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Kirsebom LA, Liu F, McClain WH. The discovery of a catalytic RNA within RNase P and its legacy. J Biol Chem 2024; 300:107318. [PMID: 38677513 PMCID: PMC11143913 DOI: 10.1016/j.jbc.2024.107318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.
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Affiliation(s)
- Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, California, USA.
| | - William H McClain
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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Liu Y, Chen YC, Yan B, Liu F. Suppressing Kaposi's Sarcoma-Associated Herpesvirus Lytic Gene Expression and Replication by RNase P Ribozyme. Molecules 2023; 28:molecules28083619. [PMID: 37110852 PMCID: PMC10142857 DOI: 10.3390/molecules28083619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Kaposi's sarcoma, an AIDS-defining illness, is caused by Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic virus. In this study, we engineered ribozymes derived from ribonuclease P (RNase P) catalytic RNA with targeting against the mRNA encoding KSHV immediate early replication and transcription activator (RTA), which is vital for KSHV gene expression. The functional ribozyme F-RTA efficiently sliced the RTA mRNA sequence in vitro. In cells, KSHV production was suppressed with ribozyme F-RTA expression by 250-fold, and RTA expression was suppressed by 92-94%. In contrast, expression of control ribozymes hardly affected RTA expression or viral production. Further studies revealed both overall KSHV early and late gene expression and viral growth decreased because of F-RTA-facilitated suppression of RTA expression. Our results indicate the first instance of RNase P ribozymes having potential for use in anti-KSHV therapy.
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Affiliation(s)
- Yujun Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Yuan-Chuan Chen
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
| | - Bin Yan
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
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3
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Trang P, Smith A, Liu F. Mapping of RNase P Ribozyme Regions in Proximity with a Human RNase P Subunit Protein Using Fe(II)-EDTA Cleavage and Nuclease Footprint Analyses. Methods Mol Biol 2023; 2666:55-67. [PMID: 37166656 DOI: 10.1007/978-1-0716-3191-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ribonuclease P (RNase P), which may consist of both protein subunits and a catalytic RNA part, is responsible for 5' maturation of tRNA by cleaving the 5'-leader sequence. In Escherichia coli, RNase P contains a catalytic RNA subunit (M1 RNA) and a protein factor (C5 protein). In human cells, RNase P holoenzyme consists of an RNA subunit (H1 RNA) and multiple protein subunits that include human RPP29 protein. M1GS, a sequence specific targeting ribozyme derived from M1 RNA, can be constructed to target a specific mRNA to degrade it in vitro. Recent studies have shown that M1GS ribozymes are efficient in blocking the expression of viral mRNAs in cultured cells and in animals. These results suggest that RNase P ribozymes have the potential to be useful in basic research and in clinical applications. It has been shown that RNase P binding proteins, such as C5 protein and RPP29, can enhance the activities of M1GS RNA in processing a natural tRNA substrate and a target mRNA. Understanding how RPP29 binds to M1GS RNA and enhances the enzyme's catalytic activity will provide great insight into developing more robust gene-targeting ribozymes for in vivo application. In this chapter, we describe the methods of using Fe(II)-ethylenediaminetetraacetic acid (EDTA) cleavage and nuclease footprint analyses to determine the regions of a M1GS ribozyme that are in proximity to RPP29 protein.
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Affiliation(s)
- Phong Trang
- School of Public Health, University of California, Berkeley, CA, USA.
| | - Adam Smith
- Program in Comparative Biochemistry, University of California, Berkeley, CA, USA
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, CA, USA.
- Program in Comparative Biochemistry, University of California, Berkeley, CA, USA.
