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Mirzaei R, Karampoor S, Korotkova NL. The emerging role of miRNA-122 in infectious diseases: Mechanisms and potential biomarkers. Pathol Res Pract 2023; 249:154725. [PMID: 37544130 DOI: 10.1016/j.prp.2023.154725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
microRNAs (miRNAs) are small, non-coding RNA molecules that play crucial regulatory roles in numerous cellular processes. Recent investigations have highlighted the significant involvement of miRNA-122 (miR-122) in the pathogenesis of infectious diseases caused by diverse pathogens, encompassing viral, bacterial, and parasitic infections. In the context of viral infections, miR-122 exerts regulatory control over viral replication by binding to the viral genome and modulating the host's antiviral response. For instance, in hepatitis B virus (HBV) infection, miR-122 restricts viral replication, while HBV, in turn, suppresses miR-122 expression. Conversely, miR-122 interacts with the hepatitis C virus (HCV) genome, facilitating viral replication. Regarding bacterial infections, miR-122 has been found to regulate host immune responses by influencing inflammatory cytokine production and phagocytosis. In Vibrio anguillarum infections, there is a significant reduction in miR-122 expression, contributing to the pathophysiology of bacterial infections. Toll-like receptor 14 (TLR14) has been identified as a novel target gene of miR-122, affecting inflammatory and immune responses. In the context of parasitic infections, miR-122 plays a crucial role in regulating host lipid metabolism and immune responses. For example, during Leishmania infection, miR-122-containing extracellular vesicles from liver cells are unable to enter infected macrophages, leading to a suppression of the inflammatory response. Furthermore, miR-122 exhibits promise as a potential biomarker for various infectious diseases. Its expression level in body fluids, particularly in serum and plasma, correlates with disease severity and treatment response in patients affected by HCV, HBV, and tuberculosis. This paper also discusses the potential of miR-122 as a biomarker in infectious diseases. In summary, this review provides a comprehensive and insightful overview of the emerging role of miR-122 in infectious diseases, detailing its mechanism of action and potential implications for the development of novel therapeutic strategies.
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Affiliation(s)
- Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Nadezhda Lenoktovna Korotkova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Russia; Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH Russia), Russia
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2
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Toon K, Kalemera MD, Palor M, Rose NJ, Takeuchi Y, Grove J, Mattiuzzo G. GB Virus B and Hepatitis C Virus, Distantly Related Hepaciviruses, Share an Entry Factor, Claudin-1. J Virol 2023; 97:e0046923. [PMID: 37310242 PMCID: PMC10373534 DOI: 10.1128/jvi.00469-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/10/2023] [Indexed: 06/14/2023] Open
Abstract
Due to increased and broadened screening efforts, the last decade has seen a rapid expansion in the number of viral species classified into the Hepacivirus genus. Conserved genetic features of hepaciviruses suggest that they have undergone specific adaptation and have evolved to hijack similar host proteins for efficient propagation in the liver. Here, we developed pseudotyped viruses to elucidate the entry factors of GB virus B (GBV-B), the first hepacivirus described in an animal after hepatitis C virus (HCV). GBV-B-pseudotyped viral particles (GBVBpp) were shown to be uniquely sensitive to the sera of tamarins infected with GBV-B, validating their usefulness as a surrogate for GBV-B entry studies. We screened GBVBpp infection of human hepatoma cell lines that were CRISPR/Cas9 engineered to ablate the expression of individual HCV receptors/entry factors and found that claudin-1 is essential for GBV-B infection, indicating the GBV-B and HCV share an entry factor. Our data suggest that claudin-1 facilitates HCV and GBV-B entry through distinct mechanisms since the former requires the first extracellular loop and the latter is reliant on a C-terminal region containing the second extracellular loop. The observation that claudin-1 is an entry factor shared between these two hepaciviruses suggests that the tight junction protein is of fundamental mechanistic importance during cell entry. IMPORTANCE Hepatitis C virus (HCV) is a major public health burden; approximately 58 million individuals have chronic HCV infection and are at risk of developing cirrhosis and liver cancer. To achieve the World Health Organization's target of eliminating hepatitis by 2030, new therapeutics and vaccines are needed. Understanding how HCV enters cells can inform the design of new vaccines and treatments targeting the first stage of infection. However, the HCV cell entry mechanism is complex and has been sparsely described. Studying the entry of related hepaciviruses will increase the knowledge of the molecular mechanisms of the first stages of HCV infection, such as membrane fusion, and inform structure-guided HCV vaccine design; in this work, we have identified a protein, claudin-1, that facilitates the entry of an HCV-related hepacivirus but with a mechanism not described for HCV. Similar work on other hepaciviruses may unveil a commonality of entry factors and, possibly, new mechanisms.
