1
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Sarkar R, Chhabra S, Tanwar M, Agarwal N, Kalia M. Japanese encephalitis virus hijacks ER-associated degradation regulators for its replication. J Gen Virol 2024; 105. [PMID: 38787366 DOI: 10.1099/jgv.0.001995] [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: 05/25/2024] Open
Abstract
Flaviviruses target their replication on membranous structures derived from the ER, where both viral and host proteins play crucial structural and functional roles. Here, we have characterized the involvement of the ER-associated degradation (ERAD) pathway core E3 ligase complex (SEL1L-HRD1) regulator proteins in the replication of Japanese encephalitis virus (JEV). Through high-resolution immunofluorescence imaging of JEV-infected HeLa cells, we observe that the virus replication complexes marked by NS1 strongly colocalize with the ERAD adapter SEL1L, lectin OS9, ER-membrane shuttle factor HERPUD1, E3 ubiquitin ligase HRD1 and rhomboid superfamily member DERLIN1. NS5 positive structures also show strong overlap with SEL1L. While these effectors show significant transcriptional upregulation, their protein levels remain largely stable in infected cells. siRNA mediated depletion of OS9, SEL1L, HERPUD1 and HRD1 significantly inhibit viral RNA replication and titres, with SEL1L depletion showing the maximum attenuation of replication. By performing protein translation arrest experiments, we show that SEL1L, and OS9 are stabilised upon JEV infection. Overall results from this study suggest that these ERAD effector proteins are crucial host-factors for JEV replication.
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Affiliation(s)
- Riya Sarkar
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
- Centre for Tuberculosis Research, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
- Present address: Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Simran Chhabra
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Mukesh Tanwar
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Nisheeth Agarwal
- Centre for Tuberculosis Research, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Manjula Kalia
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
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2
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Jobe NB, Huijben S, Paaijmans KP. Non-target effects of chemical malaria vector control on other biological and mechanical infectious disease vectors. Lancet Planet Health 2023; 7:e706-e717. [PMID: 37558351 DOI: 10.1016/s2542-5196(23)00136-5] [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: 07/28/2022] [Revised: 06/09/2023] [Accepted: 06/17/2023] [Indexed: 08/11/2023]
Abstract
Public health insecticides play a crucial role in malaria control and elimination programmes. Many other arthropods, including mechanical and biological vectors of infectious diseases, have similar indoor feeding or resting behaviours, or both, as malaria mosquitoes, and could be exposed to the same insecticides. In this Personal View, we show that little is known about the insecticide susceptibility status and the extent of exposure to malaria interventions of other arthropod species. We highlight that there is an urgent need to better understand the selection pressure for insecticide resistance in those vectors, to ensure current and future active ingredients remain effective in targeting a broad range of arthropod species, allowing us to prevent and control future outbreaks of infectious diseases other than malaria.
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Affiliation(s)
- Ndey Bassin Jobe
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Silvie Huijben
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Simon A Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA
| | - Krijn P Paaijmans
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Simon A Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA; The Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA; ISGlobal, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.
