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Sheng X, Yang Y, Zhu M, Zhou L, Zhu F, Zhu Y, Dong S, Kong H, Wang H, Jiang J, Wan M, Feng M, Deng Q, Xu Y, You Q, Hu R. Non-proteolytic ubiquitination of HBx controls HBV replication. Virol Sin 2024; 39:338-342. [PMID: 38307415 PMCID: PMC11074638 DOI: 10.1016/j.virs.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
•The expression level of TRIM21 in patients is negatively correlated with the replication and integration of HBV. •TRIM21 was found to trigger non-proteolytic ubiquitination of X protein of HBV. •This study proposes that the PRYSPRY and RING domains in TRIM21 dimer can form a docking conformation for HBx binding. •TRIM21-mediated HBx ubiquitination disrupts the DDB1 recruitment to HBx and stabilize Smc6.
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Affiliation(s)
- Xiangpeng Sheng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Yi Yang
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Min Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Linlin Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Fang Zhu
- School of Medicine, Guizhou University, Guiyang 550025, China
| | - Yuanfei Zhu
- Key Laboratory of Medical Molecular Virology (MOE & MOH), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Siying Dong
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Kong
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Honghua Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Ji Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mingyue Wan
- Department of Hospital Infection Management, Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingyang Feng
- Department of Hospital Infection Management, Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qiang Deng
- Key Laboratory of Medical Molecular Virology (MOE & MOH), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yumin Xu
- Department of Hospital Infection Management, Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Qing You
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ronggui Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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2
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Aloise C, Schipper JG, van Vliet A, Oymans J, Donselaar T, Hurdiss DL, de Groot RJ, van Kuppeveld FJM. SARS-CoV-2 nucleocapsid protein inhibits the PKR-mediated integrated stress response through RNA-binding domain N2b. PLoS Pathog 2023; 19:e1011582. [PMID: 37607209 PMCID: PMC10473545 DOI: 10.1371/journal.ppat.1011582] [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: 03/07/2023] [Revised: 09/01/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding-prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Similar observations were made for the N protein of human coronavirus 229E, suggesting that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
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Affiliation(s)
- Chiara Aloise
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jelle G. Schipper
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Arno van Vliet
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Judith Oymans
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tim Donselaar
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L. Hurdiss
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raoul J. de Groot
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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3
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Samanta A, Lufkin T, Kraus P. Intervertebral disc degeneration-Current therapeutic options and challenges. Front Public Health 2023; 11:1156749. [PMID: 37483952 PMCID: PMC10359191 DOI: 10.3389/fpubh.2023.1156749] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Degeneration of the intervertebral disc (IVD) is a normal part of aging. Due to the spine's declining function and the development of pain, it may affect one's physical health, mental health, and socioeconomic status. Most of the intervertebral disc degeneration (IVDD) therapies today focus on the symptoms of low back pain rather than the underlying etiology or mechanical function of the disc. The deteriorated disc is typically not restored by conservative or surgical therapies that largely focus on correcting symptoms and structural abnormalities. To enhance the clinical outcome and the quality of life of a patient, several therapeutic modalities have been created. In this review, we discuss genetic and environmental causes of IVDD and describe promising modern endogenous and exogenous therapeutic approaches including their applicability and relevance to the degeneration process.
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4
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Nemes B, László S, Zsidó BZ, Hetényi C, Feher A, Papp F, Varga Z, Szőke É, Sándor Z, Pintér E. Elucidation of the binding mode of organic polysulfides on the human TRPA1 receptor. Front Physiol 2023; 14:1180896. [PMID: 37351262 PMCID: PMC10282659 DOI: 10.3389/fphys.2023.1180896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction: Previous studies have established that endogenous inorganic polysulfides have significant biological actions activating the Transient Receptor Potential Ankyrin 1 (TRPA1) receptor. Organic polysulfides exert similar effects, but they are much more stable molecules, therefore these compounds are more suitable as drugs. In this study, we aimed to better understand the mechanism of action of organic polysulfides by identification of their binding site on the TRPA1 receptor. Methods: Polysulfides can readily interact with the thiol side chain of the cysteine residues of the protein. To investigate their role in the TRPA1 activation, we replaced several cysteine residues by alanine via site-directed mutagenesis. We searched for TRPA1 mutant variants with decreased or lost activating effect of the polysulfides, but with other functions remaining intact (such as the effects of non-electrophilic agonists and antagonists). The binding properties of the mutant receptors were analyzed by in silico molecular docking. Functional changes were tested by in vitro methods: calcium sensitive fluorescent flow cytometry, whole-cell patch-clamp and radioactive calcium-45 liquid scintillation counting. Results: The cysteines forming the conventional binding site of electrophilic agonists, namely C621, C641 and C665 also bind the organic polysulfides, with the key role of C621. However, only their combined mutation abolished completely the organic polysulfide-induced activation of the receptor. Discussion: Since previous papers provided evidence that organic polysulfides exert analgesic and anti-inflammatory actions in different in vivo animal models, we anticipate that the development of TRPA1-targeted, organic polysulfide-based drugs will be promoted by this identification of the binding site.
