Pancreatic Beta-Cell Enteroviral Infection. Microorganisms 2020; 8:microorganisms8091419. [PMID: 32942706 PMCID: PMC7565444 DOI: 10.3390/microorganisms8091419] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) have long been implicated in the pathogenesis of type 1 diabetes (T1D), and accumulating evidence has associated virus-induced autoimmunity with the loss of pancreatic beta cells in T1D. Inflammatory cytokines including interferons (IFN) form a primary line of defence against viral infections, and their chronic elevation is a hallmark feature of many autoimmune diseases. IFNs play a key role in activating and regulating innate and adaptive immune responses, and to do so they modulate the expression of networks of genes and transcription factors known generically as IFN stimulated genes (ISGs). ISGs in turn modulate critical cellular processes ranging from cellular metabolism and growth regulation to endoplasmic reticulum (ER) stress and apoptosis. More recent studies have revealed that IFNs also modulate gene expression at an epigenetic as well as post-transcriptional and post-translational levels. As such, IFNs form a key link connecting the various genetic, environmental and immunological factors involved in the initiation and progression of T1D. Therefore, gaining an improved understanding of the mechanisms by which IFNs modulate beta cell function and survival is crucial in explaining the pathogenesis of virally-induced T1D. This should provide the means to prevent, decelerate or even reverse beta cell impairment.
Collapse
|
38
|
Lello LS, Utt A, Bartholomeeusen K, Wang S, Rausalu K, Kendall C, Coppens S, Fragkoudis R, Tuplin A, Alphey L, Ariën KK, Merits A. Cross-utilisation of template RNAs by alphavirus replicases. PLoS Pathog 2020; 16:e1008825. [PMID: 32886709 PMCID: PMC7498090 DOI: 10.1371/journal.ppat.1008825] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/17/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Most alphaviruses (family Togaviridae) including Sindbis virus (SINV) and other human pathogens, are transmitted by arthropods. The first open reading frame in their positive strand RNA genome encodes for the non-structural polyprotein, a precursor to four separate subunits of the replicase. The replicase interacts with cis-acting elements located near the intergenic region and at the ends of the viral RNA genome. A trans-replication assay was developed and used to analyse the template requirements for nine alphavirus replicases. Replicases of alphaviruses of the Semliki Forest virus complex were able to cross-utilize each other’s templates as well as those of outgroup alphaviruses. Templates of outgroup alphaviruses, including SINV and the mosquito-specific Eilat virus, were promiscuous; in contrast, their replicases displayed a limited capacity to use heterologous templates, especially in mosquito cells. The determinants important for efficient replication of template RNA were mapped to the 5' region of the genome. For SINV these include the extreme 5'- end of the genome and sequences corresponding to the first stem-loop structure in the 5' untranslated region. Mutations introduced in these elements drastically reduced infectivity of recombinant SINV genomes. The trans-replicase tools and approaches developed here can be instrumental in studying alphavirus recombination and evolution, but can also be applied to study other viruses such as picornaviruses, flaviviruses and coronaviruses. Alphaviruses are positive-strand RNA viruses, most of which use mosquitoes to spread between vertebrate hosts; many are human pathogens with potentially severe medical consequences. Some alphavirus species are believed to have resulted from the recombination between different members of the genus and there is evidence of movement of alphaviruses between continents. Here, a novel assay uncoupling viral replicase and template RNA production was developed and used to analyse cross-utilization of alphavirus template RNAs. We observed that replicases of closely related alphaviruses belonging to the Semliki Forest virus complex can generally use each other’s template RNAs as well as those of distantly related outgroup viruses. In contrast, replicases of outgroup viruses clearly preferred homologous template RNAs. These trends were observed in both mammalian and mosquito cells, with template preferences generally more pronounced in mosquito cells. Interestingly, the template RNA of the mosquito-specific Eilat virus was efficiently used by other alphavirus replicases while Eilat replicase could not use heterologous templates. Determinants for template selectivity were mapped to the beginning of the RNA genome and template recognition was more likely based on the recognition of RNA sequences than recognition of structural elements formed by the RNAs.
Collapse
Affiliation(s)
| | - Age Utt
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Koen Bartholomeeusen
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kai Rausalu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Catherine Kendall
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sandra Coppens
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Rennos Fragkoudis
- University of Nottingham, School of Veterinary Medicine and Science, Loughborough, United Kingdom
| | - Andrew Tuplin
- Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Luke Alphey
- The Pirbright Institute, Woking, United Kingdom
| | - Kevin K. Ariën
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerpen, Belgium
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
| |
Collapse
|
39
|
Structures and Functions of Viral 5' Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections. Viruses 2020; 12:v12090919. [PMID: 32839386 PMCID: PMC7552046 DOI: 10.3390/v12090919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022] Open
Abstract
Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5′ end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (internal ribosome entry site, IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5′ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I (Retinoic acid inducible gene I) or MDA5 (melanoma differentiation-associated protein 5) receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host–cell interactions driving the development of acute or persistent EV-B infections.