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Affiliation(s)
- Kamilla Toon
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mphatso D. Kalemera
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Machaela Palor
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nicola J. Rose
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
| | - Yasuhiro Takeuchi
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Joe Grove
- Division of Infection and Immunity, University College London, London, United Kingdom
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Giada Mattiuzzo
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
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3
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Panigrahi M, Palmer MA, Wilson JA. MicroRNA-122 Regulation of HCV Infections: Insights from Studies of miR-122-Independent Replication. Pathogens 2022; 11:pathogens11091005. [PMID: 36145436 PMCID: PMC9504723 DOI: 10.3390/pathogens11091005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the advancement in antiviral therapy, Hepatitis C remains a global health challenge and one of the leading causes of hepatitis related deaths worldwide. Hepatitis C virus, the causative agent, is a positive strand RNA virus that requires a liver specific microRNA called miR-122 for its replication. Unconventional to the canonical role of miRNAs in translation suppression by binding to 3′Untranslated Region (UTR) of messenger RNAs, miR-122 binds to two sites on the 5′UTR of viral genome and promotes viral propagation. In this review, we describe the unique relationship between the liver specific microRNA and HCV, the current knowledge on the mechanisms by which the virus uses miR-122 to promote the virus life cycle, and how miR-122 impacts viral tropism and pathogenesis. We will also discuss the use of anti-miR-122 therapy and its impact on viral evolution of miR-122-independent replication. This review further provides insight into how viruses manipulate host factors at the initial stage of infection to establish a successful infection.
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4
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The Role of the Liver-Specific microRNA, miRNA-122 in the HCV Replication Cycle. Int J Mol Sci 2020; 21:ijms21165677. [PMID: 32784807 PMCID: PMC7460827 DOI: 10.3390/ijms21165677] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C virus (HCV) replication requires annealing of a liver specific microRNA, miR-122 to 2 sites on 5' untranslated region (UTR). While, microRNAs downregulate gene expression by binding to the 3' untranslated region of the target mRNA, in this case, the microRNA anneals to the 5'UTR of the viral genomes and upregulates the viral lifecycle. In this review, we explore the current understandings of the mechanisms by which miR-122 promotes the HCV lifecycle, and its contributions to pathogenesis. Annealing of miR-122 has been reported to (a) stimulate virus translation by promoting the formation of translationally active internal ribosome entry site (IRES) RNA structure, (b) stabilize the genome, and (c) induce viral genomic RNA replication. MiR-122 modulates lipid metabolism and suppresses tumor formation, and sequestration by HCV may influence virus pathogenesis. We also discuss the possible use of miR-122 as a biomarker for chronic hepatitis and as a therapeutic target. Finally, we discuss roles for miR-122 and other microRNAs in promoting other viruses.
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Amador-Cañizares Y, Panigrahi M, Huys A, Kunden RD, Adams HM, Schinold MJ, Wilson JA. miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5' UTR RNA to stabilize and promote viral RNA accumulation. Nucleic Acids Res 2019; 46:9776-9792. [PMID: 30053137 PMCID: PMC6182169 DOI: 10.1093/nar/gky662] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 07/11/2018] [Indexed: 01/01/2023] Open
Abstract
Annealing of the liver-specific microRNA, miR-122, to the Hepatitis C virus (HCV) 5′ UTR is required for efficient virus replication. By using siRNAs to pressure escape mutations, 30 replication-competent HCV genomes having nucleotide changes in the conserved 5′ untranslated region (UTR) were identified. In silico analysis predicted that miR-122 annealing induces canonical HCV genomic 5′ UTR RNA folding, and mutant 5′ UTR sequences that promoted miR-122-independent HCV replication favored the formation of the canonical RNA structure, even in the absence of miR-122. Additionally, some mutant viruses adapted to use the siRNA as a miR-122-mimic. We further demonstrate that small RNAs that anneal with perfect complementarity to the 5′ UTR stabilize and promote HCV genome accumulation. Thus, HCV genome stabilization and life-cycle promotion does not require the specific annealing pattern demonstrated for miR-122 nor 5′ end annealing or 3′ overhanging nucleotides. Replication promotion by perfect-match siRNAs was observed in Ago2 knockout cells revealing that other Ago isoforms can support HCV replication. At last, we present a model for miR-122 promotion of the HCV life cycle in which miRNA annealing to the 5′ UTR, in conjunction with any Ago isoform, modifies the 5′ UTR structure to stabilize the viral genome and promote HCV RNA accumulation.
