1
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Langeberg CJ, Szucs MJ, Sherlock ME, Vicens Q, Kieft JS. Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure. Nat Commun 2025; 16:4515. [PMID: 40374626 PMCID: PMC12081666 DOI: 10.1038/s41467-025-59657-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 04/28/2025] [Indexed: 05/17/2025] Open
Abstract
Viruses from the Flaviviridae family contain human relevant pathogens that generate subgenomic noncoding RNAs during infection using structured exoribonuclease resistant RNAs (xrRNAs). These xrRNAs block progression of host cell's 5' to 3' exoribonucleases. The structures of several xrRNAs from mosquito-borne and insect-specific flaviviruses reveal a conserved fold in which a ring-like motif encircles the 5' end of the xrRNA. However, the xrRNAs found in tick-borne and no known vector flaviviruses have distinct characteristics, and their 3-D fold was unsolved. Here, we verify the presence of xrRNAs in the encephalitis-causing tick-borne Powassan Virus. We characterize their secondary structure and obtain a mid-resolution map of one of these xrRNAs using cryo-EM, revealing a unique double-loop ring element. Integrating these results with covariation analysis, biochemical data, and existing high-resolution structural information yields a model in which the core of the fold matches the previously solved xrRNA fold, but the expanded double loop ring is remodeled upon encountering the exoribonuclease. These results are representative of a broad class of xrRNAs and reveal a conserved strategy of structure-based exoribonuclease resistance achieved through a unique topology across a viral family of importance to global health.
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Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Matthew J Szucs
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- New York Structural Biology Center, New York, NY, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA.
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- RNA BioScience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- New York Structural Biology Center, New York, NY, USA.
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2
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Bourgeois NM, Wei L, Kaushansky A, Aitchison JD. Exploiting Host Kinases to Combat Dengue Virus Infection and Disease. Antiviral Res 2025:106172. [PMID: 40348023 DOI: 10.1016/j.antiviral.2025.106172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 04/03/2025] [Accepted: 04/23/2025] [Indexed: 05/14/2025]
Abstract
The burden of dengue on human health has dramatically increased in recent years, underscoring the urgent need for effective therapeutic interventions. Despite decades of research since the discovery of the dengue virus, no specific antiviral treatments are available and strategies to reliably prevent severe disease remain limited. Direct-acting antivirals against dengue are under active investigation but have shown limited efficacy to date. An underappreciated Achille's heal of the virus is its dependence on host factors for infection and pathogenesis, each of which presents a potential avenue for therapeutic intervention. We and others have demonstrated that dengue virus relies on multiple host kinases, some of which are already targeted by clinically approved inhibitors. These offer drug repurposing opportunities for host-directed dengue treatment. Here, we summarize findings on the role of kinases in dengue infection and disease and highlight potential kinase targets for the development of innovative host-directed therapeutics.
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Affiliation(s)
- Natasha M Bourgeois
- Department of Global Health, University of Washington, Seattle WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA 98109, USA
| | - Ling Wei
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA 98109, USA
| | - Alexis Kaushansky
- Department of Global Health, University of Washington, Seattle WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA 98109, USA.
| | - John D Aitchison
- Department of Global Health, University of Washington, Seattle WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA 98109, USA.
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3
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Ravi V, Khare K, Mohite R, Mishra P, Halder S, Shukla R, Liu CSC, Yadav A, Soni J, Kanika, Chaudhary K, Neha, Tarai B, Budhiraja S, Khosla P, Sethi T, Imran M, Pandey R. Genomic hotspots in the DENV-2 serotype (E, NS4B, and NS5 genes) are associated with dengue disease severity in the endemic region of India. PLoS Negl Trop Dis 2025; 19:e0013034. [PMID: 40299925 PMCID: PMC12040166 DOI: 10.1371/journal.pntd.0013034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Accepted: 04/04/2025] [Indexed: 05/01/2025] Open
Abstract
Dengue virus (DENV) infection manifests a wide spectrum of clinical outcomes, ranging from mild fever to severe and potentially fatal disease, yet the factors driving this variability remain poorly understood. This study aims to unravel the relationship between clinical manifestations of dengue and the genetic diversity of the virus, providing insights into the genomic variability driving disease severity. To achieve this, serum samples were collected during a dengue outbreak in National Capital Region-Delhi, India, from June to November 2023. Serotyping of RNA isolated from 4,045 clinical serum samples revealed DENV-2 as the predominant serotype in circulation (n = 3702). Whole-genome sequencing for 3702 clinical samples was performed using Oxford Nanopore Technology (ONT) further yielding 3254 DENV-2 genomes with >50% coverage. However, all of them identified the cosmopolitan genotype of DENV-2, forming a distinct monophyletic cluster in the global phylogenetic tree. Comprehensive variant analysis uncovered 1,618,158 single nucleotide variations (SNVs) across the sequenced DENV-2 population. The clinico-genomic approach carried out in 1294 samples, mild (n = 473), moderate (n = 405) and clinically severe (n = 416), reveals a significant burden of SNVs in various genomic regions linked to differential disease outcomes. Statistical analyses, including Fisher's exact test and phi-correlation, identified hotspot regions in the Envelope (E), NS4B, and NS5 genes, where SNVs were strongly associated with mild and clinically severe phenotypes, providing insights into the genomic determinants of disease severity. Interestingly, the clustering of severity-associated SNVs in these genomic hotspot regions highlights their potential as therapeutic targets within the DENV genome. These findings offer a promising direction for developing early mitigation strategies and targeted interventions to manage the progression of severe DENV infections.
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Affiliation(s)
- Varsha Ravi
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Indraprastha Institute of Information Technology, Delhi, India
| | - Kriti Khare
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Pallavi Mishra
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Sayanti Halder
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Richa Shukla
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Chinky Shiu Chen Liu
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Aanchal Yadav
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jyoti Soni
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanika
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Komal Chaudhary
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Neha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | | | | | - Md Imran
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Rajesh Pandey
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Zhaguparov D, Zhao M, Sekar RV, Woodside MT. Identifying the interactions conferring functional mechanical rigidity on RNase-resistant RNA from Zika virus. Proc Natl Acad Sci U S A 2025; 122:e2417234122. [PMID: 40063803 PMCID: PMC11929477 DOI: 10.1073/pnas.2417234122] [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: 08/23/2024] [Accepted: 01/14/2025] [Indexed: 03/25/2025] Open
Abstract
Some viruses counter host-cell efforts to digest invading viral RNA by using special structures resistant to host RNases, known as exoribonuclease-resistant RNAs (xrRNAs). xrRNAs typically form an unusual fold with the 5'-end threaded through a ring consisting of a multihelix junction closed by a pseudoknot. By using single-molecule force spectroscopy (SMFS), we previously showed that a Zika virus xrRNA is extremely rigid mechanically, withstanding very high forces, and that this mechanical resistance-not simply the knot-like fold topology-is essential for RNase resistance. Here, we have determined which interactions are most important for generating mechanical rigidity in the Zika virus xrRNA, by systematically mutating tertiary contacts. We found that removing any of the tertiary contacts involving the threaded 5' end was sufficient to abrogate mechanical resistance. In contrast, breaking a single pseudoknot base pair was not sufficient to do so: Two broken pairs were needed. This hierarchy of interaction importance for mechanical rigidity was supported by simulations mapping how mechanical tension was distributed within the xrRNA. For all mutants, RNase resistance varied in lock-step with mechanical resistance, confirming the primary role of mechanical rigidity in xrRNA function. This work reveals which interactions are most important for Zika xrRNA function, with implications for targeting the xrRNA therapeutically.
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Affiliation(s)
- Daniiar Zhaguparov
- Department of Physics, University of Alberta, Edmonton, ABT6G2E1, Canada
| | - Meng Zhao
- Department of Physics, University of Alberta, Edmonton, ABT6G2E1, Canada
| | | | - Michael T. Woodside
- Department of Physics, University of Alberta, Edmonton, ABT6G2E1, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, ABT6G2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, ABT6G2E1, Canada
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5
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Khanra M, Ghosh I, Khatun S, Ghosh N, Gayen S. Dengue virus-host interactions: Structural and mechanistic insights for future therapeutic strategies. J Struct Biol 2025; 217:108196. [PMID: 40090430 DOI: 10.1016/j.jsb.2025.108196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 01/14/2025] [Accepted: 03/11/2025] [Indexed: 03/18/2025]
Abstract
Dengue pathogen, transmitted by mosquitoes, poses a growing threat as it is capable of inflicting severe illness in humans. Around 40% of the global population is currently affected by the virus, resulting in thousands of fatalities each year. The genetic blueprint of the virus comprises 10 proteins. Three proteins serve as structural components: the capsid (C), the precursor of the membrane protein (PrM/M), and the envelope protein (E). The other proteins serve as non-structural (NS) proteins, consisting of NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5. The virus relies on these NS proteins to expropriate host proteins for its replication. During their intracellular replication, these viruses engage with numerous host components and exploit the cellular machinery for tasks such as entry into various organs, propagation, and transmission. This review explores mainly the relationship between dengue viral protein and host proteins elucidating the development of viral-host interactions. These relationships between the virus and the host give important information on the processes behind viral replication and the etiology of disease, which in turn facilitates the creation of more potent treatment strategies.
