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Nouwen LV, Breeuwsma M, Zaal EA, van de Lest CHA, Buitendijk I, Zwaagstra M, Balić P, Filippov DV, Berkers CR, van Kuppeveld FJM. Modulation of nucleotide metabolism by picornaviruses. PLoS Pathog 2024; 20:e1012036. [PMID: 38457376 PMCID: PMC10923435 DOI: 10.1371/journal.ppat.1012036] [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: 06/28/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Viruses actively reprogram the metabolism of the host to ensure the availability of sufficient building blocks for virus replication and spreading. However, relatively little is known about how picornaviruses-a large family of small, non-enveloped positive-strand RNA viruses-modulate cellular metabolism for their own benefit. Here, we studied the modulation of host metabolism by coxsackievirus B3 (CVB3), a member of the enterovirus genus, and encephalomyocarditis virus (EMCV), a member of the cardiovirus genus, using steady-state as well as 13C-glucose tracing metabolomics. We demonstrate that both CVB3 and EMCV increase the levels of pyrimidine and purine metabolites and provide evidence that this increase is mediated through degradation of nucleic acids and nucleotide recycling, rather than upregulation of de novo synthesis. Finally, by integrating our metabolomics data with a previously acquired phosphoproteomics dataset of CVB3-infected cells, we identify alterations in phosphorylation status of key enzymes involved in nucleotide metabolism, providing insight into the regulation of nucleotide metabolism during infection.
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Affiliation(s)
- Lonneke V. Nouwen
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martijn Breeuwsma
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Esther A. Zaal
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chris H. A. van de Lest
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge Buitendijk
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Pascal Balić
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Celia R. Berkers
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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2
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Hatfield D, Rodriguez W, Mehrmann T, Muller M. The antiviral protein Shiftless blocks p-body formation during KSHV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567185. [PMID: 38014318 PMCID: PMC10680731 DOI: 10.1101/2023.11.16.567185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
P-bodies (PB) are non-membranous foci involved in determining mRNA fate by affecting translation and mRNA decay. In this study, we identify the anti-viral factor SHFL as a potent disassembly factor of PB. We show that PBs remain sparse in the presence of SHFL even in the context of oxidative stress, a major trigger for PB induction. Mutational approaches revealed that SHFL RNA binding activity is not required for its PB disassembly function. However, we have identified a new region of SHFL which bridges two distant domains as responsible for PB disassembly. Furthermore, we show that SHFL ability to disrupt PB formation is directly linked to its anti-viral activity during KSHV infection. While WT SHFL efficiently restricts KSHV lytic cycle, PB disruption defective mutants no longer lead to reactivation defects. SHFL-mediated PB disassembly also leads to increased expression of key anti-viral cytokines, further expanding SHFL dependent anti-viral state. Taken together, our observations suggest a role of SHFL in PB disassembly, which could have important anti-viral consequences during infection.
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Boccaccio GL, Thomas MG, García CC. Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses. J Mol Biol 2023; 435:167976. [PMID: 36702393 DOI: 10.1016/j.jmb.2023.167976] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.
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Affiliation(s)
- Graciela Lidia Boccaccio
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Gabriela Thomas
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina. https://www.twitter.com/_gabithomas
| | - Cybele Carina García
- Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEN), and IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) and Universidad de Buenos Aires, Buenos Aires, Argentina
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4
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The main protease of SARS-CoV-2 cleaves histone deacetylases and DCP1A, attenuating the immune defense of the interferon-stimulated genes. J Biol Chem 2023; 299:102990. [PMID: 36758802 PMCID: PMC9907797 DOI: 10.1016/j.jbc.2023.102990] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019, constitutes an emerging human pathogen of zoonotic origin. A critical role in protecting the host against invading pathogens is carried out by interferon-stimulated genes (ISGs), the primary effectors of the type I interferon (IFN) response. All coronaviruses studied thus far have to first overcome the inhibitory effects of the IFN/ISG system before establishing efficient viral replication. However, whether SARS-CoV-2 evades IFN antiviral immunity by manipulating ISG activation remains to be elucidated. Here, we show that the SARS-CoV-2 main protease (Mpro) significantly suppresses the expression and transcription of downstream ISGs driven by IFN-stimulated response elements in a dose-dependent manner, and similar negative regulations were observed in two mammalian epithelial cell lines (simian Vero E6 and human A549). Our analysis shows that to inhibit the ISG production, Mpro cleaves histone deacetylases (HDACs) rather than directly targeting IFN signal transducers. Interestingly, Mpro also abolishes the activity of ISG effector mRNA-decapping enzyme 1a (DCP1A) by cleaving it at residue Q343. In addition, Mpro from different genera of coronaviruses has the protease activity to cleave both HDAC2 and DCP1A, even though the alphacoronaviruse Mpro exhibits weaker catalytic activity in cleaving HDAC2. In conclusion, our findings clearly demonstrate that SARS-CoV-2 Mpro constitutes a critical anti-immune effector that modulates the IFN/ISG system at multiple levels, thus providing a novel molecular explanation for viral immune evasion and allowing for new therapeutic approaches against coronavirus disease 2019 infection.
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5
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Pro-Viral and Anti-Viral Roles of the RNA-Binding Protein G3BP1. Viruses 2023; 15:v15020449. [PMID: 36851663 PMCID: PMC9959972 DOI: 10.3390/v15020449] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Viruses depend on host cellular resources to replicate. Interaction between viral and host proteins is essential for the pathogens to ward off immune responses as well as for virus propagation within the infected cells. While different viruses employ unique strategies to interact with diverse sets of host proteins, the multifunctional RNA-binding protein G3BP1 is one of the common targets for many viruses. G3BP1 controls several key cellular processes, including mRNA stability, translation, and immune responses. G3BP1 also serves as the central hub for the protein-protein and protein-RNA interactions within a class of biomolecular condensates called stress granules (SGs) during stress conditions, including viral infection. Increasing evidence suggests that viruses utilize distinct strategies to modulate G3BP1 function-either by degradation, sequestration, or redistribution-and control the viral life cycle positively and negatively. In this review, we summarize the pro-viral and anti-viral roles of G3BP1 during infection among different viral families.
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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7
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Kleer M, Mulloy RP, Robinson CA, Evseev D, Bui-Marinos MP, Castle EL, Banerjee A, Mubareka S, Mossman K, Corcoran JA. Human coronaviruses disassemble processing bodies. PLoS Pathog 2022; 18:e1010724. [PMID: 35998203 PMCID: PMC9439236 DOI: 10.1371/journal.ppat.1010724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/02/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
A dysregulated proinflammatory cytokine response is characteristic of severe coronavirus infections caused by SARS-CoV-2, yet our understanding of the underlying mechanism responsible for this imbalanced immune response remains incomplete. Processing bodies (PBs) are cytoplasmic membraneless ribonucleoprotein granules that control innate immune responses by mediating the constitutive decay or suppression of mRNA transcripts, including many that encode proinflammatory cytokines. PB formation promotes turnover or suppression of cytokine RNAs, whereas PB disassembly corresponds with the increased stability and/or translation of these cytokine RNAs. Many viruses cause PB disassembly, an event that can be viewed as a switch that rapidly relieves cytokine RNA repression and permits the infected cell to respond to viral infection. Prior to this submission, no information was known about how human coronaviruses (CoVs) impacted PBs. Here, we show SARS-CoV-2 and the common cold CoVs, OC43 and 229E, induced PB loss. We screened a SARS-CoV-2 gene library and identified that expression of the viral nucleocapsid (N) protein from SARS-CoV-2 was sufficient to mediate PB disassembly. RNA fluorescent in situ hybridization revealed that transcripts encoding TNF and IL-6 localized to PBs in control cells. PB loss correlated with the increased cytoplasmic localization of these transcripts in SARS-CoV-2 N protein-expressing cells. Ectopic expression of the N proteins from five other human coronaviruses (OC43, MERS, 229E, NL63 and SARS-CoV) did not cause significant PB disassembly, suggesting that this feature is unique to SARS-CoV-2 N protein. These data suggest that SARS-CoV-2-mediated PB disassembly contributes to the dysregulation of proinflammatory cytokine production observed during severe SARS-CoV-2 infection.