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Affiliation(s)
- Yalena Amador-Cañizares
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Mamata Panigrahi
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Adam Huys
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Rasika D Kunden
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Halim M Adams
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Michael J Schinold
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Joyce A Wilson
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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6
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Damas ND, Fossat N, Scheel TKH. Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals. Noncoding RNA 2019; 5:ncrna5010007. [PMID: 30646609 PMCID: PMC6468702 DOI: 10.3390/ncrna5010007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/31/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
Exploring virus–host interactions is key to understand mechanisms regulating the viral replicative cycle and any pathological outcomes associated with infection. Whereas interactions at the protein level are well explored, RNA interactions are less so. Novel sequencing methodologies have helped uncover the importance of RNA–protein and RNA–RNA interactions during infection. In addition to messenger RNAs (mRNAs), mammalian cells express a great number of regulatory non-coding RNAs, some of which are crucial for regulation of the immune system whereas others are utilized by viruses. It is thus becoming increasingly clear that RNA interactions play important roles for both sides in the arms race between virus and host. With the emerging field of RNA therapeutics, such interactions are promising antiviral targets. In this review, we discuss direct and indirect RNA interactions occurring between RNA viruses or retroviruses and host non-coding transcripts upon infection. In addition, we review RNA virus derived non-coding RNAs affecting immunological and metabolic pathways of the host cell typically to provide an advantage to the virus. The relatively few known examples of virus–host RNA interactions suggest that many more await discovery.
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Affiliation(s)
- Nkerorema Djodji Damas
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA.
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Bernier A, Sagan SM. The Diverse Roles of microRNAs at the Host⁻Virus Interface. Viruses 2018; 10:v10080440. [PMID: 30126238 PMCID: PMC6116274 DOI: 10.3390/v10080440] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression at the post-transcriptional level. Through this activity, they are implicated in almost every cellular process investigated to date. Hence, it is not surprising that miRNAs play diverse roles in regulation of viral infections and antiviral responses. Diverse families of DNA and RNA viruses have been shown to take advantage of cellular miRNAs or produce virally encoded miRNAs that alter host or viral gene expression. MiRNA-mediated changes in gene expression have been demonstrated to modulate viral replication, antiviral immune responses, viral latency, and pathogenesis. Interestingly, viruses mediate both canonical and non-canonical interactions with miRNAs to downregulate specific targets or to promote viral genome stability, translation, and/or RNA accumulation. In this review, we focus on recent findings elucidating several key mechanisms employed by diverse virus families, with a focus on miRNAs at the host–virus interface during herpesvirus, polyomavirus, retroviruses, pestivirus, and hepacivirus infections.
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Affiliation(s)
- Annie Bernier
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada.
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montréal, QC H3G 1Y6, Canada.
- Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada.
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8
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Trivedi S, Murthy S, Sharma H, Hartlage AS, Kumar A, Gadi S, Simmonds P, Chauhan LV, Scheel TKH, Billerbeck E, Burbelo PD, Rice CM, Lipkin WI, Vandergrift K, Cullen JM, Kapoor A. Viral persistence, liver disease, and host response in a hepatitis C-like virus rat model. Hepatology 2018; 68:435-448. [PMID: 28859226 PMCID: PMC5832584 DOI: 10.1002/hep.29494] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/01/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022]
Abstract
UNLABELLED The lack of a relevant, tractable, and immunocompetent animal model for hepatitis C virus (HCV) has severely impeded investigations of viral persistence, immunity, and pathogenesis. In the absence of immunocompetent models with robust HCV infection, homolog hepaciviruses in their natural host could potentially provide useful surrogate models. We isolated a rodent hepacivirus from wild rats (Rattus norvegicus), RHV-rn1; acquired the complete viral genome sequence; and developed an infectious reverse genetics system. RHV-rn1 resembles HCV in genomic features including the pattern of polyprotein cleavage sites and secondary structures in the viral 5' and 3' untranslated regions. We used site-directed and random mutagenesis to determine that only the first of the two microRNA-122 seed sites in the viral 5' untranslated region is required for viral replication and persistence in rats. Next, we used the clone-derived virus progeny to infect several inbred and outbred rat strains. Our results determined that RHV-rn1 possesses several HCV-defining hallmarks: hepatotropism, propensity to persist, and the ability to induce gradual liver damage. Histological examination of liver samples revealed the presence of lymphoid aggregates, parenchymal inflammation, and macrovesicular and microvesicular steatosis in chronically infected rats. Gene expression analysis demonstrated that the intrahepatic response during RHV-rn1 infection in rats mirrors that of HCV infection, including persistent activation of interferon signaling pathways. Finally, we determined that the backbone drug of HCV direct-acting antiviral therapy, sofosbuvir, effectively suppresses chronic RHV-rn1 infection in rats. CONCLUSION We developed RHV-rn1-infected rats as a fully immunocompetent and informative surrogate model to delineate the mechanisms of HCV-related viral persistence, immunity, and pathogenesis. (Hepatology 2018).
