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Liu Y, Li L, Timani KA, He JJ. A Unique Robust Dual-Promoter-Driven and Dual-Reporter-Expressing SARS-CoV-2 Replicon: Construction and Characterization. Viruses 2022; 14:974. [PMID: 35632716 PMCID: PMC9143625 DOI: 10.3390/v14050974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs, even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe, and readily scalable platform for high-throughput screening, identification, and evaluation of antiviral drugs against positive-stranded RNA viruses. In the study, we report a unique robust HIV long terminal repeat (LTR)/T7 dual-promoter-driven and dual-reporter firefly luciferase (fLuc) and green fluorescent protein (GFP)-expressing SARS2 replicon. The genomic organization of the replicon was designed with quite a few features that were to ensure the replication fidelity of the replicon, to maximize the expression of the full-length replicon, and to offer the monitoring flexibility of the replicon replication. We showed the success of the construction of the replicon and expression of reporter genes fLuc and GFP and SARS structural N from the replicon DNA or the RNA that was in vitro transcribed from the replicon DNA. We also showed detection of the negative-stranded genomic RNA (gRNA) and subgenomic RNA (sgRNA) intermediates, a hallmark of replication of positive-stranded RNA viruses from the replicon. Lastly, we showed that expression of the reporter genes, N gene, gRNA, and sgRNA from the replicon was sensitive to inhibition by Remdesivir. Taken together, our results support use of the replicon for identification of anti-SARS2 drugs and development of new anti-SARS strategies targeted at the step of virus replication.
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Affiliation(s)
- Ying Liu
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Lu Li
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Khalid A. Timani
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J. He
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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Bräutigam J, Scheidig AJ, Egge-Jacobsen W. Mass spectrometric analysis of hepatitis C viral envelope protein E2 reveals extended microheterogeneity of mucin-type O-linked glycosylation. Glycobiology 2012; 23:453-74. [PMID: 23242014 DOI: 10.1093/glycob/cws171] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The infectious liver disease hepatitis C is caused by the small, enveloped, positive single-strand RNA hepatitis C virus (HCV). The HCV genome encodes for a single polyprotein precursor of ∼3010 amino acid residues. Host and cellular proteases co- and posttranslational process the precursor creating six nonstructural (NS) proteins and four structural components. Properly folded forms of the envelope proteins E1 and E2 form the associated E1-E2 complex. This complex represents a significant antigenic component at the viral surface that can interact with several target cell receptors. Extent and type of glycosylation is an important factor for virulence and escape from the immune system. Detailed characterization of the glycosylated sites is helpful for the understanding of different phenotypes as well as for the development of E1/E2-related treatments of HCV infection. Here, we have investigated in detail the O-linked glycosylation of the HCV envelope protein E2 expressed in and isolated from human embryonic kidney (HEK 293) cells. Using nano-liquid chromatography and tandem mass spectrometry approaches, we clearly have identified six residues for O-linked glycosylation within isolated glycopeptides (Ser393, Thr396, Ser401, Ser404, Thr473 and Thr518), carrying mainly Core 1 and Core 2 mucin-type structures. Based on our data, Thr385 is probably glycosylated as well. In addition, we could show that Ser479 within the hyper variable region (HVR) I is not O-glycosylated. For most of these sites, different degrees of microheterogeneity could be verified. Concerning HCV E2, this is the first case of experimentally proven O-linked glycosylation in detail via mass spectrometry.