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3
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Rainey SM, Geoghegan V, Lefteri DA, Ant TH, Martinez J, McNamara CJ, Kamel W, de Laurent ZR, Castello A, Sinkins SP. Differences in proteome perturbations caused by the Wolbachia strain wAu suggest multiple mechanisms of Wolbachia-mediated antiviral activity. Sci Rep 2023; 13:11737. [PMID: 37474590 PMCID: PMC10359319 DOI: 10.1038/s41598-023-38127-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
Some strains of the inherited bacterium Wolbachia have been shown to be effective at reducing the transmission of dengue virus (DENV) and other RNA viruses by Aedes aegypti in both laboratory and field settings and are being deployed for DENV control. The degree of virus inhibition varies between Wolbachia strains. Density and tissue tropism can contribute to these differences but there are also indications that this is not the only factor involved: for example, strains wAu and wAlbA are maintained at similar intracellular densities but only wAu produces strong DENV inhibition. We previously reported perturbations in lipid transport dynamics, including sequestration of cholesterol in lipid droplets, with strains wMel/wMelPop in Ae. aegypti. To further investigate the cellular basis underlying these differences, proteomic analysis of midguts was carried out on Ae. aegypti lines carrying strains wAu and wAlbA: with the hypothesis that differences in perturbations may underline Wolbachia-mediated antiviral activity. Surprisingly, wAu-carrying midguts not only showed distinct proteome perturbations when compared to non-Wolbachia carrying and wAlbA-carrying midguts but also wMel-carrying midguts. There are changes in RNA processing pathways and upregulation of a specific set of RNA-binding proteins in the wAu-carrying line, including genes with known antiviral activity. Lipid transport and metabolism proteome changes also differ between strains, and we show that strain wAu does not produce the same cholesterol sequestration phenotype as wMel. Moreover, in contrast to wMel, wAu antiviral activity was not rescued by cyclodextrin treatment. Together these results suggest that wAu could show unique features in its inhibition of arboviruses compared to previously characterized Wolbachia strains.
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Affiliation(s)
| | - Vincent Geoghegan
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
- The University of York, York, UK
| | | | - Thomas H Ant
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Julien Martinez
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Wael Kamel
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Alfredo Castello
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Steven P Sinkins
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK.
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4
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Belavilas-Trovas A, Tastsoglou S, Dong S, Kefi M, Tavadia M, Mathiopoulos KD, Dimopoulos G. Long non-coding RNAs regulate Aedes aegypti vector competence for Zika virus and reproduction. PLoS Pathog 2023; 19:e1011440. [PMID: 37319296 DOI: 10.1371/journal.ppat.1011440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various cellular and metabolic processes in mosquitoes and all other organisms studied thus far. In particular, their involvement in essential processes such as reproduction makes them potential targets for the development of novel pest control approaches. However, their function in mosquito biology remains largely unexplored. To elucidate the role of lncRNAs in mosquitoes' reproduction and vector competence for arboviruses, we have implemented a computational and experimental pipeline to mine, screen, and characterize lncRNAs related to these two biological processes. Through analysis of publicly available Zika virus (ZIKV) infection-regulated Aedes aegypti transcriptomes, at least six lncRNAs were identified as being significantly upregulated in response to infection in various mosquito tissues. The roles of these ZIKV-regulated lncRNAs (designated Zinc1, Zinc2, Zinc3, Zinc9, Zinc10 and Zinc22), were further investigated by dsRNA-mediated silencing studies. Our results show that silencing of Zinc1, Zinc2, and Zinc22 renders mosquitoes significantly less permissive to ZIKV infection, while silencing of Zinc22 also reduces fecundity, indicating a potential role for Zinc22 in trade-offs between vector competence and reproduction. We also found that silencing of Zinc9 significantly increases fecundity but has no effect on ZIKV infection, suggesting that Zinc9 may be a negative regulator of oviposition. Our work demonstrates that some lncRNAs play host factor roles by facilitating viral infection in mosquitoes. We also show that lncRNAs can influence both mosquito reproduction and permissiveness to virus infection, two biological systems with important roles in mosquito vectorial capacity.
