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Xu C, Wang M, Cheng A, Yang Q, Huang J, Ou X, Sun D, He Y, Wu Z, Wu Y, Zhang S, Tian B, Zhao X, Liu M, Zhu D, Jia R, Chen S. Multiple functions of the nonstructural protein 3D in picornavirus infection. Front Immunol 2024; 15:1365521. [PMID: 38629064 PMCID: PMC11018997 DOI: 10.3389/fimmu.2024.1365521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
3D polymerase, also known as RNA-dependent RNA polymerase, is encoded by all known picornaviruses, and their structures are highly conserved. In the process of picornavirus replication, 3D polymerase facilitates the assembly of replication complexes and directly catalyzes the synthesis of viral RNA. The nuclear localization signal carried by picornavirus 3D polymerase, combined with its ability to interact with other viral proteins, viral RNA and cellular proteins, indicate that its noncatalytic role is equally important in viral infections. Recent studies have shown that 3D polymerase has multiple effects on host cell biological functions, including inducing cell cycle arrest, regulating host cell translation, inducing autophagy, evading immune responses, and triggering inflammasome formation. Thus, 3D polymerase would be a very valuable target for the development of antiviral therapies. This review summarizes current studies on the structure of 3D polymerase and its regulation of host cell responses, thereby improving the understanding of picornavirus-mediated pathogenesis caused by 3D polymerase.
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Affiliation(s)
- Chenxia Xu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu He
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhen Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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Real-Hohn A, Blaas D. Rhinovirus Inhibitors: Including a New Target, the Viral RNA. Viruses 2021; 13:1784. [PMID: 34578365 PMCID: PMC8473194 DOI: 10.3390/v13091784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Rhinoviruses (RVs) are the main cause of recurrent infections with rather mild symptoms characteristic of the common cold. Nevertheless, RVs give rise to enormous numbers of absences from work and school and may become life-threatening in particular settings. Vaccination is jeopardised by the large number of serotypes eliciting only poorly cross-neutralising antibodies. Conversely, antivirals developed over the years failed FDA approval because of a low efficacy and/or side effects. RV species A, B, and C are now included in the fifteen species of the genus Enteroviruses based upon the high similarity of their genome sequences. As a result of their comparably low pathogenicity, RVs have become a handy model for other, more dangerous members of this genus, e.g., poliovirus and enterovirus 71. We provide a short overview of viral proteins that are considered potential drug targets and their corresponding drug candidates. We briefly mention more recently identified cellular enzymes whose inhibition impacts on RVs and comment novel approaches to interfere with infection via aggregation, virus trapping, or preventing viral access to the cell receptor. Finally, we devote a large part of this article to adding the viral RNA genome to the list of potential drug targets by dwelling on its structure, folding, and the still debated way of its exit from the capsid. Finally, we discuss the recent finding that G-quadruplex stabilising compounds impact on RNA egress possibly via obfuscating the unravelling of stable secondary structural elements.
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Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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Chen P, Li Z, Cui S. Picornaviral 2C proteins: A unique ATPase family critical in virus replication. Enzymes 2021; 49:235-264. [PMID: 34696834 DOI: 10.1016/bs.enz.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 2C proteins of Picornaviridae are unique members of AAA+ protein family. Although picornavirus 2C shares many conserved motifs with Super Family 3 DNA helicases, duplex unwinding activity of many 2C proteins remains undetected, and high-resolution structures of 2C hexamers are unavailable. All characterized 2C proteins exhibit ATPase activity, but the purpose of ATP hydrolysis is not fully understood. 2C is highly conserved among picornaviruses and plays crucial roles in nearly all steps of the virus lifecycle. It is therefore considered as an effective target for broad-spectrum antiviral drug development. Crystallographic investigation of enterovirus 2C proteins provide structural details important for the elucidation of 2C function and development of antiviral drugs. This chapter summarizes not only the findings of enzymatic activities, biochemical and structural characterizations of the 2C proteins, but also their role in virus replication, immune evasion and morphogenesis. The linkage between structure and function of the 2C proteins is discussed in detail. Inhibitors targeting the 2C proteins are also summarized to provide an overview of drug development. Finally, we raise several key questions to be addressed in this field and provide future research perspective on this unique class of ATPases.
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Affiliation(s)
- Pu Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhijian Li
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sheng Cui
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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5
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Development of Group B Coxsackievirus as an Oncolytic Virus: Opportunities and Challenges. Viruses 2021; 13:v13061082. [PMID: 34198859 PMCID: PMC8227215 DOI: 10.3390/v13061082] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Oncolytic viruses have emerged as a promising strategy for cancer therapy due to their dual ability to selectively infect and lyse tumor cells and to induce systemic anti-tumor immunity. Among various candidate viruses, coxsackievirus group B (CVBs) have attracted increasing attention in recent years. CVBs are a group of small, non-enveloped, single-stranded, positive-sense RNA viruses, belonging to species human Enterovirus B in the genus Enterovirus of the family Picornaviridae. Preclinical studies have demonstrated potent anti-tumor activities for CVBs, particularly type 3, against multiple cancer types, including lung, breast, and colorectal cancer. Various approaches have been proposed or applied to enhance the safety and specificity of CVBs towards tumor cells and to further increase their anti-tumor efficacy. This review summarizes current knowledge and strategies for developing CVBs as oncolytic viruses for cancer virotherapy. The challenges arising from these studies and future prospects are also discussed in this review.