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Affiliation(s)
- Joachim Bräutigam
- Department of Structural Biology, Centre for Biochemistry and Molecular Biology, Christian-Albrechts Universität, 24118 Kiel, Germany
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Zheng J, Sugrue RJ, Tang K. Mass spectrometry based proteomic studies on viruses and hosts--a review. Anal Chim Acta 2011; 702:149-59. [PMID: 21839192 PMCID: PMC7094357 DOI: 10.1016/j.aca.2011.06.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 02/07/2023]
Abstract
In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied using this approach. As more virus and host genomes are being sequenced, MS-based proteomics is becoming an indispensable tool for virology. In this paper, we provide a brief review of the current technologies and their applications in studying selected viruses and hosts.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Richard J. Sugrue
- Division of Molecular and Cell Biology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kai Tang
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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4
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Ryu K, Kim KH, Yoo SY, Lee EY, Lim KH, Min MK, Kim H, Choi SI, Seong BL. Production and characterization of active hepatitis C virus RNA-dependent RNA polymerase. Protein Expr Purif 2010; 71:147-52. [DOI: 10.1016/j.pep.2010.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/28/2009] [Accepted: 01/04/2010] [Indexed: 01/24/2023]
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Cheng JC, Yeh YJ, Pai LM, Chang ML, Yeh CT. 293 cells over-expressing human ADI1 and CD81 are permissive for serum-derived hepatitis C virus infection. J Med Virol 2009; 81:1560-8. [PMID: 19626614 DOI: 10.1002/jmv.21495] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Human aci-reductone dioxygenase 1 (ADI1) is a member of the Cupin superfamily. It binds to and inhibits the activities of membrane-type 1 matrix metalloproteinase, a protein known to interact with the tight junction protein, claudin-1. Previously, a variant protein, named submergence-induced protein-like factor (Sip-L), consisting of ADI1 amino acids 64-179, was found to support hepatitis C virus (HCV) infection and replication in 293 cells. In the present study, it was discovered that over-expression of human ADI1 in 293 cells (293-ADI1 cells) also supported HCV infection and replication. Using serum-derived HCV as an infectious source, enhanced cell uptake of HCV to a Northern blot detectable level was found in 293 cells over-expressing both CD81 and ADI1 (293-ADI1-CD81 cells). The enhanced cell entry was confirmed by the use of the vesicular stomatitis virus-based HCV pseudotype particles. However, transfection of HCV replicon RNA by electroporation into naïve 293 and 293-ADI1 cells revealed no difference in replication efficiency. Using the infectious J6/JFH chimera as an infectious source, the infectivity was compared between 293-ADI1-CD81 and Huh-7.5 cells. More infection foci were formed in the 293-ADI1-CD81 cells in the first round of infection. In conclusion, human ADI1 over-expression in 293 cells enhances cell entry but not replication of HCV. 293-ADI1-CD81 cells are permissive for serum-derived HCV infection.
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Affiliation(s)
- Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
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6
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Raymond VA, Selliah S, Ethier C, Houle R, Jouan L, Maniere T, Lamarre D, Willems B, Bilodeau M. Primary cultures of human hepatocytes isolated from hepatitis C virus-infected cirrhotic livers as a model to study hepatitis C infection. Liver Int 2009; 29:942-9. [PMID: 19302183 DOI: 10.1111/j.1478-3231.2009.01996.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND/AIM Since the discovery of hepatitis C virus (HCV), researchers have encountered difficulties with in vitro models. The aim of this study was to determine whether HCV-infected human primary hepatocytes, isolated from cirrhotic livers at liver transplantation, can be used as a model to study HCV infection. METHODS Hepatocytes were isolated with collagenase and cultured over a 20-day period on different matrices. Viral kinetics was monitored with/without treatment by real-time polymerase chain reaction. RESULTS Cell yield and viability were higher with uninfected/non-cirrhotic livers (77.2+/-1.8%) in comparison with HCV-infected cirrhotic livers (68.8+/-12%). HCV-infected hepatocytes behaved similar to non-infected cells and expressed albumin and cytochrome P4502E1. HCV-positive strand was identified in supernatants and cell lysates. HCV-negative strand was only found inside cells and correlated with viral RNA recovery in the medium. Improvement in the degree of hepatocyte differentiation was associated with better HCV recovery. Antiviral treatment with interferon-alpha, EX4 and cyclosporine A induced significant reductions in HCV RNA. CONCLUSION Primary cultures of HCV-infected human hepatocytes from end-stage cirrhotic livers is feasible, represents an excellent model to study specific virus-host interactions and can be used to assess viral replication.