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Affiliation(s)
- Moumita Khanra
- Molecular Pharmacology Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Indrani Ghosh
- Molecular Pharmacology Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Nilanjan Ghosh
- Molecular Pharmacology Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
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6
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Lin RJ, Lin LH, Chen ZP, Liu BC, Ko PC, Liao CL. The zinc finger protein ZFP36L2 inhibits flavivirus infection via the 5'-3' XRN1-mediated RNA decay pathway in the replication complexes. J Biomed Sci 2025; 32:27. [PMID: 39972499 PMCID: PMC11841009 DOI: 10.1186/s12929-025-01122-0] [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: 04/02/2024] [Accepted: 01/24/2025] [Indexed: 02/21/2025] Open
Abstract
BACKGROUND The zinc finger protein 36-like (ZFP36L) family is a CCCH-type group consisting of RNA-binding proteins, i.e., ZFP36L1 and ZFP36L2, which regulate cellular mRNA through the RNA decay pathway. ZFP36L1 combats flavivirus infections through the 5'-3' XRN1 and 3'-5' RNA exosome decay pathways. The present study clarified the role of human ZFP36L2 in the defense response of the host against flavivirus infection. METHODS Cell lines with overexpression or knockdown of ZFP36L2 were established using lentiviral vectors carrying genes for overexpression and short-hairpin RNA targeting specific genes, respectively. A plaque assay was employed to determine the viral titer. Immunofluorescence and real-time quantitative polymerase chain reaction were used to measure the viral RNA levels. The in vitro-transcribed RNA transcript derived from a replication-dead Japanese encephalitis virus (JEV) replicon containing the renilla luciferase reporter gene (J-R2A-NS5mt) was used to assess the stability of the flavivirus RNA. An RNA immunoprecipitation assay was used to detect the protein-RNA binding ability. Confocal microscopic images were captured to analyze protein colocalization. RESULTS ZFP36L2 served as an innate host defender against JEV and dengue virus. ZFP36L2 inhibited flavivirus infection solely through the 5'-3' XRN1 RNA decay pathway, whereas ZFP36L1 inhibited JEV infection via the 5'-3' XRN1 and 3'-5' RNA exosome RNA decay pathways. The direct binding between viral RNA and ZFP36L2 via its CCCH-type zinc finger motifs facilitated the degradation of flavivirus RNA mediated by 5'-3' XRN1. Furthermore, ZFP36L2 was localized in processing bodies (PBs), which participate in the 5'-3' XRN1-mediated RNA decay pathway. Nonetheless, the disruption of PBs did not affect the antiviral activity of ZFP36L2, suggesting that its localization is not essential for the function of the protein. Interestingly, the colocalization of ZFP36L2 and XRN1 with viral RNA and NS3 revealed that the antiviral activity of ZFP36L2 occurred within the replication complexes (RCs). CONCLUSIONS In summary, ZFP36L2 bound to and degraded viral RNA through the XRN1-mediated RNA decay pathway in the RCs, thereby inhibiting flavivirus replication. These findings provide valuable insights into the diverse antiviral mechanisms of the ZFP36-like family of proteins in the innate immune response against flavivirus infection.
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Affiliation(s)
- Ren-Jye Lin
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institute, Taipei, Taiwan.
| | - Li-Hsiung Lin
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institute, Taipei, Taiwan
| | - Zih-Ping Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Bing-Cheng Liu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Pin-Chen Ko
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Ching-Len Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
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7
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Freppel W, Barragan Torres VA, Uyar O, Anton A, Nouhi Z, Broquière M, Mazeaud C, Sow AA, Léveillé A, Gilbert C, Tremblay N, Owen JE, Bemis CL, Laulhé X, Lamarre A, Neufeldt CJ, Rodrigue-Gervais IG, Pichlmair A, Girard D, Scaturro P, Hulea L, Chatel-Chaix L. Dengue virus and Zika virus alter endoplasmic reticulum-mitochondria contact sites to regulate respiration and apoptosis. iScience 2025; 28:111599. [PMID: 39834870 PMCID: PMC11743106 DOI: 10.1016/j.isci.2024.111599] [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] [Received: 03/16/2023] [Revised: 07/17/2024] [Accepted: 12/11/2024] [Indexed: 01/22/2025] Open
Abstract
During infection, dengue virus (DENV) and Zika virus (ZIKV), two (ortho)flaviviruses of public health concern worldwide, induce alterations of mitochondria morphology to favor viral replication, suggesting a viral co-opting of mitochondria functions. Here, we performed an extensive transmission electron microscopy-based quantitative analysis to demonstrate that both DENV and ZIKV alter endoplasmic reticulum-mitochondria contact sites (ERMC). This correlated at the molecular level with an impairment of ERMC tethering protein complexes located at the surface of both organelles. Furthermore, virus infection modulated the mitochondrial oxygen consumption rate. Consistently, metabolomic and mitoproteomic analyses revealed a decrease in the abundance of several metabolites of the Krebs cycle and changes in the stoichiometry of the electron transport chain. Most importantly, ERMC destabilization by protein knockdown increased virus replication while dampening ZIKV-induced apoptosis. Overall, our results support the notion that flaviviruses hijack ERMCs to generate a cytoplasmic environment beneficial for sustained and efficient replication.
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Affiliation(s)
- Wesley Freppel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Viviana Andrea Barragan Torres
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Olus Uyar
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Anaïs Anton
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Zaynab Nouhi
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec H1T 2M4, Canada
| | - Mathilde Broquière
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Clément Mazeaud
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Aïssatou Aïcha Sow
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Alexanne Léveillé
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Claudia Gilbert
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Nicolas Tremblay
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Jonathan Eintrez Owen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheyanne L. Bemis
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xavier Laulhé
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Alain Lamarre
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Christopher J. Neufeldt
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian Gaël Rodrigue-Gervais
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, School of Medicine 81675 Munich, Germany
- German Center of Infection Research (DZIF), Munich partner site, Munich, Germany
| | - Denis Girard
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
| | - Pietro Scaturro
- Institute of Virology, Technical University of Munich, School of Medicine 81675 Munich, Germany
- Leibniz Institute of Virology 20251 Hamburg, Germany
| | - Laura Hulea
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada
| | - Laurent Chatel-Chaix
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada
- Center of Excellence in Orphan Diseases Research-Fondation Courtois, Québec, Canada
- Regroupement Intersectoriel de Recherche en Santé de l’Université du Québec, Québec, Canada
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8
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Eberhardt W, Nasrullah U, Pfeilschifter J. TRIM25: A Global Player of Cell Death Pathways and Promising Target of Tumor-Sensitizing Therapies. Cells 2025; 14:65. [PMID: 39851496 PMCID: PMC11764315 DOI: 10.3390/cells14020065] [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: 10/31/2024] [Revised: 12/16/2024] [Accepted: 12/20/2024] [Indexed: 01/26/2025] Open
Abstract
Therapy resistance still constitutes a common hurdle in the treatment of many human cancers and is a major reason for treatment failure and patient relapse, concomitantly with a dismal prognosis. In addition to "intrinsic resistance", e.g., acquired by random mutations, cancer cells typically escape from certain treatments ("acquired resistance") by a large variety of means, including suppression of apoptosis and other cell death pathways via upregulation of anti-apoptotic factors or through inhibition of tumor-suppressive proteins. Therefore, ideally, the tumor-cell-restricted induction of apoptosis is still considered a promising avenue for the development of novel, tumor (re)sensitizing therapies. A growing body of evidence has highlighted the multifaceted role of tripartite motif 25 (TRIM25) in controlling different aspects of tumorigenesis, including chemotherapeutic drug resistance. Accordingly, overexpression of TRIM25 is observed in many tumors and frequently correlates with a poor patient survival. In addition to its originally described function in antiviral innate immune response, TRIM25 can play critical yet context-dependent roles in apoptotic- and non-apoptotic-regulated cell death pathways, including pyroposis, necroptosis, ferroptosis, and autophagy. The review summarizes current knowledge of molecular mechanisms by which TRIM25 can interfere with different cell death modalities and thereby affect the success of currently used chemotherapeutics. A better understanding of the complex repertoire of cell death modulatory effects by TRIM25 is an essential prerequisite for validating TRIM25 as a potential target for future anticancer therapy to surmount the high failure rate of currently used chemotherapies.
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Affiliation(s)
- Wolfgang Eberhardt
- Institute of General Pharmacology and Toxicology, Goethe University Frankfurt, 60590 Frankfurt, Germany; (U.N.); (J.P.)
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9
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Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL. The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.17.628992. [PMID: 39763890 PMCID: PMC11702639 DOI: 10.1101/2024.12.17.628992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
Abstract
Exoribonuclease-resistant RNAs (xrRNAs) are viral RNA structures that block degradation by cellular 5'-3' exoribonucleases to produce subgenomic viral RNAs during infection. Initially discovered in flaviviruses, xrRNAs have since been identified in wide range of RNA viruses, including those that infect plants. High sequence variability among viral xrRNAs raises questions about the shared molecular features that characterize this functional RNA class. Here, we present the first structure of a plant-virus xrRNA in its active exoribonuclease-resistant conformation. The xrRNA forms a 9 base pair pseudoknot that creates a knot-like topology similar to that of flavivirus xrRNAs, despite lacking sequence similarity. Biophysical assays confirm a compact pseudoknot structure in solution, and functional studies validate its relevance both in vitro and during infection. Our study reveals how viral RNAs achieve a common functional outcome through highly divergent sequences and identifies the knot-like topology as a defining feature of xrRNAs.
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Affiliation(s)
- Jeanine G. Gezelle
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sophie M. Korn
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jayden T. McDonald
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Zhen Gong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna Erickson
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Chih-Hung Huang
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Feiyue Yang
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Matt Cronin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Yen-Wen Kuo
- Department of Plant Pathology, University of California, Davis, CA, USA
| | | | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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10
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Kalam N, Balasubramaniam V. Emerging Therapeutics in the Fight Against EV-D68: A Review of Current Strategies. Influenza Other Respir Viruses 2024; 18:e70064. [PMID: 39702696 PMCID: PMC11659119 DOI: 10.1111/irv.70064] [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: 07/21/2024] [Revised: 10/28/2024] [Accepted: 12/04/2024] [Indexed: 12/21/2024] Open
Abstract
Enterovirus-D68 (EV-D68) was first identified in 1962 in pediatric patients with acute respiratory conditions in California, USA (US). From the 1970s to 2005, EV-D68 was underestimated due to limited data and serotyping methods. In 2014, the United States experienced outbreaks of acute flaccid myelitis (AFM) in children EV-D68 positive. WIN-like compounds (pleconaril, pocapavir, and vapendavir) bind to the virus capsid and have been tested against various enteroviruses (EVs) in clinical trials. However, these compounds encountered issues with resistance and adverse effects, which impeded their approval by the Food and Drug Administration (FDA). Presently, the medical field lacks FDA-approved antiviral treatments or vaccines for EV-D68. Ongoing research efforts are dedicated to identifying viable therapeutics to address EV-D68 infections. This review explores the current advancements in antiviral therapies and potential therapeutics to mitigate the significant impact of EV-D68 infection control.