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4
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Schang LM, Hu M, Cortes EF, Sun K. Chromatin-mediated epigenetic regulation of HSV-1 transcription as a potential target in antiviral therapy. Antiviral Res 2021; 192:105103. [PMID: 34082058 PMCID: PMC8277756 DOI: 10.1016/j.antiviral.2021.105103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
The ability to establish, and reactivate from, latent infections is central to the biology and pathogenesis of HSV-1. It also poses a strong challenge to antiviral therapy, as latent HSV-1 genomes do not replicate or express any protein to be targeted. Although the processes regulating the establishment and maintenance of, and reactivation from, latency are not fully elucidated, the current general consensus is that epigenetics play a major role. A unifying model postulates that whereas HSV-1 avoids or counteracts chromatin silencing in lytic infections, it becomes silenced during latency, silencing which is somewhat disrupted during reactivation. Many years of work by different groups using a variety of approaches have also shown that the lytic HSV-1 chromatin is distinct and has unique biophysical properties not shared with most cellular chromatin. Nonetheless, the lytic and latent viral chromatins are typically enriched in post translational modifications or histone variants characteristic of active or repressed transcription, respectively. Moreover, a variety of small molecule epigenetic modulators inhibit viral replication and reactivation from latency. Despite these successes in culture and animal models, it is not obvious how epigenetic modulation would be used in antiviral therapy if the same epigenetic mechanisms governed viral and cellular gene expression. Recent work has highlighted several important differences between the viral and cellular chromatins, which appear to be of consequence to their respective epigenetic regulations. In this review, we will discuss the distinctiveness of the viral chromatin, and explore whether it is regulated by mechanisms unique enough to be exploited in antiviral therapy.
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Affiliation(s)
- Luis M Schang
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
| | - MiYao Hu
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA; Departments of Biochemistry and Medical Microbiology and Immunology, University of Alberta. 470 MSB, Edmonton, AB, T6G 2H7, Canada.
| | - Esteban Flores Cortes
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
| | - Kairui Sun
- Department of Microbiology and Immunology and Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University. 235 Hungerford Hill Road, Ithaca, NY, 14850, USA.
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Sutton VR, Andoniou C, Leeming MG, House CM, Watt SV, Verschoor S, Ciccone A, Voskoboinik I, Degli-Esposti M, Trapani JA. Differential cleavage of viral polypeptides by allotypic variants of granzyme B skews immunity to mouse cytomegalovirus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140457. [PMID: 32473350 DOI: 10.1016/j.bbapap.2020.140457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Abstract
We investigated the molecular basis for the remarkably different survival outcomes of mice expressing different alloforms of the pro-apoptotic serine protease granzyme B to mouse cytomegalovirus infection. Whereas C57BL/6 mice homozygous for granzyme BP (GzmBP/P) raise cytotoxic T lymphocytes that efficiently kill infected cells, those of C57BL/6 mice congenic for the outbred allele (GzmBW/W) fail to kill MCMV-infected cells and died from uncontrolled hepatocyte infection and acute liver failure. We identified subtle differences in how GzmBP and GzmBW activate cell death signalling - both alloforms predominantly activated pro-caspases directly, and cleaved pro-apoptotic Bid poorly. Consequently, neither alloform initiated mitochondrial outer membrane permeabilization, or was blocked by Bcl-2, Bcl-XL or co-expression of MCMV proteins M38.5/M41.1, which together stabilize mitochondria by sequestering Bak/Bax. Remarkably, mass spectrometric analysis of proteins from MCMV-infected primary mouse embryonic fibroblasts identified 13 cleavage sites in nine viral proteins (M18, M25, M28, M45, M80, M98, M102, M155, M164) that were cleaved >20-fold more efficiently by either GzmBP or GzmBW. Notably, M18, M28, M45, M80, M98, M102 and M164 were cleaved 20- >100-fold more efficiently by GzmBW, and so, would persist in infected cells targeted by CTLs from GzmBP/P mice. Conversely, M155 was cleaved >100-fold more efficiently by GzmBP, and would persist in cells targeted by CTLs of GzmBW/W mice. M25 was cleaved efficiently by both proteases, but at different sites. We conclude that different susceptibility to MCMV does not result from skewed endogenous cell death pathways, but rather, to as yet uncharacterised MCMV-intrinsic pathways that ultimately inhibit granzyme B-induced cell death.