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Affiliation(s)
- Valérie-Ann Raymond
- Laboratoire d'hépatologie cellulaire, Centre hospitalier de l'Université de Montréal (CHUM)-Hôpital Saint-Luc, Montréal, QC, Canada
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7
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Hepatitis C virus infection in mouse hepatoma cells co-expressing human CD81 and Sip-L. Biochem Biophys Res Commun 2008; 372:157-61. [PMID: 18474223 DOI: 10.1016/j.bbrc.2008.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 05/01/2008] [Indexed: 11/22/2022]
Abstract
Although human CD81 has been shown to be essential for hepatitis C virus (HCV) infection, non-hepatic cells or transgenic animals expressing human CD81 alone did not support HCV replication. Co-expression of other cofactors was thus necessary for HCV replication. Previously, a hepatic factor named Sip-L was found to support HCV replication in an otherwise non-permissive cell line. To understand the species specificity of hepatic factors required for HCV replication, mouse hepatoma cells co-expressing human CD81 and Sip-L (Hepa1-6-CD81-Sip-L cells) were subjected for HCV infection assay. It was discovered that Hepa1-6-CD81-Sip-L cells were permissive for HCV infection and replication. An animal model was thus established by subcutaneous injection of the permissive cells into nude mice to generate tumors. Viral passages could be achieved in these animals. The antiviral effects of interferon and sodium stibogluconate administrated as a single agent or in combination were demonstrated in this animal model.
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Iacob RE, Perdivara I, Przybylski M, Tomer KB. Mass spectrometric characterization of glycosylation of hepatitis C virus E2 envelope glycoprotein reveals extended microheterogeneity of N-glycans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:428-444. [PMID: 18187336 PMCID: PMC2287207 DOI: 10.1016/j.jasms.2007.11.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/27/2007] [Accepted: 11/28/2007] [Indexed: 05/25/2023]
Abstract
Hepatitis C virus (HCV) causes acute and chronic liver disease in humans, including chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The polyprotein encoded in the HCV genome is co- and post-translationally processed by host and viral peptidases, generating the structural proteins Core, E1, E2, and p7, and five nonstructural proteins. The two envelope proteins E1 and E2 are heavily glycosylated. Studying the glycan moieties attached to the envelope E2 glycoprotein is important because the N-linked glycans on E2 envelope protein are involved in the interaction with some human neutralizing antibodies, and may also have a direct or indirect effect on protein folding. In the present study, we report the mass spectrometric characterization of the glycan moieties attached to the E2 glycoprotein. The mass spectrometric analysis clearly identified the nature, composition, and microheterogeneity of the sugars attached to the E2 glycopeptides. All 11 sites of glycosylation on E2 protein were characterized, and the majority of these sites proved to be occupied by high mannose glycans. However, complex type oligosaccharides, which have not been previously identified, were exclusively observed at two N-linked sites, and their identity and heterogeneity were determined.
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Affiliation(s)
- Roxana E. Iacob
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
| | - Irina Perdivara
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
- Department of Chemistry, Laboratory of Analytical Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Przybylski
- Department of Chemistry, Laboratory of Analytical Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
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Agaugué S, Perrin-Cocon L, André P, Lotteau V. Hepatitis C lipo-Viro-particle from chronically infected patients interferes with TLR4 signaling in dendritic cell. PLoS One 2007; 2:e330. [PMID: 17389921 PMCID: PMC1828622 DOI: 10.1371/journal.pone.0000330] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 02/18/2007] [Indexed: 01/27/2023] Open
Abstract
Background Hepatitis C virus (HCV) can be purified from serum of chronically-infected patients in the form of Lipo-Viro-Particles (LVP), which are triglycerid-rich lipoprotein-like particles containing viral RNA and proteins. Since LVP is a constant feature of chronically infected patients, we asked whether purified LVP could interfere with the immune response by acting directly on dendritic cell (DC) function. Methods and Findings We have analyzed the impact of LVP on the maturation monocyte-derived DC induced by TLR3 or TLR4 ligands. Following incubation with LVP, immature DC supported weak transient HCV-RNA replication and type I IFN synthesis. This, however, did not lead to viral particle production nor to maturation of DC. LVP-treatment prior to TLR3 stimulation by polyI:C only enhanced the secretion of IL-12, IL-6 and TNFα yielding typical mature DC. In contrast, LVP-treated DC activated by the TLR4 ligand LPS yielded phenotypically mature DC with reduced capacity to secrete both pro- and anti-inflammatory cytokines. Their ability to stimulate allogeneic T lymphocytes was strongly affected since activated T cells produced IL-5 and IL-13 instead of IFNγ. Addition of IFNα prevented the effect of LVP on DC function. Restoration of IFNγ secretion by T cells was obtained by blocking ERK activation in DC, while induction of IL-5 and IL-13 secretion was inhibited by blocking the p38-MAPK pathway in DC. Conclusions LVP can interfere with TLR4-triggered maturation of DC, inducing a shift in DC function that stimulates Th2 cells instead of Th1, by a mechanism that is ERK- and p38-MAPK-dependent. The effect of LVP on DC polarization was reversed by IFNα, providing an additional rationale for the interferon therapy of chronically-infected patients. By acting on TLR4 pathway with LVP, HCV may thus exploit a natural protective mechanism of the liver and the intestine normally used to control inflammation and immunity to commensal microorganisms.