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Affiliation(s)
- Sheetal Trivedi
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Satyapramod Murthy
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Himanshu Sharma
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Alex S. Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA,Medical Scientist Training Program, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210
| | - Arvind Kumar
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Sashi Gadi
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | - Troels K. H. Scheel
- Copenhagen Hepatitis C Program, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | - Eva Billerbeck
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | | | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | - Kurt Vandergrift
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - John M. Cullen
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210,Corresponding author. , Amit Kapoor, Ph.D., Associate Professor, Department of Pediatrics, College of Medicine, The Ohio State University, Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, Ohio 43205
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9
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Schult P, Roth H, Adams RL, Mas C, Imbert L, Orlik C, Ruggieri A, Pyle AM, Lohmann V. microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site. Nat Commun 2018; 9:2613. [PMID: 29973597 PMCID: PMC6031695 DOI: 10.1038/s41467-018-05053-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/11/2018] [Indexed: 12/24/2022] Open
Abstract
The liver-specific microRNA-122 (miR-122) recognizes two conserved sites at the 5′ end of the hepatitis C virus (HCV) genome and contributes to stability, translation, and replication of the viral RNA. We show that stimulation of the HCV internal ribosome entry site (IRES) by miR-122 is essential for efficient viral replication. The mechanism relies on a dual function of the 5′ terminal sequence in the complementary positive (translation) and negative strand (replication), requiring different secondary structures. Predictions and experimental evidence argue for several alternative folds involving the miR-binding region (MBR) adjacent to the IRES and interfering with its function. Mutations in the MBR, designed to suppress these dysfunctional structures indeed stimulate translation independently of miR-122. Conversely, MBR mutants favoring alternative folds show impaired IRES activity. Our results therefore suggest that miR-122 binding assists the folding of a functional IRES in an RNA chaperone-like manner by suppressing energetically favorable alternative secondary structures. The liver-specific microRNA-122 is an essential proviral host factor of Hepatitis C virus replication. Here the authors show that microRNA-122 functions as an RNA chaperone that guides the formation of a functional internal ribosome entry site by preventing energetically more favorable secondary structures within the HCV RNA genome.
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Affiliation(s)
- Philipp Schult
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Hanna Roth
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Rebecca L Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St, New Haven, CT, 06511, USA
| | - Caroline Mas
- University Grenoble Alpes, CNRS, CEA, IBS, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble CEDEX 9, France
| | - Lionel Imbert
- University Grenoble Alpes, CNRS, CEA, IBS, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble CEDEX 9, France
| | - Christian Orlik
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.,Department of Immunology, Molecular Immunology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St, New Haven, CT, 06511, USA.,Howard Hughes Medical Institute, 219 Prospect St, New Haven, CT, 06511, USA
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.