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Affiliation(s)
- Alexandros Belavilas-Trovas
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - Shengzhang Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Mary Kefi
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Mihra Tavadia
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Kostas D Mathiopoulos
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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5
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He J, Yang L, Chang P, Yang S, Wang Y, Lin S, Tang Q, Zhang Y. Zika Virus Induces Degradation of the Numb Protein Required through Embryonic Neurogenesis. Viruses 2023; 15:1258. [PMID: 37376558 DOI: 10.3390/v15061258] [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: 04/14/2023] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus and causes an infection associated with congenital Zika syndrome and Guillain-Barre syndrome. The mechanism of ZIKV-mediated neuropathogenesis is not well understood. In this study, we discovered that ZIKV induces degradation of the Numb protein, which plays a crucial role in neurogenesis by allowing asymmetric cell division during embryonic development. Our data show that ZIKV reduced the Numb protein level in a time- and dose-dependent manner. However, ZIKV infection appears to have minimal effect on the Numb transcript. Treatment of ZIKV-infected cells with a proteasome inhibitor restores the Numb protein level, which suggests the involvement of the ubiquitin-proteasome pathway. In addition, ZIKV infection shortens the half-life of the Numb protein. Among the ZIKV proteins, the capsid protein significantly reduces the Numb protein level. Immunoprecipitation of the Numb protein co-precipitates the capsid protein, indicating the interaction between these two proteins. These results provide insights into the ZIKV-cell interaction that might contribute to its impact on neurogenesis.
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Affiliation(s)
- Jia He
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Liping Yang
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Peixi Chang
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Shixing Yang
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Yu Wang
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Shaoli Lin
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Yanjin Zhang
- Molecular Virology Laboratory, Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
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6
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Arbovirus-vector protein interactomics identifies Loquacious as a co-factor for dengue virus replication in Aedes mosquitoes. PLoS Pathog 2022; 18:e1010329. [PMID: 36074777 PMCID: PMC9488832 DOI: 10.1371/journal.ppat.1010329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/20/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Efficient virus replication in Aedes vector mosquitoes is essential for the transmission of arboviral diseases such as dengue virus (DENV) in human populations. Like in vertebrates, virus-host protein-protein interactions are essential for viral replication and immune evasion in the mosquito vector. Here, 79 mosquito host proteins interacting with DENV non-structural proteins NS1 and NS5 were identified by label-free mass spectrometry, followed by a functional screening. We confirmed interactions with host factors previously observed in mammals, such as the oligosaccharyltransferase complex, and we identified protein-protein interactions that seem to be specific for mosquitoes. Among the interactors, the double-stranded RNA (dsRNA) binding protein Loquacious (Loqs), an RNA interference (RNAi) cofactor, was found to be essential for efficient replication of DENV and Zika virus (ZIKV) in mosquito cells. Loqs did not affect viral RNA stability or translation of a DENV replicon and its proviral activity was independent of its RNAi regulatory activity. Interestingly, Loqs colocalized with DENV dsRNA replication intermediates in infected cells and directly interacted with high affinity with DENV RNA in the 3’ untranslated region in vitro (KD = 48–62 nM). Our study provides an interactome for DENV NS1 and NS5 and identifies Loqs as a key proviral host factor in mosquitoes. We propose that DENV hijacks a factor of the RNAi mechanism for replication of its own RNA. Dengue virus is a mosquito-transmitted virus endemic to the tropics and subtropics, affecting an estimated 390 million people yearly. While the mechanisms of infection, pathogenesis and immune evasion have been extensively studied in humans, replication in Aedes mosquitoes has received much less attention, despite being a critical step in the arbovirus transmission cycle. Here, we used a proteomic approach to identify Aedes mosquito proteins recruited by dengue virus non-structural proteins NS1 and NS5. In addition to previously established host proteins that interact with DENV in mammals, we identified Loquacious, a double-stranded RNA binding protein involved in the RNAi-based antiviral immune response of mosquitoes. Unexpectedly, our data showed that Loquacious functions as a proviral factor that is recruited to replication organelles to facilitate viral replication. We propose that DENV exploits host immune components, such as Loquacious, for its own benefit.