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Affiliation(s)
- Sophie Agaugué
- Institut National de la Santé et de la Recherche Médicale (INSERM), U851, Lyon, France
- Université de Lyon, Lyon-Gerland, France
| | - Laure Perrin-Cocon
- Institut National de la Santé et de la Recherche Médicale (INSERM), U851, Lyon, France
- Université de Lyon, Lyon-Gerland, France
| | - Patrice André
- Institut National de la Santé et de la Recherche Médicale (INSERM), U851, Lyon, France
- Université de Lyon, Lyon-Gerland, France
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratoire de Virologie, France
| | - Vincent Lotteau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U851, Lyon, France
- Université de Lyon, Lyon-Gerland, France
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratoire de Virologie, France
- * To whom correspondence should be addressed. E-mail:
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Sainz B, Chisari FV. Production of infectious hepatitis C virus by well-differentiated, growth-arrested human hepatoma-derived cells. J Virol 2006; 80:10253-7. [PMID: 17005703 PMCID: PMC1617281 DOI: 10.1128/jvi.01059-06] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dimethyl sulfoxide (DMSO) has been shown to induce the differentiation of primary hepatocytes in vitro. When actively dividing poorly differentiated human hepatoma-derived (Huh7) cells were cultured in the presence of 1% DMSO, cells became cytologically differentiated and transitioned into a nondividing state, characterized by the induction of hepatocyte-specific genes. Moreover, these cells were highly permissive for acute hepatitis C virus (HCV) infection, and persistent long term infection of these cultures could also be achieved. As HCV naturally replicates in highly differentiated nondividing human hepatocytes, this system may more accurately mimic the conditions under which HCV replicates in vivo than previous models using poorly differentiated rapidly dividing hepatoma cells.
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Affiliation(s)
- Bruno Sainz
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, SBR-10, La Jolla, CA 92037, USA
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11
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Dahari H, Ribeiro RM, Rice CM, Perelson AS. Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells. J Virol 2006; 81:750-60. [PMID: 17035310 PMCID: PMC1797446 DOI: 10.1128/jvi.01304-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell-based hepatitis C virus (HCV) replicon systems have provided a means for understanding HCV replication mechanisms and for testing new antiviral agents. We describe here a mathematical model of HCV replication that assumes that the translation of the HCV polyprotein occurs in the cytoplasm, that HCV RNA synthesis occurs in vesicular-membrane structures, and that the strategy of replication involves a double-stranded RNA intermediate. Our results shed light on the intracellular dynamics of subgenomic HCV RNA replication from transfection to steady state within Huh-7 cells. We predict the following: (i) about 6 x 10(3) ribosomes are involved in generating millions of HCV NS5B-polymerase molecules in a Huh-7 cell, (ii) the observed 10:1 asymmetry of plus- to minus-strand RNA levels can be explained by a higher-affinity (200-fold) interaction of HCV NS5B polymerase-containing replication complexes with HCV minus-strand RNA over HCV plus-strand RNA in order to initiate synthesis, (iii) the latter higher affinity can also account for the observed approximately 6:1 plus-strand/minus-strand ratio in vesicular-membrane structures, and (iv) the introduction of higher numbers of HCV plus-strand RNA by transfection leads to faster attainment of steady-state but does not change the steady-state HCV RNA level. Fully permissive HCV replication systems have been developed, and the model presented here is a first step toward building a comprehensive model for complete HCV replication. Moreover, the model can serve as an important tool in understanding HCV replication mechanisms and should prove useful in designing and evaluating new antivirals against HCV.