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Affiliation(s)
- Vivien R Sutton
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Christopher Andoniou
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Centre for Experimental Immunology, Lions Eye Institute, Perth, Western Australia 6009, Australia
| | - Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, Australia; School of Chemistry, The University of Melbourne, Melbourne, Australia
| | - Colin M House
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Sally V Watt
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Sandra Verschoor
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Annette Ciccone
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Ilia Voskoboinik
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia
| | - Mariapia Degli-Esposti
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Centre for Experimental Immunology, Lions Eye Institute, Perth, Western Australia 6009, Australia
| | - Joseph A Trapani
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street Melbourne 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne 3050, Australia.
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Li W, Liu Y, Wang Y, Li R, Trang P, Tang W, Yang Z, Wang Y, Sun X, Xing X, Lu S, Liu F. Engineered RNase P Ribozymes Effectively Inhibit the Infection of Murine Cytomegalovirus in Animals. Am J Cancer Res 2018; 8:5634-5644. [PMID: 30555569 PMCID: PMC6276291 DOI: 10.7150/thno.27776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/03/2018] [Indexed: 01/30/2023] Open
Abstract
Rationales: Gene-targeting ribozymes represent promising nucleic acid-based gene interference agents for therapeutic application. We previously used an in vitro selection procedure to engineer novel RNase P-based ribozyme variants with enhanced targeting activity. However, it has not been reported whether these ribozyme variants also exhibit improved activity in blocking gene expression in animals. Methods and Results: In this report, R388-AS, a new engineered ribozyme variant, was designed to target the mRNA of assemblin (AS) of murine cytomegalovirus (MCMV), which is essential for viral progeny production. Variant R338-AS cleaved AS mRNA sequence in vitro at least 200 times more efficiently than ribozyme M1-AS, which originated from the wild type RNase P catalytic RNA sequence. In cultured MCMV-infected cells, R338-AS exhibited better antiviral activity than M1-AS and decreased viral AS expression by 98-99% and virus production by 15,000 fold. In MCMV-infected mice, R388-AS was more active in inhibiting AS expression, blocking viral replication, and improving animal survival than M1-AS. Conclusions: Our results provide the first direct evidence that novel engineered RNase P ribozyme variants with more active catalytic activity in vitro are also more effective in inhibiting viral gene expression in animals. Moreover, our studies imply the potential of engineering novel RNase P ribozyme variants with unique mutations to improve ribozyme activity for therapeutic application.
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Sun X, Chen W, He L, Sheng J, Liu Y, Vu GP, Yang Z, Li W, Trang P, Wang Y, Hai R, Zhu H, Lu S, Liu F. Inhibition of human cytomegalovirus immediate early gene expression and growth by a novel RNase P ribozyme variant. PLoS One 2017; 12:e0186791. [PMID: 29059242 PMCID: PMC5653336 DOI: 10.1371/journal.pone.0186791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/08/2017] [Indexed: 11/25/2022] Open
Abstract
We have previously engineered new RNase P-based ribozyme variants with improved in vitro catalytic activity. In this study, we employed a novel engineered variant to target a shared mRNA region of human cytomegalovirus (HCMV) immediate early proteins 1 (IE1) and 2 (IE2), which are essential for the expression of viral early and late genes as well as viral growth. Ribozyme F-R228-IE represents a novel variant that possesses three unique base substitution point mutations at the catalytic domain of RNase P catalytic RNA. Compared to F-M1-IE that is the ribozyme derived from the wild type RNase P catalytic RNA sequence, the functional variant F-R228-IE cleaved the target mRNA sequence in vitro at least 100 times more efficiently. In cultured cells, expression of F-R228-IE resulted in IE1/IE2 expression reduction by 98–99% and in HCMV production reduction by 50,000 folds. In contrast, expression of F-M1-IE resulted in IE1/IE2 expression reduction by less than 80% and in viral production reduction by 200 folds. Studies of the ribozyme-mediated antiviral effects in cultured cells suggest that overall viral early and late gene expression and viral growth were inhibited due to the ribozyme-mediated reduction of HCMV IE1 and IE2 expression. Our results provide direct evidence that engineered RNase P ribozymes, such as F-R228-IE, can serve as a novel class of inhibitors for the treatment and prevention of HCMV infection. Moreover, these results suggest that F-R228-IE, with novel and unique mutations at the catalytic domain to enhance ribozyme activity, can be a candidate for the construction of effective agents for anti-HCMV therapy.