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7
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Sun RC, Hu JH, Li XH, Liu CC, Liu YY, Chen J, Yang YC, Zhou B. Valosin-containing protein (VCP/p97) is responsible for the endocytotic trafficking of classical swine fever virus. Vet Microbiol 2022; 272:109511. [PMID: 35849988 DOI: 10.1016/j.vetmic.2022.109511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 11/25/2022]
Abstract
Classical swine fever virus (CSFV), a member of the Flaviviridae enveloped RNA virus family, results in an epidemic disease that brings serious economic losses to the pig industry worldwide. Valosin-containing protein (VCP/p97), a multifunctional active protein in cells, is related to the life activities of many viruses. However, the role of VCP in CSFV infection remains unknown. In this study, it was first found that treatment of VCP inhibitors impaired CSFV propagation. Furthermore, overexpression or knockdown of VCP showed that it was essential for CSFV infection. Moreover, confocal microscopy and immunoprecipitation assay showed that VCP was recruited for intracellular transport from early endosomes to lysosomes. Importantly, knockdown of VCP prevented CSFV to release from early endosomes, suggesting that VCP is a key factor for CSFV trafficking. Taken together, our findings first demonstrate that the endocytosis of CSFV into PK-15 cells requires the participation of VCP, providing the alternative approach for the discovery of novel anti-flaviviridae drugs.
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Affiliation(s)
- Rui-Cong Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jia-Huan Hu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Han Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chun-Chun Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ya-Yun Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jing Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yi-Chen Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Animal Bacteriology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China.
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8
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Ramos LFC, Martins M, Murillo JR, Domont GB, de Oliveira DMP, Nogueira FCS, Maciel-de-Freitas R, Junqueira M. Interspecies Isobaric Labeling-Based Quantitative Proteomics Reveals Protein Changes in the Ovary of Aedes aegypti Coinfected With ZIKV and Wolbachia. Front Cell Infect Microbiol 2022; 12:900608. [PMID: 35873163 PMCID: PMC9302590 DOI: 10.3389/fcimb.2022.900608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
Zika is a vector-borne disease caused by an arbovirus (ZIKV) and overwhelmingly transmitted by Ae. aegypti. This disease is linked to adverse fetal outcomes, mostly microcephaly in newborns, and other clinical aspects such as acute febrile illness and neurologic complications, for example, Guillain-Barré syndrome. One of the most promising strategies to mitigate arbovirus transmission involves releasing Ae. aegypti mosquitoes carrying the maternally inherited endosymbiont bacteria Wolbachia pipientis. The presence of Wolbachia is associated with a reduced susceptibility to arboviruses and a fitness cost in mosquito life-history traits such as fecundity and fertility. However, the mechanisms by which Wolbachia influences metabolic pathways leading to differences in egg production remains poorly known. To investigate the impact of coinfections on the reproductive tract of the mosquito, we applied an isobaric labeling-based quantitative proteomic strategy to investigate the influence of Wolbachia wMel and ZIKV infection in Ae. aegypti ovaries. To the best of our knowledge, this is the most complete proteome of Ae. aegypti ovaries reported so far, with a total of 3913 proteins identified, were also able to quantify 1044 Wolbachia proteins in complex sample tissue of Ae. aegypti ovary. Furthermore, from a total of 480 mosquito proteins modulated in our study, we discuss proteins and pathways altered in Ae. aegypti during ZIKV infections, Wolbachia infections, coinfection Wolbachia/ZIKV, and compared with no infection, focusing on immune and reproductive aspects of Ae. aegypti. The modified aspects mainly were related to the immune priming enhancement by Wolbachia presence and the modulation of the Juvenile Hormone pathway caused by both microorganism’s infection.