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Affiliation(s)
- Harel Dahari
- Theoretical Biology and Biophysics, MS-K710, Los Alamos National Laboratory, NM 87545, USA
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12
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Fillebeen C, Rivas-Estilla AM, Bisaillon M, Ponka P, Muckenthaler M, Hentze MW, Koromilas AE, Pantopoulos K. Iron inactivates the RNA polymerase NS5B and suppresses subgenomic replication of hepatitis C Virus. J Biol Chem 2005; 280:9049-57. [PMID: 15637067 DOI: 10.1074/jbc.m412687200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clinical data suggest that iron is a negative factor in chronic hepatitis C; however, the molecular mechanisms by which iron modulates the infectious cycle of hepatitis C virus (HCV) remain elusive. To explore this, we utilized cells expressing a HCV replicon as a well-established model for viral replication. We demonstrate that iron administration dramatically inhibits the expression of viral proteins and RNA, without significantly affecting its translation or stability. Experiments with purified recombinant HCV RNA polymerase (NS5B) revealed that iron binds specifically and with high affinity (apparent Kd: 6 and 60 microM for Fe2+ and Fe3+, respectively) to the protein's Mg2+-binding pocket, thereby inhibiting its enzymatic activity. We propose that iron impairs HCV replication by inactivating NS5B and that its negative effects in chronic hepatitis C may be primarily due to attenuation of antiviral immune responses. Our data provide a direct molecular link between iron and HCV replication.
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Affiliation(s)
- Carine Fillebeen
- Lady Davis Institute for Medical Research, Sir Mortimer B Davis Jewish General Hospital, 3755 Cote-Sainte-Catherine Road, Montreal, Quebec H3T 1E2, Canada
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13
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Castanotto D, Scherer L. Targeting Cellular Genes with PCR Cassettes Expressing Short Interfering RNAs. Methods Enzymol 2005; 392:173-85. [PMID: 15644181 DOI: 10.1016/s0076-6879(04)92010-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The synthesis and transfection of PCR short interfering/short hairpin RNA (si/shRNA) expression cassettes described in this chapter can be used to rapidly test siRNA targeting and function in cells. One critical element in the design of effective siRNAs is the selection of siRNA-target sequence combinations that yield the best inhibitory activity. This can be accomplished by using synthetic siRNAs and transfection procedures, but these can be costly and time consuming. By using the PCR strategy, it is possible to create several expression cassettes and simultaneously screen for the best target sites on any given mRNA. This PCR strategy allows a rapid and inexpensive approach for intracellular expression of si/shRNAs and subsequent testing of target site sensitivity to downregulation by RNA interference (RNAi).
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Affiliation(s)
- Daniela Castanotto
- City of Hope Medical Center, Division of Molecular Biology, Beckman Research Institute, Duarte, CA 91010-3000, USA
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14
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Hertzig T, Scandella E, Schelle B, Ziebuhr J, Siddell SG, Ludewig B, Thiel V. Rapid identification of coronavirus replicase inhibitors using a selectable replicon RNA. J Gen Virol 2004; 85:1717-1725. [PMID: 15166457 DOI: 10.1099/vir.0.80044-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A previously unknown coronavirus (CoV) is the aetiological agent causing severe acute respiratory syndrome (SARS), for which an effective antiviral treatment is urgently needed. To enable the rapid and biosafe identification of coronavirus replicase inhibitors, we have generated a non-cytopathic, selectable replicon RNA (based on human CoV 229E) that can be stably maintained in eukaryotic cells. Most importantly, the replicon RNA mediates reporter gene expression as a marker for coronavirus replication. We have used a replicon RNA-containing cell line to test the inhibitory effect of several compounds that are currently being assessed for SARS treatment. Amongst those, interferon-alpha displayed the strongest inhibitory activity. Our results demonstrate that coronavirus replicon cell lines provide a versatile and safe assay for the identification of coronavirus replicase inhibitors. Once this technology is adapted to SARS-CoV replicon RNAs, it will allow high throughput screening for SARS-CoV replicase inhibitors without the need to grow infectious SARS-CoV.