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Affiliation(s)
- Nida Kalam
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaBandar SunwayMalaysia
| | - Vinod R. M. T. Balasubramaniam
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaBandar SunwayMalaysia
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11
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Delli Ponti R, Vandelli A, Tartaglia GG. Subgenomic flaviviral RNAs and human proteins: in silico exploration of anti-host defense mechanisms. Comput Struct Biotechnol J 2024; 23:3527-3536. [PMID: 39435344 PMCID: PMC11492465 DOI: 10.1016/j.csbj.2024.09.029] [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] [Received: 06/21/2024] [Revised: 09/29/2024] [Accepted: 09/29/2024] [Indexed: 10/23/2024] Open
Abstract
Flaviviruses pose significant global health threats, infecting over 300 million people annually. Among their evasion strategies, the production of subgenomic flaviviral RNAs (sfRNAs) from the 3' UTR of viral genomes is particularly notable. Utilizing a comprehensive in silico approach with the catRAPID algorithm, we analyzed over 300,000 interactions between sfRNAs and human proteins derived from more than 8000 flavivirus genomes, including Dengue, Zika, Yellow Fever, West Nile, and Japanese Encephalitis viruses. By providing the first extensive atlas of sfRNA interactions, we offer new insights into how flaviviruses can manipulate host cellular machinery to facilitate viral survival and persistence. Our study not only validated known interactions but also revealed novel human proteins that could be involved in sfRNA-mediated host defense evasion, including helicases, splicing factors, and chemokines. These findings significantly expand the known interactome of sfRNAs with human proteins, underscoring their role in modulating host cellular pathways. Intriguingly, we predict interaction with stress granules, a critical component of the cellular response to viral infection, suggesting a mechanism by which flaviviruses inhibit their formation to evade host defenses. Moreover, a set of highly-interacting proteins in common among the sfRNAs showed predictive power to identify sfRNA-forming regions, highlighting how protein signatures could be used to annotate viruses. This atlas not only serves as a resource for exploring therapeutic targets but also aids in the identification of sfRNA biomarkers for improved flavivirus diagnostics.
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Affiliation(s)
- Riccardo Delli Ponti
- Centre for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, Genova GE 16152, Italy
| | - Andrea Vandelli
- Centre for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, Genova GE 16152, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, Genova GE 16152, Italy
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12
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Ko HY, Li YT, Yu HP, Li YY, Chiang MT, Simanjuntak Y, Lee YL, Dai SS, Chung PJ, Yu GY, Chao DY, Lin YL. Emergence and increased epidemic potential of dengue variants with the NS5 V357E mutation after consecutive years of transmission. iScience 2024; 27:110899. [PMID: 39524326 PMCID: PMC11550591 DOI: 10.1016/j.isci.2024.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/13/2024] [Accepted: 09/04/2024] [Indexed: 11/16/2024] Open
Abstract
Arboviruses can intensify epidemics by acquiring single nucleotide variants, leading to clade replacement and severe outbreaks. We investigated dengue virus serotype 2 evolution in consecutive outbreaks from 2001 to 2003 in Taiwan, coinciding with overwintering and increased epidemic severity. The virus evolved from the early-epidemic strain (Ia) to the late-epidemic strains (Ib and II), featuring three amino acid differences. The later strains demonstrated increased replication at lower temperatures, and the NS5V357E mutation significantly boosts virus replication and virulence, regardless of the other two mutations (ET46I and NS5I271T). Crucially, the late NS5V357E signature swiftly emerged after infecting mosquitos with the early Ia strain, through thoracic injection or by feeding on Ia-infected mice. Thus, we discover the molecular events involved in overwintering and increased disease severity between consecutive dengue outbreaks. This study enhances our understanding of dengue epidemiology, aiding in predicting and monitoring the emergence of dengue strains with increased epidemic potential.
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Affiliation(s)
- Hui-Ying Ko
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Microbiology and Public Health, National Chung-Hsing University, Taichung, Taiwan
| | - Yao-Tsun Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Han-Peng Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Yuan Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Tsai Chiang
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Yogy Simanjuntak
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shih-Syong Dai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Jung Chung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, National Chung-Hsing University, Taichung, Taiwan
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung City, Taiwan
- Department of Post-Baccalaureate Medicine, National Chung Hsing University, Taichung City, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
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13
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Sayyad Z, Acharya D, Gack MU. TRIM Proteins: Key Regulators of Immunity to Herpesvirus Infection. Viruses 2024; 16:1738. [PMID: 39599852 PMCID: PMC11599090 DOI: 10.3390/v16111738] [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: 09/27/2024] [Revised: 10/31/2024] [Accepted: 11/01/2024] [Indexed: 11/29/2024] Open
Abstract
Herpesviruses are ubiquitous DNA viruses that can establish latency and cause a range of mild to life-threatening diseases in humans. Upon infection, herpesviruses trigger the activation of several host antiviral defense programs that play critical roles in curbing virus replication and dissemination. Recent work from many groups has integrated our understanding of TRIM (tripartite motif) proteins, a specific group of E3 ligase enzymes, as pivotal orchestrators of mammalian antiviral immunity. In this review, we summarize recent advances in the modulation of innate immune signaling by TRIM proteins during herpesvirus infection, with a focus on the detection of herpes simplex virus type 1 (HSV-1, a prototype herpesvirus) by cGAS-STING, RIG-I-like receptors, and Toll-like receptors. We also review the latest progress in understanding the intricate relationship between herpesvirus replication and TRIM protein-regulated autophagy and apoptosis. Finally, we discuss the maneuvers used by HSV-1 and other herpesviruses to overcome TRIM protein-mediated virus restriction.
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Affiliation(s)
| | - Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, 9801 SW Discovery Way, Port St. Lucie, FL 34987, USA;
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, 9801 SW Discovery Way, Port St. Lucie, FL 34987, USA;
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14
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Napit R, Elong Ngono A, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha BK, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak. BMC Genomics 2024; 25:998. [PMID: 39449117 PMCID: PMC11515306 DOI: 10.1186/s12864-024-10879-x] [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: 05/27/2024] [Accepted: 10/08/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. METHODS AND RESULTS During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. CONCLUSION These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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Affiliation(s)
- Rajindra Napit
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Annie Elong Ngono
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aunji Pradhan
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Binod Khadka
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Smita Shrestha
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lata Karki
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rabindra Khatiwada
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Mamata Tamang
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Bimal Sharma Chalise
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | - Manisha Rawal
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | | | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sujan Shresta
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, USA.
| | - Krishna Das Manandhar
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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15
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Guo W, Jiang T, Rao J, Zhang Z, Zhang X, Su J, Yin C, Lu M, Hu X, Shan C. A safer cell-based yellow fever live attenuated vaccine protects mice against YFV infection. iScience 2024; 27:110972. [PMID: 39398246 PMCID: PMC11470684 DOI: 10.1016/j.isci.2024.110972] [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] [Received: 05/02/2024] [Revised: 07/07/2024] [Accepted: 09/13/2024] [Indexed: 10/15/2024] Open
Abstract
The live attenuated yellow fever vaccine (YF17D) has caused controversial safety issues in history with low-yield problems, which has led to a large population being unable to be vaccinated and vaccine shortage in facing recent outbreaks. Here, we report a safer live attenuated vaccine candidate, YF17D-Δ77, which contains 77 nucleotides deletion in the 3' untranslated region (3' UTR) of the YF17D genome. YF17D-Δ77 exhibited no neurotropism and decreased viscerotropism and caused significantly lower lethality in mice compared to YF17D. Mechanistically, the deletion enhanced the sensitivity of the virus to type I and type II interferon responses, which hindered viral replication. Encouragingly, YF17D-Δ77 provided comparable immune protection in mice as did YF17D. Even 10 PFU of YF17D-Δ77 completely protected mice against YFV-Asibi challenge. In addition, the Δ77 mutation showed excellent stability after successive passages in Vero cells. Collectively, the data suggest that further development of YF17D-Δ77 as vaccine candidate is warranted.
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Affiliation(s)
- Weiwei Guo
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Tingting Jiang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Juhong Rao
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zihan Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Xuekai Zhang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jiaoling Su
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Chunhong Yin
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Mingqing Lu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Xue Hu
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chao Shan
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
- Hubei Jiangxia Laboratory, Wuhan 430200, China
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16
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Pallarés H, González López Ledesma M, Oviedo-Rouco S, Castellano L, Costa Navarro G, Fernández-Alvarez A, D’Andreiz M, Aldas-Bulos V, Alvarez D, Bazzini A, Gamarnik A. Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest. Nucleic Acids Res 2024; 52:11128-11147. [PMID: 38917323 PMCID: PMC11472168 DOI: 10.1093/nar/gkae507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/08/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that causes severe outbreaks in human populations. ZIKV infection leads to the accumulation of small non-coding viral RNAs (known as sfRNAs) that are crucial for evasion of antiviral responses and for viral pathogenesis. However, the mechanistic understanding of how sfRNAs function remains incomplete. Here, we use recombinant ZIKVs and ribosome profiling of infected human cells to show that sfRNAs block translation of antiviral genes. Mechanistically, we demonstrate that specific RNA structures present in sfRNAs trigger PKR activation, which instead of limiting viral replication, enhances viral particle production. Although ZIKV infection induces mRNA expression of antiviral genes, translation efficiency of type I interferon and interferon stimulated genes were significantly downregulated by PKR activation. Our results reveal a novel viral adaptation mechanism mediated by sfRNAs, where ZIKV increases its fitness by repurposing the antiviral role of PKR into a proviral factor.
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Affiliation(s)
- Horacio M Pallarés
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Mora González López Ledesma
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Santiago Oviedo-Rouco
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Guadalupe S Costa Navarro
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana J Fernández-Alvarez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Josefina D’Andreiz
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Buenos Aires, Argentina
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
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17
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Castello A, Álvarez L, Kamel W, Iselin L, Hennig J. Exploring the expanding universe of host-virus interactions mediated by viral RNA. Mol Cell 2024; 84:3706-3721. [PMID: 39366356 DOI: 10.1016/j.molcel.2024.08.027] [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: 06/17/2024] [Revised: 08/16/2024] [Accepted: 08/23/2024] [Indexed: 10/06/2024]
Abstract
RNA is a central molecule in RNA virus biology; however, the interactions that it establishes with the host cell are only starting to be elucidated. In recent years, a methodology revolution has dramatically expanded the scope of host-virus interactions involving the viral RNA (vRNA). A second wave of method development has enabled the precise study of these protein-vRNA interactions in a life cycle stage-dependent manner, as well as providing insights into the interactome of specific vRNA species. This review discusses these technical advances and describes the new regulatory mechanisms that have been identified through their use. Among these, we discuss the importance of vRNA in regulating protein function through a process known as riboregulation. We envision that the elucidation of vRNA interactomes will open new avenues of research, including pathways to the discovery of host factors with therapeutic potential against viruses.