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10
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Roles of the 5' Untranslated Region of Nonprimate Hepacivirus in Translation Initiation and Viral Replication. J Virol 2018; 92:JVI.01997-17. [PMID: 29343570 DOI: 10.1128/jvi.01997-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/09/2018] [Indexed: 12/26/2022] Open
Abstract
The 5' untranslated region (UTR) of hepatitis C virus (HCV), which is composed of four domains (I, II, III, and IV) and a pseudoknot, is essential for translation and viral replication. Equine nonprimate hepacivirus (EHcV) harbors a 5' UTR consisting of a large 5'-terminal domain (I); three additional domains (I', II, and III), which are homologous to domains I, II, and III, respectively, of HCV; and a pseudoknot, in the order listed. In this study, we investigated the roles of the EHcV 5' UTR in translation and viral replication. The internal ribosome entry site (IRES) activity of the EHcV 5' UTR was lower than that of the HCV 5' UTR in several cell lines due to structural differences in domain III. Domains I and III of EHcV were functional in the HCV 5' UTR in terms of IRES activity and the replication of the subgenomic replicon (SGR), although domain II was not exchangeable between EHcV and HCV for SGR replication. Furthermore, the region spanning domains I and I' of EHcV (the 5'-proximal EHcV-specific region) improved RNA stability and provided the HCV SGR with microRNA 122 (miR-122)-independent replication capability, while EHcV domain I alone improved SGR replication and RNA stability irrespective of miR-122. These data suggest that the region spanning EHcV domains I and I' improves RNA stability and viral replication regardless of miR-122 expression. The 5'-proximal EHcV-specific region may represent an inherent mechanism to facilitate viral replication in nonhepatic tissues.IMPORTANCE EHcV is the closest viral homolog to HCV among other hepaciviruses. HCV exhibits a narrow host range and liver-specific tropism, while epidemiological reports suggest that EHcV infects the liver and respiratory organs in horses, donkeys, and dogs. However, the mechanism explaining the differences in host or organ tropism between HCV and EHcV is unknown. In this study, our data suggest that the 5' untranslated region (UTR) of EHcV is composed of an internal ribosome entry site (IRES) element that is functionally exchangeable with HCV IRES elements. Furthermore, the 5'-proximal EHcV-specific region enhances viral replication and RNA stability in a miR-122-independent manner. Our data suggest that the region upstream of domain II in the EHcV 5' UTR contributes to the differences in tissue tropism observed between these hepaciviruses.
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11
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Boukadida C, Fritz M, Blumen B, Fogeron ML, Penin F, Martin A. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities. PLoS Pathog 2018; 14:e1006863. [PMID: 29415072 PMCID: PMC5819835 DOI: 10.1371/journal.ppat.1006863] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/20/2018] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Over the recent years, several homologues with varying degrees of genetic relatedness to hepatitis C virus (HCV) have been identified in a wide range of mammalian species. HCV infectious life cycle relies on a first critical proteolytic event of its single polyprotein, which is carried out by nonstructural protein 2 (NS2) and allows replicase assembly and genome replication. In this study, we characterized and evaluated the conservation of the proteolytic mode of action and regulatory mechanisms of NS2 across HCV and animal hepaciviruses. We first demonstrated that NS2 from equine, bat, rodent, New and Old World primate hepaciviruses also are cysteine proteases. Using tagged viral protein precursors and catalytic triad mutants, NS2 of equine NPHV and simian GBV-B, which are the most closely and distantly related viruses to HCV, respectively, were shown to function, like HCV NS2 as dimeric proteases with two composite active sites. Consistent with the reported essential role for NS3 N-terminal domain (NS3N) as HCV NS2 protease cofactor via NS3N key hydrophobic surface patch, we showed by gain/loss of function mutagenesis studies that some heterologous hepacivirus NS3N may act as cofactors for HCV NS2 provided that HCV-like hydrophobic residues are conserved. Unprecedently, however, we also observed efficient intrinsic proteolytic activity of NS2 protease in the absence of NS3 moiety in the context of C-terminal tag fusions via flexible linkers both in transiently transfected cells for all hepaciviruses studied and in the context of HCV dicistronic full-length genomes. These findings suggest that NS3N acts as a regulatory rather than essential cofactor for hepacivirus NS2 protease. Overall, unique features of NS2 including enzymatic function as dimers with two composite active sites and additional NS3-independent proteolytic activity are conserved across hepaciviruses regardless of their genetic distances, highlighting their functional significance in hepacivirus life cycle. Despite remarkable progress in the development of therapeutic options, more than 70 million individuals are chronically infected by hepatitis C virus (HCV) worldwide and major challenges in basic and translational research remain. Phylogenetically-related HCV homologues have recently been identified in the wild in several mammalian species, whose host restriction and potential for zoonosis remain largely unknown. We comparatively characterized the functions and properties of nonstructural proteins 2 (NS2) from several animal hepaciviruses and HCV. We demonstrated that NS2 from animal hepaciviruses, like HCV NS2, are cysteine proteases, which function as dimers with two composite active sites to ensure a key proteolytic event of the single viral polyprotein at the NS2/NS3 junction. In addition to the activation of HCV NS2 protease by NS3 N-terminal domain, our data revealed a novel NS3-independent substrate specificity and efficient intrinsic proteolytic activity of NS2. The conservation of its properties and peculiar mode of action among distantly related hepaciviruses supports an important regulatory role for NS2 protein in the life cycle of these viruses. It also strengthens the value of animal, notably rodent hepaciviruses for the development of surrogate, immunocompetent models of HCV infection to address HCV-associated pathogenesis and vaccine strategies.