Collapse
|
40
|
Cunha MS, Costa PAG, Correa IA, de Souza MRM, Calil PT, da Silva GPD, Costa SM, Fonseca VWP, da Costa LJ. Chikungunya Virus: An Emergent Arbovirus to the South American Continent and a Continuous Threat to the World. Front Microbiol 2020; 11:1297. [PMID: 32670231 PMCID: PMC7332961 DOI: 10.3389/fmicb.2020.01297] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/20/2020] [Indexed: 01/23/2023] Open
Abstract
Chikungunya virus (CHIKV) is an arthropod-borne virus (arbovirus) of epidemic concern, transmitted by Aedes ssp. mosquitoes, and is the etiologic agent of a febrile and incapacitating arthritogenic illness responsible for millions of human cases worldwide. After major outbreaks starting in 2004, CHIKV spread to subtropical areas and western hemisphere coming from sub-Saharan Africa, South East Asia, and the Indian subcontinent. Even though CHIKV disease is self-limiting and non-lethal, more than 30% of the infected individuals will develop chronic disease with persistent severe joint pain, tenosynovitis, and incapacitating polyarthralgia that can last for months to years, negatively impacting an individual's quality of life and socioeconomic productivity. The lack of specific drugs or licensed vaccines to treat or prevent CHIKV disease associated with the global presence of the mosquito vector in tropical and temperate areas, representing a possibility for CHIKV to continually spread to different territories, make this virus an agent of public health burden. In South America, where Dengue virus is endemic and Zika virus was recently introduced, the impact of the expansion of CHIKV infections, and co-infection with other arboviruses, still needs to be estimated. In Brazil, the recent spread of the East/Central/South Africa (ECSA) and Asian genotypes of CHIKV was accompanied by a high morbidity rate and acute cases of abnormal disease presentation and severe neuropathies, which is an atypical outcome for this infection. In this review, we will discuss what is currently known about CHIKV epidemics, clinical manifestations of the human disease, the basic concepts and recent findings in the mechanisms underlying virus-host interaction, and CHIKV-induced chronic disease for both in vitro and in vivo models of infection. We aim to stimulate scientific debate on how the characterization of replication, host-cell interactions, and the pathogenic potential of the new epidemic viral strains can contribute as potential developments in the virology field and shed light on strategies for disease control.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Luciana J. da Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
41
|
An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells. Nat Commun 2020; 11:2584. [PMID: 32444635 PMCID: PMC7244579 DOI: 10.1038/s41467-020-16327-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Interferon-α (IFNα), a type I interferon, is expressed in the islets of type 1 diabetic individuals, and its expression and signaling are regulated by T1D genetic risk variants and viral infections associated with T1D. We presently characterize human beta cell responses to IFNα by combining ATAC-seq, RNA-seq and proteomics assays. The initial response to IFNα is characterized by chromatin remodeling, followed by changes in transcriptional and translational regulation. IFNα induces changes in alternative splicing (AS) and first exon usage, increasing the diversity of transcripts expressed by the beta cells. This, combined with changes observed on protein modification/degradation, ER stress and MHC class I, may expand antigens presented by beta cells to the immune system. Beta cells also up-regulate the checkpoint proteins PDL1 and HLA-E that may exert a protective role against the autoimmune assault. Data mining of the present multi-omics analysis identifies two compound classes that antagonize IFNα effects on human beta cells. The cytokine IFNα is expressed in the islets of individuals with type 1 diabetes and contributes to local inflammation and destruction of beta cells. Here, the authors provide a global multiomics view of IFNα-induced changes in human beta cells at the level of chromatin, mRNA and protein expression.
Collapse
|
42
|
On the Host Side of the Hepatitis E Virus Life Cycle. Cells 2020; 9:cells9051294. [PMID: 32456000 PMCID: PMC7291229 DOI: 10.3390/cells9051294] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Hepatitis E virus (HEV) infection is one of the most common causes of acute hepatitis in the world. HEV is an enterically transmitted positive-strand RNA virus found as a non-enveloped particle in bile as well as stool and as a quasi-enveloped particle in blood. Current understanding of the molecular mechanisms and host factors involved in productive HEV infection is incomplete, but recently developed model systems have facilitated rapid progress in this area. Here, we provide an overview of the HEV life cycle with a focus on the host factors required for viral entry, RNA replication, assembly and release. Further developments of HEV model systems and novel technologies should yield a broader picture in the future.
