1
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Sharma N, Kessler P, Sen GC. Cell-type-specific need of Ddx3 and PACT for interferon induction by RNA viruses. J Virol 2023; 97:e0130423. [PMID: 37982645 PMCID: PMC10734550 DOI: 10.1128/jvi.01304-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Interferon-stimulated genes (ISGs) are induced in response to interferon expression due to viral infections. Role of these ISGs can be variable in different cells or organs. Our study highlights such cell-specific role of an ISG, Ddx3, which regulates the translation of mRNAs essential for interferon induction (PACT) and interferon signaling (STAT1) in a cell-specific manner. Our study also highlights the role of PACT in RNA virus-induced RLR signaling. Our study depicts how Ddx3 regulates innate immune signaling pathways in an indirect manner. Such cell-specific behavior of ISGs helps us to better understand viral pathogenesis and highlights the complexities of viral tropism and innate immune responses.
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Affiliation(s)
- Nikhil Sharma
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Patricia Kessler
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ganes C. Sen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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2
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Wilkins KC, Schroeder T, Gu S, Revalde JL, Floor SN. Determinants of DDX3X sensitivity uncovered using a helicase activity in translation reporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557805. [PMID: 37745530 PMCID: PMC10515938 DOI: 10.1101/2023.09.14.557805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DDX3X regulates the translation of a subset of human transcripts containing complex 5' untranslated regions (5' UTRs). In this study we developed the helicase activity reporter for translation (HART) which uses DDX3X-sensitive 5' UTRs to measure DDX3X mediated translational activity in cells. To dissect the structural underpinnings of DDX3X dependent translation, we first used SHAPE-MaP to determine the secondary structures present in DDX3X-sensitive 5' UTRs and then employed HART to investigate how their perturbation impacts DDX3X-sensitivity. Additionally, we identified residues 38-44 as potential mediators of DDX3X's interaction with the translational machinery. HART revealed that both DDX3X's association with the ribosome complex as well as its helicase activity are required for its function in promoting the translation of DDX3X-sensitive 5' UTRs. These findings suggest DDX3X plays a crucial role regulating translation through its interaction with the translational machinery during ribosome scanning, and establish the HART reporter as a robust, lentivirally encoded measurement of DDX3X-dependent translation in cells.
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Affiliation(s)
- Kevin C. Wilkins
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, 94143, USA
- Graduate Division, University of California, San Francisco, San Francisco, CA, United States
| | - Till Schroeder
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, 94143, USA
- Julius-Maximilians-University of Würzburg, Würzburg, 97070, Germany
| | - Sohyun Gu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Jezrael L. Revalde
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143, United States
| | - Stephen N. Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, 94143, USA
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3
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Ryan CS, Schröder M. The human DEAD-box helicase DDX3X as a regulator of mRNA translation. Front Cell Dev Biol 2022; 10:1033684. [PMID: 36393867 PMCID: PMC9642913 DOI: 10.3389/fcell.2022.1033684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/07/2022] [Indexed: 08/27/2023] Open
Abstract
The human DEAD-box protein DDX3X is an RNA remodelling enzyme that has been implicated in various aspects of RNA metabolism. In addition, like many DEAD-box proteins, it has non-conventional functions that are independent of its enzymatic activity, e.g., DDX3X acts as an adaptor molecule in innate immune signalling pathways. DDX3X has been linked to several human diseases. For example, somatic mutations in DDX3X were identified in various human cancers, and de novo germline mutations cause a neurodevelopmental condition now termed 'DDX3X syndrome'. DDX3X is also an important host factor in many different viral infections, where it can have pro-or anti-viral effects depending on the specific virus. The regulation of translation initiation for specific mRNA transcripts is likely a central cellular function of DDX3X, yet many questions regarding its exact targets and mechanisms of action remain unanswered. In this review, we explore the current knowledge about DDX3X's physiological RNA targets and summarise its interactions with the translation machinery. A role for DDX3X in translational reprogramming during cellular stress is emerging, where it may be involved in the regulation of stress granule formation and in mediating non-canonical translation initiation. Finally, we also discuss the role of DDX3X-mediated translation regulation during viral infections. Dysregulation of DDX3X's function in mRNA translation likely contributes to its involvement in disease pathophysiology. Thus, a better understanding of its exact mechanisms for regulating translation of specific mRNA targets is important, so that we can potentially develop therapeutic strategies for overcoming the negative effects of its dysregulation.
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4
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De Colibus L, Stunnenberg M, Geijtenbeek TB. DDX3X structural analysis: Implications in the pharmacology and innate immunity. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:100-109. [PMID: 35647523 PMCID: PMC9133689 DOI: 10.1016/j.crimmu.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
The human DEAD-Box Helicase 3 X-Linked (DDX3X) is an ATP-dependent RNA helicase involved in virtually every step of RNA metabolism, ranging from transcription regulation in the nucleus to translation initiation and stress granule (SG) formation, and plays crucial roles in innate immunity, as well as tumorigenesis and viral infections. This review discusses latest advances in DDX3X biology and structure-function relationship, including the implications of the recent DDX3X crystal structure in complex with double stranded RNA for RNA metabolism, DDX3X involvement in the cross-talk between innate immune responses and cell stress adaptation, and the roles of DDX3X in controlling cell fate. The human DDX3X, an ATP-dependent RNA helicase, plays a central role in a variety of cellular processes involving RNA. DDX3X is implicated in antiviral signalling pathways. DDX3X interacts with full-length NLRP3 and its NACHT domain. The recent crystal structure of DDX3X in complex with dsRNA offers a model for understanding its binding to the HIV-1 TAR hairpin sequence.