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Affiliation(s)
- Balázs Nemes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
| | - Szabolcs László
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
| | - Adam Feher
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ferenc Papp
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Éva Szőke
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán Sándor
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
| | - Erika Pintér
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
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5
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Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility. mBio 2022; 13:e0098122. [PMID: 36000733 PMCID: PMC9600491 DOI: 10.1128/mbio.00981-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for crp, ompR, phoP, and flhD genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhD4C2), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of flhD, is involved in the fine-tuning of flhD expression and thus participates in the control of motility.
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6
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Role of Stress Granules in Suppressing Viral Replication by the Infectious Bronchitis Virus Endoribonuclease. J Virol 2022; 96:e0068622. [PMID: 35638780 DOI: 10.1128/jvi.00686-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infectious bronchitis virus (IBV), a γ-coronavirus, causes the economically important poultry disease infectious bronchitis. Cellular stress response is an effective antiviral strategy that leads to stress granule (SG) formation. Previous studies suggested that SGs were involved in the antiviral activity of host cells to limit viral propagation. Here, we aimed to delineate the molecular mechanisms regulating the SG response to pathogenic IBV strain infection. We found that most chicken embryo kidney (CEK) cells formed no SGs during IBV infection and IBV replication inhibited arsenite-induced SG formation. This inhibition was not caused by changes in the integrity or abundance of SG proteins during infection. IBV nonstructural protein 15 (Nsp15) endoribonuclease activity suppressed SG formation. Regardless of whether Nsp15 was expressed alone, with recombinant viral infection with Newcastle disease virus as a vector, or with EndoU-deficient IBV, the Nsp15 endoribonuclease activity was the main factor inhibiting SG formation. Importantly, uridine-specific endoribonuclease (EndoU)-deficient IBV infection induced colocalization of IBV N protein/dsRNA and SG-associated protein TIA1 in infected cells. Additionally, overexpressing TIA1 in CEK cells suppressed IBV replication and may be a potential antiviral factor for impairing viral replication. These data provide a novel foundation for future investigations of the mechanisms by which coronavirus endoribonuclease activity affects viral replication. IMPORTANCE Endoribonuclease is conserved in coronaviruses and affects viral replication and pathogenicity. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal, and reproductive systems, causing millions of dollars in lost revenue to the poultry industry worldwide annually. Mutating the viral endoribonuclease poly(U) resulted in SG formation, and TIA1 protein colocalized with the viral N protein and dsRNA, thus damaging IBV replication. These results suggest a new antiviral target design strategy for coronaviruses.
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7
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Fus-Kujawa A, Prus P, Bajdak-Rusinek K, Teper P, Gawron K, Kowalczuk A, Sieron AL. An Overview of Methods and Tools for Transfection of Eukaryotic Cells in vitro. Front Bioeng Biotechnol 2021; 9:701031. [PMID: 34354988 PMCID: PMC8330802 DOI: 10.3389/fbioe.2021.701031] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Transfection is a powerful analytical tool enabling studies of gene products and functions in eukaryotic cells. Successful delivery of genetic material into cells depends on DNA quantity and quality, incubation time and ratio of transfection reagent to DNA, the origin, type and the passage of transfected cells, and the presence or absence of serum in the cell culture. So far a number of transfection methods that use viruses, non-viral particles or physical factors as the nucleic acids carriers have been developed. Among non-viral carriers, the cationic polymers are proposed as the most attractive ones due to the possibility of their chemical structure modification, low toxicity and immunogenicity. In this review the delivery systems as well as physical, biological and chemical methods used for eukaryotic cells transfection are described and discussed.