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Affiliation(s)
- Xu Sun
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Weijie Chen
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Lingling He
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Jingxue Sheng
- School of Public Health, University of California, Berkeley, CA, United States of America
| | - Yujun Liu
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
- School of Medicine, St. George’s University, Grenada, West Indies
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Gia-Phong Vu
- School of Public Health, University of California, Berkeley, CA, United States of America
| | - Zhu Yang
- Guangzhou Qinheli Biotechnologies, Inc., Guangzhou, Guangdong, China
- Jiangsu Affynigen Biotechnologies, Inc., Taizhou, Jiangsu, China
- Taizhou Institute of Virology, Taizhou, Jiangsu, China
| | - Wei Li
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Phong Trang
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Yu Wang
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
- Guangzhou Qinheli Biotechnologies, Inc., Guangzhou, Guangdong, China
- Jiangsu Affynigen Biotechnologies, Inc., Taizhou, Jiangsu, China
| | - Rong Hai
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Hua Zhu
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Sangwei Lu
- School of Public Health, University of California, Berkeley, CA, United States of America
- * E-mail: (FL); (SL)
| | - Fenyong Liu
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
- School of Public Health, University of California, Berkeley, CA, United States of America
- * E-mail: (FL); (SL)
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RNase P Ribozymes Inhibit the Replication of Human Cytomegalovirus by Targeting Essential Viral Capsid Proteins. Viruses 2015; 7:3345-60. [PMID: 26114473 PMCID: PMC4517104 DOI: 10.3390/v7072775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/08/2015] [Accepted: 06/18/2015] [Indexed: 11/17/2022] Open
Abstract
An engineered RNase P-based ribozyme variant, which was generated using the in vitro selection procedure, was used to target the overlapping mRNA region of two proteins essential for human cytomegalovirus (HCMV) replication: capsid assembly protein (AP) and protease (PR). In vitro studies showed that the generated variant, V718-A, cleaved the target AP mRNA sequence efficiently and its activity was about 60-fold higher than that of wild type ribozyme M1-A. Furthermore, we observed a reduction of 98%–99% in AP/PR expression and an inhibition of 50,000 fold in viral growth in cells with V718-A, while a 75% reduction in AP/PR expression and a 500-fold inhibition in viral growth was found in cells with M1-A. Examination of the antiviral effects of the generated ribozyme on the HCMV replication cycle suggested that viral DNA encapsidation was inhibited and as a consequence, viral capsid assembly was blocked when the expression of AP and PR was inhibited by the ribozyme. Thus, our study indicates that the generated ribozyme variant is highly effective in inhibiting HCMV gene expression and blocking viral replication, and suggests that engineered RNase P ribozyme can be potentially developed as a promising gene-targeting agent for anti-HCMV therapy.