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Affiliation(s)
- Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK.
| | - Lucía Álvarez
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany
| | - Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK
| | - Louisa Iselin
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G611QH, Scotland, UK
| | - Janosch Hennig
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany; Department of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
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18
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Zoladek J, El Kazzi P, Caval V, Vivet-Boudou V, Cannac M, Davies EL, Rossi S, Bribes I, Rouilly L, Simonin Y, Jouvenet N, Decroly E, Paillart JC, Wilson SJ, Nisole S. A specific domain within the 3' untranslated region of Usutu virus confers resistance to the exonuclease ISG20. Nat Commun 2024; 15:8528. [PMID: 39358425 PMCID: PMC11447015 DOI: 10.1038/s41467-024-52870-w] [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: 02/27/2024] [Accepted: 09/18/2024] [Indexed: 10/04/2024] Open
Abstract
Usutu virus (USUV) and West Nile virus (WNV) are two closely related emerging mosquito-borne flaviviruses. Their natural hosts are wild birds, but they can also cause severe neurological disorders in humans. Both viruses are efficiently suppressed by type I interferon (IFN), which interferes with viral replication, dissemination, pathogenesis and transmission. Here, we show that the replication of USUV and WNV are inhibited through a common set of IFN-induced genes (ISGs), with the notable exception of ISG20, which USUV is resistant to. Strikingly, USUV was the only virus among all the other tested mosquito-borne flaviviruses that demonstrated resistance to the 3'-5' exonuclease activity of ISG20. Our findings highlight that the intrinsic resistance of the USUV genome, irrespective of the presence of cellular or viral proteins or protective post-transcriptional modifications, relies on a unique sequence present in its 3' untranslated region. Importantly, this genomic region alone can confer ISG20 resistance to a susceptible flavivirus, without compromising its infectivity, suggesting that it could be acquired by other flaviviruses. This study provides new insights into the strategy employed by emerging flaviviruses to overcome host defense mechanisms.
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Affiliation(s)
- Jim Zoladek
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Priscila El Kazzi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix Marseille Université, CNRS UMR 7257, Marseille, France
| | - Vincent Caval
- Virus Sensing and Signaling Unit, CNRS UMR 3569, Institut Pasteur, Université Paris Cité, Paris, France
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Marion Cannac
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Emma L Davies
- MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Soléna Rossi
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Inès Bribes
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Lucile Rouilly
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix Marseille Université, CNRS UMR 7257, Marseille, France
| | - Yannick Simonin
- Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), INSERM, Etablissement Français du Sang, Université de Montpellier, Montpellier, France
| | - Nolwenn Jouvenet
- Virus Sensing and Signaling Unit, CNRS UMR 3569, Institut Pasteur, Université Paris Cité, Paris, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix Marseille Université, CNRS UMR 7257, Marseille, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Sam J Wilson
- MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, Glasgow, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sébastien Nisole
- Viral Trafficking, Restriction and Innate Signaling, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France.
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19
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Álvarez L, Haubrich K, Iselin L, Gillioz L, Ruscica V, Lapouge K, Augsten S, Huppertz I, Choudhury NR, Simon B, Masiewicz P, Lethier M, Cusack S, Rittinger K, Gabel F, Leitner A, Michlewski G, Hentze MW, Allain FHT, Castello A, Hennig J. The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity. Nat Commun 2024; 15:8485. [PMID: 39353916 PMCID: PMC11445558 DOI: 10.1038/s41467-024-52918-x] [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: 12/07/2023] [Accepted: 09/23/2024] [Indexed: 10/03/2024] Open
Abstract
TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25's RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9). Using iCLIP2 in virus-infected and uninfected cells, we identified TRIM25's RNA sequence and structure specificity, that it binds specifically to viral RNA, and that the interaction with RNA is critical for its antiviral activity.
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Affiliation(s)
- Lucía Álvarez
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Kevin Haubrich
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - Laurent Gillioz
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Vincenzo Ruscica
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - Karine Lapouge
- Protein expression and purification facility, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Sandra Augsten
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Ina Huppertz
- Director's Research, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Nila Roy Choudhury
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Infection Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK
| | - Bernd Simon
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Pawel Masiewicz
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Mathilde Lethier
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, Grenoble Cedex, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, Grenoble Cedex, France
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Frank Gabel
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut de Biologie Structurale, Grenoble, France; Centre National de la Recherche Scientifique, Institut de Biologie Structurale, Grenoble, France
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Gracjan Michlewski
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Infection Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK
| | - Matthias W Hentze
- Director's Research, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany
| | - Frédéric H T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK.
| | - Janosch Hennig
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117, Heidelberg, Germany.
- Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95447, Bayreuth, Germany.
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20
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Meganck RM, Ogurlu R, Liu J, Moller-Tank S, Tse V, Blondel LO, Rosales A, Hall AC, Vincent HA, Moorman NJ, Marzluff WF, Asokan A. Sub-genomic flaviviral RNA elements increase the stability and abundance of recombinant AAV vector transcripts. J Virol 2024; 98:e0009524. [PMID: 39082815 PMCID: PMC11334430 DOI: 10.1128/jvi.00095-24] [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: 01/14/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Many viruses have evolved structured RNA elements that can influence transcript abundance and translational efficiency, and help evade host immune factors by hijacking cellular machinery during replication. Here, we evaluated the functional impact of sub-genomic flaviviral RNAs (sfRNAs) known to stall exoribonuclease activity, by incorporating these elements into recombinant adeno-associated viral (AAV) genome cassettes. Specifically, sfRNAs from Dengue, Zika, Japanese Encephalitis, Yellow Fever, Murray Valley Encephalitis, and West Nile viruses increased transcript stability and transgene expression compared to a conventional woodchuck hepatitis virus element (WPRE). Further dissection of engineered transcripts revealed that sfRNA elements (i) require incorporation in cis within the 3' untranslated region (UTR) of AAV genomes, (ii) require minimal dumbbell structures to exert the observed effects, and (iii) can stabilize AAV transcripts independent of 5'-3' exoribonuclease 1 (XRN1)-mediated decay. Additionally, preliminary in vivo assessment of AAV vectors bearing sfRNA elements in mice achieved increased transcript abundance and expression in cardiac tissue. Leveraging the functional versatility of engineered viral RNA elements may help improve the potency of AAV vector-based gene therapies. IMPORTANCE Viral RNA elements can hijack host cell machinery to control stability of transcripts and consequently, infection. Studies that help better understand such viral elements can provide insights into antiviral strategies and also potentially leverage these features for therapeutic applications. In this study, by incorporating structured flaviviral RNA elements into recombinant adeno-associated viral (AAV) vector genomes, we show improved AAV transcript stability and transgene expression can be achieved, with implications for gene transfer.
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Affiliation(s)
- Rita M. Meganck
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Roza Ogurlu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Jiacheng Liu
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Cornell University, Ithaca, New York, USA
| | - Sven Moller-Tank
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Regeneron Pharmaceutical, Inc., Tarrytown, New York, USA
| | - Victor Tse
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Leo O. Blondel
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan Rosales
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Aaron C. Hall
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather A. Vincent
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- TorqueBio, Inc., Durham, North Carolina, USA
| | - Nathaniel J. Moorman
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William F. Marzluff
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aravind Asokan
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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21
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Cannac M, Nisole S. TRIMming down Flavivirus Infections. Viruses 2024; 16:1262. [PMID: 39205236 PMCID: PMC11359179 DOI: 10.3390/v16081262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Flaviviruses comprise a large number of arthropod-borne viruses, some of which are associated with life-threatening diseases. Flavivirus infections are rising worldwide, mainly due to the proliferation and geographical expansion of their vectors. The main human pathogens are mosquito-borne flaviviruses, including dengue virus, Zika virus, and West Nile virus, but tick-borne flaviviruses are also emerging. As with any viral infection, the body's first line of defense against flavivirus infections is the innate immune defense, of which type I interferon is the armed wing. This cytokine exerts its antiviral activity by triggering the synthesis of hundreds of interferon-induced genes (ISGs), whose products can prevent infection. Among the ISGs that inhibit flavivirus replication, certain tripartite motif (TRIM) proteins have been identified. Although involved in other biological processes, TRIMs constitute a large family of antiviral proteins active on a wide range of viruses. Furthermore, whereas some TRIM proteins directly block viral replication, others are positive regulators of the IFN response. Therefore, viruses have developed strategies to evade or counteract TRIM proteins, and some even hijack certain TRIM proteins to their advantage. In this review, we summarize the current state of knowledge on the interactions between flaviviruses and TRIM proteins, covering both direct and indirect antiviral mechanisms.
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Affiliation(s)
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, 34090 Montpellier, France
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22
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Choi ANX, Siriphanitchakorn T, Choy MM, Ooi JSG, Manuel M, Tan HC, Lin LZ, Yap X, Gubler DJ, Ooi EE. A prM mutation that attenuates dengue virus replication in human cells enhances midgut infection in mosquitoes. Sci Transl Med 2024; 16:eadk4769. [PMID: 39083584 DOI: 10.1126/scitranslmed.adk4769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/10/2024] [Indexed: 08/02/2024]
Abstract
Dengue viruses (DENVs), like all viruses, evolve to perpetuate transmission of their species in their hosts. However, how DENV genetics influences dengue disease outbreaks remains poorly understood. Here, we examined isolates of the South Pacific dengue virus type 2 (DENV-2) that emerged in the 1970s and caused major dengue outbreaks in islands in this region until it reached Tonga, where only a few mild cases were reported. Phylogenetically, the DENV-2 strain isolated in Tonga segregated into a clade different from those clades infecting populations in other South Pacific islands. We found that this epidemiological observation could be explained by a single histidine-to-arginine substitution in position 86 of the premembrane (prM) protein of the Tonga DENV-2 strain. This mutation attenuated viral protein translation in mammalian cells but not in midgut cells of the mosquito vector Aedes aegypti. In mammalian cells, the prM mutation resulted in reduced translation of the viral genome and subsequent reduced virus replication. In contrast, in mosquito midgut cells, the prM mutation conferred a selective infection advantage, possibly because of the positively charged arginine residue introduced by the mutation. These findings provide molecular insights into the year-long silent transmission of attenuated DENV-2 in Tonga during the 1970s dengue outbreak in the South Pacific.