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Affiliation(s)
- Agnieszka Fus-Kujawa
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Pawel Prus
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
- Students’ Scientific Society, Katowice, Poland
| | - Karolina Bajdak-Rusinek
- Department of Medical Genetics, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Paulina Teper
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland
| | - Katarzyna Gawron
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Agnieszka Kowalczuk
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland
| | - Aleksander L. Sieron
- Department of Molecular Biology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
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8
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Di Blasi R, Marbiah MM, Siciliano V, Polizzi K, Ceroni F. A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation. Nat Commun 2021; 12:2545. [PMID: 33953169 PMCID: PMC8099865 DOI: 10.1038/s41467-021-22795-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 02/08/2023] Open
Abstract
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammalian cells highlight how resource competition for gene expression leads to biases in data interpretation, with a direct impact on co-transfection experiments. Here we define the connection between resource competition and transient transfection experiments and discuss possible alternatives. Our aim is to raise awareness within the community and stimulate discussion to include such considerations in future experimental designs, for the development of better transfection controls.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples (ITA), Italy
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK. .,Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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9
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Chong ZX, Yeap SK, Ho WY. Transfection types, methods and strategies: a technical review. PeerJ 2021; 9:e11165. [PMID: 33976969 PMCID: PMC8067914 DOI: 10.7717/peerj.11165] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells' genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
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Affiliation(s)
- Zhi Xiong Chong
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wan Yong Ho
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
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10
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Coronavirus Endoribonuclease Ensures Efficient Viral Replication and Prevents Protein Kinase R Activation. J Virol 2021; 95:JVI.02103-20. [PMID: 33361429 PMCID: PMC8092692 DOI: 10.1128/jvi.02103-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus (CoV) nsp15 is an endoribonuclease conserved throughout the CoV family. The enzymatic activity and crystal structure of infectious bronchitis virus (IBV) nsp15 are undefined, and the protein's role in replication remains unclear. We verified the uridylate-specific endoribonuclease (EndoU) activity of IBV and found that the EndoU active sites were located in the C-terminus of nsp15 and included His223, His238, Lys278 and Tyr334. We further constructed an infectious clone of the IBV-rSD strain (rSD-wild-type [WT]) and EndoU-deficient IBVs by changing the codon for the EndoU catalytic residues to alanine. Both the rSD-WT and EndoU-deficient viruses propagated efficiently in embryonated chicken eggs. Conversely, EndoU-deficient viral propagation was severely impaired in chicken embryonic kidney cells, which was reflected in the lower viral mRNA accumulation and protein synthesis. After infecting chickens with the parental rSD-WT strain and EndoU-deficient viruses, the EndoU-deficient-virus-infected chickens presented reduced mortality, tissue injury and viral shedding.IMPORTANCE Coronaviruses can emerge from animal reservoirs into naive host species to cause pandemic respiratory and gastrointestinal diseases with significant mortality in humans and domestic animals. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal and reproductive systems, causing millions of dollars in lost revenue worldwide annually. Mutating the viral endoribonuclease resulted in an attenuated virus and prevented protein kinase R activation. Therefore, EndoU activity is a virulence factor in IBV infections, thus providing an approach for generating live-attenuated vaccine candidates for emerging coronaviruses.
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11
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Rabouw HH, Visser LJ, Passchier TC, Langereis MA, Liu F, Giansanti P, van Vliet ALW, Dekker JG, van der Grein SG, Saucedo JG, Anand AA, Trellet ME, Bonvin AMJJ, Walter P, Heck AJR, de Groot RJ, van Kuppeveld FJM. Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association. Nat Microbiol 2020; 5:1361-1373. [PMID: 32690955 DOI: 10.1038/s41564-020-0759-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/22/2020] [Indexed: 11/09/2022]
Abstract
Eukaryotic cells, when exposed to environmental or internal stress, activate the integrated stress response (ISR) to restore homeostasis and promote cell survival. Specific stress stimuli prompt dedicated stress kinases to phosphorylate eukaryotic initiation factor 2 (eIF2). Phosphorylated eIF2 (p-eIF2) in turn sequesters the eIF2-specific guanine exchange factor eIF2B to block eIF2 recycling, thereby halting translation initiation and reducing global protein synthesis. To circumvent stress-induced translational shutdown, viruses encode ISR antagonists. Those identified so far prevent or reverse eIF2 phosphorylation. We now describe two viral proteins-one from a coronavirus and the other from a picornavirus-that have independently acquired the ability to counteract the ISR at its very core by acting as a competitive inhibitor of p-eIF2-eIF2B interaction. This allows continued formation of the eIF2-GTP-Met-tRNAi ternary complex and unabated global translation at high p-eIF2 levels that would otherwise cause translational arrest. We conclude that eIF2 and p-eIF2 differ in their interaction with eIF2B to such effect that p-eIF2-eIF2B association can be selectively inhibited.