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Affiliation(s)
- Mariel Kleer
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rory P. Mulloy
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Carolyn-Ann Robinson
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Danyel Evseev
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maxwell P. Bui-Marinos
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo; Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, Master University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer A. Corcoran
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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8
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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9
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Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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10
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Epstein-Barr Virus BGLF2 commandeers RISC to interfere with cellular miRNA function. PLoS Pathog 2022; 18:e1010235. [PMID: 35007297 PMCID: PMC8782528 DOI: 10.1371/journal.ppat.1010235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/21/2022] [Accepted: 12/27/2021] [Indexed: 01/27/2023] Open
Abstract
The Epstein-Barr virus (EBV) BGLF2 protein is a tegument protein with multiple effects on the cellular environment, including induction of SUMOylation of cellular proteins. Using affinity-purification coupled to mass-spectrometry, we identified the miRNA-Induced Silencing Complex (RISC), essential for miRNA function, as a top interactor of BGLF2. We confirmed BGLF2 interaction with the Ago2 and TNRC6 components of RISC in multiple cell lines and their co-localization in cytoplasmic bodies that also contain the stress granule marker G3BP1. In addition, BGLF2 expression led to the loss of processing bodies in multiple cell types, suggesting disruption of RISC function in mRNA regulation. Consistent with this observation, BGLF2 disrupted Ago2 association with multiple miRNAs. Using let-7 miRNAs as a model, we tested the hypothesis that BGLF2 interfered with the function of RISC in miRNA-mediated mRNA silencing. Using multiple reporter constructs with 3’UTRs containing let-7a regulated sites, we showed that BGLF2 inhibited let-7a miRNA activity dependent on these 3’UTRs, including those from SUMO transcripts which are known to be regulated by let-7 miRNAs. In keeping with these results, we showed that BGLF2 increased the cellular level of unconjugated SUMO proteins without affecting the level of SUMO transcripts. Such an increase in free SUMO is known to drive SUMOylation and would account for the effect of BGLF2 in inducing SUMOylation. We further showed that BGLF2 expression inhibited the loading of let-7 miRNAs into Ago2 proteins, and conversely, that lytic infection with EBV lacking BGLF2 resulted in increased interaction of let-7a and SUMO transcripts with Ago2, relative to WT EBV infection. Therefore, we have identified a novel role for BGLF2 as a miRNA regulator and shown that one outcome of this activity is the dysregulation of SUMO transcripts that leads to increased levels of free SUMO proteins and SUMOylation. Epstein-Barr virus (EBV) infects most people worldwide, persists for life and is associated with several kinds of cancer. In order to undergo efficient lytic infection, EBV must manipulate multiple cellular pathways. BGLF2 is an EBV lytic protein known to modulate several cellular processes including increasing the modification of cellular proteins with the Small Ubiquitin-Like Modifier (SUMO), a process referred to as SUMOylation. Here we show for the first time that BGLF2 interacts with a cellular complex (RISC) required for miRNA function and interferes with the function of some cellular miRNAs by sequestering this complex. One of the consequences of this effect is the increased expression of SUMO proteins, due to inhibition of the miRNAs that normally downregulate their expression. The resulting increase in SUMO proteins drives SUMOylation, providing a mechanism for the previously reported BGLF2-induced SUMOylation of cellular proteins. In addition, the discovery of BGLF2 as a miRNA regulator suggests that this EBV protein can control many cellular pathways by interfering with cellular miRNAs that normally regulate them.
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Saito A, Shofa M, Ode H, Yumiya M, Hirano J, Okamoto T, Yoshimura SH. How Do Flaviviruses Hijack Host Cell Functions by Phase Separation? Viruses 2021; 13:v13081479. [PMID: 34452345 PMCID: PMC8402827 DOI: 10.3390/v13081479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Viral proteins interact with different sets of host cell components throughout the viral life cycle and are known to localize to the intracellular membraneless organelles (MLOs) of the host cell, where formation/dissolution is regulated by phase separation of intrinsically disordered proteins and regions (IDPs/IDRs). Viral proteins are rich in IDRs, implying that viruses utilize IDRs to regulate phase separation of the host cell organelles and augment replication by commandeering the functions of the organelles and/or sneaking into the organelles to evade the host immune response. This review aims to integrate current knowledge of the structural properties and intracellular localizations of viral IDPs to understand viral strategies in the host cell. First, the properties of viral IDRs are reviewed and similarities and differences with those of eukaryotes are described. The higher IDR content in viruses with smaller genomes suggests that IDRs are essential characteristics of viral proteins. Then, the interactions of the IDRs of flaviviruses with the MLOs of the host cell are investigated with emphasis on the viral proteins localized in the nucleoli and stress granules. Finally, the possible roles of viral IDRs in regulation of the phase separation of organelles and future possibilities for antiviral drug development are discussed.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan;
| | - Maho Yumiya
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Junki Hirano
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Toru Okamoto
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
- Center for Infectious Diseases Education and Research, Osaka University, Osaka 565-0871, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Shige H. Yoshimura
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
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Abstract
Several viruses were proved to inhibit the formation of RNA processing bodies (P-bodies); however, knowledge regarding whether enterovirus blocks P-body formation remains unclear, and the detailed molecular mechanisms and functions of picornavirus regulation of P-bodies are limited. Here we show the crucial role of 2A protease in inhibiting P-bodies to promote viral replication during enterovirus 71 infection. Moreover, we found that the activity of 2A protease is essential to inhibit P-body formation, which was proved by the result that infection of EV71-2AC110S, the 2A protease activity-inactivated recombinant virus, failed to block the formation of P-bodies. Furthermore, we showed DDX6, a scaffolding protein of P-bodies, interacted with viral RNA to facilitate viral replication rather than viral translation, by using a Renilla luciferase mRNA reporter system and capturing the nascent RNA assay. Altogether, our data firstly demonstrate that the 2A protease of enterovirus inhibits P-body formation to facilitate viral RNA synthesis by recruiting the P-body components to viral RNA. IMPORTANCE Processing bodies (P-bodies) are constitutively present in eukaryotic cells and play an important role in the mRNA cycle, including regulating gene expression and mRNA degradation. P-bodies are the structure that viruses to manipulate to facilitate their survival. Here, we show that the 2A protease alone was efficient to block P-body formation during enterovirus 71 infection and its activity was essential. When the assembly of P-bodies was blocked by 2A, DDX6 and 4E-T which were required for P-body formation bound to viral RNA to facilitate viral RNA synthesis. We propose a model revealing that EV71 manipulates P-body formation to generate an environment that is conducive to viral replication by facilitating viral RNA synthesis: 2A protease blocked P-body assembly to make it possible for virus to take advantage of P-body components.
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13
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Embarc-Buh A, Francisco-Velilla R, Martinez-Salas E. RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements. Viruses 2021; 13:952. [PMID: 34064059 PMCID: PMC8224014 DOI: 10.3390/v13060952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Importantly, not only the RNA sequence but also the RNA architecture imposed by the presence of specific structural domains mediates the interaction with host RNA-binding proteins (RBPs), ultimately affecting virus multiplication and spreading. In marked difference with other biological systems, the genome of positive strand RNA viruses is also the mRNA. Here we focus on distinct types of positive strand RNA viruses that differ in the regulatory elements used to promote translation of the viral RNA, as well as in the mechanisms used to evade the series of events connected to antiviral response, including translation shutoff induced in infected cells, assembly of stress granules, and trafficking stress.
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Affiliation(s)
| | | | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, 28049 Madrid, Spain; (A.E.-B.); (R.F.-V.)