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5
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Zapatero-Belinchón FJ, Moeller R, Lasswitz L, van Ham M, Becker M, Brogden G, Rosendal E, Bi W, Carriquí-Madroñal B, Islam K, Lenman A, Gunesch AP, Kirui J, Pietschmann T, Överby AK, Jänsch L, Gerold G. Fluvastatin mitigates SARS-CoV-2 infection in human lung cells. iScience 2021; 24:103469. [PMID: 34812415 PMCID: PMC8599137 DOI: 10.1016/j.isci.2021.103469] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/08/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Clinical data of patients suffering from COVID-19 indicates that statin therapy, used to treat hypercholesterolemia, is associated with a better disease outcome. Whether statins directly affect virus replication or influence the clinical outcome through modulation of immune responses is unknown. We therefore investigated the effect of statins on SARS-CoV-2 infection in human lung cells and found that only fluvastatin inhibited low and high pathogenic coronaviruses in vitro and ex vivo in a dose-dependent manner. Quantitative proteomics revealed that fluvastatin and other tested statins modulated the cholesterol synthesis pathway without altering innate antiviral immune responses in infected lung epithelial cells. However, fluvastatin treatment specifically downregulated proteins that modulate protein translation and viral replication. Collectively, these results support the notion that statin therapy poses no additional risk to individuals exposed to SARS-CoV-2 and that fluvastatin has a moderate beneficial effect on SARS-CoV-2 infection of human lung cells.
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Affiliation(s)
- Francisco J. Zapatero-Belinchón
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90185 Umeå, Sweden
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Rebecca Moeller
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Miriam Becker
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90185 Umeå, Sweden
| | - Graham Brogden
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Ebba Rosendal
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), R893+F4 Umeå, Sweden
| | - Wenjie Bi
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Belén Carriquí-Madroñal
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Koushikul Islam
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90185 Umeå, Sweden
| | - Annasara Lenman
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90185 Umeå, Sweden
| | - Antonia P. Gunesch
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Jared Kirui
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Anna K. Överby
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), R893+F4 Umeå, Sweden
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
- Department of Clinical Microbiology, Virology, Umeå University, 90185 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90185 Umeå, Sweden
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany
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6
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DEAD/H-box helicases:Anti-viral and pro-viral roles during infections. Virus Res 2021; 309:198658. [PMID: 34929216 DOI: 10.1016/j.virusres.2021.198658] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
DEAD/H-box RNA helicases make the prominent family of helicases super family-2 which take part in almost all RNA-related processes, from initiation of transcription to RNA decay pathways. In addition to these RNA-related activities, in recent years a certain number of these helicases are reported to play important roles in anti-viral immunity through various ways. Along with RLHs, endosomal TLRs, and cytosolic DNA receptors, many RNA helicases including DDX3, DHX9, DDX6, DDX41, DHX33, DDX60, DHX36 and DDX1-DDX21-DHX36 complex act as viral nucleic acid sensors or co-sensors. These helicases mostly follow RLHs-MAVS and STING mediated signaling cascades to trigger induction of type-I interferons and pro-inflammatory cytokines. Many of them also function as downstream adaptor molecules (DDX3), segments of stress and processing bodies (DDX3 and DDX6) or negative regulators (DDX19, DDX24, DDX25, DDX39A and DDX46). On the contrary, many studies indicated that several DEAD/H-box helicases such as DDX1, DDX3, DDX6, DDX24, and DHX9 could be exploited by viruses to evade innate immune responses, suggesting that these helicases seem to have a dual function as anti-viral innate immune mediators and viral replication cofactors. In this review, we summarized the current knowledge on several representative DEAD/H-box helicases, with an emphasis on their functions in innate immunity responses, involved in their anti-viral and pro-viral roles.