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Affiliation(s)
- Huib H Rabouw
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Linda J Visser
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tim C Passchier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Martijn A Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Fan Liu
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Arno L W van Vliet
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - José G Dekker
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Susanne G van der Grein
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jesús G Saucedo
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Aditya A Anand
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Mikael E Trellet
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Raoul J de Groot
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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12
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Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli. mBio 2020; 11:mBio.00485-20. [PMID: 32518184 PMCID: PMC7373196 DOI: 10.1128/mbio.00485-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabilizes ∼21-nucleotide (nt) dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA. RNase III-produced small dsRNA were formed at most bacterial genes in the bacterial genome and in a plasmid. Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabilizes ∼21-nucleotide (nt) dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA. RNase III-produced small dsRNA were formed at most bacterial genes in the bacterial genome and in a plasmid. We classified the types of asRNA in genomic clusters producing the most abundant p19-captured dsRNA and confirmed RNase III regulation of asRNA and sense RNA decay at three type I toxin-antitoxin loci and at a coding gene, rsd. Furthermore, we provide potential evidence for the RNase III-dependent regulation of CspD protein by asRNA. The analysis of p19-captured dsRNA revealed an RNase III sequence preference for AU-rich sequences 3 nucleotides on either side of the cleavage sites and for GC-rich sequences in the 2-nt overhangs. Unexpectedly, GC-rich sequences were enriched in the middle section of p19-captured dsRNA, suggesting some unexpected sequence bias in p19 protein binding. Nonetheless, the ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in dsRNA formed by overlapping sense and antisense transcripts in bacteria.
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Lungu-Mitea S, Lundqvist J. Potentials and pitfalls of transient in vitro reporter bioassays: interference by vector geometry and cytotoxicity in recombinant zebrafish cell lines. Arch Toxicol 2020; 94:2769-2784. [PMID: 32447522 PMCID: PMC7395025 DOI: 10.1007/s00204-020-02783-6] [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: 02/18/2020] [Accepted: 05/07/2020] [Indexed: 12/03/2022]
Abstract
The water framework directive re-evaluation proposes the integration of effect-based tools, increasing the need for alternative methods. Especially within aquatic toxicology, coverage of specific toxicity pathways is scarce, and most applications are based on mammalian or bacterial models, not reflecting realistic exposure scenarios. The use of transient reporter gene assays in cells from organisms of interest could be a quick and inexpensive solution. However, interference with cellular homeostasis may impact the system beyond the function of the manipulated gene and thus lead to non-specific results. We describe how varying vector geometry and different regulatory gene elements on plasmids used for transfection in zebrafish hepatocytes and embryonic fibroblasts may lead up to a tenfold difference in potency. Cells were transiently co-transfected with an Nrf2-responsive Firefly luciferase reporter plasmid and eight different Renilla luciferase normalization plasmids. Transfected cells were exposed to two different regimes (0.1–100 µM and 7.8–250 µM) of the oxidative stress-inducing compounds, sulforaphane, tertbutylhydroquinone, and metazachlor. Nrf2 activity was measured in dual-luciferase assays. In parallel, cytotoxicity was assessed for different endpoints (energy metabolism, protein amount, membrane stability, and cell proliferation) in non-transfected cells and cells co-transfected with constructs of increasing size, to be used for normalization. Transfected cells were more susceptible to cytotoxicity in a vector size-dependent manner. Conclusively, we report that vector geometries (size, backbones, gene-regulatory units), cell line (tissue origin), applied transfection methods, and signal normalization may alter the sensitivity of reporter bioassays in a synergistic manner. Further, we propose that thorough bioassay design is needed to ensure reliability and regulatory acceptance.