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Affiliation(s)
- Allyson N X Choi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Tanamas Siriphanitchakorn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Milly M Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Justin S G Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Menchie Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Lowell Z Lin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Xin Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Duane J Gubler
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Department of Clinical Research, Singapore General Hospital, Singapore 169608, Singapore
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23
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Nogueira CDO, Lopes da Silva MO, de Lima EV, Christoff RR, Gavino-Leopoldino D, Lemos FS, da Silva NE, Da Poian AT, Assunção-Miranda I, Figueiredo CP, Clarke JR. Immunosuppression-induced Zika virus reactivation causes brain inflammation and behavioral deficits in mice. iScience 2024; 27:110178. [PMID: 38993676 PMCID: PMC11237861 DOI: 10.1016/j.isci.2024.110178] [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] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
Zika virus (ZIKV) is a neurotropic flavivirus that can persist in several tissues. The late consequences of ZIKV persistence and whether new rounds of active replication can occur, remain unaddressed. Here, we investigated whether neonatally ZIKV-infected mice are susceptible to viral reactivation in adulthood. We found that when ZIKV-infected mice are treated with immunosuppressant drugs, they present increased susceptibility to chemically induced seizures. Levels of subgenomic flavivirus RNAs (sfRNAs) were increased, relative to the amounts of genomic RNAs, in the brains of mice following immunosuppression and were associated with changes in cytokine expression. We investigated the impact of immunosuppression on the testicles and found that ZIKV genomic RNA levels are increased in mice following immunosuppression, which also caused significant testicular damage. These findings suggest that ZIKV can establish new rounds of active replication long after acute stages of disease, so exposed patients should be monitored to ensure complete viral eradication.
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Affiliation(s)
- Clara de O Nogueira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | | | - Emanuelle V de Lima
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Raíssa Rilo Christoff
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Daniel Gavino-Leopoldino
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Felipe S Lemos
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Nicolas E da Silva
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Andrea T Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Iranaia Assunção-Miranda
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Claudia P Figueiredo
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
| | - Julia R Clarke
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, RJ, Brazil
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24
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Zarate-Sanchez E, George SC, Moya ML, Robertson C. Vascular dysfunction in hemorrhagic viral fevers: opportunities for organotypic modeling. Biofabrication 2024; 16:032008. [PMID: 38749416 PMCID: PMC11151171 DOI: 10.1088/1758-5090/ad4c0b] [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: 12/14/2023] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
The hemorrhagic fever viruses (HFVs) cause severe or fatal infections in humans. Named after their common symptom hemorrhage, these viruses induce significant vascular dysfunction by affecting endothelial cells, altering immunity, and disrupting the clotting system. Despite advances in treatments, such as cytokine blocking therapies, disease modifying treatment for this class of pathogen remains elusive. Improved understanding of the pathogenesis of these infections could provide new avenues to treatment. While animal models and traditional 2D cell cultures have contributed insight into the mechanisms by which these pathogens affect the vasculature, these models fall short in replicatingin vivohuman vascular dynamics. The emergence of microphysiological systems (MPSs) offers promising avenues for modeling these complex interactions. These MPS or 'organ-on-chip' models present opportunities to better mimic human vascular responses and thus aid in treatment development. In this review, we explore the impact of HFV on the vasculature by causing endothelial dysfunction, blood clotting irregularities, and immune dysregulation. We highlight how existing MPS have elucidated features of HFV pathogenesis as well as discuss existing knowledge gaps and the challenges in modeling these interactions using MPS. Understanding the intricate mechanisms of vascular dysfunction caused by HFV is crucial in developing therapies not only for these infections, but also for other vasculotropic conditions like sepsis.
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Affiliation(s)
- Evelyn Zarate-Sanchez
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States of America
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States of America
| | - Monica L Moya
- Materials Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Claire Robertson
- Materials Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
- UC Davis Comprehensive Cancer Center, Davis, CA, United States of America
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25
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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [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: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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26
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Bampali M, Kouvela A, Kesesidis N, Kassela K, Dovrolis N, Karakasiliotis I. West Nile Virus Subgenomic RNAs Modulate Gene Expression in a Neuronal Cell Line. Viruses 2024; 16:812. [PMID: 38793693 PMCID: PMC11125720 DOI: 10.3390/v16050812] [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: 02/19/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are small non-coding products of the incomplete degradation of viral genomic RNA. They accumulate during flaviviral infection and have been associated with many functional roles inside the host cell. Studies so far have demonstrated that sfRNA plays a crucial role in determining West Nile virus (WNV) pathogenicity. However, its modulatory role on neuronal homeostasis has not been studied in depth. In this study, we investigated the mechanism of sfRNA biosynthesis and its importance for WNV replication in neuronal cells. We found that sfRNA1 is functionally redundant for both replication and translation of WNV. However, the concurrent absence of sfRNA1 and sfRNA2 species is detrimental for the survival of the virus. Differential expression analysis on RNA-seq data from WT and ΔsfRNA replicon cell lines revealed transcriptional changes induced by sfRNA and identified a number of putative targets. Overall, it was shown that sfRNA contributes to the viral evasion by suppressing the interferon-mediated antiviral response. An additional differential expression analysis among replicon and control Neuro2A cells also clarified the transcriptional changes that support WNV replication in neuronal cells. Increased levels of translation and oxidative phosphorylation, post-translational modification processes, and activated DNA repair pathways were observed in replicon cell lines, while developmental processes such as axonal growth were deficient.
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Affiliation(s)
| | | | | | | | | | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.B.); (A.K.); (N.K.); (K.K.); (N.D.)
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27
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Bermudez-Santana CI, Gallego-Gómez JC. Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses 2024; 16:804. [PMID: 38793685 PMCID: PMC11125801 DOI: 10.3390/v16050804] [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: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.
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Affiliation(s)
- Clara Isabel Bermudez-Santana
- Computational and theoretical RNomics Group, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Gallego-Gómez
- Grupo de Medicina de Traslación, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
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28
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Malavige GN, Ogg GS. Molecular mechanisms in the pathogenesis of dengue infections. Trends Mol Med 2024; 30:484-498. [PMID: 38582622 DOI: 10.1016/j.molmed.2024.03.006] [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: 01/01/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Dengue is the most rapidly emerging climate-sensitive infection, and morbidity/mortality and disease incidence are rising markedly, leading to healthcare systems being overwhelmed. There are currently no specific treatments for dengue or prognostic markers to identify those who will progress to severe disease. Owing to an increase in the burden of illness and a change in epidemiology, many patients experience severe disease. Our limited understanding of the complex mechanisms of disease pathogenesis has significantly hampered the development of safe and effective treatments, vaccines, and biomarkers. We discuss the molecular mechanisms of dengue pathogenesis, the gaps in our knowledge, and recent advances, as well as the most crucial questions to be answered to enable the development of therapeutics, biomarkers, and vaccines.
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Affiliation(s)
- Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Sri Lanka; Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Graham S Ogg
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Sri Lanka; Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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Wu L, Zhang L, Feng S, Chen L, Lin C, Wang G, Zhu Y, Wang P, Cheng G. An evolutionarily conserved ubiquitin ligase drives infection and transmission of flaviviruses. Proc Natl Acad Sci U S A 2024; 121:e2317978121. [PMID: 38593069 PMCID: PMC11032495 DOI: 10.1073/pnas.2317978121] [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: 10/17/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
Mosquito-borne flaviviruses such as dengue (DENV) and Zika (ZIKV) cause hundreds of millions of infections annually. The single-stranded RNA genome of flaviviruses is translated into a polyprotein, which is cleaved equally into individual functional proteins. While structural proteins are packaged into progeny virions and released, most of the nonstructural proteins remain intracellular and could become cytotoxic if accumulated over time. However, the mechanism by which nonstructural proteins are maintained at the levels optimal for cellular fitness and viral replication remains unknown. Here, we identified that the ubiquitin E3 ligase HRD1 is essential for flaviviruses infections in both mammalian hosts and mosquitoes. HRD1 directly interacts with flavivirus NS4A and ubiquitylates a conserved lysine residue for ER-associated degradation. This mechanism avoids excessive accumulation of NS4A, which otherwise interrupts the expression of processed flavivirus proteins in the ER. Furthermore, a small-molecule inhibitor of HRD1 named LS-102 effectively interrupts DENV2 infection in both mice and Aedes aegypti mosquitoes, and significantly disturbs DENV transmission from the infected hosts to mosquitoes owing to reduced viremia. Taken together, this study demonstrates that flaviviruses have evolved a sophisticated mechanism to exploit the ubiquitination system to balance the homeostasis of viral proteins for their own advantage and provides a potential therapeutic target to interrupt flavivirus infection and transmission.
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Affiliation(s)
- Linjuan Wu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Liming Zhang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Shengyong Feng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Lu Chen
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Cai Lin
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
| | - Gang Wang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Yibin Zhu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
- Southwest United Graduate School, Kunming650092, China
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30
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Yuan H, Zou JH, Luo Y, Zhang J, Pan H, Cao S, Chen H, Song Y. Cellular nuclear-localized U2AF2 protein is hijacked by the flavivirus 3'UTR for viral replication complex formation and RNA synthesis. Vet Microbiol 2024; 290:109977. [PMID: 38185072 DOI: 10.1016/j.vetmic.2023.109977] [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: 09/20/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024]
Abstract
Japanese encephalitis virus (JEV) is a zoonotic pathogen belonging to the Flavivirus genus, causing viral encephalitis in humans and reproductive failure in swine. The 3' untranslated region (3'UTR) of JEV contains highly conservative secondary structures required for viral translation, RNA synthesis, and pathogenicity. Identification of host factors interacting with JEV 3'UTR is crucial for elucidating the underlying mechanism of flavivirus replication and pathogenesis. In this study, U2 snRNP auxiliary factor 2 (U2AF2) was identified as a novel cellular protein that interacts with the JEV genomic 3'UTR (the SL-I, SL-II, SL-III, and DB region) via its 1 to 148 amino acids. JEV infection or JEV 3' UTR on its own triggered the nuclear-localized U2AF2 redistributed to the cytoplasm and colocalized with viral replication complex. U2AF2 also interacts with JEV NS3 and NS5 protein, the downregulation of U2AF2 nearly abolished the formation of flavivirus replication vesicles. The production of JEV protein, RNA, and viral titers were all increased by U2AF2 overexpression and decreased by knockdown. U2AF2 also functioned as a pro-viral factor for Zika virus (ZIKV) and West Nile virus (WNV), but not for vesicular stomatitis virus (VSV). Mechanically, U2AF2 facilitated the synthesis of both positive- and negative-strand flavivirus RNA without affecting viral attachment, internalization or release process. Collectively, our work paves the way for developing U2AF2 as a potential flavivirus therapeutic target.