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Affiliation(s)
- Célia Boukadida
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Matthieu Fritz
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Brigitte Blumen
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Annette Martin
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
- * E-mail:
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12
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Abstract
Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus.
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Affiliation(s)
- Alex S Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205;
| | - John M Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina 27606
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; .,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, Ohio 43210
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13
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Yu Y, Scheel TKH, Luna JM, Chung H, Nishiuchi E, Scull MA, Echeverría N, Ricardo-Lax I, Kapoor A, Lipkin IW, Divers TJ, Antczak DF, Tennant BC, Rice CM. miRNA independent hepacivirus variants suggest a strong evolutionary pressure to maintain miR-122 dependence. PLoS Pathog 2017; 13:e1006694. [PMID: 29084265 PMCID: PMC5679655 DOI: 10.1371/journal.ppat.1006694] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 11/09/2017] [Accepted: 10/14/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) requires the liver specific micro-RNA (miRNA), miR-122, to replicate. This was considered unique among RNA viruses until recent discoveries of HCV-related hepaciviruses prompting the question of a more general miR-122 dependence. Among hepaciviruses, the closest known HCV relative is the equine non-primate hepacivirus (NPHV). Here, we used Argonaute cross-linking immunoprecipitation (AGO-CLIP) to confirm AGO binding to the single predicted miR-122 site in the NPHV 5'UTR in vivo. To study miR-122 requirements in the absence of NPHV-permissive cell culture systems, we generated infectious NPHV/HCV chimeric viruses with the 5' end of NPHV replacing orthologous HCV sequences. These chimeras were viable even in cells lacking miR-122, although miR-122 presence enhanced virus production. No other miRNAs bound this region. By random mutagenesis, we isolated HCV variants partially dependent on miR-122 as well as robustly replicating NPHV/HCV variants completely independent of any miRNAs. These miRNA independent variants even replicate and produce infectious particles in non-hepatic cells after exogenous delivery of apolipoprotein E (ApoE). Our findings suggest that miR-122 independent HCV and NPHV variants have arisen and been sampled during evolution, yet miR-122 dependence has prevailed. We propose that hepaciviruses may use this mechanism to guarantee liver tropism and exploit the tolerogenic liver environment to avoid clearance and promote chronicity.
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Affiliation(s)
- Yingpu Yu
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Troels K. H. Scheel
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
- Copenhagen Hepatitis C Program, Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joseph M. Luna
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Hachung Chung
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Eiko Nishiuchi
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Margaret A. Scull
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Natalia Echeverría
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
| | - Amit Kapoor
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States of America
| | - Ian W. Lipkin
- Center for Infection and Immunity, Mailman School of Public Health and College of Physicians & Surgeons, Columbia University, New York, NY, United States of America
| | - Thomas J. Divers
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Douglas F. Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Bud C. Tennant
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States of America
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14
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Sarnow P, Sagan SM. Unraveling the Mysterious Interactions Between Hepatitis C Virus RNA and Liver-Specific MicroRNA-122. Annu Rev Virol 2016; 3:309-332. [PMID: 27578438 DOI: 10.1146/annurev-virology-110615-042409] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many viruses encode or subvert cellular microRNAs (miRNAs) to aid in their gene expression, amplification strategies, or pathogenic signatures. miRNAs typically downregulate gene expression by binding to the 3' untranslated region of their mRNA targets. As a result, target mRNAs are translationally repressed and subsequently deadenylated and degraded. Curiously, hepatitis C virus (HCV), a member of the Flaviviridae family, recruits two molecules of liver-specific microRNA-122 (miR-122) to the 5' end of its genome. In contrast to the canonical activity of miRNAs, the interactions of miR-122 with the viral genome promote viral RNA accumulation in cultured cells and in animal models of HCV infection. Sequestration of miR-122 results in loss of viral RNA both in cell culture and in the livers of chronic HCV-infected patients. This review discusses the mechanisms by which miR-122 is thought to enhance viral RNA abundance and the consequences of miR-122-HCV interactions. We also describe preliminary findings from phase II clinical trials in patients treated with miR-122 antisense oligonucleotides.