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14
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Markiewicz L, Drazkowska K, Sikorski PJ. Tricks and threats of RNA viruses - towards understanding the fate of viral RNA. RNA Biol 2021; 18:669-687. [PMID: 33618611 PMCID: PMC8078519 DOI: 10.1080/15476286.2021.1875680] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 12/24/2022] Open
Abstract
Human innate cellular defence pathways have evolved to sense and eliminate pathogens, of which, viruses are considered one of the most dangerous. Their relatively simple structure makes the identification of viral invasion a difficult task for cells. In the course of evolution, viral nucleic acids have become one of the strongest and most reliable early identifiers of infection. When considering RNA virus recognition, RNA sensing is the central mechanism in human innate immunity, and effectiveness of this sensing is crucial for triggering an appropriate antiviral response. Although human cells are armed with a variety of highly specialized receptors designed to respond only to pathogenic viral RNA, RNA viruses have developed an array of mechanisms to avoid being recognized by human interferon-mediated cellular defence systems. The repertoire of viral evasion strategies is extremely wide, ranging from masking pathogenic RNA through end modification, to utilizing sophisticated techniques to deceive host cellular RNA degrading enzymes, and hijacking the most basic metabolic pathways in host cells. In this review, we aim to dissect human RNA sensing mechanisms crucial for antiviral immune defences, as well as the strategies adopted by RNA viruses to avoid detection and degradation by host cells. We believe that understanding the fate of viral RNA upon infection, and detailing the molecular mechanisms behind virus-host interactions, may be helpful for developing more effective antiviral strategies; which are urgently needed to prevent the far-reaching consequences of widespread, highly pathogenic viral infections.
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15
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Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C-like protease? Rev Med Virol 2021; 31:1-22. [PMID: 33624382 PMCID: PMC7883238 DOI: 10.1002/rmv.2206] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 is the etiological agent of the ongoing pandemic of coronavirus disease-2019, a multi-organ disease that has triggered an unprecedented global health and economic crisis. The virally encoded 3C-like protease (3CLpro ), which is named after picornaviral 3C protease (3Cpro ) due to their similarities in substrate recognition and enzymatic activity, is essential for viral replication and has been considered as the primary drug target. However, information regarding the cellular substrates of 3CLpro and its interaction with the host remains scarce, though recent work has begun to shape our understanding more clearly. Here we summarized and compared the mechanisms by which picornaviruses and coronaviruses have evolved to evade innate immune surveillance, with a focus on the established role of 3Cpro in this process. Through this comparison, we hope to highlight the potential action and mechanisms that are conserved and shared between 3Cpro and 3CLpro . In this review, we also briefly discussed current advances in the development of broad-spectrum antivirals targeting both 3Cpro and 3CLpro .
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Honglin Luo
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
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16
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Ng CS, Kasumba DM, Fujita T, Luo H. Spatio-temporal characterization of the antiviral activity of the XRN1-DCP1/2 aggregation against cytoplasmic RNA viruses to prevent cell death. Cell Death Differ 2020; 27:2363-2382. [PMID: 32034313 PMCID: PMC7370233 DOI: 10.1038/s41418-020-0509-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
Host nucleases are implicated in antiviral response through the processing of pathogen-derived nucleic acids. Among many host RNases, decapping enzymes DCP1 and 2, and 5'→3' exonuclease XRN1, which are components of the RNA decay machinery, have been extensively studied in prokaryotes, plants, and invertebrates but less so in mammalian systems. As a result, the implication of XRN1 and DCPs in viral replication, in particular, the spatio-temporal dynamics during RNA viral infections remains elusive. Here, we highlight that XRN1 and DCPs play a critical role in limiting several groups of RNA viral infections. This antiviral activity was not obvious in wild-type cells but clearly observed in type I interferon (IFN-I)-deficient cells. Mechanistically, infection with RNA viruses induced the enrichment of XRN1 and DCPs in viral replication complexes (vRCs), hence forming distinct cytoplasmic aggregates. These aggregates served as sites for direct interaction between XRN1, DCP1/2, and viral ribonucleoprotein that contains viral RNA (vRNA). Although these XRN1-DCP1/2-vRC-containing foci resemble antiviral stress granules (SGs) or P-body (PB), they did not colocalize with known SG markers and did not correlate with critical PB functions. Furthermore, the presence of 5' mono- and 5' triphosphate structures on vRNA was not required for the formation of XRN1-DCP1/2-vRC-containing foci. On the other hand, single-, double-stranded, and higher-ordered vRNA species play a role but are not deterministic for efficient formation of XRN1-DCP1/2 foci and consequent antiviral activity in a manner proportional to RNA length. These results highlight the mechanism behind the antiviral function of XRN1-DCP1/2 in RNA viral infections independent of IFN-I response, protein kinase R and PB function.
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Dacquin M Kasumba
- Centre de Recherche du Centre Hospitalier de I'Université de Montréal, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Honglin Luo
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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17
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Zhang ZJ, Gao Q, Fang XD, Ding ZH, Gao DM, Xu WY, Cao Q, Qiao JH, Yang YZ, Han C, Wang Y, Yuan X, Li D, Wang XB. CCR4, a RNA decay factor, is hijacked by a plant cytorhabdovirus phosphoprotein to facilitate virus replication. eLife 2020; 9:53753. [PMID: 32207684 PMCID: PMC7105381 DOI: 10.7554/elife.53753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
Carbon catabolite repression 4 (CCR4) is a conserved mRNA deadenylase regulating posttranscriptional gene expression. However, regulation of CCR4 in virus infections is less understood. Here, we characterized a pro-viral role of CCR4 in replication of a plant cytorhabdovirus, Barley yellow striate mosaic virus (BYSMV). The barley (Hordeum vulgare) CCR4 protein (HvCCR4) was identified to interact with the BYSMV phosphoprotein (P). The BYSMV P protein recruited HvCCR4 from processing bodies (PBs) into viroplasm-like bodies. Overexpression of HvCCR4 promoted BYSMV replication in plants. Conversely, knockdown of the small brown planthopper CCR4 inhibited viral accumulation in the insect vector. Biochemistry experiments revealed that HvCCR4 was recruited into N–RNA complexes by the BYSMV P protein and triggered turnover of N-bound cellular mRNAs, thereby releasing RNA-free N protein to bind viral genomic RNA for optimal viral replication. Our results demonstrate that the co-opted CCR4-mediated RNA decay facilitates cytorhabdovirus replication in plants and insects.
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Affiliation(s)
- Zhen-Jia Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Gao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao-Dong Fang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhi-Hang Ding
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dong-Min Gao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Ya Xu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Cao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ji-Hui Qiao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi-Zhou Yang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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18
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Holmes AC, Zagnoli-Vieira G, Caldecott KW, Semler BL. Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation. Viruses 2020; 12:E166. [PMID: 32023921 PMCID: PMC7077319 DOI: 10.3390/v12020166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we characterized the role of host cell protein tyrosyl-DNA phosphodiesterase 2 (TDP2) activity, also known as VPg unlinkase, in picornavirus infections in a human cell model of infection. TDP2/VPg unlinkase is used by picornaviruses to remove the small polypeptide, VPg (Virus Protein genome-linked, the primer for viral RNA synthesis), from virus genomic RNA. We utilized a CRISPR/Cas-9-generated TDP2 knock out (KO) human retinal pigment epithelial-1 (hRPE-1) cell line, in addition to the wild type (WT) counterpart for our studies. We determined that in the absence of TDP2, virus growth kinetics for two enteroviruses (poliovirus and coxsackievirus B3) were delayed by about 2 h. Virus titers were reduced by ~2 log10 units for poliovirus and 0.5 log10 units for coxsackievirus at 4 hours post-infection (hpi), and by ~1 log10 unit at 6 hpi for poliovirus. However, virus titers were nearly indistinguishable from those of control cells by the end of the infectious cycle. We determined that this was not the result of an alternative source of VPg unlinkase activity being activated in the absence of TPD2 at late times of infection. Viral protein production in TDP2 KO cells was also substantially reduced at 4 hpi for poliovirus infection, consistent with the observed growth kinetics delay, but reached normal levels by 6 hpi. Interestingly, this result differs somewhat from what has been reported previously for the TDP2 KO mouse cell model, suggesting that either cell type or species-specific differences might be playing a role in the observed phenotype. We also determined that catalytically inactive TDP2 does not rescue the growth defect, confirming that TDP2 5' phosphodiesterase activity is required for efficient virus replication. Importantly, we show for the first time that polysomes can assemble efficiently on VPg-linked RNA after the initial round of translation in a cell culture model, but both positive and negative strand RNA production is impaired in the absence of TDP2 at mid-times of infection, indicating that the presence of VPg on the viral RNA affects a step in the replication cycle downstream of translation (e.g., RNA synthesis). In agreement with this conclusion, we found that double-stranded RNA production (a marker of viral RNA synthesis) is delayed in TDP2 KO RPE-1 cells. Moreover, we show that premature encapsidation of nascent, VPg-linked RNA is not responsible for the observed virus growth defect. Our studies provide the first lines of evidence to suggest that either negative- or positive-strand RNA synthesis (or both) is a likely candidate for the step that requires the removal of VPg from the RNA for an enterovirus infection to proceed efficiently.