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Affiliation(s)
- Honggen Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jia Hui Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jinhua Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hong Pan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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Chen X, Li RT, Chen RY, Shi PD, Liu ZX, Lou YN, Wu M, Zhang RR, Tang W, Li XF, Qin CF. The subgenomic flaviviral RNA suppresses RNA interference through competing with siRNAs for binding RISC components. J Virol 2024; 98:e0195423. [PMID: 38289102 PMCID: PMC10878275 DOI: 10.1128/jvi.01954-23] [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: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 02/21/2024] Open
Abstract
During the life cycle of mosquito-borne flaviviruses, substantial subgenomic flaviviral RNA (sfRNA) is produced via incomplete degradation of viral genomic RNA by host XRN1. Zika virus (ZIKV) sfRNA has been detected in mosquito and mammalian somatic cells. Human neural progenitor cells (hNPCs) in the developing brain are the major target cells of ZIKV, and antiviral RNA interference (RNAi) plays a critical role in hNPCs. However, whether ZIKV sfRNA was produced in ZIKV-infected hNPCs as well as its function remains not known. In this study, we demonstrate that abundant sfRNA was produced in ZIKV-infected hNPCs. RNA pulldown and mass spectrum assays showed ZIKV sfRNA interacted with host proteins RHA and PACT, both of which are RNA-induced silencing complex (RISC) components. Functionally, ZIKV sfRNA can antagonize RNAi by outcompeting small interfering RNAs (siRNAs) in binding to RHA and PACT. Furthermore, the 3' stem loop (3'SL) of sfRNA was responsible for RISC components binding and RNAi inhibition, and 3'SL can enhance the replication of a viral suppressor of RNAi (VSR)-deficient virus in a RHA- and PACT-dependent manner. More importantly, the ability of binding to RISC components is conversed among multiple flaviviral 3'SLs. Together, our results identified flavivirus 3'SL as a potent VSR in RNA format, highlighting the complexity in virus-host interaction during flavivirus infection.IMPORTANCEZika virus (ZIKV) infection mainly targets human neural progenitor cells (hNPCs) and induces cell death and dysregulated cell-cycle progression, leading to microcephaly and other central nervous system abnormalities. RNA interference (RNAi) plays critical roles during ZIKV infections in hNPCs, and ZIKV has evolved to encode specific viral proteins to antagonize RNAi. Herein, we first show that abundant sfRNA was produced in ZIKV-infected hNPCs in a similar pattern to that in other cells. Importantly, ZIKV sfRNA acts as a potent viral suppressor of RNAi (VSR) by competing with siRNAs for binding RISC components, RHA and PACT. The 3'SL of sfRNA is responsible for binding RISC components, which is a conserved feature among mosquito-borne flaviviruses. As most known VSRs are viral proteins, our findings highlight the importance of viral non-coding RNAs during the antagonism of host RNAi-based antiviral innate immunity.
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Affiliation(s)
- Xiang Chen
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rui-Ting Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ru-Yi Chen
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Pan-Deng Shi
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zi-Xin Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ya-Nan Lou
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mei Wu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rong-Rong Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Tang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, China
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32
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [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: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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33
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Nemes K, Gil JF, Liebe S, Mansi M, Poimenopoulou E, Lennefors BL, Varrelmann M, Savenkov EI. Intermolecular base-pairing interactions, a unique topology and exoribonuclease-resistant noncoding RNAs drive formation of viral chimeric RNAs in plants. THE NEW PHYTOLOGIST 2024; 241:861-877. [PMID: 37897070 DOI: 10.1111/nph.19346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
In plants, exoribonuclease-resistant RNAs (xrRNAs) are produced by many viruses. Whereas xrRNAs contribute to the pathogenicity of these viruses, the role of xrRNAs in the virus infectious cycle remains elusive. Here, we show that xrRNAs produced by a benyvirus (a multipartite RNA virus with four genomic segments) in plants are involved in the formation of monocistronic coat protein (CP)-encoding chimeric RNAs. Naturally occurring chimeric RNAs, we discovered, are composed of 5'-end of RNA 2 and 3'-end of either RNA 3 or RNA 4 bearing conservative exoribonuclease-resistant 'coremin' region. Using computational tools and site-directed mutagenesis, we show that de novo formation of chimeric RNAs requires intermolecular base-pairing interaction between 'coremin' and 3'-proximal part of the CP gene of RNA 2 as well as a stem-loop structure immediately adjacent to the CP gene. Moreover, knockdown of the expression of the XRN4 gene, encoding 5'→3' exoribonuclease, inhibits biogenesis of both xrRNAs and chimeric RNAs. Our findings suggest a novel mechanism involving a unique tropology of the intermolecular base-pairing complex between xrRNAs and RNA2 to promote formation of chimeric RNAs in plants. XrRNAs, essential for chimeric RNA biogenesis, are generated through the action of cytoplasmic Xrn 4 5'→3' exoribonuclease conserved in all plant species.
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Affiliation(s)
- Katalin Nemes
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | - Jose F Gil
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
- VEDAS Corporación de Investigación e Innovación (VEDAS CII), Medellín, 050024, Colombia
| | - Sebastian Liebe
- Department of Phytopathology, Institute of Sugar Beet Research, Göttingen, 37079, Germany
| | - Mansi Mansi
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | - Efstratia Poimenopoulou
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | | | - Mark Varrelmann
- Department of Phytopathology, Institute of Sugar Beet Research, Göttingen, 37079, Germany
| | - Eugene I Savenkov
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
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Pronyk PM, de Alwis R, Rockett R, Basile K, Boucher YF, Pang V, Sessions O, Getchell M, Golubchik T, Lam C, Lin R, Mak TM, Marais B, Twee-Hee Ong R, Clapham HE, Wang L, Cahyorini Y, Polotan FGM, Rukminiati Y, Sim E, Suster C, Smith GJD, Sintchenko V. Advancing pathogen genomics in resource-limited settings. CELL GENOMICS 2023; 3:100443. [PMID: 38116115 PMCID: PMC10726422 DOI: 10.1016/j.xgen.2023.100443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genomic sequencing has emerged as a powerful tool to enhance early pathogen detection and characterization with implications for public health and clinical decision making. Although widely available in developed countries, the application of pathogen genomics among low-resource, high-disease burden settings remains at an early stage. In these contexts, tailored approaches for integrating pathogen genomics within infectious disease control programs will be essential to optimize cost efficiency and public health impact. We propose a framework for embedding pathogen genomics within national surveillance plans across a spectrum of surveillance and laboratory capacities. We adopt a public health approach to genomics and examine its application to high-priority diseases relevant in resource-limited settings. For each grouping, we assess the value proposition for genomics to inform public health and clinical decision-making, alongside its contribution toward research and development of novel diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Paul Michael Pronyk
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore.
| | - Ruklanthi de Alwis
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore; Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Rebecca Rockett
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Yann Felix Boucher
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 117549, Singapore; Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117549, Singapore; Nanyang Technological University, Singapore 639798, Singapore
| | - Vincent Pang
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - October Sessions
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Marya Getchell
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tanya Golubchik
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Connie Lam
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Raymond Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Tze-Minn Mak
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore
| | - Ben Marais
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Hannah Eleanor Clapham
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Linfa Wang
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Programme for Research in Epidemic Preparedness and Response (PREPARE), Ministry of Health, Singapore 169854, Singapore
| | - Yorin Cahyorini
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, Muntinlupa 1781, Metro Manila, Philippines
| | - Yuni Rukminiati
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Eby Sim
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Carl Suster
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Gavin J D Smith
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Vitali Sintchenko
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
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Rey-Cadilhac F, Rachenne F, Missé D, Pompon J. Viral Components Trafficking with(in) Extracellular Vesicles. Viruses 2023; 15:2333. [PMID: 38140574 PMCID: PMC10747788 DOI: 10.3390/v15122333] [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: 11/07/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The global public health burden exerted by viruses partially stems from viruses' ability to subdue host cells into creating an environment that promotes their multiplication (i.e., pro-viral). It has been discovered that viruses alter cell physiology by transferring viral material through extracellular vesicles (EVs), which serve as vehicles for intercellular communication. Here, we aim to provide a conceptual framework of all possible EV-virus associations and their resulting functions in infection output. First, we describe the different viral materials potentially associated with EVs by reporting that EVs can harbor entire virions, viral proteins and viral nucleic acids. We also delineate the different mechanisms underlying the internalization of these viral components into EVs. Second, we describe the potential fate of EV-associated viral material cargo by detailing how EV can circulate and target a naive cell once secreted. Finally, we itemize the different pro-viral strategies resulting from EV associations as the Trojan horse strategy, an alternative mode of viral transmission, an expansion of viral cellular tropism, a pre-emptive alteration of host cell physiology and an immunity decoy. With this conceptual overview, we aim to stimulate research on EV-virus interactions.
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Affiliation(s)
- Félix Rey-Cadilhac
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (F.R.-C.); (F.R.); (D.M.)
- Faculty of Science, Université de Montpellier, 34095 Montpellier, France
| | - Florian Rachenne
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (F.R.-C.); (F.R.); (D.M.)
- Faculty of Science, Université de Montpellier, 34095 Montpellier, France
| | - Dorothée Missé
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (F.R.-C.); (F.R.); (D.M.)
| | - Julien Pompon
- MIVEGEC, Université de Montpellier, IRD, CNRS, 34394 Montpellier, France; (F.R.-C.); (F.R.); (D.M.)