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Affiliation(s)
- Tobias Hertzig
- Institute of Virology and Immunology, University of Würzburg, Würzburg, Germany
| | - Elke Scandella
- Research Department, Cantonal Hospital St Gallen, CH-9007 St Gallen, Switzerland
| | - Barbara Schelle
- Institute of Virology and Immunology, University of Würzburg, Würzburg, Germany
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Würzburg, Germany
| | - Stuart G Siddell
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol, UK
| | - Burkhard Ludewig
- Research Department, Cantonal Hospital St Gallen, CH-9007 St Gallen, Switzerland
| | - Volker Thiel
- Research Department, Cantonal Hospital St Gallen, CH-9007 St Gallen, Switzerland
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15
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Abstract
The emergence of RNA interference (RNAi) as a powerful tool for silencing gene expression has spurred considerable interest in its experimental and therapeutic potential. RNAi is a cellular process of gene silencing in which small duplexes of RNA specifically target a homologous sequence for cleavage by cellular ribonucleases. The introduction of 21-23 nucleotide RNA duplexes, termed small interfering RNAs (siRNAs), into mammalian cells can specifically degrade homologous mRNAs. RNAi efficiently silences the expression of both cellular and viral RNAs. A number of groups have demonstrated that siRNAs interfere with hepatitis C virus (HCV) gene expression and replication. Additionally, cellular genes are efficiently silenced in the presence of replicating HCV. These studies lay the foundation for using RNAi as an experimental tool for studying HCV replication and defining host genes that are significant for viral replication. The potential for RNAi as an antiviral therapy remains less clear, as it will face many of the challenges that have hindered nucleic acid therapies in the past.
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Affiliation(s)
- Glenn Randall
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, Box 64, New York, NY 10021, USA
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16
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Scherer L, Rossi JJ. Therapeutic applications of RNA interference: recent advances in siRNA design. ADVANCES IN GENETICS 2004; 52:1-21. [PMID: 15522731 DOI: 10.1016/s0065-2660(04)52001-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Lisa Scherer
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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Aizaki H, Nagamori S, Matsuda M, Kawakami H, Hashimoto O, Ishiko H, Kawada M, Matsuura T, Hasumura S, Matsuura Y, Suzuki T, Miyamura T. Production and release of infectious hepatitis C virus from human liver cell cultures in the three-dimensional radial-flow bioreactor. Virology 2003; 314:16-25. [PMID: 14517056 DOI: 10.1016/s0042-6822(03)00383-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lack of efficient culture systems for hepatitis C virus (HCV) has been a major obstacle in HCV research. Human liver cells grown in a three-dimensional radial-flow bioreactor were successfully infected following inoculation with plasma from an HCV carrier. Subsequent detection of increased HCV RNA suggested viral replication. Furthermore, transfection of HCV RNA transcribed from full-length cDNA also resulted in the production and release of HCV virions into supernatant. Infectivity was shown by successful secondary passage to a new culture. Introduction of mutations in RNA helicase and polymerase regions of HCV cDNA abolished virus replication, indicating that reverse genetics of this system is possible. The ability to replicate and detect the extracellular release of HCV might provide clues with regard to the persistent nature of HCV infection. It will also accelerate research into the pathogenicity of HCV, as well as the development of prophylactic agents and new therapy.
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Affiliation(s)
- Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
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Randall G, Grakoui A, Rice CM. Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc Natl Acad Sci U S A 2003; 100:235-40. [PMID: 12518066 PMCID: PMC140937 DOI: 10.1073/pnas.0235524100] [Citation(s) in RCA: 273] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2002] [Indexed: 12/19/2022] Open
Abstract
RNA interference is a cellular process of gene silencing in which small duplexes of RNA specifically target a homologous sequence for cleavage by cellular ribonucleases. The introduction of approximately 22-nt small interfering RNAs (siRNAs) into mammalian cells can specifically silence cellular mRNAs without induction of the nonspecific IFN responses that are activated by longer RNA duplexes. We investigate in this article whether siRNAs can also silence the expression of the cytoplasmically replicating hepatitis C virus (HCV) RNAs by using a replicon system that supports robust HCV replication, but not the production of infectious virions. We report the efficient silencing of both cellular lamin AC and HCV RNAs in Huh-7 hepatoma cell lines supporting HCV replication. Silencing of HCV RNAs was dose dependent and specific, inasmuch as two HCV variants that differ by 3 nt within the target sequence were only silenced by the exact homologous sequence for each. siRNAs designed to target HCV RNA triggered an exponential decrease in HCV RNA, resulting in an 80-fold decrease in HCV RNA after 4 days. The introduction of siRNAs into cells with established HCV replication cured >98% of these cells of detectable HCV antigen and replication-competent HCV RNAs. These data support the principle of siRNA-based HCV antiviral therapy.
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Affiliation(s)
- Glenn Randall
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10021, USA
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