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Murine cytomegalovirus protein pM79 is a key regulator for viral late transcription. J Virol 2013; 87:9135-47. [PMID: 23760242 DOI: 10.1128/jvi.00688-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Herpesvirus genes are temporally expressed during permissive infections, but how their expression is regulated at late times is poorly understood. Previous studies indicate that the human cytomegalovirus (CMV) gene, UL79, is required for late gene expression. However, the mechanism remains to be fully elucidated, and UL79 homologues in other CMVs have not been studied. Here, we characterized the role of the conserved murine CMV (MCMV) gene M79. We showed that M79 encoded a protein (pM79) which was expressed with early-late kinetics and localized to nuclear viral replication compartments. M79 transcription was significantly decreased in the absence of viral DNA synthesis but markedly stimulated by pM79. To investigate its role, we created the recombinant virus SMin79, in which pM79 expression was disrupted. While marker-rescued virus grew efficiently in fibroblasts, SMin79 failed to produce infectious progeny but was rescued by pM79 expression in trans. During SMin79 infection, representative viral immediate-early and early gene products as well as viral DNA accumulated sufficiently. Formation of viral replication compartments also appeared normal. Pulsed-field gel electrophoresis analysis indicated that the overall structure of replicating viral DNA was indistinguishable between wild-type and SMin79 infection. Viral tiled array and quantitative PCR analysis revealed that many late transcripts sensitive to a viral DNA synthesis inhibitor (phosphonoacetic acid) were markedly reduced by pM79 mutation. This study indicates that cytomegaloviruses use a conserved mechanism to promote transcription at late stages of infection and that pM79 is a critical regulator for at least a subset of viral DNA synthesis-dependent transcripts.
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Motard J, Rouxel R, Paun A, von Messling V, Bisaillon M, Perreault JP. A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One 2011; 6:e27327. [PMID: 22110627 PMCID: PMC3215696 DOI: 10.1371/journal.pone.0027327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/13/2011] [Indexed: 12/17/2022] Open
Abstract
Influenza A virus seasonal outbreaks and occasional pandemics represent a global health threat. The high genetic instability of this virus permits rapid escape from the host immune system and emergence of resistance to antivirals. There is thus an urgent need to develop novel approaches for efficient treatment of newly emerging strains. Based on a sequence alignment of representatives from every subtype known to infect humans, we identified nucleic acid regions that are conserved amongst these influenza A populations. We then engineered SOFA-HDV-Ribozymes as therapeutic tools recognizing these conserved regions to catalytically cleave the corresponding viral mRNA targets. The most promising ribozymes were chosen based on an initial in silico screening, and their efficacy was assessed using in vitro cleavage assays. Further characterization of their antiviral effect in cell culture and in mice led to the gradual identification of prophylactic SOFA-HDV-Ribozyme combinations, providing proof-of-principle for the potential of this novel strategy to develop antivirals against genetically highly variable viruses.
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MESH Headings
- Animals
- Antiviral Agents/metabolism
- Antiviral Agents/pharmacology
- Base Sequence
- Biocatalysis
- Female
- HEK293 Cells
- Hepatitis Delta Virus/enzymology
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Mice
- Nucleoproteins/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/pharmacology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombinant Proteins/pharmacology
- Virus Replication/drug effects
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Affiliation(s)
- Julie Motard
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Ronan Rouxel
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Canada
| | - Alexandra Paun
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Martin Bisaillon
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
| | - Jean-Pierre Perreault
- Département de biochimie, RNA group/Groupe ARN, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (JPP); (MB)
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11
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Abstract
INTRODUCTION Cytomegalovirus (CMV) is a ubiquitous pathogen that establishes a lifelong asymptomatic infection in healthy individuals. Infection of immunesuppressed individuals causes serious illness. Transplant and AIDS patients are highly susceptible to CMV leading to life-threatening end-organ disease. Another vulnerable population is the developing fetus in utero, where congenital infection can result in surviving newborns with long-term developmental problems. There is no vaccine licensed for CMV and current antivirals suffer from complications associated with prolonged treatment. These include drug toxicity and emergence of resistant strains. There is an obvious need for new antivirals. Candidate intervention strategies are tested in controlled preclinical animal models but species specificity of human CMV precludes the direct study of the virus in an animal model. AREAS COVERED This review explores the current status of CMV antivirals and development of new drugs. This includes the use of animal models and the development of new improved models such as humanized animal CMV and bioluminescent imaging of virus in animals in real time. EXPERT OPINION Various new CMV antivirals are in development, some with greater spectrum of activity against other viruses. Although the greatest need is in the setting of transplant patients, there remains an unmet need for a safe antiviral strategy against congenital CMV. This is especially important as an effective CMV vaccine remains an elusive goal. In this regard, greater emphasis should be placed on suitable preclinical animal models and greater collaboration between industry and academia.