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Affiliation(s)
- Luís Felipe Costa Ramos
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michele Martins
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jimmy Rodriguez Murillo
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Gilberto Barbosa Domont
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Fábio César Sousa Nogueira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Maciel-de-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Department of Arbovirology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- *Correspondence: Magno Junqueira, ; Rafael Maciel-de-Freitas,
| | - Magno Junqueira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Magno Junqueira, ; Rafael Maciel-de-Freitas,
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9
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Shah PS, Beesabathuni NS, Fishburn AT, Kenaston MW, Minami SA, Pham OH, Tucker I. Systems Biology of Virus-Host Protein Interactions: From Hypothesis Generation to Mechanisms of Replication and Pathogenesis. Annu Rev Virol 2022; 9:397-415. [PMID: 35576593 PMCID: PMC10150767 DOI: 10.1146/annurev-virology-100520-011851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As obligate intracellular parasites, all viruses must co-opt cellular machinery to facilitate their own replication. Viruses often co-opt these cellular pathways and processes through physical interactions between viral and host proteins. In addition to facilitating fundamental aspects of virus replication cycles, these virus-host protein interactions can also disrupt physiological functions of host proteins, causing disease that can be advantageous to the virus or simply a coincidence. Consequently, unraveling virus-host protein interactions can serve as a window into molecular mechanisms of virus replication and pathogenesis. Identifying virus-host protein interactions using unbiased systems biology approaches provides an avenue for hypothesis generation. This review highlights common systems biology approaches for identification of virus-host protein interactions and the mechanistic insights revealed by these methods. We also review conceptual innovations using comparative and integrative systems biology that can leverage global virus-host protein interaction data sets to more rapidly move from hypothesis generation to mechanism. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Priya S Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA; .,Department of Chemical Engineering, University of California, Davis, California, USA
| | - Nitin S Beesabathuni
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Adam T Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Matthew W Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Shiaki A Minami
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Oanh H Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Inglis Tucker
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
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10
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Wang L, Moreira EA, Kempf G, Miyake Y, Oliveira Esteves BI, Fahmi A, Schaefer JV, Dreier B, Yamauchi Y, Alves MP, Plückthun A, Matthias P. Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways. Cell Rep 2022; 39:110736. [PMID: 35476995 PMCID: PMC9065369 DOI: 10.1016/j.celrep.2022.110736] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 11/11/2021] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
The deacetylase HDAC6 has tandem catalytic domains and a zinc finger domain (ZnF) binding ubiquitin (Ub). While the catalytic domain has an antiviral effect, the ZnF facilitates influenza A virus (IAV) infection and cellular stress responses. By recruiting Ub via the ZnF, HDAC6 promotes the formation of aggresomes and stress granules (SGs), dynamic structures associated with pathologies such as neurodegeneration. IAV subverts the aggresome/HDAC6 pathway to facilitate capsid uncoating during early infection. To target this pathway, we generate designed ankyrin repeat proteins (DARPins) binding the ZnF; one of these prevents interaction with Ub in vitro and in cells. Crystallographic analysis shows that it blocks the ZnF pocket where Ub engages. Conditional expression of this DARPin reversibly impairs infection by IAV and Zika virus; moreover, SGs and aggresomes are downregulated. These results validate the HDAC6 ZnF as an attractive target for drug discovery. A small synthetic protein (DARPin) blocks interaction between HDAC6 and ubiquitin This DARPin impairs infection by influenza and Zika virus at the uncoating step Both viruses contain ubiquitin associated with their capsid The DARPin also impacts the formation of aggresomes and stress granules
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Etori Aguiar Moreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Yasuyuki Miyake
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Blandina I Oliveira Esteves
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Amal Fahmi
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Marco P Alves
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland.
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11
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Wang S, Wang D, Duan Y, Zhou Z, Gao W, Zhang L. Cellular Nanosponges for Biological Neutralization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107719. [PMID: 34783078 DOI: 10.1002/adma.202107719] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Biological neutralization represents a general strategy that deploys therapeutic agents to bind with harmful molecules or infectious pathogens, block their bioactivity, and thus prevent them from causing the diseases. Here, a comprehensive review of using cell-membrane-coated nanoparticles, namely "cellular nanosponges," as host decoys for a wide range of biological neutralization applications is provided. Compared to traditional neutralization strategies, the cellular nanosponges stand out by mimicking susceptible host cells rather than accommodating the structures of the causative agents for the design of therapeutics. As all pathological agents must interact with host cells for bioactivity, nanosponges bypass the diversity of these agents and create function-driven and broad-spectrum neutralization solutions. The review focuses on the recent progress of using this new nanomedicine platform for neutralization against five primary pathological agents, including bacterial toxins, chemical toxicants, inflammatory cytokines, pathological antibodies, and viruses. Existing studies have established cellular nanosponges as versatile tools for biological neutralization. A thorough review of the cellular nanosponge technology is expected to inspire more refined cellular nanosponge designs and unique neutralization applications to address unsolved medical problems.