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Affiliation(s)
- Peter Sarnow
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;
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15
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Charley PA, Wilusz J. Standing your ground to exoribonucleases: Function of Flavivirus long non-coding RNAs. Virus Res 2016; 212:70-7. [PMID: 26368052 PMCID: PMC4744573 DOI: 10.1016/j.virusres.2015.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/04/2015] [Accepted: 09/10/2015] [Indexed: 01/18/2023]
Abstract
Members of the Flaviviridae (e.g., Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomic flavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis.
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Affiliation(s)
- Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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16
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Scheel TKH, Simmonds P, Kapoor A. Surveying the global virome: identification and characterization of HCV-related animal hepaciviruses. Antiviral Res 2015; 115:83-93. [PMID: 25545071 PMCID: PMC5081135 DOI: 10.1016/j.antiviral.2014.12.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 12/25/2022]
Abstract
Recent advances in sequencing technologies have greatly enhanced our abilities to identify novel microbial sequences. Thus, our understanding of the global virome and the virome of specific host species in particular is rapidly expanding. Identification of animal viruses is important for understanding animal disease, the origin and evolution of human viruses, as well as zoonotic reservoirs for emerging infections. Although the human hepacivirus, hepatitis C virus (HCV), was identified 25years ago, its origin has remained elusive. In 2011, the first HCV homolog was reported in dogs but subsequent studies showed the virus to be widely distributed in horses. This indicated a wider hepacivirus host range and paved the way for identification of rodent, bat and non-human primate hepaciviruses. The equine non-primate hepacivirus (NPHV) remains the closest relative of HCV and is so far the best characterized. Identification and characterization of novel hepaciviruses may in addition lead to development of tractable animal models to study HCV persistence, immune responses and pathogenesis. This could be particular important, given the current shortage of immunocompetent models for robust HCV infection. Much remains to be learned on the novel hepaciviruses, including their association with disease, and thereby how relevant they will become as HCV model systems and for studies of animal disease. This review discusses how virome analysis led to identification of novel hepaci- and pegiviruses, their genetic relationship and characterization and the potential use of animal hepaciviruses as models to study hepaciviral infection, immunity and pathogenesis. This article forms part of a symposium in Antiviral Research on "Hepatitis C: Next steps toward global eradication."
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Affiliation(s)
- Troels K H Scheel
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, United States; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Disease and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark; Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Amit Kapoor
- Center for Infection and Immunity, Columbia University, New York, NY, United States.
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17
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Sagan SM, Chahal J, Sarnow P. cis-Acting RNA elements in the hepatitis C virus RNA genome. Virus Res 2015; 206:90-8. [PMID: 25576644 DOI: 10.1016/j.virusres.2014.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/12/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
Abstract
Hepatitis C virus (HCV) infection is a rapidly increasing global health problem with an estimated 170 million people infected worldwide. HCV is a hepatotropic, positive-sense RNA virus of the family Flaviviridae. As a positive-sense RNA virus, the HCV genome itself must serve as a template for translation, replication and packaging. The viral RNA must therefore be a dynamic structure that is able to readily accommodate structural changes to expose different regions of the genome to viral and cellular proteins to carry out the HCV life cycle. The ∼ 9600 nucleotide viral genome contains a single long open reading frame flanked by 5' and 3' non-coding regions that contain cis-acting RNA elements important for viral translation, replication and stability. Additional cis-acting RNA elements have also been identified in the coding sequences as well as in the 3' end of the negative-strand replicative intermediate. Herein, we provide an overview of the importance of these cis-acting RNA elements in the HCV life cycle.
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Affiliation(s)
- Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Jasmin Chahal
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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18
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Cox JE, Sullivan CS. Balance and Stealth: The Role of Noncoding RNAs in the Regulation of Virus Gene Expression. Annu Rev Virol 2014; 1:89-109. [PMID: 26958716 DOI: 10.1146/annurev-virology-031413-085439] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past two decades, our knowledge of gene regulation has been greatly expanded by the discovery of microRNAs (miRNAs). miRNAs are small (19-24 nt) noncoding RNAs (ncRNAs) found in metazoans, plants, and some viruses. They have been shown to regulate many cellular processes, including differentiation, maintenance of homeostasis, apoptosis, and the immune response. At present, there are over 300 known viral miRNAs encoded by diverse virus families. One well-characterized function of some viral miRNAs is the regulation of viral transcripts. Host miRNAs can also regulate viral gene expression. We propose that viruses take advantage of both host and viral ncRNA regulation to balance replication and infectious state (for example, latent versus lytic infection). As miRNA regulation can be reversed upon certain cellular stresses, we hypothesize that ncRNAs can serve viruses as barometers for cellular stress.