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7
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Alqazlan N, Emam M, Nagy É, Bridle B, Sargolzaei M, Sharif S. Transcriptomics of chicken cecal tonsils and intestine after infection with low pathogenic avian influenza virus H9N2. Sci Rep 2021; 11:20462. [PMID: 34650121 PMCID: PMC8517014 DOI: 10.1038/s41598-021-99182-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
Influenza viruses cause severe respiratory infections in humans and birds, triggering global health concerns and economic burden. Influenza infection is a dynamic process involving complex biological host responses. The objective of this study was to illustrate global biological processes in ileum and cecal tonsils at early time points after chickens were infected with low pathogenic avian influenza virus (LPAIV) H9N2 through transcriptome analysis. Total RNA isolated from ileum and cecal tonsils of non-infected and infected layers at 12-, 24- and 72-h post-infection (hpi) was used for mRNA sequencing analyses to characterize differentially expressed genes and overrepresented pathways. Statistical analysis highlighted transcriptomic signatures significantly occurring 24 and 72 hpi, but not earlier at 12 hpi. Interferon (IFN)-inducible and IFN-stimulated gene (ISG) expression was increased, followed by continued expression of various heat-shock proteins (HSP), including HSP60, HSP70, HSP90 and HSP110. Some upregulated genes involved in innate antiviral responses included DDX60, MX1, RSAD2 and CMPK2. The ISG15 antiviral mechanism pathway was highly enriched in ileum and cecal tonsils at 24 hpi. Overall, most affected pathways were related to interferon production and the heat-shock response. Research on these candidate genes and pathways is warranted to decipher underlying mechanisms of immunity against LPAIV in chickens.
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Affiliation(s)
- Nadiyah Alqazlan
- grid.34429.380000 0004 1936 8198Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Mehdi Emam
- grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC H3A 0E7 Canada
| | - Éva Nagy
- grid.34429.380000 0004 1936 8198Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Byram Bridle
- grid.34429.380000 0004 1936 8198Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Mehdi Sargolzaei
- grid.34429.380000 0004 1936 8198Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada ,Select Sires, Inc., Plain City, OH 43064 USA
| | - Shayan Sharif
- grid.34429.380000 0004 1936 8198Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
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8
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Lai MC, Chen YP, Li DA, Yu JS, Hung HY, Tarn WY. DDX3 interacts with USP9X and participates in deubiquitination of the anti-apoptotic protein MCL1. FEBS J 2021; 289:1043-1061. [PMID: 34606682 DOI: 10.1111/febs.16219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/26/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
Here, we describe a novel interaction between the RNA helicase DDX3 and the deubiquitinase ubiquitin-specific peptidase 9 X-linked (USP9X) in human cells. Domain mapping studies reveal that the C-terminal region of DDX3 interacted with the N terminus of USP9X. USP9X was predominantly localized in the cytoplasm where the interaction between DDX3 and USP9X occurred. USP9X was not visibly enriched in cytoplasmic stress granules (SGs) under oxidative stress conditions, whereas overexpression of GFP-DDX3 induced SG formation and recruited USP9X to SGs in HeLa cells. Luciferase reporter assays showed that depletion of USP9X had no significant effect on DDX3-mediated translation. Given that DDX3 is not ubiquitinated upon ubiquitin overexpression, it is unlikely that DDX3 serves as a substrate of USP9X. Importantly, we found that ubiquitinated MCL1 was accumulated upon depletion of USP9X and/or DDX3 in MG132-treated cells, suggesting that USP9X and DDX3 play a role in regulating MCL1 protein stability and anti-apoptotic function. This study indicates that DDX3 exerts anti-apoptotic effects probably by coordinating with USP9X in promoting MCL1 deubiquitination.
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Affiliation(s)
- Ming-Chih Lai
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Colorectal Surgery, New Taipei Municipal Tucheng Hospital, Taiwan
| | - Yi-Pin Chen
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Ding-An Li
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yuan Hung
- Department of Colorectal Surgery, New Taipei Municipal Tucheng Hospital, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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9
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RNA Helicase DDX3: A Double-Edged Sword for Viral Replication and Immune Signaling. Microorganisms 2021; 9:microorganisms9061206. [PMID: 34204859 PMCID: PMC8227550 DOI: 10.3390/microorganisms9061206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
DDX3 is a cellular ATP-dependent RNA helicase involved in different aspects of RNA metabolism ranging from transcription to translation and therefore, DDX3 participates in the regulation of key cellular processes including cell cycle progression, apoptosis, cancer and the antiviral immune response leading to type-I interferon production. DDX3 has also been described as an essential cellular factor for the replication of different viruses, including important human threats such HIV-1 or HCV, and different small molecules targeting DDX3 activity have been developed. Indeed, increasing evidence suggests that DDX3 can be considered not only a promising but also a viable target for anticancer and antiviral treatments. In this review, we summarize distinct functional aspects of DDX3 focusing on its participation as a double-edged sword in the host immune response and in the replication cycle of different viruses.