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Affiliation(s)
- Sebastian Lungu-Mitea
- Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, SE-750 07, Uppsala, Sweden.
| | - Johan Lundqvist
- Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, SE-750 07, Uppsala, Sweden
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Sebrow J, Goff SP, Griffin DO. Successfully transfected primary peripherally mobilized human CD34+ hematopoietic stem and progenitor cells (HSPCs) demonstrate increased susceptibility to retroviral infection. Virol J 2020; 17:22. [PMID: 32039735 PMCID: PMC7008578 DOI: 10.1186/s12985-020-1297-3] [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: 11/06/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Transfection, the process of introducing purified nucleic acids into cells, and viral transduction, viral-mediated nucleic acid transfer, are two commonly utilized techniques for gene delivery in the research setting. Transfection allows purified nucleic acid to be introduced into target cells through chemical-based techniques, nonchemical methods or particle-based methods, while viral transduction employs genomes or vectors based on adenoviruses, retroviruses (e.g. lentiviruses), adeno-associated viruses, or hybrid viruses. Transfected DNAs are often tested for potential effects on subsequent transduction, but it is not clear whether transfection itself rather than the particular nucleic acid being introduced might impact subsequent viral transfection. We observed a significant association between successfully transfected mobilized peripheral blood CD34+ human stem and progenitor cells (HSPCs) and permissiveness to subsequent lentiviral transduction, which was not evident in other cells such as 293 T cells and Jurkat cells. This association, apparently specific to CD34+ human stem and progenitor cells (HSPCs), is critical to both research and clinical applications as these cells are a frequent target of transfection and viral transduction owing to the durable nature of these cells in living systems. This finding may also present a significant opportunity to enhance the success of viral transduction for clinical applications.
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Affiliation(s)
- Jeffrey Sebrow
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168th Street, HHSC 1310, New York, NY, 10032, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168th Street, HHSC 1310, New York, NY, 10032, USA.,HHMI, Department of Biochemistry and Molecular Biophysics, and Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel O Griffin
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168th Street, HHSC 1310, New York, NY, 10032, USA. .,Department of Medicine, Division of Infectious Diseases, Columbia University, College of Physicians and Surgeons, New York, NY, 10032, USA.
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15
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Demeter T, Vaskovicova M, Malik R, Horvat F, Pasulka J, Svobodova E, Flemr M, Svoboda P. Main constraints for RNAi induced by expressed long dsRNA in mouse cells. Life Sci Alliance 2019; 2:2/1/e201800289. [PMID: 30808654 PMCID: PMC6391682 DOI: 10.26508/lsa.201800289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
A systematic survey of dsRNA expression in mouse fibroblasts and embryonic stem cells shows main constraints for RNAi. RNAi activity depends on the initial Dicer cleavage of dsRNA, having implications for the evolution of mammalian RNAi functions. RNAi is the sequence-specific mRNA degradation guided by siRNAs produced from long dsRNA by RNase Dicer. Proteins executing RNAi are present in mammalian cells but rather sustain the microRNA pathway. Aiming for a systematic analysis of mammalian RNAi, we report here that the main bottleneck for RNAi efficiency is the production of functional siRNAs, which integrates Dicer activity, dsRNA structure, and siRNA targeting efficiency. Unexpectedly, increased expression of Dicer cofactors TARBP2 or PACT reduces RNAi but not microRNA function. Elimination of protein kinase R, a key dsRNA sensor in the interferon response, had minimal positive effects on RNAi activity in fibroblasts. Without high Dicer activity, RNAi can still occur when the initial Dicer cleavage of the substrate yields an efficient siRNA. Efficient mammalian RNAi may use substrates with some features of microRNA precursors, merging both pathways even more than previously suggested. Although optimized endogenous Dicer substrates mimicking miRNA features could evolve for endogenous regulations, the same principles would make antiviral RNAi inefficient as viruses would adapt to avoid efficacy.