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36
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Liu Y, Guan W, Liu H. Subgenomic Flaviviral RNAs of Dengue Viruses. Viruses 2023; 15:2306. [PMID: 38140548 PMCID: PMC10747610 DOI: 10.3390/v15122306] [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: 10/24/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are produced during flavivirus infections in both arthropod and vertebrate cells. They are undegraded products originating from the viral 3' untranslated region (3' UTR), a result of the action of the host 5'-3' exoribonuclease, Xrn1, when it encounters specific RNA structures known as Xrn1-resistant RNAs (xrRNAs) within the viral 3' UTR. Dengue viruses generate three to four distinct species of sfRNAs through the presence of two xrRNAs and two dumbbell structures (DBs). The tertiary structures of xrRNAs have been characterized to form a ringlike structure around the 5' end of the viral RNA, effectively inhibiting the activity of Xrn1. The most important role of DENV sfRNAs is to inhibit host antiviral responses by interacting with viral and host proteins, thereby influencing viral pathogenicity, replicative fitness, epidemiological fitness, and transmission. In this review, we aimed to summarize the biogenesis, structures, and functions of DENV sfRNAs, exploring their implications for viral interference.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Wuxiang Guan
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
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37
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Jain S, Vimal N, Angmo N, Sengupta M, Thangaraj S. Dengue Vaccination: Towards a New Dawn of Curbing Dengue Infection. Immunol Invest 2023; 52:1096-1149. [PMID: 37962036 DOI: 10.1080/08820139.2023.2280698] [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] [Indexed: 11/15/2023]
Abstract
Dengue is an infectious disease caused by dengue virus (DENV) and is a serious global burden. Antibody-dependent enhancement and the ability of DENV to infect immune cells, along with other factors, lead to fatal Dengue Haemorrhagic Fever and Dengue Shock Syndrome. This necessitates the development of a robust and efficient vaccine but vaccine development faces a number of hurdles. In this review, we look at the epidemiology, genome structure and cellular targets of DENV and elaborate upon the immune responses generated by human immune system against DENV infection. The review further sheds light on various challenges in development of a potent vaccine against DENV which is followed by presenting a current account of different vaccines which are being developed or have been licensed.
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Affiliation(s)
- Sidhant Jain
- Independent Researcher, Institute for Globally Distributed Open Research and Education (IGDORE), Rewari, India
| | - Neha Vimal
- Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| | - Nilza Angmo
- Maitreyi College, University of Delhi, Delhi, India
| | - Madhumita Sengupta
- Janki Devi Bajaj Government Girls College, University of Kota, Kota, India
| | - Suraj Thangaraj
- Swami Ramanand Teerth Rural Government Medical College, Maharashtra University of Health Sciences, Ambajogai, India
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Jaeger AS, Marano J, Riemersma KK, Castaneda D, Pritchard EM, Pritchard JC, Bohm EK, Baczenas JJ, O'Connor SL, Weger-Lucarelli J, Friedrich TC, Aliota MT. Gain without pain: adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector. J Virol 2023; 97:e0116223. [PMID: 37800949 PMCID: PMC10653995 DOI: 10.1128/jvi.01162-23] [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: 07/27/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
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Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kasen K. Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David Castaneda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Elise M. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
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Zoladek J, Nisole S. Mosquito-borne flaviviruses and type I interferon: catch me if you can! Front Microbiol 2023; 14:1257024. [PMID: 37965539 PMCID: PMC10642725 DOI: 10.3389/fmicb.2023.1257024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Mosquito-borne flaviviruses include many viruses that are important human pathogens, including Yellow fever virus, Dengue virus, Zika virus and West Nile virus. While these viruses have long been confined to tropical regions, they now pose a global public health concern, as the geographical distribution of their mosquito vectors has dramatically expanded. The constant threat of flavivirus emergence and re-emergence underlines the need for a better understanding of the relationships between these viruses and their hosts. In particular, unraveling how these viruses manage to bypass antiviral immune mechanisms could enable the design of countermeasures to limit their impact on human health. The body's first line of defense against viral infections is provided by the interferon (IFN) response. This antiviral defense mechanism takes place in two waves, namely the induction of type I IFNs triggered by viral infection, followed by the IFN signaling pathway, which leads to the synthesis of interferon-stimulated genes (ISGs), whose products inhibit viral replication. In order to spread throughout the body, viruses must race against time to replicate before this IFN-induced antiviral state hinders their dissemination. In this review, we summarize our current knowledge on the multiple strategies developed by mosquito-borne flaviviruses to interfere with innate immune detection and signaling pathways, in order to delay, if not prevent, the establishment of an antiviral response.
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Affiliation(s)
| | - Sébastien Nisole
- Viral Trafficking, Restriction and Innate Signaling, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
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Wen X, Irshad A, Jin H. The Battle for Survival: The Role of RNA Non-Canonical Tails in the Virus-Host Interaction. Metabolites 2023; 13:1009. [PMID: 37755289 PMCID: PMC10537345 DOI: 10.3390/metabo13091009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Terminal nucleotidyltransferases (TENTs) could generate a 'mixed tail' or 'U-rich tail' consisting of different nucleotides at the 3' end of RNA by non-templated nucleotide addition to protect or degrade cellular messenger RNA. Recently, there has been increasing evidence that the decoration of virus RNA terminus with a mixed tail or U-rich tail is a critical way to affect viral RNA stability in virus-infected cells. This paper first briefly introduces the cellular function of the TENT family and non-canonical tails, then comprehensively reviews their roles in virus invasion and antiviral immunity, as well as the significance of the TENT family in antiviral therapy. This review will contribute to understanding the role and mechanism of non-canonical RNA tailing in survival competition between the virus and host.
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Affiliation(s)
| | | | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China; (X.W.); (A.I.)
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Wang W, Dai S, Liu L, Fu Z, Yang R, Yu G, Ma Z, Zong H. Daily Rhythmicity of Muscle-Related and Rhythm Genes Expression in Mackerel Tuna ( Euthynnus affinis). BIOLOGY 2023; 12:1211. [PMID: 37759610 PMCID: PMC10525508 DOI: 10.3390/biology12091211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
The aim of this study was to investigate the circadian rhythm of muscle-related gene expression in mackerel tuna under different weather conditions. The experiment was carried out under two weather conditions at four sampling times (6:00, 12:00, 18:00, and 24:00) to determine the expression of growth, function, and rhythm genes: white muscle rhythm genes were rhythmic on sunny and cloudy days, except for PER3 and RORA; all functional genes had daily rhythmicity. Red muscle had daily rhythmicity on both sunny and cloudy days; functional genes had daily rhythmicity except for MBNL. The expression levels of the rhythm gene PER1 were determined to be significantly different by independent t-test samples in white muscle at 6:00, 12:00, 18:00, and 24:00 under different weather conditions; the expression levels of the functional genes MBNL and MSTN were both significantly different. In the red muscle, the expression of the rhythm genes PER3, REVERBA, and BMAL1 was determined by independent t-test samples at 6:00, 12:00, 18:00, and 24:00 on cloudy and sunny days; the functional gene MBNL was significantly different. The present study showed that mackerel tuna muscle rhythm genes and functional genes varied significantly in expression levels depending on weather, time of day, and light intensity and that the expression levels of myogenic genes were closely related to clock gene expression. The fish were also able to adapt to changes in light intensity in different weather conditions through positive physiological regulation.
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Affiliation(s)
- Wenwen Wang
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Shiming Dai
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Longlong Liu
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Zhengyi Fu
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Rui Yang
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Gang Yu
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Zhenhua Ma
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Humin Zong
- National Marine Environmental Center, Dalian 116023, China
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Chiffi G, Grandgirard D, Leib SL, Chrdle A, Růžek D. Tick-borne encephalitis: A comprehensive review of the epidemiology, virology, and clinical picture. Rev Med Virol 2023; 33:e2470. [PMID: 37392370 DOI: 10.1002/rmv.2470] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Tick-borne encephalitis virus (TBEV) is a flavivirus commonly found in at least 27 European and Asian countries. It is an emerging public health problem, with steadily increasing case numbers over recent decades. Tick-borne encephalitis virus affects between 10,000 and 15,000 patients annually. Infection occurs through the bite of an infected tick and, much less commonly, through infected milk consumption or aerosols. The TBEV genome comprises a positive-sense single-stranded RNA molecule of ∼11 kilobases. The open reading frame is > 10,000 bases long, flanked by untranslated regions (UTR), and encodes a polyprotein that is co- and post-transcriptionally processed into three structural and seven non-structural proteins. Tick-borne encephalitis virus infection results in encephalitis, often with a characteristic biphasic disease course. After a short incubation time, the viraemic phase is characterised by non-specific influenza-like symptoms. After an asymptomatic period of 2-7 days, more than half of patients show progression to a neurological phase, usually characterised by central and, rarely, peripheral nervous system symptoms. Mortality is low-around 1% of confirmed cases, depending on the viral subtype. After acute tick-borne encephalitis (TBE), a minority of patients experience long-term neurological deficits. Additionally, 40%-50% of patients develop a post-encephalitic syndrome, which significantly impairs daily activities and quality of life. Although TBEV has been described for several decades, no specific treatment exists. Much remains unknown regarding the objective assessment of long-lasting sequelae. Additional research is needed to better understand, prevent, and treat TBE. In this review, we aim to provide a comprehensive overview of the epidemiology, virology, and clinical picture of TBE.
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Affiliation(s)
- Gabriele Chiffi
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Denis Grandgirard
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Aleš Chrdle
- Department of Infectious Diseases, Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic
- Faculty of Health and Social Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic
- Royal Liverpool University Hospital, Liverpool, UK
| | - Daniel Růžek
- Veterinary Research Institute, Emerging Viral Diseases, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
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Rahimi-Tesiye M, Zaersabet M, Salehiyeh S, Jafari SZ. The role of TRIM25 in the occurrence and development of cancers and inflammatory diseases. Biochim Biophys Acta Rev Cancer 2023; 1878:188954. [PMID: 37437700 DOI: 10.1016/j.bbcan.2023.188954] [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: 03/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
The tripartite motif (TRIM) family proteins are a group of proteins involved in different signaling pathways. The changes in the expression regulation, function, and signaling of this protein family are associated with the occurrence and progression of a wide range of disorders. Given the importance of these proteins in pathogenesis, they can be considered as potential therapeutic targets for many diseases. TRIM25, as an E3-ubiquitin ligase, is involved in the development of various diseases and cellular mechanisms, including antiviral innate immunity and cell proliferation. The clinical studies conducted on restricting the function of this protein have reached promising results that can be further evaluated in the future. Here, we review the regulation of TRIM25 and its function in different diseases and signaling pathways, especially the retinoic acid-inducible gene-I (RIG-I) signaling which prompts many kinds of cancers and inflammatory disorders.