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Affiliation(s)
- Autumn C. Holmes
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
| | - Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Bert L. Semler
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
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19
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Odon V, Fros JJ, Goonawardane N, Dietrich I, Ibrahim A, Alshaikhahmed K, Nguyen D, Simmonds P. The role of ZAP and OAS3/RNAseL pathways in the attenuation of an RNA virus with elevated frequencies of CpG and UpA dinucleotides. Nucleic Acids Res 2019; 47:8061-8083. [PMID: 31276592 PMCID: PMC6735852 DOI: 10.1093/nar/gkz581] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/17/2022] Open
Abstract
Zinc finger antiviral protein (ZAP) is a powerful restriction factor for viruses with elevated CpG dinucleotide frequencies. We report that ZAP similarly mediates antiviral restriction against echovirus 7 (E7) mutants with elevated frequencies of UpA dinucleotides. Attenuation of both CpG- and UpA-high viruses and replicon mutants was reversed in ZAP k/o cell lines, and restored by plasmid-derived reconstitution of expression in k/o cells. In pull-down assays, ZAP bound to viral RNA transcripts with either CpG- and UpA-high sequences inserted in the R2 region. We found no evidence that attenuation of CpG- or UpA-high mutants was mediated through either translation inhibition or accelerated RNA degradation. Reversal of the attenuation of CpG-high, and UpA-high E7 viruses and replicons was also achieved through knockout of RNAseL and oligodenylate synthetase 3 (OAS3), but not OAS1. WT levels of replication of CpG- and UpA-high mutants were observed in OAS3 k/o cells despite abundant expression of ZAP, indicative of synergy or complementation of these hitherto unconnected pathways. The dependence on expression of ZAP, OAS3 and RNAseL for CpG/UpA-mediated attenuation and the variable and often low level expression of these pathway proteins in certain cell types, such as those of the central nervous system, has implications for the use of CpG-elevated mutants as attenuated live vaccines against neurotropic viruses.
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Affiliation(s)
- Valerie Odon
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Jelke J Fros
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.,Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Niluka Goonawardane
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Isabelle Dietrich
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Ahmad Ibrahim
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Kinda Alshaikhahmed
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
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20
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Gaete-Argel A, Márquez CL, Barriga GP, Soto-Rifo R, Valiente-Echeverría F. Strategies for Success. Viral Infections and Membraneless Organelles. Front Cell Infect Microbiol 2019; 9:336. [PMID: 31681621 PMCID: PMC6797609 DOI: 10.3389/fcimb.2019.00336] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of RNA homeostasis or “RNAstasis” is a central step in eukaryotic gene expression. From transcription to decay, cellular messenger RNAs (mRNAs) associate with specific proteins in order to regulate their entire cycle, including mRNA localization, translation and degradation, among others. The best characterized of such RNA-protein complexes, today named membraneless organelles, are Stress Granules (SGs) and Processing Bodies (PBs) which are involved in RNA storage and RNA decay/storage, respectively. Given that SGs and PBs are generally associated with repression of gene expression, viruses have evolved different mechanisms to counteract their assembly or to use them in their favor to successfully replicate within the host environment. In this review we summarize the current knowledge about the viral regulation of SGs and PBs, which could be a potential novel target for the development of broad-spectrum antiviral therapies.
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Affiliation(s)
- Aracelly Gaete-Argel
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Chantal L Márquez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Gonzalo P Barriga
- Emerging Viruses Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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21
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Liu L, Weiss E, Panas MD, Götte B, Sellberg S, Thaa B, McInerney GM. RNA processing bodies are disassembled during Old World alphavirus infection. J Gen Virol 2019; 100:1375-1389. [DOI: 10.1099/jgv.0.001310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RNA processing bodies (P-bodies) are non-membranous cytoplasmic aggregates of mRNA and proteins involved in mRNA decay and translation repression. P-bodies actively respond to environmental stresses, associated with another type of RNA granules, known as stress granules (SGs). Alphaviruses were previously shown to block SG induction at late stages of infection, which is important for efficient viral growth. In this study, we found that P-bodies were disassembled or reduced in number very early in infection with Semliki Forest virus (SFV) or chikungunya virus (CHIKV) in a panel of cell lines. Similar to SGs, reinduction of P-bodies by a second stress (sodium arsenite) was also blocked in infected cells. The disassembly of P-bodies still occurred in non-phosphorylatable eIF2α mouse embryonal fibroblasts (MEFs) that are impaired in SG assembly. Studies of translation status by ribopuromycylation showed that P-body disassembly is independent of host translation shutoff, which requires the phosphorylation of eIF2α in the SFV- or CHIKV-infected cells. Labelling of newly synthesized RNA with bromo-UTP showed that host transcription shutoff correlated with P-body disassembly at the same early stage (3–4 h) after infection. However, inhibition of global transcription with actinomycin D (ActD) failed to disassemble P-bodies as effectively as the viruses did. Interestingly, blocking nuclear import with importazole led to an efficient P-bodies loss. Our data reveal that P-bodies are disassembled independently from SG formation at early stages of Old World alphavirus infection and that nuclear import is involved in the dynamic of P-bodies.
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Affiliation(s)
- Lifeng Liu
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Eva Weiss
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Benjamin Götte
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Stina Sellberg
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Bastian Thaa
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
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22
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Sharma NR, Majerciak V, Kruhlak MJ, Yu L, Kang JG, Yang A, Gu S, Fritzler MJ, Zheng ZM. KSHV RNA-binding protein ORF57 inhibits P-body formation to promote viral multiplication by interaction with Ago2 and GW182. Nucleic Acids Res 2019; 47:9368-9385. [PMID: 31400113 PMCID: PMC6755100 DOI: 10.1093/nar/gkz683] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 01/16/2023] Open
Abstract
Cellular non-membranous RNA-granules, P-bodies (RNA processing bodies, PB) and stress granules (SG), are important components of the innate immune response to virus invasion. Mechanisms governing how a virus modulates PB formation remain elusive. Here, we report the important roles of GW182 and DDX6, but not Dicer, Ago2 and DCP1A, in PB formation, and that Kaposi's sarcoma-associated herpesvirus (KSHV) lytic infection reduces PB formation through several specific interactions with viral RNA-binding protein ORF57. The wild-type ORF57, but not its N-terminal dysfunctional mutant, inhibits PB formation by interacting with the N-terminal GW-domain of GW182 and the N-terminal domain of Ago2, two major components of PB. KSHV ORF57 also induces nuclear Ago2 speckles. Homologous HSV-1 ICP27, but not EBV EB2, shares this conserved inhibitory function with KSHV ORF57. By using time-lapse confocal microscopy of HeLa cells co-expressing GFP-tagged GW182, we demonstrated that viral ORF57 inhibits primarily the scaffolding of GW182 at the initial stage of PB formation. Consistently, KSHV-infected iSLK/Bac16 cells with reduced GW182 expression produced far fewer PB and SG, but 100-fold higher titer of infectious KSHV virions when compared to cells with normal GW182 expression. Altogether, our data provide the first evidence that a DNA virus evades host innate immunity by encoding an RNA-binding protein that promotes its replication by blocking PB formation.