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Affiliation(s)
- Tomas Demeter
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michaela Vaskovicova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Pasulka
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Matyas Flemr
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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16
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Ralston MT, Papoutsakis ET. RNAseq‐based transcriptome assembly of
Clostridium acetobutylicum
for functional genome annotation and discovery. AIChE J 2018. [DOI: 10.1002/aic.16396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew T. Ralston
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711
| | - Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE 19711
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
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Brustikova K, Sedlak D, Kubikova J, Skuta C, Solcova K, Malik R, Bartunek P, Svoboda P. Cell-Based Reporter System for High-Throughput Screening of MicroRNA Pathway Inhibitors and Its Limitations. Front Genet 2018. [PMID: 29535760 PMCID: PMC5835079 DOI: 10.3389/fgene.2018.00045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs repressing gene expression. They contribute to many physiological processes and pathologies. Consequently, strategies for manipulation of the miRNA pathway are of interest as they could provide tools for experimental or therapeutic interventions. One of such tools could be small chemical compounds identified through high-throughput screening (HTS) with reporter assays. While a number of chemical compounds have been identified in such high-throughput screens, their application potential remains elusive. Here, we report our experience with cell-based HTS of a library of 12,816 chemical compounds to identify miRNA pathway modulators. We used human HeLa and mouse NIH 3T3 cell lines with stably integrated or transiently expressed luciferase reporters repressed by endogenous miR-30 and let-7 miRNAs and identified 163 putative miRNA inhibitors. We report that compounds relieving miRNA-mediated repression via stress induction are infrequent; we have found only two compounds that reproducibly induced stress granules and relieved miRNA-targeted reporter repression. However, we have found that this assay type readily yields non-specific (miRNA-independent) stimulators of luciferase reporter activity. Furthermore, our data provide partial support for previously published miRNA pathway modulators; the most notable intersections were found among anthracyclines, dopamine derivatives, flavones, and stilbenes. Altogether, our results underscore the importance of appropriate negative controls in development of small compound inhibitors of the miRNA pathway. This particularly concerns validation strategies, which would greatly profit from assays that fundamentally differ from the routinely employed miRNA-targeted reporter assays.
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Affiliation(s)
- Katerina Brustikova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - David Sedlak
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Kubikova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Ctibor Skuta
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Solcova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Bartunek
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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18
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Muerdter F, Boryń ŁM, Woodfin AR, Neumayr C, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A. Resolving systematic errors in widely used enhancer activity assays in human cells. Nat Methods 2018; 15:141-149. [PMID: 29256496 PMCID: PMC5793997 DOI: 10.1038/nmeth.4534] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022]
Abstract
The identification of transcriptional enhancers in the human genome is a prime goal in biology. Enhancers are typically predicted via chromatin marks, yet their function is primarily assessed with plasmid-based reporter assays. Here, we show that such assays are rendered unreliable by two previously reported phenomena relating to plasmid transfection into human cells: (i) the bacterial plasmid origin of replication (ORI) functions as a conflicting core promoter and (ii) a type I interferon (IFN-I) response is activated. These cause confounding false positives and negatives in luciferase assays and STARR-seq screens. We overcome both problems by employing the ORI as core promoter and by inhibiting two IFN-I-inducing kinases, enabling genome-wide STARR-seq screens in human cells. In HeLa-S3 cells, we uncover strong enhancers, IFN-I-induced enhancers, and enhancers endogenously silenced at the chromatin level. Our findings apply to all episomal enhancer activity assays in mammalian cells and are key to the characterization of human enhancers.
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Affiliation(s)
- Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Łukasz M Boryń
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Ashley R Woodfin
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Christoph Neumayr
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Katharina Schernhuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Cosmas D Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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19
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Stepanenko AA, Heng HH. Transient and stable vector transfection: Pitfalls, off-target effects, artifacts. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:91-103. [DOI: 10.1016/j.mrrev.2017.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/09/2017] [Accepted: 05/13/2017] [Indexed: 12/15/2022]
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20
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Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet 2017; 49:1073-1081. [PMID: 28581502 DOI: 10.1038/ng.3884] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/01/2017] [Indexed: 12/15/2022]
Abstract
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters. Extensive CRISPR-Cas9 genomic manipulation demonstrated the involvement of these promoters in the cis regulation of expression of distal genes in their natural loci. Our results have important implications for the understanding of complex gene regulation in normal development and disease.