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Affiliation(s)
- Maryam Rahimi-Tesiye
- Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mona Zaersabet
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Sajad Salehiyeh
- Department of Physiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyedeh Zahra Jafari
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Graham ME, Merrick C, Akiyama BM, Szucs MJ, Leach S, Kieft JS, Beckham JD. Zika virus dumbbell-1 structure is critical for sfRNA presence and cytopathic effect during infection. mBio 2023; 14:e0110823. [PMID: 37417764 PMCID: PMC10470596 DOI: 10.1128/mbio.01108-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
All flaviviruses contain conserved RNA structures in the 3' untranslated region (3' UTR) that are important for flavivirus RNA replication, translation, and pathogenesis. Flaviviruses like Zika virus (ZIKV) contain multiple conserved RNA structures in the viral 3' UTR, including the structure known as dumbbell-1 (DB-1). Previous research has shown that the DB-1 structure is important for flavivirus positive-strand genome replication, but the functional role of the flavivirus DB-1 structure and the mechanism by which it contributes to viral pathogenesis are not known. Using the recently solved flavivirus DB RNA structural data, we designed two DB-1 mutant ZIKV infectious clones, termed ZIKV-TL.PK and ZIKV-p.2.5', which disrupt DB-1 tertiary folding. We found that viral positive-strand genome replication of both ZIKV DB-1 mutant clones is similar to wild-type (WT) ZIKV, but ZIKV DB-1 mutants exhibit significantly decreased cytopathic effect due to reduced caspase-3 activation. We next show that ZIKV DB-1 mutants exhibit decreased levels of sfRNA species compared to ZIKV-WT during infection. However, ZIKV DB-1 mutant 3' UTRs exhibit unchanged sfRNA biogenesis following XRN1 degradation in vitro. We also found that ZIKV DB-1 mutant virus (ZIKV-p.2.5') exhibited enhanced sensitivity to type I interferon treatment, and both ZIKV-DB-1 mutants exhibit reduced morbidity and mortality due to tissue-specific attenuated viral replication in brain tissue of interferon type I/II receptor knockout mice. We propose that the flavivirus DB-1 RNA structure maintains sfRNA levels during infection despite maintained sfRNA biogenesis, and these results indicate that ZIKV DB-dependent maintenance of sfRNA levels support caspase-3-dependent, cytopathic effect, type I interferon resistance, and viral pathogenesis in mammalian cells and in a ZIKV murine model of disease. IMPORTANCE The group of viruses termed flaviviruses cause important disease throughout the world and include dengue virus, Zika virus, Japanese encephalitis virus, and many more. All of these flaviviruses have highly conserved RNA structures in the untranslated regions of the virus genome. One of the shared RNA structures, termed the dumbbell region, is not well studied, but mutations in this region are important for vaccine development. In this study, we made structure-informed targeted mutations in the Zika virus dumbbell region and studied the effect on the virus. We found that Zika virus dumbbell mutants are significantly weakened or attenuated due to a decreased ability to produce non-coding RNA that is needed to support infection, support virus-induced cell death, and support escape from the host immune system. These data show that targeted mutations in the flavivirus dumbbell RNA structure may be an important approach to develop future vaccine candidates.
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Affiliation(s)
- Monica E. Graham
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Camille Merrick
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Benjamin M. Akiyama
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Matthew J. Szucs
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Sarah Leach
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jeffery S. Kieft
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J. David Beckham
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
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Campbell LK, Peery RM, Magor KE. Evolution and expression of the duck TRIM gene repertoire. Front Immunol 2023; 14:1220081. [PMID: 37622121 PMCID: PMC10445537 DOI: 10.3389/fimmu.2023.1220081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.
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Affiliation(s)
- Lee K. Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Katharine E. Magor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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Modahl CM, Chowdhury A, Low DHW, Manuel MC, Missé D, Kini RM, Mendenhall IH, Pompon J. Midgut transcriptomic responses to dengue and chikungunya viruses in the vectors Aedes albopictus and Aedes malayensis. Sci Rep 2023; 13:11271. [PMID: 37438463 DOI: 10.1038/s41598-023-38354-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/06/2023] [Indexed: 07/14/2023] Open
Abstract
Dengue (DENV) and chikungunya (CHIKV) viruses are among the most preponderant arboviruses. Although primarily transmitted through the bite of Aedes aegypti mosquitoes, Aedes albopictus and Aedes malayensis are competent vectors and have an impact on arbovirus epidemiology. Here, to fill the gap in our understanding of the molecular interactions between secondary vectors and arboviruses, we used transcriptomics to profile the whole-genome responses of A. albopictus to CHIKV and of A. malayensis to CHIKV and DENV at 1 and 4 days post-infection (dpi) in midguts. In A. albopictus, 1793 and 339 genes were significantly regulated by CHIKV at 1 and 4 dpi, respectively. In A. malayensis, 943 and 222 genes upon CHIKV infection, and 74 and 69 genes upon DENV infection were significantly regulated at 1 and 4 dpi, respectively. We reported 81 genes that were consistently differentially regulated in all the CHIKV-infected conditions, identifying a CHIKV-induced signature. We identified expressed immune genes in both mosquito species, using a de novo assembled midgut transcriptome for A. malayensis, and described the immune architectures. We found the JNK pathway activated in all conditions, generalizing its antiviral function to Aedines. Our comprehensive study provides insight into arbovirus transmission by multiple Aedes vectors.
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Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Liverpool School of Tropical Medicine, Liverpool, U.K
| | - Avisha Chowdhury
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Toronto Centre for Liver Disease, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | - Dolyce H W Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Menchie C Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France.
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47
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Ooi EE, Kalimuddin S. Insights into dengue immunity from vaccine trials. Sci Transl Med 2023; 15:eadh3067. [PMID: 37437017 DOI: 10.1126/scitranslmed.adh3067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The quest for an effective dengue vaccine has culminated in two approved vaccines and another that has completed phase 3 clinical trials. However, shortcomings exist in each, suggesting that the knowledge on dengue immunity used to develop these vaccines was incomplete. Vaccine trial findings could refine our understanding of dengue immunity, because these are experimentally derived, placebo-controlled data. Results from these trials suggest that neutralizing antibody titers alone are insufficient to inform protection against symptomatic infection, implicating a role for cellular immunity in protection. These findings have relevance for both future dengue vaccine development and application of current vaccines for maximal public health benefit.
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Affiliation(s)
- Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore 169856, Singapore
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Álvarez-Díaz DA, Usme-Ciro JA, Corchuelo S, Naizaque JR, Rivera JA, Castiblanco-Martínez HD, Torres-Fernández O, Rengifo AC. 5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus. Arch Virol 2023; 168:204. [PMID: 37428234 DOI: 10.1007/s00705-023-05820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/19/2023] [Indexed: 07/11/2023]
Abstract
The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-genome sequencing technologies to resolve the sequences of the genome ends. We modified a protocol for rapid amplification of cDNA ends (RACE) to determine the complete sequences of the 5' and 3' UTRs of a previously reported ZIKV isolate (GenBank no. MH544701.1). This strategy is useful for determining 5' and 3' UTR sequences of ZIKV isolates and will be useful for comparative genomics applications.
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Affiliation(s)
- Diego Alejandro Álvarez-Díaz
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
- Grupo de Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
| | - José Aldemar Usme-Ciro
- Centro de Investigación en Salud para el Trópico-CIST, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Sheryll Corchuelo
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
| | - Julián Ricardo Naizaque
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
| | - Jorge Alonso Rivera
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
| | | | - Orlando Torres-Fernández
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia
| | - Aura Caterine Rengifo
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
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Abstract
Re-emerging and new viral pathogens have caused significant morbidity and mortality around the world, as evidenced by the recent monkeypox, Ebola and Zika virus outbreaks and the ongoing COVID-19 pandemic. Successful viral infection relies on tactical viral strategies to derail or antagonize host innate immune defenses, in particular the production of type I interferons (IFNs) by infected cells. Viruses can thwart intracellular sensing systems that elicit IFN gene expression (that is, RIG-I-like receptors and the cGAS-STING axis) or obstruct signaling elicited by IFNs. In this Cell Science at a Glance article and the accompanying poster, we review the current knowledge about the major mechanisms employed by viruses to inhibit the activity of intracellular pattern-recognition receptors and their downstream signaling cascades leading to IFN-based antiviral host defenses. Advancing our understanding of viral immune evasion might spur unprecedented opportunities to develop new antiviral compounds or vaccines to prevent viral infectious diseases.
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Affiliation(s)
- Junji Zhu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
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50
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Hu H, Feng Y, He ML. Targeting Type I Interferon Induction and Signaling: How Zika Virus Escapes from Host Innate Immunity. Int J Biol Sci 2023; 19:3015-3028. [PMID: 37416780 PMCID: PMC10321277 DOI: 10.7150/ijbs.83056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Zika virus (ZIKV) infection causes neurological disorders and draws great attention. ZIKV infection can elicit a wide range of immune response. Type I interferons (IFNs) as well as its signaling cascade play crucial role in innate immunity against ZIKV infection and in turn ZIKV can antagonize them. ZIKV genome are mainly recognized by Toll-like receptors 3 (TLR3), TLR7/8 and RIG-I-like receptor 1 (RIG-1), which induces the expression of Type I IFNs and interferon-stimulated genes (ISGs). ISGs exert antiviral activity at different stages of the ZIKV life cycle. On the other hand, ZIKV takes multiple strategies to antagonize the Type Ⅰ IFN induction and its signaling pathway to establish a pathogenic infection, especially by using the viral nonstructural (NS) proteins. Most of the NS proteins can directly interact with the factors in the pathways to escape the innate immunity. In addition, structural proteins also participate in the innate immune evasion and activation of antibody-binding of blood dendritic cell antigen 2 (BDCA2) or inflammasome also be used to enhance ZIKV replication. In this review, we summarize the recent findings about the interaction between ZIKV infection and type I IFNs pathways and suggest potential strategies for antiviral drug development.
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Affiliation(s)
- Huan Hu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yaxiu Feng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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