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10
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Hua Q, Liu Y, Li M, Chen Y, Diao Q, Zeng H, Jiang Y. Tobacco-Related Exposure Upregulates Circ_0035266 to Exacerbate Inflammatory Responses in Human Bronchial Epithelial Cells. Toxicol Sci 2021; 179:70-83. [PMID: 33107911 DOI: 10.1093/toxsci/kfaa163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
One of the most carcinogenic chemicals found in cigarette tobacco smoke is 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), which has been confirmed to be associated with the etiology of diverse cancers. Lipopolysaccharide (LPS), another biologically active component of cigarette smoke, is a risk factor which enhances NNK-induced lung tumorigenesis due to chronic lung inflammation. Although inflammatory responses play critical roles in the initiation of many tumors, our knowledge about the mechanisms of NNK+LPS on inflammation is currently limited. Here, we investigated the inflammatory effects of NNK+LPS in human bronchial epithelial cells (BEAS-2B) and explored the underlying mechanisms mediated by circular RNAs (circRNAs). We identified a novel circRNA, circ_0035266, which was strongly upregulated in NNK+LPS-induced BEAS-2B cells and enhanced the inflammatory responses to NNK+LPS by regulating the secretion of pro-inflammatory cytokines interleukin (IL)-6 and IL-8. Specifically, circ_0035266 knockdown alleviated NNK+LPS-induced inflammatory responses, whereas overexpression of circ_0035266 had the opposite effect. Moreover, dual-luciferase reporter and fluorescence in situ hybridization (FISH) assays verified that circ_0035266 bound to miR-181d-5p directly in the cytoplasm. qRT-PCR, dual-luciferase reporter assays, and Western blot analyses showed that DDX3X (DDX3) was the downstream target of miR-181d-5p and that DDX3X expression levels were modulated by circ_0035266. These results suggested that circ_0035266 served as a competitive endogenous RNA for miR-181d-5p to regulate DDX3X expression, which is involved in the modulation of NNK+LPS-induced inflammatory responses in BEAS-2B cells.
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Affiliation(s)
- Qiuhan Hua
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yufei Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Meizhen Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yingnan Chen
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Qinqin Diao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Huixian Zeng
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
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11
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Cui BC, Sikirzhytski V, Aksenova M, Lucius MD, Levon GH, Mack ZT, Pollack C, Odhiambo D, Broude E, Lizarraga SB, Wyatt MD, Shtutman M. Pharmacological inhibition of DEAD-Box RNA Helicase 3 attenuates stress granule assembly. Biochem Pharmacol 2020; 182:114280. [PMID: 33049245 DOI: 10.1016/j.bcp.2020.114280] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022]
Abstract
Stress granules (SGs) are non-membranous cytosolic protein-RNA aggregates that process mRNAs through stalled translation initiation in response to cellular stressors and in disease. DEAD-Box RNA helicase 3 (DDX3) is an active target of drug development for the treatment of viral infections, cancers, and neurodegenerative diseases. DDX3 plays a critical role in RNA metabolism, including SGs, but the role of DDX3 enzymatic activity in SG dynamics is not well understood. Here, we address this question by determining the effects of DDX3 inhibition on the dynamics of SG assembly and disassembly. We use two small molecule inhibitors of DDX3, RK33 and 16D, with distinct inhibitory mechanisms that target DDX3's ATPase activity and RNA helicase site, respectively. We find that both DDX3 inhibitors reduce the assembly of SGs, with a more pronounced reduction from RK-33. In contrast, both compounds only marginally affect the disassembly of SGs. RNA-mediated knockdown of DDX3 caused a similar reduction in SG assembly and minimal effect on SG disassembly. Collectively, these results reveal that the enzymatic activity of DDX3 is required for the assembly of SGs and pharmacological inhibition of DDX3 could be relevant for the treatment of SG-dependent pathologies.
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Affiliation(s)
- B Celia Cui
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Vitali Sikirzhytski
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Marina Aksenova
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Matthew D Lucius
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Gabrielle H Levon
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Zachary T Mack
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Charlotte Pollack
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Diana Odhiambo
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Eugenia Broude
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Sofia B Lizarraga
- Department of Biological Sciences, College of Arts and Sciences, University of South Carolina, Columbia, SC, USA
| | - Michael D Wyatt
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA.
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12
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Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12:v12090984. [PMID: 32899736 PMCID: PMC7552005 DOI: 10.3390/v12090984] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades.
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Affiliation(s)
- Nina Eiermann
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Katharina Haneke
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Zhaozhi Sun
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
- Correspondence:
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13
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Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins. Viruses 2020; 12:v12070784. [PMID: 32708250 PMCID: PMC7412275 DOI: 10.3390/v12070784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022] Open
Abstract
Endemic to West Africa and South America, mammalian arenaviruses can cross the species barrier from their natural rodent hosts to humans, resulting in illnesses ranging from mild flu-like syndromes to severe and fatal haemorrhagic zoonoses. The increased frequency of outbreaks and associated high fatality rates of the most prevalent arenavirus, Lassa, in West African countries, highlights the significant risk to public health and to the socio-economic development of affected countries. The devastating impact of these viruses is further exacerbated by the lack of approved vaccines and effective treatments. Differential immune responses to arenavirus infections that can lead to either clearance or rapid, widespread and uncontrolled viral dissemination are modulated by the arenavirus multifunctional proteins, NP and Z. These two proteins control the antiviral response to infection by targeting multiple cellular pathways; and thus, represent attractive targets for antiviral development to counteract infection. The interplay between the host immune responses and viral replication is a key determinant of virus pathogenicity and disease outcome. In this review, we examine the current understanding of host immune defenses against arenavirus infections and summarise the host protein interactions of NP and Z and the mechanisms that govern immune evasion strategies.