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21
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Middle East Respiratory Coronavirus Accessory Protein 4a Inhibits PKR-Mediated Antiviral Stress Responses. PLoS Pathog 2016; 12:e1005982. [PMID: 27783669 PMCID: PMC5081173 DOI: 10.1371/journal.ppat.1005982] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory infections that can be life-threatening. To establish an infection and spread, MERS-CoV, like most other viruses, must navigate through an intricate network of antiviral host responses. Besides the well-known type I interferon (IFN-α/β) response, the protein kinase R (PKR)-mediated stress response is being recognized as an important innate response pathway. Upon detecting viral dsRNA, PKR phosphorylates eIF2α, leading to the inhibition of cellular and viral translation and the formation of stress granules (SGs), which are increasingly recognized as platforms for antiviral signaling pathways. It is unknown whether cellular infection by MERS-CoV activates the stress response pathway or whether the virus has evolved strategies to suppress this infection-limiting pathway. Here, we show that cellular infection with MERS-CoV does not lead to the formation of SGs. By transiently expressing the MERS-CoV accessory proteins individually, we identified a role of protein 4a (p4a) in preventing activation of the stress response pathway. Expression of MERS-CoV p4a impeded dsRNA-mediated PKR activation, thereby rescuing translation inhibition and preventing SG formation. In contrast, p4a failed to suppress stress response pathway activation that is independent of PKR and dsRNA. MERS-CoV p4a is a dsRNA binding protein. Mutation of the dsRNA binding motif in p4a disrupted its PKR antagonistic activity. By inserting p4a in a picornavirus lacking its natural PKR antagonist, we showed that p4a exerts PKR antagonistic activity also under infection conditions. However, a recombinant MERS-CoV deficient in p4a expression still suppressed SG formation, indicating the expression of at least one other stress response antagonist. This virus also suppressed the dsRNA-independent stress response pathway. Thus, MERS-CoV interferes with antiviral stress responses using at least two different mechanisms, with p4a suppressing the PKR-dependent stress response pathway, probably by sequestering dsRNA. MERS-CoV p4a represents the first coronavirus stress response antagonist described.
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22
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Olejniczak M, Urbanek MO, Jaworska E, Witucki L, Szczesniak MW, Makalowska I, Krzyzosiak WJ. Sequence-non-specific effects generated by various types of RNA interference triggers. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:306-14. [DOI: 10.1016/j.bbagrm.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 10/26/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022]
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23
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Pros and cons of pDNA and mRNA transfection to study mRNA translation in mammalian cells. Gene 2015; 578:1-6. [PMID: 26680098 DOI: 10.1016/j.gene.2015.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/07/2015] [Indexed: 02/02/2023]
Abstract
Protein synthesis in eukaryotes is subject to stringent control. The misregulation of translation of certain mRNAs is often a hallmark of many diseases, including malignancies and autoimmune disorders. To understand why and how it happens, it is important to investigate the translational control of specific mRNAs. In this case, one could use reporter mRNAs in order to identify cis-acting elements responsible for regulation. Here we overview plasmid DNA (pDNA) and mRNA transfections, their pitfalls and limitations, as well as some emerging applications for mRNA transfection.
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Dušková E, Hnilicová J, Staněk D. CRE promoter sites modulate alternative splicing via p300-mediated histone acetylation. RNA Biol 2014; 11:865-74. [PMID: 25019513 DOI: 10.4161/rna.29441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Histone acetylation modulates alternative splicing of several hundred genes. Here, we tested the role of the histone acetyltransferase p300 in alternative splicing and showed that knockdown of p300 promotes inclusion of the fibronectin (FN1) alternative EDB exon. p300 associates with CRE sites in the promoter via the CREB transcription factor. We created mini-gene reporters driven by an artificial promoter containing CRE sites. Both deletion and mutation of the CRE site affected EDB alternative splicing in the same manner as p300 knockdown. Next we showed that p300 controls histone H4 acetylation along the FN1 gene. Consistently, p300 depletion and CRE deletion/mutation both reduced histone H4 acetylation on mini-gene reporters. Finally, we provide evidence that the effect of CRE inactivation on H4 acetylation and alternative splicing is counteracted by the inhibition of histone deacetylases. Together, these data suggest that histone acetylation could be one of the mechanisms how promoter and promoter binding proteins influence alternative splicing.