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Affiliation(s)
- Shuyan Wang
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dan Wang
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yaou Duan
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhidong Zhou
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Weiwei Gao
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
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12
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Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SS, Roos DS, McDowell MA. VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100860. [PMID: 34864248 PMCID: PMC9133010 DOI: 10.1016/j.cois.2021.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 06/12/2023]
Abstract
VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.
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Affiliation(s)
- Gloria I Giraldo-Calderón
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA; Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Calle 18 No 122-135, Cali, Colombia
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Sarah A Kelly
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Samuel Sc Rund
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA.
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13
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Koliński M, Kałużna E, Piwecka M. RNA–protein interactomes as invaluable resources to study RNA viruses: Insights from SARS CoV‐2 studies. WIRES RNA 2022; 13:e1727. [PMID: 35343064 PMCID: PMC9111084 DOI: 10.1002/wrna.1727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is essential for the successful development of therapeutic strategies against the COVID‐19 pandemic. Numerous studies have focused on the identification of host factors and cellular pathways involved in the viral replication cycle. The speed and magnitude of hijacking the translation machinery of host mRNA, and shutting down host transcription are still not well understood. Since SARS‐CoV‐2 relies on host RNA‐binding proteins for the infection progression, several efforts have been made to define the SARS‐CoV‐2 RNA‐bound proteomes (RNA–protein interactomes). Methodologies that enable the systemic capture of protein interactors of given RNA in vivo have been adapted for the identification of the SARS‐CoV‐2 RNA interactome. The obtained proteomic data aided by genome‐wide and targeted CRISPR perturbation screens, revealed host factors with either pro‐ or anti‐viral activity and highlighted cellular processes and factors involved in host response. We focus here on the recent studies on SARS‐CoV‐2 RNA–protein interactomes, with regard to both the technological aspects of RNA interactome capture methods and the obtained results. We also summarize several related studies, which were used in the interpretation of the SARS‐CoV‐2 RNA–protein interactomes. These studies provided the selection of host factors that are potentially suitable candidates for antiviral therapy. Finally, we underscore the importance of RNA–protein interactome studies in regard to the effective development of antiviral strategies against current and future threats. This article is categorized under:RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells
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Affiliation(s)
- Marcin Koliński
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Ewelina Kałużna
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Monika Piwecka
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
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14
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Schneider WM, Hoffmann HH. Flavivirus-host interactions: an expanding network of proviral and antiviral factors. Curr Opin Virol 2022; 52:71-77. [PMID: 34896863 PMCID: PMC8655497 DOI: 10.1016/j.coviro.2021.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
Flaviviruses are zoonotic pathogens transmitted by the bite of infected mosquitos and ticks and represent a constant burden to human health. Here we review recent literature aimed at uncovering how flaviviruses interact with the cells that they infect. A better understanding of these interactions may ultimately lead to novel therapeutic targets. We highlight several studies that employed low-biased methods to discover new protein-protein, protein-RNA, and genetic interactions, and spotlight recent work characterizing the host protein, TMEM41B, which has been shown to be critical for infection by diverse flaviviruses and coronaviruses.