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Affiliation(s)
- Nishi R Sharma
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Michael J Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda 20892, MD, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Jeong Gu Kang
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Marvin J Fritzler
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada T2N 4N1
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
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23
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Abstract
RNA granules are cytoplasmic, microscopically visible, non-membrane ribo-nucleoprotein structures and are important posttranscriptional regulators in gene expression by controlling RNA translation and stability. TIA/G3BP/PABP-specific stress granules (SG) and GW182/DCP-specific RNA processing bodies (PB) are two major distinguishable RNA granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, RNA-binding proteins, RNA decay enzymes and helicases to exclude mRNAs from the cellular active translational pool. Although SG formation is inducible due to cellular stress, PB exist physiologically in every cell. Both RNA granules are important components of the host antiviral defense. Virus infection imposes stress on host cells and thus induces SG formation. However, both RNA and DNA viruses must confront the hostile environment of host innate immunity and apply various strategies to block the formation of SG and PB for their effective infection and multiplication. This review summarizes the current research development in the field and the mechanisms of how individual viruses suppress the formation of host SG and PB for virus production.
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Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
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25
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Du S, Liu X, Cai Q. Viral-Mediated mRNA Degradation for Pathogenesis. Biomedicines 2018; 6:biomedicines6040111. [PMID: 30501096 PMCID: PMC6315618 DOI: 10.3390/biomedicines6040111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/21/2022] Open
Abstract
Cellular RNA decay machinery plays a vital role in regulating gene expression by altering the stability of mRNAs in response to external stresses, including viral infection. In the primary infection, viruses often conquer the host cell’s antiviral immune response by controlling the inherently cellular mRNA degradation machinery to facilitate viral gene expression and establish a successful infection. This review summarizes the current knowledge about the diverse strategies of viral-mediated regulatory RNA shutoff for pathogenesis, and particularly sheds a light on the mechanisms that viruses evolve to elude immune surveillance during infection.
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Affiliation(s)
- Shujuan Du
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Xiaoqing Liu
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiliang Cai
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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26
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Tao R, Fang L, Bai D, Ke W, Zhou Y, Wang D, Xiao S. Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 4 Cleaves Porcine DCP1a To Attenuate Its Antiviral Activity. THE JOURNAL OF IMMUNOLOGY 2018; 201:2345-2353. [DOI: 10.4049/jimmunol.1701773] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/07/2018] [Indexed: 12/12/2022]
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Li F, Wang A. RNA decay is an antiviral defense in plants that is counteracted by viral RNA silencing suppressors. PLoS Pathog 2018; 14:e1007228. [PMID: 30075014 PMCID: PMC6101400 DOI: 10.1371/journal.ppat.1007228] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/20/2018] [Accepted: 07/17/2018] [Indexed: 11/19/2022] Open
Abstract
Exonuclease-mediated RNA decay in plants is known to be involved primarily in endogenous RNA degradation, and several RNA decay components have been suggested to attenuate RNA silencing possibly through competing for RNA substrates. In this paper, we report that overexpression of key cytoplasmic 5'-3' RNA decay pathway gene-encoded proteins (5'RDGs) such as decapping protein 2 (DCP2) and exoribonuclease 4 (XRN4) in Nicotiana benthamiana fails to suppress sense transgene-induced post-transcriptional gene silencing (S-PTGS). On the contrary, knock-down of these 5'RDGs attenuates S-PTGS and supresses the generation of small interfering RNAs (siRNAs). We show that 5'RDGs degrade transgene transcripts via the RNA decay pathway when the S-PTGS pathway is disabled. Thus, RNA silencing and RNA decay degrade exogenous gene transcripts in a hierarchical and coordinated manner. Moreover, we present evidence that infection by turnip mosaic virus (TuMV) activates RNA decay and 5'RDGs also negatively regulate TuMV RNA accumulation. We reveal that RNA silencing and RNA decay can mediate degradation of TuMV RNA in the same way that they target transgene transcripts. Furthermore, we demonstrate that VPg and HC-Pro, the two known viral suppressors of RNA silencing (VSRs) of potyviruses, bind to DCP2 and XRN4, respectively, and the interactions compromise their antiviral function. Taken together, our data highlight the overlapping function of the RNA silencing and RNA decay pathways in plants, as evidenced by their hierarchical and concerted actions against exogenous and viral RNA, and VSRs not only counteract RNA silencing but also subvert RNA decay to promote viral infection.
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Affiliation(s)
- Fangfang Li
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
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28
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Zhai X, Wu S, Lin L, Wang T, Zhong X, Chen Y, Xu W, Tong L, Wang Y, Zhao W, Zhong Z. Stress Granule Formation is One of the Early Antiviral Mechanisms for Host Cells Against Coxsackievirus B Infection. Virol Sin 2018; 33:314-322. [PMID: 29959686 DOI: 10.1007/s12250-018-0040-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 12/11/2022] Open
Abstract
Stress granules (SGs) are intracellular granules formed when cellular translation is blocked and have been reported to be involved in a variety of viral infections. Our previous studies revealed that SGs are involved in the coxsackievirus B (CVB) infection process, but the role of SGs in CVB infection has not been fully explored. In this study, we found that CVB type 3 (CVB3) could induce SG formation in the early phase of infection. Results showed that levels of CVB3 RNA and protein were significantly inhibited during the early stage of CVB3 infection by the elevated formation of SGs, while viral RNA and protein synthesis were significantly promoted when SG formation was blocked. Our findings suggest that SG formation is one of the early antiviral mechanisms for host cells against CVB infection.
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Affiliation(s)
- Xia Zhai
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Shuo Wu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Lexun Lin
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Tianying Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Xiaoyan Zhong
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Yang Chen
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Weizhen Xu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Lei Tong
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin, 150081, China.
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.
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29
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Delorme-Axford E, Abernathy E, Lennemann NJ, Bernard A, Ariosa A, Coyne CB, Kirkegaard K, Klionsky DJ. The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy. Autophagy 2018; 14:898-912. [PMID: 29465287 DOI: 10.1080/15548627.2018.1441648] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast Saccharomyces cerevisiae and in mammalian cells. In yeast, chromosomal deletion of XRN1 enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (ATG) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
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Affiliation(s)
| | - Emma Abernathy
- b Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | | | - Amélie Bernard
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
| | - Aileen Ariosa
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
| | - Carolyn B Coyne
- c Department of Pediatrics , University of Pittsburgh , Pittsburgh , PA , USA
| | - Karla Kirkegaard
- b Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Daniel J Klionsky
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
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Fernández-Carrillo C, Pérez-Vilaró G, Díez J, Pérez-Del-Pulgar S. Hepatitis C virus plays with fire and yet avoids getting burned. A review for clinicians on processing bodies and stress granules. Liver Int 2018; 38:388-398. [PMID: 28782251 DOI: 10.1111/liv.13541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 08/02/2017] [Indexed: 02/13/2023]
Abstract
Over the last few years, many reports have defined several types of RNA cell granules composed of proteins and messenger RNA (mRNA) that regulate gene expression on a post-transcriptional level. Processing bodies (P-bodies) and stress granules (SGs) are among the best-known RNA granules, only detectable when they accumulate into very dynamic cytosolic foci. Recently, a tight association has been found between positive-stranded RNA viruses, including hepatitis C virus (HCV), and these granules. The present article offers a comprehensive review on the complex and paradoxical relationship between HCV, P-bodies and SGs from a translational perspective. Despite the fact that components of P-bodies and SGs have assiduously controlled mRNA expression, either by sequestration or degradation, for thousands of years, HCV has learned how to dangerously exploit certain of them for its own benefit in an endless biological war. Thus, HCV has gained the ability to hack ancient host machineries inherited from prokaryotic times. While P-bodies and SGs are crucial to the HCV cycle, in the interferon-free era we still lack detailed knowledge of the mechanisms involved, processes that may underlie the long-term complications of HCV infection.