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14
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Quaranta P, Lottini G, Chesi G, Contrafatto F, Russotto R, Macera L, Lai M, Spezia PG, Brai A, Botta M, Freer G, Pistello M. DDX3 inhibitors show antiviral activity against positive-sense single-stranded RNA viruses but not against negative-sense single-stranded RNA viruses: The coxsackie B model. Antiviral Res 2020; 178:104750. [DOI: 10.1016/j.antiviral.2020.104750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/08/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
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15
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The Drosophila RNA Helicase Belle (DDX3) Non-Autonomously Suppresses Germline Tumorigenesis Via Regulation of a Specific mRNA Set. Cells 2020; 9:cells9030550. [PMID: 32111103 PMCID: PMC7140462 DOI: 10.3390/cells9030550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 12/28/2022] Open
Abstract
DDX3 subfamily DEAD-box RNA helicases are essential developmental regulators of RNA metabolism in eukaryotes. belle, the single DDX3 ortholog in Drosophila, is required for fly viability, fertility, and germline stem cell maintenance. Belle is involved both in translational activation and repression of target mRNAs in different tissues; however, direct targets of Belle in the testes are essentially unknown. Here we showed that belle RNAi knockdown in testis cyst cells caused a disruption of adhesion between germ and cyst cells and generation of tumor-like clusters of stem-like germ cells. Ectopic expression of β-integrin in cyst cells rescued early stages of spermatogenesis in belle knockdown testes, indicating that integrin adhesion complexes are required for the interaction between somatic and germ cells in a cyst. To address Belle functions in spermatogenesis in detail we performed cross-linking immunoprecipitation and sequencing (CLIP-seq) analysis and identified multiple mRNAs that interacted with Belle in the testes. The set of Belle targets includes transcripts of proteins that are essential for preventing the tumor-like clusters of germ cells and for sustaining spermatogenesis. By our hypothesis, failures in the translation of a number of mRNA targets additively contribute to developmental defects observed in the testes with belle knockdowns both in cyst cells and in the germline.
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16
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Liao SE, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle posttranscriptionally promotes gene expression in an ATPase activity-dependent manner. RNA (NEW YORK, N.Y.) 2019; 25:825-839. [PMID: 30979781 PMCID: PMC6573787 DOI: 10.1261/rna.070268.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Drosophila Belle (human ortholog DDX3) is a conserved DEAD-box RNA helicase implicated in regulating gene expression. However, the molecular mechanisms by which Belle/DDX3 regulates gene expression are poorly understood. Here we performed systematic mutational analysis to determine the contributions of conserved motifs within Belle to its in vivo function. We found that Belle RNA-binding and RNA-unwinding activities and intrinsically disordered regions (IDRs) are required for Belle in vivo function. Expression of Belle ATPase mutants that cannot bind, hydrolyze, or release ATP resulted in dominant toxic phenotypes. Mechanistically, we discovered that Belle up-regulates reporter protein level when tethered to reporter mRNA, without corresponding changes at the mRNA level, indicating that Belle promotes translation of mRNA that it binds. Belle ATPase activity and amino-terminal IDR were required for this translational promotion activity. We also found that ectopic ovary expression of dominant Belle ATPase mutants decreases levels of cyclin proteins, including Cyclin B, without corresponding changes in their mRNA levels. Finally, we found that Belle binds endogenous cyclin B mRNA. We propose that Belle promotes translation of specific target mRNAs, including cyclin B mRNA, in an ATPase activity-dependent manner.
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Affiliation(s)
- Susan E Liao
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Suresh K Kandasamy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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17
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Perčulija V, Ouyang S. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases. HELICASES FROM ALL DOMAINS OF LIFE 2019. [PMCID: PMC7158350 DOI: 10.1016/b978-0-12-814685-9.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DEAD/DEAH-box helicases are enzymes that belong to the DEAD/H-box family of SF2 helicase superfamily. These enzymes are essential in RNA metabolism, where they are involved in a number of processes that require manipulation of RNA structure. Recent studies have found that some DEAD/DEAH-box helicases play important roles in innate immunity, where they act as sensors of cytosolic DNA/RNA, as adaptor proteins, or as regulators of signaling and gene expression. In spite of their function in immunity, DEAD/DEAH-box helicases can also be hijacked and exploited by viruses to circumvent detection and aid in viral replication. These findings not only imply that DEAD/DEAH-box helicases have a broader function than previously thought, but also give us a much better understanding of immune mechanisms and diseases that arise due to the dysregulation or evasion thereof. In this chapter, we demonstrate the known scope of activities of human DEAD/DEAH-box helicases in innate immunity and interaction with viruses or other pathogens. Additionally, we give an outline of diseases in which they are, or may be, involved in the context of immunity.