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Affiliation(s)
- William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
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15
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Zhang L, Zhou D, Li Q, Zhu S, Imran M, Duan H, Cao S, Ke S, Ye J. The Antiviral Effect of Novel Steroidal Derivatives on Flaviviruses. Front Microbiol 2021; 12:727236. [PMID: 34690968 PMCID: PMC8527100 DOI: 10.3389/fmicb.2021.727236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Flaviviruses are the major emerging arthropod-borne pathogens globally. However, there is still no practical anti-flavivirus approach. Therefore, existing and emerging flaviviruses desperately need active broad-spectrum drugs. In the present study, the antiviral effect of steroidal dehydroepiandrosterone (DHEA) and 23 synthetic derivatives against flaviviruses such as Japanese encephalitis virus (JEV), Zika virus (ZIKV), and Dengue virus (DENV) were appraised by examining the characteristics of virus infection both in vitro and in vivo. Our results revealed that AV1003, AV1004 and AV1017 were the most potent inhibitors of flavivirus propagation in cells. They mainly suppress the viral infection in the post-invasion stage in a dose-dependent manner. Furthermore, orally administered compound AV1004 protected mice from lethal JEV infection by increasing the survival rate and reducing the viral load in the brain of infected mice. These results indicate that the compound AV1004 might be a potential therapeutic drug against JEV infection. These DHEA derivatives may provide lead scaffolds for further design and synthesis of potential anti-flavivirus potential drugs.
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Affiliation(s)
- Luping Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Dengyuan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiuyan Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shuo Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Imran
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shaoyong Ke
- National Biopesticide Engineering Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jing Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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16
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The Biogenesis of Dengue Virus Replication Organelles Requires the ATPase Activity of Valosin-Containing Protein. Viruses 2021; 13:v13102092. [PMID: 34696522 PMCID: PMC8540793 DOI: 10.3390/v13102092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 12/03/2022] Open
Abstract
The dengue virus (DENV) causes the most prevalent arthropod-borne viral disease worldwide. While its incidence is increasing in many countries, there is no approved antiviral therapy currently available. In infected cells, the DENV induces extensive morphological alterations of the endoplasmic reticulum (ER) to generate viral replication organelles (vRO), which include convoluted membranes (CM) and vesicle packets (VP) hosting viral RNA replication. The viral non-structural protein NS4B localizes to vROs and is absolutely required for viral replication through poorly defined mechanisms, which might involve cellular protein partners. Previous interactomic studies identified the ATPase valosin-containing protein (VCP) as a DENV NS4B-interacting host factor in infected cells. Using both pharmacological and dominant-negative inhibition approaches, we show, in this study, that VCP ATPase activity is required for efficient DENV replication. VCP associates with NS4B when expressed in the absence of other viral proteins while in infected cells, both proteins colocalize within large DENV-induced cytoplasmic structures previously demonstrated to be CMs. Consistently, VCP inhibition dramatically reduces the abundance of DENV CMs in infected cells. Most importantly, using a recently reported replication-independent plasmid-based vRO induction system, we show that de novo VP biogenesis is dependent on VCP ATPase activity. Overall, our data demonstrate that VCP ATPase activity is required for vRO morphogenesis and/or stability. Considering that VCP was shown to be required for the replication of other flaviviruses, our results argue that VCP is a pan-flaviviral host dependency factor. Given that new generation VCP-targeting drugs are currently evaluated in clinical trials for cancer treatment, VCP may constitute an attractive broad-spectrum antiviral target in drug repurposing approaches.
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Das P, Dudley JP. How Viruses Use the VCP/p97 ATPase Molecular Machine. Viruses 2021; 13:1881. [PMID: 34578461 PMCID: PMC8473244 DOI: 10.3390/v13091881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/22/2022] Open
Abstract
Viruses are obligate intracellular parasites that are dependent on host factors for their replication. One such host protein, p97 or the valosin-containing protein (VCP), is a highly conserved AAA ATPase that facilitates replication of diverse RNA- and DNA-containing viruses. The wide range of cellular functions attributed to this ATPase is consistent with its participation in multiple steps of the virus life cycle from entry and uncoating to viral egress. Studies of VCP/p97 interactions with viruses will provide important information about host processes and cell biology, but also viral strategies that take advantage of these host functions. The critical role of p97 in viral replication might be exploited as a target for development of pan-antiviral drugs that exceed the capability of virus-specific vaccines or therapeutics.
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Affiliation(s)
- Poulami Das
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Jaquelin P. Dudley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA;
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX 78712, USA
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