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Affiliation(s)
- Alistair McGregor
- University of Minnesota Medical School, Center for Infectious Diseases and Microbiology Translational Research, 2001 6th Street SE, MN 55455, USA.
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12
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Melnick M, Abichaker G, Htet K, Sedghizadeh P, Jaskoll T. Small molecule inhibitors of the host cell COX/AREG/EGFR/ERK pathway attenuate cytomegalovirus-induced pathogenesis. Exp Mol Pathol 2011; 91:400-10. [PMID: 21565184 DOI: 10.1016/j.yexmp.2011.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 04/18/2011] [Indexed: 11/17/2022]
Abstract
As with other herpesviruses, human cytomegalovirus (hCMV) has the ability to establish lifelong persistence and latent infection following primary exposure, salivary glands (SMGs) being the primary site of both. In the immunocompromised patient, hCMV is a common cause of opportunistic infections, and subsequent morbidity and mortality. Elucidating the molecular pathogenesis of CMV-induced disease is critical to the development of more effective and safer drug therapies. In the present study, we used a novel mouse postnatal SMG organ culture model of mCMV-induced dysplasia to investigate a candidate signaling network suggested by our prior studies (COX-2/AREG/EGFR/ERK). The objective was to employ small molecule inhibitors to target several key steps in the autocrine loop, and in this way ameliorate pathology. Our results indicate that upregulation of ERK phosphorylation is necessary for initial mCMV-induced pathogenesis, and that ErbB receptor family phosphorylation and downstream signaling are highly relevant targets for drug discovery.
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Affiliation(s)
- Michael Melnick
- Laboratory for Developmental Genetics, USC, Los Angeles, CA 90089-0641, USA.
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13
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Abstract
The use of RNase P ribozyme (M1GS catalytic RNA) for inhibition of murine cytomegalovirus (MCMV) propagation in mice is described in this chapter. General information about RNase P based technology is included and followed by detailed protocols focused on (1) construction and in vitro cleavage assay of the customized M1GS ribozyme, (2) stable expression of the M1GS RNA and evaluation of its activity in inhibition of viral gene expression and growth in cultured cells, and (3) investigation of M1GS-mediated inhibition of viral infection and pathogenesis in animals. Using these methods, we have successfully constructed catalytic M1-1 RNA against the MCMV assembly protein (mAP) and M80 mRNA. Our recent study has demonstrated that an 80% reduction in the expression of mAP and M80 and a 2,000-fold reduction in viral growth were observed in cells expressing the ribozyme. Furthermore, after the functional ribozyme-expressing constructs were delivered into MCMV-infected SCID mice, a significant reduction of viral gene expression and infection was detected, and the survival of the infected animals was significantly improved. Collectively, our data demonstrate the feasibility of the use of RNase P ribozyme for inhibition of viral gene expression in animals and support the utility of RNase P ribozyme for gene-targeting applications in vivo.