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Affiliation(s)
| | - Gemma Pérez-Vilaró
- Department of Experimental and Health Sciences, Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juana Díez
- Department of Experimental and Health Sciences, Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain
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31
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Abstract
Viruses alter host-cell gene expression at many biochemical levels, such as transcription, translation, mRNA splicing and mRNA decay in order to create a cellular environment suitable for viral replication. In this review, we discuss mechanisms by which viruses manipulate host-gene expression at the level of mRNA decay in order to enable the virus to evade host antiviral responses to allow viral survival and replication. We discuss different cellular RNA decay pathways, including the deadenylation-dependent mRNA decay pathway, and various strategies that viruses exploit to manipulate these pathways in order to create a virus-friendly cellular environment.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St Louis
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul R Bohjanen
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
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32
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Balagopal V, Beemon KL. Rous Sarcoma Virus RNA Stability Element Inhibits Deadenylation of mRNAs with Long 3'UTRs. Viruses 2017; 9:v9080204. [PMID: 28763028 PMCID: PMC5580461 DOI: 10.3390/v9080204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/14/2017] [Accepted: 07/26/2017] [Indexed: 12/15/2022] Open
Abstract
All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3′ untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), there is a 7 kb 3′UTR downstream of the gag terminator, containing the pol, env, and src genes. mRNAs containing long 3′UTRs, like those with premature termination codons, are frequently recognized by the cellular nonsense-mediated mRNA decay (NMD) machinery and targeted for degradation. To prevent this, RSV has evolved an RNA stability element (RSE) in the RNA immediately downstream of the gag termination codon. This 400-nt RNA sequence stabilizes premature termination codons (PTCs) in gag. It also stabilizes globin mRNAs with long 3′UTRs, when placed downstream of the termination codon. It is not clear how the RSE stabilizes the mRNA and prevents decay. We show here that the presence of RSE inhibits deadenylation severely. In addition, the RSE also impairs decapping (DCP2) and 5′-3′ exonucleolytic (XRN1) function in knockdown experiments in human cells.
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Affiliation(s)
- Vidya Balagopal
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Karen L Beemon
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA.
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33
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Wu YY, Hou BH, Lee WC, Lu SH, Yang CJ, Vaucheret H, Chen HM. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1064-1078. [PMID: 28267232 DOI: 10.1111/tpj.13528] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/02/2017] [Accepted: 02/28/2017] [Indexed: 05/25/2023]
Abstract
DICER-LIKE (DCL) enzymes process double-stranded RNA into small RNAs that act as regulators of gene expression. Arabidopsis DCL4 and DCL2 each allow the post-transcriptional gene silencing (PTGS) of viruses and transgenes, but primary PTGS-prone DCL4 outcompetes transitive PTGS-prone DCL2 in wild-type plants. This hierarchy likely prevents DCL2 having any detrimental effects on endogenous genes. Indeed, dcl4 mutants exhibit developmental defects and increased sensitivity to genotoxic stress. In this study, the mechanism underlying dcl4 defects was investigated using genetic, biochemical and high-throughput sequencing approaches. We show that the purple phenotype of dcl4 leaves correlates with carbohydrate over-accumulation and defective phloem transport, and depends on the activity of SUPPRESSOR OF GENE SILENCING 3, RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) and DCL2. This phenotype correlates with the downregulation of two genes expressed in the apex and the vasculature, SMAX1-LIKE 4 (SMXL4) and SMXL5, and the accumulation of DCL2- and RDR6-dependent small interfering RNAs derived from these two genes. Supporting a causal effect, smxl4 smxl5 double mutants exhibit leaf pigmentation, enhanced starch accumulation and defective phloem transport, similar to dcl4 plants. Overall, this study elucidates the detrimental action of DCL2 when DCL4 is absent, and indicates that DCL4 outcompeting DCL2 in wild-type plants is crucial to prevent the degradation of endogenous transcripts by DCL2- and RDR6-dependent transitive PTGS.
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Affiliation(s)
- Yu-Yi Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin-Hua Lu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen-Jui Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
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IRAV ( FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10. J Virol 2017; 91:JVI.01606-16. [PMID: 27974568 PMCID: PMC5309953 DOI: 10.1128/jvi.01606-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/05/2016] [Indexed: 12/23/2022] Open
Abstract
Dengue virus (DENV) is a member of the genus Flavivirus and can cause severe febrile illness. Here, we show that FLJ11286, which we refer to as IRAV, is induced by DENV in an interferon-dependent manner, displays antiviral activity against DENV, and localizes to the DENV replication complex. IRAV is an RNA binding protein and localizes to cytoplasmic processing bodies (P bodies) in uninfected cells, where it interacts with the MOV10 RISC complex RNA helicase, suggesting a role for IRAV in the processing of viral RNA. After DENV infection, IRAV, along with MOV10 and Xrn1, localizes to the DENV replication complex and associates with DENV proteins. Depletion of IRAV or MOV10 results in an increase in viral RNA. These data serve to characterize an interferon-stimulated gene with antiviral activity against DENV, as well as to propose a mechanism of activity involving the processing of viral RNA.
IMPORTANCE Dengue virus, a member of the family Flaviviridae, can result in a life-threatening illness and has a significant impact on global health. Dengue virus has been shown to be particularly sensitive to the effects of type I interferon; however, little is known about the mechanisms by which interferon-stimulated genes function to inhibit viral replication. A better understanding of the interferon-mediated antiviral response to dengue virus may aid in the development of novel therapeutics. Here, we examine the influence of the interferon-stimulated gene IRAV (FLJ11286) on dengue virus replication. We show that IRAV associates with P bodies in uninfected cells and with the dengue virus replication complex after infection. IRAV also interacts with MOV10, depletion of which is associated with increased viral replication. Our results provide insight into a newly identified antiviral gene, as well as broadening our understanding of the innate immune response to dengue virus infection.
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Attacked from All Sides: RNA Decay in Antiviral Defense. Viruses 2017; 9:v9010002. [PMID: 28054965 PMCID: PMC5294971 DOI: 10.3390/v9010002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/22/2016] [Accepted: 12/26/2016] [Indexed: 12/22/2022] Open
Abstract
The innate immune system has evolved a number of sensors that recognize viral RNA (vRNA) to restrict infection, yet the full spectrum of host-encoded RNA binding proteins that target these foreign RNAs is still unknown. The RNA decay machinery, which uses exonucleases to degrade aberrant RNAs largely from the 5′ or 3′ end, is increasingly recognized as playing an important role in antiviral defense. The 5′ degradation pathway can directly target viral messenger RNA (mRNA) for degradation, as well as indirectly attenuate replication by limiting specific pools of endogenous RNAs. The 3′ degradation machinery (RNA exosome) is emerging as a downstream effector of a diverse array of vRNA sensors. This review discusses our current understanding of the roles of the RNA decay machinery in controlling viral infection.
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36
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Mäkinen K, Lõhmus A, Pollari M. Plant RNA Regulatory Network and RNA Granules in Virus Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:2093. [PMID: 29312371 PMCID: PMC5732267 DOI: 10.3389/fpls.2017.02093] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual components contribute to these processes. In this review we discuss the roles of cellular RNA regulatory mechanisms and RNA granules in plant virus infection in the light of current knowledge and compare the findings to those made in animal virus studies.
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37
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Jungfleisch J, Blasco-Moreno B, Díez J. Use of Cellular Decapping Activators by Positive-Strand RNA Viruses. Viruses 2016; 8:v8120340. [PMID: 28009841 PMCID: PMC5192400 DOI: 10.3390/v8120340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/06/2016] [Accepted: 12/19/2016] [Indexed: 12/14/2022] Open
Abstract
Positive-strand RNA viruses have evolved multiple strategies to not only circumvent the hostile decay machinery but to trick it into being a priceless collaborator supporting viral RNA translation and replication. In this review, we describe the versatile interaction of positive-strand RNA viruses and the 5′-3′ mRNA decay machinery with a focus on the viral subversion of decapping activators. This highly conserved viral trickery is exemplified with the plant Brome mosaic virus, the animal Flock house virus and the human hepatitis C virus.