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18
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DDX3 Participates in Translational Control of Inflammation Induced by Infections and Injuries. Mol Cell Biol 2018; 39:MCB.00285-18. [PMID: 30373933 DOI: 10.1128/mcb.00285-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022] Open
Abstract
Recent studies have suggested that DDX3 functions in antiviral innate immunity, but the underlying mechanism remains elusive. We previously identified target mRNAs whose translation is controlled by DDX3. Pathway enrichment analysis of these targets indicated that DDX3 is involved in various infections and inflammation. Using immunoblotting, we confirmed that PACT, STAT1, GNB2, Rac1, TAK1, and p38 mitogen-activated protein kinase (MAPK) proteins are downregulated by DDX3 knockdown in human monocytic THP-1 cells and epithelial HeLa cells. Polysome profiling revealed that DDX3 knockdown reduces the translational efficiency of target mRNAs. We further demonstrated DDX3-mediated translational control of target mRNAs by luciferase reporter assays. To examine the effects of DDX3 knockdown on macrophage migration and phagocytosis, we performed in vitro cell migration assay and flow cytometry analysis of the uptake of green fluorescent protein-expressing Escherichia coli in THP-1 cells. The DDX3 knockdown cells exhibited impaired macrophage migration and phagocytosis. Moreover, we used a human cytokine antibody array to identify the cytokines affected by DDX3 knockdown. Several chemokines were decreased considerably in DDX3 knockdown THP-1 cells after lipopolysaccharide or poly(I·C) stimulation. Lastly, we demonstrated that DDX3 is crucial for the recruitment of phagocytes to the site of inflammation in transgenic zebrafish.
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19
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Szappanos D, Tschismarov R, Perlot T, Westermayer S, Fischer K, Platanitis E, Kallinger F, Novatchkova M, Lassnig C, Müller M, Sexl V, Bennett KL, Foong-Sobis M, Penninger JM, Decker T. The RNA helicase DDX3X is an essential mediator of innate antimicrobial immunity. PLoS Pathog 2018; 14:e1007397. [PMID: 30475900 PMCID: PMC6283616 DOI: 10.1371/journal.ppat.1007397] [Citation(s) in RCA: 53] [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: 03/29/2018] [Revised: 12/06/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
DExD/H box RNA helicases, such as the RIG-I-like receptors (RLR), are important components of the innate immune system. Here we demonstrate a pivotal and sex-specific role for the heterosomal isoforms of the DEAD box RNA helicase DDX3 in the immune system. Mice lacking DDX3X during hematopoiesis showed an altered leukocyte composition in bone marrow and spleen and a striking inability to combat infection with Listeria monocytogenes. Alterations in innate immune responses resulted from decreased effector cell availability and function as well as a sex-dependent impairment of cytokine synthesis. Thus, our data provide further in vivo evidence for an essential contribution of a non-RLR DExD/H RNA helicase to innate immunity and suggest it may contribute to sex-related differences in resistance to microbes and resilience to inflammatory disease. The establishment of innate immunity to pathogens requires cells to sense microbial molecules and to initiate a de novo transcription-based antimicrobial response. With the identification of Rig I and Mda5, two RNA helicases were shown to serve as pivotal receptors of viral RNA. Subsequently, a considerable number of RNA helicases were proposed to function as sensors or signal transducers for both microbial RNA and DNA. X-chromosome-encoded RNA helicase DDX3X was discovered as an interactor of the S/T kinase TBK1 which regulates the production of type I Interferons (IFN-I). However, the importance of DDX3X for innate immunity in an organismic context remained elusive. Here we describe and analyze mice lacking DDX3X in hematopoietic cells. We show contributions of DDX3X to hematopoiesis and a striking loss in resistance against Listeria monocytogenes. Our data reveal that DDX3X is critically involved in enhancing the expression of numerous antimicrobial genes. Consistently, production of important cytokines such as IL12 or IFNγ is reduced. Furthermore, DDX3X-deficient macrophages show reduced ability to restrict L. monocytogenes growth. Owing to partial redundancy with its close Y-chromosomal homologue, DDX3Y, the observed effects differ between mouse sexes. Thus, DDX3X may contribute to sex differences in immunity to pathogens and inflammatory disease.
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Affiliation(s)
- Daniel Szappanos
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Roland Tschismarov
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Thomas Perlot
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Sandra Westermayer
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Katrin Fischer
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Ekaterini Platanitis
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Fabian Kallinger
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Caroline Lassnig
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle Foong-Sobis
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
- * E-mail: (JMP); (TD)
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
- * E-mail: (JMP); (TD)
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20
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Brennan R, Haap-Hoff A, Gu L, Gautier V, Long A, Schröder M. Investigating nucleo-cytoplasmic shuttling of the human DEAD-box helicase DDX3. Eur J Cell Biol 2018; 97:501-511. [PMID: 30131165 DOI: 10.1016/j.ejcb.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/20/2023] Open
Abstract
The human DEAD-box helicase DDX3 is a multi-functional protein involved in the regulation of gene expression and additional non-conventional roles as signalling adaptor molecule that are independent of its enzymatic RNA remodeling activity. It is a nucleo-cytoplasmic shuttling protein and it has previously been suggested that dysregulation of its subcellular localization could contribute to tumourigenesis. Indeed, both tumour suppressor and oncogenic functions have been attributed to DDX3. In this study, we investigated the regulation of DDX3's nucleocytoplasmic shuttling. We confirmed that an N-terminal conserved Nuclear Export Signal (NES) is required for export of human DDX3 from the nucleus, and identified three regions within DDX3 that can independently facilitate its nuclear import. We also aimed to identify conditions that alter DDX3's subcellular localisation. Viral infection, cytokine treatment and DNA damage only induced minor changes in DDX3's subcellular distribution as determined by High Content Analysis. However, DDX3's nuclear localization increased in early mitotic cells (during prophase) concomitant with an increase in DDX3 expression levels. Our results are likely to have implications for the proposed use of (nuclear) DDX3 as a prognostic biomarker in cancer.