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Affiliation(s)
- Yong Bai
- Program in Comparative Biochemistry, University of California, Berkeley, CA, USA
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14
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Fernández N, Martínez-Salas E. Tailoring the switch from IRES-dependent to 5'-end-dependent translation with the RNase P ribozyme. RNA (NEW YORK, N.Y.) 2010; 16:852-862. [PMID: 20194518 PMCID: PMC2844631 DOI: 10.1261/rna.1973710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 01/04/2010] [Indexed: 05/28/2023]
Abstract
Translation initiation driven by internal ribosome entry site (IRES) elements is dependent on the structural organization of the IRES region. We have previously shown that a structural motif within the foot-and-mouth-disease virus IRES is recognized in vitro as substrate for the Synechocystis sp. RNase P ribozyme. Here we show that this structure-dependent endonuclease recognizes the IRES element in cultured cells, leading to inhibition of translation. Inhibition of IRES activity was dependent on the expression of the active ribozyme RNA subunit. Moreover, expression of the antisense sequence of the ribozyme did not inhibit IRES activity, demonstrating that stable RNA structures located upstream of the IRES element do not interfere with internal initiation. RNAs carrying defective IRES mutants that were substrates of the ribozyme in vivo revealed an increased translation of the reporter in response to the expression of the active ribozyme. In support of RNA cleavage, subsequent analysis of the translation initiation manner indicated a switch from IRES-dependent to 5'-end-dependent translation of RNase P target RNAs. We conclude that the IRES element is inactivated by expression in cis of RNase P in the cytoplasm of cultured cells, providing a promising antiviral tool to combat picornavirus infections. Furthermore, our results reinforce the essential role of the structural motif that serves as RNase P recognition motif for IRES activity.
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Affiliation(s)
- Noemi Fernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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15
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Abstract
The ability to interfere with gene expression is of crucial importance to unravel the function of genes and is also a promising therapeutic strategy. Here we discuss methodologies for inhibition of target RNAs based on the cleavage activity of the essential enzyme, Ribonuclease P (RNase P). RNase P-mediated cleavage of target RNAs can be directed by external guide sequences (EGSs) or by the use of the catalytic M1 RNA from E. coli linked to a guide sequence (M1GSs). These are not only basic tools for functional genetic studies in prokaryotic and eukaryotic cells but also promising antibacterial, anticancer and antiviral agents.
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Affiliation(s)
- Eirik Wasmuth Lundblad
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway.
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16
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McClain WH, Lai LB, Gopalan V. Trials, travails and triumphs: an account of RNA catalysis in RNase P. J Mol Biol 2010; 397:627-46. [PMID: 20100492 DOI: 10.1016/j.jmb.2010.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/12/2010] [Accepted: 01/19/2010] [Indexed: 12/16/2022]
Abstract
Last December marked the 20th anniversary of the Nobel Prize in Chemistry to Sidney Altman and Thomas Cech for their discovery of RNA catalysts in bacterial ribonuclease P (an enzyme catalyzing 5' maturation of tRNAs) and a self-splicing rRNA of Tetrahymena, respectively. Coinciding with the publication of a treatise on RNase P, this review provides a historical narrative, a brief report on our current knowledge, and a discussion of some research prospects on RNase P.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, College of Agriculture & Life Sciences, University of Wisconsin, Madison, WI 53706, USA.
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17
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Shan G. RNA interference as a gene knockdown technique. Int J Biochem Cell Biol 2009; 42:1243-51. [PMID: 19442757 DOI: 10.1016/j.biocel.2009.04.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 04/20/2009] [Accepted: 04/29/2009] [Indexed: 01/11/2023]
Abstract
Not many scientific breakthroughs bring significant advances simultaneously in both basic research and translational applications like the discovery of RNA interference. Along with the elucidation of the RNA interference pathway and the discovery of its participation in crucial biological events, a branch of science has grown to utilize the RNA interference pathway as a biotechnology for both basic and applied research. Small interference RNA, plasmid-, and virus-encoded short-hairpin RNA are now regular reagents in the tool box of biologists to knockdown the expression of specific genes posttranscriptionally. Efforts have also been made to develop RNA interference based therapeutics into reality. Many concerns about the RNA interference technique have now been answered through research and development, although hurdles are still present. In this review, the RNA interference/microRNA pathway is briefly introduced followed with a detailed summary about the design and application of the RNA interference experiments, along with examples of the utilization of the RNA interference technology in animal cells and model organisms. Recent progresses and current concerns are also highlighted. Two techniques, namely morpholino and external guide sequence, are discussed as complementary gene knockdown technology. RNA interference technology, along with several other alternative gene knockdown techniques, is now indispensable to modern biological and medical research.
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Affiliation(s)
- Ge Shan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, P. O. Box 208103, New Haven, CT 06520, USA.
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