Collapse
|
43
|
Wei X, Zhang H. Four and a half LIM domains protein 1 can be as a double-edged sword in cancer progression. Cancer Biol Med 2020; 17:270-281. [PMID: 32587768 PMCID: PMC7309467 DOI: 10.20892/j.issn.2095-3941.2019.0420] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/04/2020] [Indexed: 11/18/2022] Open
Abstract
Four and a half LIM domains protein 1 (FHL1), as the name suggests, contains four and a half LIM domains capable of interacting with various molecules, including structural proteins, kinases, and transcriptional machinery. FHL1 contains a zinc-finger domain and performs diverse roles in regulation of gene transcription, cytoarchitecture, cell proliferation, and signal transduction. Several studies have validated the importance of FHL1 in muscle development, myopathy, and cardiovascular diseases. Mutations in the FHL1 gene are associated with various myopathies. Recently, FHL1 was identified as a major host factor for chikungunya virus (CHIKV) infection in both humans and mice. Based on more recent findings over the last decade, FHL1 is proposed to play a dual role in cancer progression. On the one hand, FHL1 expression is suppressed in several cancer types, which correlates with increased metastatic disease and decreased survival. Moreover, FHL1 is reported to inhibit tumor cell growth and migration by associating with diverse signals, such as TGF-β and ER, and therefore considered a tumor suppressor. On the other hand, FHL1 can function as an oncogenic protein that promotes tumor progression upon phosphorylation, reflecting complex roles in cancer. This review primarily focuses on the dual role and underlying mechanisms of action of FHL1 in human cancer progression and its clinical relevance.
Collapse
Affiliation(s)
- Xiaofan Wei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Human Anatomy, Histology and Embryology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100191, China
| |
Collapse
|
44
|
Labeau A, Simon-Loriere E, Hafirassou ML, Bonnet-Madin L, Tessier S, Zamborlini A, Dupré T, Seta N, Schwartz O, Chaix ML, Delaugerre C, Amara A, Meertens L. A Genome-Wide CRISPR-Cas9 Screen Identifies the Dolichol-Phosphate Mannose Synthase Complex as a Host Dependency Factor for Dengue Virus Infection. J Virol 2020; 94:e01751-19. [PMID: 31915280 PMCID: PMC7081898 DOI: 10.1128/jvi.01751-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no specific therapies are available. Like other viruses, DENV relies heavily on the host cellular machinery for productive infection. In this study, we performed a genome-wide CRISPR-Cas9 screen using haploid HAP1 cells to identify host genes important for DENV infection. We identified DPM1 and -3, two subunits of the endoplasmic reticulum (ER) resident dolichol-phosphate mannose synthase (DPMS) complex, as host dependency factors for DENV and other related flaviviruses, such as Zika virus (ZIKV). The DPMS complex catalyzes the synthesis of dolichol-phosphate mannose (DPM), which serves as mannosyl donor in pathways leading to N-glycosylation, glycosylphosphatidylinositol (GPI) anchor biosynthesis, and C- or O-mannosylation of proteins in the ER lumen. Mutation in the DXD motif of DPM1, which is essential for its catalytic activity, abolished DPMS-mediated DENV infection. Similarly, genetic ablation of ALG3, a mannosyltransferase that transfers mannose to lipid-linked oligosaccharide (LLO), rendered cells poorly susceptible to DENV. We also established that in cells deficient for DPMS activity, viral RNA amplification is hampered and truncated oligosaccharides are transferred to the viral prM and E glycoproteins, affecting their proper folding. Overall, our study provides new insights into the host-dependent mechanisms of DENV infection and supports current therapeutic approaches using glycosylation inhibitors to treat DENV infection.IMPORTANCE Dengue disease, which is caused by dengue virus (DENV), has emerged as the most important mosquito-borne viral disease in humans and is a major global health concern. DENV encodes only few proteins and relies on the host cell machinery to accomplish its life cycle. The identification of the host factors important for DENV infection is needed to propose new targets for antiviral intervention. Using a genome-wide CRISPR-Cas9 screen, we identified DPM1 and -3, two subunits of the DPMS complex, as important host factors for the replication of DENV as well as other related viruses such as Zika virus. We established that DPMS complex plays dual roles during viral infection, both regulating viral RNA replication and promoting viral structural glycoprotein folding/stability. These results provide insights into the host molecules exploited by DENV and other flaviviruses to facilitate their life cycle.
Collapse
Affiliation(s)
- Athena Labeau
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | | | - Mohamed-Lamine Hafirassou
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Lucie Bonnet-Madin
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Sarah Tessier
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Alessia Zamborlini
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Dupré
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Nathalie Seta
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France
| | - Marie-Laure Chaix
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Constance Delaugerre
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Ali Amara
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Laurent Meertens
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| |
Collapse
|
45
|
Schnierle BS. A New Host Factor Essential for Chikungunya Virus. Trends Microbiol 2019; 28:2-4. [PMID: 31780232 DOI: 10.1016/j.tim.2019.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
FHL1 has been identified as a host protein that is essential for chikungunya virus (CHIKV) replication. FHL1 interacts with the chikungunya non-structural protein 3, which is thought to recruit cellular proteins to the viral replication complex. Inhibition of this interaction is a promising target for drug development.
Collapse
Affiliation(s)
- Barbara S Schnierle
- Paul-Ehrlich-Institut, Department of Virology, Paul-Ehrlich Strass 51-59, 63225 Langen, Germany.
| |
Collapse
|