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Affiliation(s)
- Jennifer Jungfleisch
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
| | - Bernat Blasco-Moreno
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
| | - Juana Díez
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
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38
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Diverse Strategies Used by Picornaviruses to Escape Host RNA Decay Pathways. Viruses 2016; 8:v8120335. [PMID: 27999393 PMCID: PMC5192396 DOI: 10.3390/v8120335] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022] Open
Abstract
To successfully replicate, viruses protect their genomic material from degradation by the host cell. RNA viruses must contend with numerous destabilizing host cell processes including mRNA decay pathways and viral RNA (vRNA) degradation resulting from the antiviral response. Members of the Picornaviridae family of small RNA viruses have evolved numerous diverse strategies to evade RNA decay, including incorporation of stabilizing elements into vRNA and re-purposing host stability factors. Viral proteins are deployed to disrupt and inhibit components of the decay machinery and to redirect decay machinery to the advantage of the virus. This review summarizes documented interactions of picornaviruses with cellular RNA decay pathways and processes.
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39
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Nikolic J, Civas A, Lama Z, Lagaudrière-Gesbert C, Blondel D. Rabies Virus Infection Induces the Formation of Stress Granules Closely Connected to the Viral Factories. PLoS Pathog 2016; 12:e1005942. [PMID: 27749929 PMCID: PMC5066959 DOI: 10.1371/journal.ppat.1005942] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022] Open
Abstract
Stress granules (SGs) are membrane-less dynamic structures consisting of mRNA and protein aggregates that form rapidly in response to a wide range of environmental cellular stresses and viral infections. They act as storage sites for translationally silenced mRNAs under stress conditions. During viral infection, SG formation results in the modulation of innate antiviral immune responses, and several viruses have the ability to either promote or prevent SG assembly. Here, we show that rabies virus (RABV) induces SG formation in infected cells, as revealed by the detection of SG-marker proteins Ras GTPase-activating protein-binding protein 1 (G3BP1), T-cell intracellular antigen 1 (TIA-1) and poly(A)-binding protein (PABP) in the RNA granules formed during viral infection. As shown by live cell imaging, RABV-induced SGs are highly dynamic structures that increase in number, grow in size by fusion events, and undergo assembly/disassembly cycles. Some SGs localize in close proximity to cytoplasmic viral factories, known as Negri bodies (NBs). Three dimensional reconstructions reveal that both structures remain distinct even when they are in close contact. In addition, viral mRNAs synthesized in NBs accumulate in the SGs during viral infection, revealing material exchange between both compartments. Although RABV-induced SG formation is not affected in MEFs lacking TIA-1, TIA-1 depletion promotes viral translation which results in an increase of viral replication indicating that TIA-1 has an antiviral effect. Inhibition of PKR expression significantly prevents RABV-SG formation and favors viral replication by increasing viral translation. This is correlated with a drastic inhibition of IFN-B gene expression indicating that SGs likely mediate an antiviral response which is however not sufficient to fully counteract RABV infection.
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Affiliation(s)
- Jovan Nikolic
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ahmet Civas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Zoé Lama
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail:
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40
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Rowley PA, Ho B, Bushong S, Johnson A, Sawyer SL. XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts. PLoS Pathog 2016; 12:e1005890. [PMID: 27711183 PMCID: PMC5053509 DOI: 10.1371/journal.ppat.1005890] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly refined, species-specific relationship between Xrn1p and the "L-A" totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, the activity of Xrn1p against totiviruses is not simply an incidental consequence of the enzymatic activity of Xrn1p, but rather Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. Consistent with this, we demonstrated that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Brandon Ho
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sarah Bushong
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Arlen Johnson
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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Abstract
Viral myocarditis remains a prominent infectious-inflammatory disease for patients throughout the lifespan. The condition presents several challenges including varied modes of clinical presentation, a range of timepoints when patients come to attention, a diversity of approaches to diagnosis, a spectrum of clinical courses, and unsettled perspectives on therapeutics in different patient settings and in the face of different viral pathogens. In this review, we examine current knowledge about viral heart disease and especially provide information on evolving understanding of mechanisms of disease and efforts by investigators to identify and evaluate potential therapeutic avenues for intervention.
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Affiliation(s)
- Gabriel Fung
- From the Department of Pathology and Laboratory Medicine (G.F., H.L., Y.Q., D.Y., B.M.), Centre for Heart Lung Innovation (G.F., H.L., Y.Q., D.Y., B.M.), Centre of Excellence for Prevention of Organ Failure (PROOF Centre), and Institute for Heart + Lung Health, St. Paul's Hospital (B.M.), University of British Columbia, Vancouver, British Columbia, Canada
| | - Honglin Luo
- From the Department of Pathology and Laboratory Medicine (G.F., H.L., Y.Q., D.Y., B.M.), Centre for Heart Lung Innovation (G.F., H.L., Y.Q., D.Y., B.M.), Centre of Excellence for Prevention of Organ Failure (PROOF Centre), and Institute for Heart + Lung Health, St. Paul's Hospital (B.M.), University of British Columbia, Vancouver, British Columbia, Canada
| | - Ye Qiu
- From the Department of Pathology and Laboratory Medicine (G.F., H.L., Y.Q., D.Y., B.M.), Centre for Heart Lung Innovation (G.F., H.L., Y.Q., D.Y., B.M.), Centre of Excellence for Prevention of Organ Failure (PROOF Centre), and Institute for Heart + Lung Health, St. Paul's Hospital (B.M.), University of British Columbia, Vancouver, British Columbia, Canada
| | - Decheng Yang
- From the Department of Pathology and Laboratory Medicine (G.F., H.L., Y.Q., D.Y., B.M.), Centre for Heart Lung Innovation (G.F., H.L., Y.Q., D.Y., B.M.), Centre of Excellence for Prevention of Organ Failure (PROOF Centre), and Institute for Heart + Lung Health, St. Paul's Hospital (B.M.), University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce McManus
- From the Department of Pathology and Laboratory Medicine (G.F., H.L., Y.Q., D.Y., B.M.), Centre for Heart Lung Innovation (G.F., H.L., Y.Q., D.Y., B.M.), Centre of Excellence for Prevention of Organ Failure (PROOF Centre), and Institute for Heart + Lung Health, St. Paul's Hospital (B.M.), University of British Columbia, Vancouver, British Columbia, Canada.
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Poblete-Durán N, Prades-Pérez Y, Vera-Otarola J, Soto-Rifo R, Valiente-Echeverría F. Who Regulates Whom? An Overview of RNA Granules and Viral Infections. Viruses 2016; 8:v8070180. [PMID: 27367717 PMCID: PMC4974515 DOI: 10.3390/v8070180] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022] Open
Abstract
After viral infection, host cells respond by mounting an anti-viral stress response in order to create a hostile atmosphere for viral replication, leading to the shut-off of mRNA translation (protein synthesis) and the assembly of RNA granules. Two of these RNA granules have been well characterized in yeast and mammalian cells, stress granules (SGs), which are translationally silent sites of RNA triage and processing bodies (PBs), which are involved in mRNA degradation. This review discusses the role of these RNA granules in the evasion of anti-viral stress responses through virus-induced remodeling of cellular ribonucleoproteins (RNPs).
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Affiliation(s)
- Natalia Poblete-Durán
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Yara Prades-Pérez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago 8330024, Chile.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
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43
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Abstract
During infection, positive-strand RNA viruses subvert cellular machinery involved in RNA metabolism to translate viral proteins and replicate viral genomes to avoid or disable the host defense mechanisms. Cytoplasmic RNA granules modulate the stabilities of cellular and viral RNAs. Understanding how hepatitis C virus and other flaviviruses interact with the host machinery required for protein synthesis, localization, and degradation of mRNAs is important for elucidating how these processes occur in both virus-infected and uninfected cells.
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Lloyd RE. Enterovirus Control of Translation and RNA Granule Stress Responses. Viruses 2016; 8:93. [PMID: 27043612 PMCID: PMC4848588 DOI: 10.3390/v8040093] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/26/2016] [Accepted: 03/29/2016] [Indexed: 12/24/2022] Open
Abstract
Enteroviruses such as poliovirus (PV) and coxsackievirus B3 (CVB3) have evolved several parallel strategies to regulate cellular gene expression and stress responses to ensure efficient expression of the viral genome. Enteroviruses utilize their encoded proteinases to take over the cellular translation apparatus and direct ribosomes to viral mRNAs. In addition, viral proteinases are used to control and repress the two main types of cytoplasmic RNA granules, stress granules (SGs) and processing bodies (P-bodies, PBs), which are stress-responsive dynamic structures involved in repression of gene expression. This review discusses these processes and the current understanding of the underlying mechanisms with respect to enterovirus infections. In addition, the review discusses accumulating data suggesting linkage exists between RNA granule formation and innate immune sensing and activation.