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Affiliation(s)
- Jennifer E Cox
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Christopher S Sullivan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
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19
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Hepatitis C virus and human miR-122: insights from the bench to the clinic. Curr Opin Virol 2014; 7:11-8. [PMID: 24721497 DOI: 10.1016/j.coviro.2014.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function as part of RNA-induced silencing complexes that repress the expression of target genes. Over the past few years, miRNAs have been found to mediate complex regulation of a wide variety of mammalian viral infections, including Hepatitis C virus (HCV) infection. Here, we focus on a highly abundant, liver-specific miRNA, miR-122. In a unique and unusual interaction, miR-122 binds to two sites in the 5' untranslated region (UTR) of the HCV genome and promotes viral RNA accumulation. We will discuss what has been learned about this important interaction to date, provide insights into how miR-122 is able to modulate HCV RNA accumulation, and how miR-122 might be exploited for antiviral intervention.
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20
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Jackowiak P, Kuls K, Budzko L, Mania A, Figlerowicz M, Figlerowicz M. Phylogeny and molecular evolution of the hepatitis C virus. INFECTION GENETICS AND EVOLUTION 2013; 21:67-82. [PMID: 24200590 DOI: 10.1016/j.meegid.2013.10.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022]
Abstract
The hepatitis C virus (HCV) is a globally prevalent human pathogen that causes persistent liver infections in most infected individuals. HCV is classified into seven phylogenetically distinct genotypes, which have different geographical distributions and levels of genetic diversity. Some of these genotypes are endemic and highly divergent, whereas others disseminate rapidly on an epidemic scale but display lower variability. HCV phylogeny has an important impact on disease epidemiology and clinical practice because the viral genotype may determine the pathogenesis and severity of the resultant chronic liver disease. In addition, there is a clear association between the HCV genotype and its susceptibility to antiviral treatment. Similarly to other RNA viruses, in a single host, HCV exists as a combination of related but genetically different variants. The whole formation is the actual target of selection exerted by a host organism and antiviral therapeutics. The genetic structure of the viral population is largely shaped by mutations that are constantly introduced during an error-prone replication. However, it appears that genetic recombination may also contribute to this process. This heterogeneous collection of variants has a significant ability to evolve towards the fitness optimum. Interestingly, negative selection, which restricts diversity, emerges as an essential force that drives HCV evolution. It is becoming clear that HCV evolves to become stably adapted to the host environment. In this article we review the HCV phylogeny and molecular evolution in the context of host-virus interactions.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Kuls
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Mania
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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21
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Wilson JA, Huys A. miR-122 promotion of the hepatitis C virus life cycle: sound in the silence. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:665-76. [PMID: 23881584 DOI: 10.1002/wrna.1186] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 12/25/2022]
Abstract
The unusual role for miR-122 in promoting the hepatitis C virus (HCV) life cycle was first identified in 2005, but its mechanism of action remains uncharacterized. The virus appears to use the microRNA (miRNA) in a way that is opposed to that of normal miRNAs. Instead of interacting with sequences in the 3'-untranslated region (UTR), miR-122 binds to two sites in the 5'-UTR, and instead of silencing gene expression or promoting the degradation of the viral RNA, it stabilizes the genome and potently augments the efficiency by which HCV RNA accumulates in infected cells. This review discusses the current knowledge and models for the mechanism by which miR-122 promotes the HCV life cycle. Annealing of miR-122 to the HCV genome requires particular base pairing, stimulates translation, and stabilizes the viral genome by blocking degradation by host exonucleases, but these functions are unlikely to be the whole story. We will discuss other possible functions for miR-122, the stages of the HCV life cycle at which miR-122 may influence HCV, and other related viruses that may be similarly regulated by miR-122. Despite our lack of detailed mechanistic information, antagonism of miR-122 is emerging as a powerful method to inhibit HCV infections, and unique to other HCV treatment strategies does not, thus far, appear to induce emergence of escape mutants. Used alone or in combination with other antiviral drugs, miR-122 antagonists could be useful to both inhibit the virus and provide selective pressure to inhibit the development of resistance.
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Affiliation(s)
- Joyce A Wilson
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada; VIDO-Intervac, University of Saskatchewan, Saskatoon, Canada
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