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Affiliation(s)
- Ruth Brennan
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antje Haap-Hoff
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Lili Gu
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Virginie Gautier
- School of Medicine, Centre for Research in Infectious Diseases (CRID), University College Dublin, Belfield, Dublin 4, Ireland
| | - Aideen Long
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Martina Schröder
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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21
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Loureiro ME, Zorzetto-Fernandes AL, Radoshitzky S, Chi X, Dallari S, Marooki N, Lèger P, Foscaldi S, Harjono V, Sharma S, Zid BM, López N, de la Torre JC, Bavari S, Zúñiga E. DDX3 suppresses type I interferons and favors viral replication during Arenavirus infection. PLoS Pathog 2018; 14:e1007125. [PMID: 30001425 PMCID: PMC6042795 DOI: 10.1371/journal.ppat.1007125] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/27/2018] [Indexed: 11/19/2022] Open
Abstract
Several arenaviruses cause hemorrhagic fever (HF) diseases that are associated with high morbidity and mortality in humans. Accordingly, HF arenaviruses have been listed as top-priority emerging diseases for which countermeasures are urgently needed. Because arenavirus nucleoprotein (NP) plays critical roles in both virus multiplication and immune-evasion, we used an unbiased proteomic approach to identify NP-interacting proteins in human cells. DDX3, a DEAD-box ATP-dependent-RNA-helicase, interacted with NP in both NP-transfected and virus-infected cells. Importantly, DDX3 deficiency compromised the propagation of both Old and New World arenaviruses, including the HF arenaviruses Lassa and Junin viruses. The DDX3 role in promoting arenavirus multiplication associated with both a previously un-recognized DDX3 inhibitory role in type I interferon production in arenavirus infected cells and a positive DDX3 effect on arenavirus RNA synthesis that was dependent on its ATPase and Helicase activities. Our results uncover novel mechanisms used by arenaviruses to exploit the host machinery and subvert immunity, singling out DDX3 as a potential host target for developing new therapies against highly pathogenic arenaviruses.
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Affiliation(s)
- María Eugenia Loureiro
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | | | - Sheli Radoshitzky
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Xiaoli Chi
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Simone Dallari
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Nuha Marooki
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Psylvia Lèger
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Sabrina Foscaldi
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Vince Harjono
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Sonia Sharma
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States of America
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Nora López
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Juan Carlos de la Torre
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, United States of America
| | - Sina Bavari
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Elina Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
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22
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Chan CP, Yuen CK, Cheung PHH, Fung SY, Lui PY, Chen H, Kok KH, Jin DY. Antiviral activity of double-stranded RNA-binding protein PACT against influenza A virus mediated via suppression of viral RNA polymerase. FASEB J 2018. [PMID: 29513570 DOI: 10.1096/fj.201701361r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PACT is a double-stranded RNA-binding protein that has been implicated in host-influenza A virus (IAV) interaction. PACT facilitates the action of RIG-I in the activation of the type I IFN response, which is suppressed by the viral nonstructural protein NS1. PACT is also known to interact with the IAV RNA polymerase subunit PA. Exactly how PACT exerts its antiviral activity during IAV infection remains to be elucidated. In the current study, we demonstrated the interplay between PACT and IAV polymerase. Induction of IFN-β by the IAV RNP complex was most robust when both RIG-I and PACT were expressed. PACT-dependent activation of IFN-β production was suppressed by the IAV polymerase subunits, polymerase acidic protein, polymerase basic protein 1 (PB1), and PB2. PACT associated with PA, PB1, and PB2. Compromising PACT in IAV-infected A549 cells resulted in the augmentation of viral RNA (vRNA) transcription and replication and IFN-β production. Furthermore, vRNA replication was boosted by knockdown of PACT in both A549 cells and IFN-deficient Vero cells. Thus, the antiviral activity of PACT is mediated primarily via its interaction with and inhibition of IAV polymerase. Taken together, our findings reveal a new facet of the host-IAV interaction in which the interplay between PACT and IAV polymerase affects the outcome of viral infection and antiviral response.-Chan, C.-P., Yuen, C.-K., Cheung, P.-H. H., Fung, S.-Y., Lui, P.-Y., Chen, H., Kok, K.-H., Jin, D.-Y. Antiviral activity of double-stranded RNA-binding protein PACT against influenza A virus mediated via suppression of viral RNA polymerase.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chun-Kit Yuen
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | | | - Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Pak-Yin Lui
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Honglin Chen
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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23
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Boldescu V, Behnam MAM, Vasilakis N, Klein CD. Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond. Nat Rev Drug Discov 2017; 16:565-586. [PMID: 28473729 PMCID: PMC5925760 DOI: 10.1038/nrd.2017.33] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.