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Affiliation(s)
- Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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Abstract
RNA granules are dynamic cellular structures essential for proper gene expression and homeostasis. The two principal types of cytoplasmic RNA granules are stress granules, which contain stalled translation initiation complexes, and processing bodies (P bodies), which concentrate factors involved in mRNA degradation. RNA granules are associated with gene silencing of transcripts; thus, viruses repress RNA granule functions to favor replication. This article discusses the breadth of viral interactions with cytoplasmic RNA granules, focusing on mechanisms that modulate the functions of RNA granules and that typically promote viral replication. Currently, mechanisms for virus manipulation of RNA granules can be loosely grouped into three nonexclusive categories: (a) cleavage of key RNA granule factors, (b) regulation of PKR activation, and (c) co-opting of RNA granule factors for new roles in viral replication. Viral modulation of RNA granules supports productive infection by inhibiting their gene-silencing functions and counteracting their role in linking stress sensing with innate immune activation.
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Affiliation(s)
- Wei-Chih Tsai
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030;
| | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030;
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Burgess HM, Mohr I. Cellular 5'-3' mRNA exonuclease Xrn1 controls double-stranded RNA accumulation and anti-viral responses. Cell Host Microbe 2015; 17:332-344. [PMID: 25766294 PMCID: PMC4826345 DOI: 10.1016/j.chom.2015.02.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/23/2014] [Accepted: 01/28/2015] [Indexed: 12/30/2022]
Abstract
By accelerating global mRNA decay, many viruses impair host protein synthesis, limiting host defenses and stimulating virus mRNA translation. Vaccinia virus (VacV) encodes two decapping enzymes (D9, D10) that remove protective 5′ caps on mRNAs, presumably generating substrates for degradation by the host exonuclease Xrn1. Surprisingly, we find VacV infection of Xrn1-depleted cells inhibits protein synthesis, compromising virus growth. These effects are aggravated by D9 deficiency and dependent upon a virus transcription factor required for intermediate and late mRNA biogenesis. Considerable double-stranded RNA (dsRNA) accumulation in Xrn1-depleted cells is accompanied by activation of host dsRNA-responsive defenses controlled by PKR and 2′-5′ oligoadenylate synthetase (OAS), which respectively inactivate the translation initiation factor eIF2 and stimulate RNA cleavage by RNase L. This proceeds despite VacV-encoded PKR and RNase L antagonists being present. Moreover, Xrn1 depletion sensitizes uninfected cells to dsRNA treatment. Thus, Xrn1 is a cellular factor regulating dsRNA accumulation and dsRNA-responsive innate immune effectors. Vaccinia virus (VacV) replication requires the host Xrn1 mRNA decay enzyme The 5′-3′ mRNA exonuclease Xrn1 limits dsRNA accumulation In the absence of Xrn1, host dsRNA-responsive innate immune defenses are activated VacV antagonists of dsRNA-responsive host defenses are Xrn1 dependent
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Affiliation(s)
- Hannah M Burgess
- Department of Microbiology and NYU Cancer Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Ian Mohr
- Department of Microbiology and NYU Cancer Institute, NYU School of Medicine, New York, NY 10016, USA.
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47
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Host cytoplasmic processing bodies assembled by Trypanosoma cruzi during infection exert anti-parasitic activity. Parasitol Int 2015; 64:540-6. [DOI: 10.1016/j.parint.2015.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 11/23/2022]
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48
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Dougherty JD, Tsai WC, Lloyd RE. Multiple Poliovirus Proteins Repress Cytoplasmic RNA Granules. Viruses 2015; 7:6127-40. [PMID: 26610553 PMCID: PMC4690851 DOI: 10.3390/v7122922] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 01/05/2023] Open
Abstract
We have previously shown that poliovirus (PV) infection induces stress granule (SG) formation early in infection and then inhibits the formation of SG and disperses processing bodies (PBs) by the mid-phase of infection. Loss of SG was linked to cleavage of G3BP1 by viral 3C proteinase (3Cpro), however dispersal of PBs was not strongly linked to cleavage of specific factors by viral proteinases, suggesting other viral proteins may play roles in inhibition of SG or PB formation. Here we have screened all viral proteins for roles in inducing or inhibiting the formation of RNA granules by creating fusions with mCherry and expressing them individually in cells. Expression of viral proteins separately revealed that the capsid region P1, 2Apro, 3A, 3Cpro, the protease precursor 3CD and 3D polymerase all affect RNA granules to varying extents, whereas 2BC does not. 2Apro, which cleaves eIF4GI, induced SGs as expected, and entered novel foci containing the SG nucleating protein G3BP1. Of the two forms of G3BP, only G3BP1 is cleaved by a virus proteinase, 3Cpro, whereas G3BP2 is not cleaved by 3Cpro or 2Apro. Surprisingly, 3CD, which contains proteinase activity, differentially repressed PBs but not SGs. Further, both 2Apro and 3Cpro expression dispersed PBs, however molecular targets were different since PB dispersal due to 2Apro and heat shock protein (Hsp)90 inhibition but not 3Cpro, could be rescued by application of oxidative stress to cells. The data indicate that PV repression of SGs and PBs is multifactorial, though protease function is dominant.
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Affiliation(s)
- Jonathan D Dougherty
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Wei-Chih Tsai
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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49
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Liu Y, Zhu Z, Zhang M, Zheng H. Multifunctional roles of leader protein of foot-and-mouth disease viruses in suppressing host antiviral responses. Vet Res 2015; 46:127. [PMID: 26511922 PMCID: PMC4625562 DOI: 10.1186/s13567-015-0273-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/07/2015] [Indexed: 12/17/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) leader protein (Lpro) is a papain-like proteinase, which plays an important role in FMDV pathogenesis. Lpro exists as two forms, Lab and Lb, due to translation being initiated from two different start codons separated by 84 nucleotides. Lpro self-cleaves from the nascent viral polyprotein precursor as the first mature viral protein. In addition to its role as a viral proteinase, Lpro also has the ability to antagonize host antiviral effects. To promote FMDV replication, Lpro can suppress host antiviral responses by three different mechanisms: (1) cleavage of eukaryotic translation initiation factor 4 γ (eIF4G) to shut off host protein synthesis; (2) inhibition of host innate immune responses through restriction of interferon-α/β production; and (3) Lpro can also act as a deubiquitinase and catalyze deubiquitination of innate immune signaling molecules. In the light of recent functional and biochemical findings regarding Lpro, this review introduces the basic properties of Lpro and the mechanisms by which it antagonizes host antiviral responses.
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Affiliation(s)
- Yingqi Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China. .,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.
| | - Miaotao Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.
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50
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Bhowmick R, Mukherjee A, Patra U, Chawla-Sarkar M. Rotavirus disrupts cytoplasmic P bodies during infection. Virus Res 2015; 210:344-54. [PMID: 26386333 DOI: 10.1016/j.virusres.2015.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/17/2022]
Abstract
Cytoplasmic Processing bodies (P bodies), the RNA-protein aggregation foci of translationally stalled and potentially decaying mRNA, have been reported to be differentially modulated by viruses. Rotavirus, the causative agent of acute infantile gastroenteritis is a double stranded RNA virus which completes its entire life-cycle exclusively in host cell cytoplasm. In this study, the fate of P bodies was investigated upon rotavirus infection. It was found that P bodies get disrupted during rotavirus infection. The disruption occurred by more than one different mechanism where deadenylating P body component Pan3 was degraded by rotavirus NSP1 and exonuclease XRN1 along with the decapping enzyme hDCP1a were relocalized from cytoplasm to nucleus. Overall the study highlights decay and subcellular relocalization of P body components as novel mechanisms by which rotavirus subverts cellular antiviral responses.
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Affiliation(s)
- Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India.
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