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Affiliation(s)
- Eva Dušková
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jarmila Hnilicová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David Staněk
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Abstract
A plethora of non-protein coding RNAs are produced throughout eukaryotic genomes, many of which are transcribed antisense to protein-coding genes and could potentially instigate RNA interference (RNAi) responses. Here we have used a synthetic RNAi system to show that gene copy number is a key factor controlling RNAi for transcripts from endogenous loci, since transcripts from multi-copy loci form double stranded RNA more efficiently than transcripts from equivalently expressed single-copy loci. Selectivity towards transcripts from high-copy DNA is therefore an emergent property of a minimal RNAi system. The ability of RNAi to selectively degrade transcripts from high-copy loci would allow suppression of newly emerging transposable elements, but such a surveillance system requires transcription. We show that low-level genome-wide pervasive transcription is sufficient to instigate RNAi, and propose that pervasive transcription is part of a defense mechanism capable of directing a sequence-independent RNAi response against transposable elements amplifying within the genome. DOI:http://dx.doi.org/10.7554/eLife.01581.001 Genes contain the codes that are needed to make the proteins used by cells. This code is transcribed to make a messenger RNA molecule that is then translated to make a protein. However, other types of RNA called non-coding RNA molecules can disrupt this process by binding to messenger RNA molecules, with matching sequences, before translation begins. This phenomenon, which is known as RNA interference, involves enzymes called Dicer and Argonaute. Many cells contain large numbers of non-coding RNA molecules—so called because they are not translated to produce proteins—and many of these are capable of starting the process of RNA interference. However, most do not, and the reasons for this are not understood. Now, work by Cruz and Houseley has provided new insight into this phenomenon by showing that it is related to the number of copies of the gene encoding such RNAs in the genome. Yeast cells normally do not have the genes for RNA interference, but Cruz and Houseley used genetically engineered yeast cells containing Dicer and Argonaute. Although most of the messenger RNA molecules in these cells showed no change, the expression of some genes with high ‘copy numbers’ was reduced. Further experiments that involved adding more and more copies of other genes showed that RNA interference could selectively target messenger RNA molecules produced from genes with an increased copy number—particularly if the copies of the genes were clustered in one location in the genome. RNA interference is also used to defend against DNA sequences that invade and multiply within a genome, such as viruses and other ‘genetic parasites’. As such, the effect observed by Cruz and Houseley could explain why entire genomes are often continuously copied to RNA at low levels. This activity would allow the monitoring of the genome for the invasion of any genetic parasites that had multiplied to high numbers. Following on from this work, the next challenge will be to understand how gene copy number and location are balanced to achieve a selective RNA interference system. DOI:http://dx.doi.org/10.7554/eLife.01581.002
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Affiliation(s)
- Cristina Cruz
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
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26
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Nejepinska J, Malik R, Wagner S, Svoboda P. Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression. PLoS One 2014; 9:e87517. [PMID: 24475301 PMCID: PMC3903663 DOI: 10.1371/journal.pone.0087517] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/23/2013] [Indexed: 11/18/2022] Open
Abstract
In mammals, double-stranded RNA (dsRNA) can mediate sequence-specific RNA interference, activate sequence-independent interferon response, or undergo RNA editing by adenosine deaminases. We showed that long hairpin dsRNA expression had negligible effects on mammalian somatic cells--expressed dsRNA was slightly edited, poorly processed into siRNAs, and it did not activate the interferon response. At the same time, we noticed reduced reporter expression in transient co-transfections, which was presumably induced by expressed dsRNA. Since transient co-transfections are frequently used for studying gene function, we systematically explored the role of expressed dsRNA in this silencing phenomenon. We demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits the expression of co-transfected reporter plasmids but not the expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent, it is found in different cell types, and it is independent of transfection method and dsRNA sequence. The inhibition occurs at the level of translation and involves protein kinase R, which binds the expressed dsRNA. Thus, dsRNA expression represents a hidden danger in transient transfection experiments and must be taken into account during interpretation of experimental results.
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Affiliation(s)
- Jana Nejepinska
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Susan Wagner
- Institute of Microbiology of the ASCR, v.v.i., Prague, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
- * E-mail:
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27
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Marker-free plasmids for biotechnological applications – implications and perspectives. Trends Biotechnol 2013; 31:539-47. [DOI: 10.1016/j.tibtech.2013.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 11/22/2022]
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Williams JA. Vector Design for Improved DNA Vaccine Efficacy, Safety and Production. Vaccines (Basel) 2013; 1:225-49. [PMID: 26344110 PMCID: PMC4494225 DOI: 10.3390/vaccines1030225] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 12/25/2022] Open
Abstract
DNA vaccination is a disruptive technology that offers the promise of a new rapidly deployed vaccination platform to treat human and animal disease with gene-based materials. Innovations such as electroporation, needle free jet delivery and lipid-based carriers increase transgene expression and immunogenicity through more effective gene delivery. This review summarizes complementary vector design innovations that, when combined with leading delivery platforms, further enhance DNA vaccine performance. These next generation vectors also address potential safety issues such as antibiotic selection, and increase plasmid manufacturing quality and yield in exemplary fermentation production processes. Application of optimized constructs in combination with improved delivery platforms tangibly improves the prospect of successful application of DNA vaccination as prophylactic vaccines for diverse human infectious disease targets or as therapeutic vaccines for cancer and allergy.
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Affiliation(s)
- James A Williams
- Nature Technology Corporation/Suite 103, 4701 Innovation Drive, Lincoln, NE 68521, USA.
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