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Affiliation(s)
- Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry of the Academy of Sciences of Moldova, Academiei 3, 2028 Chisinau, Moldova
| | - Mira A. M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Vasilakis
- Dept. of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, 2.138D Keiller Bldg, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555–0609, USA
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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24
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RNA helicase DDX3 maintains lipid homeostasis through upregulation of the microsomal triglyceride transfer protein by interacting with HNF4 and SHP. Sci Rep 2017; 7:41452. [PMID: 28128295 PMCID: PMC5269733 DOI: 10.1038/srep41452] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/19/2016] [Indexed: 01/06/2023] Open
Abstract
Multifunctional RNA helicase DDX3 participates in HCV infection, one of the major causes of hepatic steatosis. Here, we investigated the role of DDX3 in hepatic lipid metabolism. We found that HCV infection severely reduced DDX3 expression. Analysis of intracellular triglyceride and secreted ApoB indicated that lipid accumulations were increased while ApoB secretion were decreased in DDX3 knockdown HuH7 and HepG2 cell lines. Down-regulation of DDX3 significantly decreased protein and transcript expression of microsomal triglyceride transfer protein (MTP), a key regulator of liver lipid homeostasis. Moreover, DDX3 interacted with hepatocyte nuclear factor 4 (HNF4) and small heterodimer partner (SHP), and synergistically up-regulated HNF4-mediated transactivation of MTP promoter via its ATPase activity. Further investigation revealed that DDX3 interacted with CBP/p300 and increased the promoter binding affinity of HNF4 by enhancing HNF4 acetylation. Additionally, DDX3 partially relieved the SHP-mediated suppression on MTP promoter by competing with SHP for HNF4 binding which disrupted the inactive HNF4/SHP heterodimer while promoted the formation of the active HNF4 homodimer. Collectively, these results imply that DDX3 regulates MTP gene expression and lipid homeostasis through interplay with HNF4 and SHP, which may also reveal a novel mechanism of HCV-induced steatosis.
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Patent highlights: December 2015-January 2016. Pharm Pat Anal 2016; 5:147-53. [PMID: 27088860 DOI: 10.4155/ppa-2016-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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Ma TH, Lee LW, Lee CC, Yi YH, Chan SP, Tan BCM, Lo SJ. Genetic control of nucleolar size: An evolutionary perspective. Nucleus 2016; 7:112-20. [PMID: 27003693 DOI: 10.1080/19491034.2016.1166322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Exploiting a C. elegans mutant (ncl-1) exhibiting nucleolar abnormalities, we recently identified the let-7/ncl-1/fib-1 genetic cascade underlying proper rRNA abundance and nucleolar size. These 3 factors, let-7 (a miRNA), NCL-1 (a member of the TRIM-NHL family), and fibrillarin (a nucleolar methyltransferase), are evolutionarily conserved across metazoans. In this article, we provide several lines of bioinformatic evidence showing that human and Drosophila homologues of C. elegans NCL-1, TRIM-71 and Brat, respectively, likely act as translational suppressors of fibrillarin. Moreover, since their 3'-UTRs contain putative target sites, they may also be under the control of the let-7 miRNA. We hypothesize that let-7, TRIM and fibrillarin contribute activities in concert, and constitute a conserved network controlling nucleolar size in eukaryotes. We provide an in-depth literature review of various molecular pathways, including the let-7/ncl-1/fib-1 genetic cascade, implicated in the regulation of nucleolar size.
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Affiliation(s)
- Tian-Hsiang Ma
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Li-Wei Lee
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Chi-Chang Lee
- d Institute of Chemistry , Academia Sinica , Taipei , Taiwan
| | - Yung-Hsiang Yi
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Shih-Peng Chan
- e Graduate Institute of Microbiology , College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Bertrand Chin-Ming Tan
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
| | - Szecheng J Lo
- a Department of Biomedical Sciences, College of Medicine , Chang Gung University , TaoYuan , Taiwan.,b Graduate Institute of Biomedical Sciences , College of Medicine , Chang Gung University , TaoYuan , Taiwan.,c Molecular Medicine Research Center , College of Medicine , Chang Gung University , TaoYuan , Taiwan
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Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3. J Biol Chem 2015; 291:2412-21. [PMID: 26598523 DOI: 10.1074/jbc.m115.700625] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 11/06/2022] Open
Abstract
DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins.
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Affiliation(s)
- Stephen N Floor
- From the Department of Molecular and Cell Biology, Howard Hughes Medical Institute
| | | | - Deepak Sharma
- the Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Eckhard Jankowsky
- the Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Jennifer A Doudna
- From the Department of Molecular and Cell Biology, Howard Hughes Medical Institute, Department of Chemistry, and Innovative Genomics Initiative, University of California, Berkeley, California 94720, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and
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