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6
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Jackson T, Belsham GJ. Picornaviruses: A View from 3A. Viruses 2021; 13:v13030456. [PMID: 33799649 PMCID: PMC7999760 DOI: 10.3390/v13030456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
Picornaviruses are comprised of a positive-sense RNA genome surrounded by a protein shell (or capsid). They are ubiquitous in vertebrates and cause a wide range of important human and animal diseases. The genome encodes a single large polyprotein that is processed to structural (capsid) and non-structural proteins. The non-structural proteins have key functions within the viral replication complex. Some, such as 3Dpol (the RNA dependent RNA polymerase) have conserved functions and participate directly in replicating the viral genome, whereas others, such as 3A, have accessory roles. The 3A proteins are highly divergent across the Picornaviridae and have specific roles both within and outside of the replication complex, which differ between the different genera. These roles include subverting host proteins to generate replication organelles and inhibition of cellular functions (such as protein secretion) to influence virus replication efficiency and the host response to infection. In addition, 3A proteins are associated with the determination of host range. However, recent observations have challenged some of the roles assigned to 3A and suggest that other viral proteins may carry them out. In this review, we revisit the roles of 3A in the picornavirus life cycle. The 3AB precursor and mature 3A have distinct functions during viral replication and, therefore, we have also included discussion of some of the roles assigned to 3AB.
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Affiliation(s)
- Terry Jackson
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, UK;
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Correspondence:
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Lee KM, Wu CC, Wu SE, Lin YH, Wang LT, Chang CR, Huang PN, Shih SR, Kuo RL. The RNA-dependent RNA polymerase of enterovirus A71 associates with ribosomal proteins and positively regulates protein translation. RNA Biol 2020; 17:608-622. [PMID: 32009553 DOI: 10.1080/15476286.2020.1722448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Enteroviruses, which may cause neurological complications, have become a public health threat worldwide in recent years. Interactions between cellular proteins and enteroviral proteins could interfere with cellular biological processes to facilitate viral replication in infected cells. Enteroviral RNA-dependent RNA polymerase (RdRP), known as 3D protein, mainly functions as a replicase for viral RNA synthesis in infected cells. However, the 3D protein encoded by enterovirus A71 (EV-A71) could also interact with several cellular proteins to regulate cellular events and responses during infection. To globally investigate the functions of the EV-A71 3D protein in regulating biological processes in host cells, we performed immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify host proteins that may associate with the 3D protein. We found that the 3D protein interacts with factors involved in translation-related biological processes, including ribosomal proteins. In addition, polysome profiling analysis showed that the 3D protein cosediments with small and large subunits of ribosomes. We further discovered that the EV-A71 3D protein could enhance EV-A71 internal ribosome entry site (IRES)-dependent translation as well as cap-dependent translation. Collectively, this research demonstrated that the RNA polymerase encoded by EV-A71 could join a functional ribosomal complex and positively regulate viral and host translation.
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Affiliation(s)
- Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Shang-En Wu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Han Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li-Ting Wang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Ru Chang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Virology Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Rei-Lin Kuo
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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8
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Viral Generated Inter-Organelle Contacts Redirect Lipid Flux for Genome Replication. Cell 2019; 178:275-289.e16. [PMID: 31204099 DOI: 10.1016/j.cell.2019.05.030] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/05/2018] [Accepted: 05/14/2019] [Indexed: 11/24/2022]
Abstract
Positive-stranded RNA viruses extensively remodel host cell architecture to enable viral replication. Here, we examined the poorly understood formation of specialized membrane compartments that are critical sites for the synthesis of the viral genome. We show that the replication compartments (RCs) of enteroviruses are created through novel membrane contact sites that recruit host lipid droplets (LDs) to the RCs. Viral proteins tether the RCs to the LDs and interact with the host lipolysis machinery to enable transfer of fatty acids from LDs, thereby providing lipids essential for RC biogenesis. Inhibiting the formation of the membrane contact sites between LDs and RCs or inhibition of the lipolysis pathway disrupts RC biogenesis and enterovirus replication. Our data illuminate mechanistic and functional aspects of organelle remodeling in viral infection and establish that pharmacological targeting of contact sites linking viral and host compartments is a potential strategy for antiviral development.
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9
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Abstract
Enteroviruses (EVs) are the most common human pathogens worldwide. Recent international outbreaks in North America and South East Asia have emphasized the need for more effective anti-viral therapies. As obligate parasites, EVs rely on the host cellular machinery for effective viral propagation. Accumulating evidence has indicated that EVs subvert and disrupt the cellular autophagy pathway to facilitate productive infection, and consequently leading to host pathogenesis. Given that defective autophagy is a common factor in various human diseases, including neurodegeneration, cardiomyopathy, and metabolic disorders, a clear understanding of the relationship between EV infection and autophagy is warranted. In this review, we highlight recent advances in understanding the molecular mechanisms by which EVs exploit the autophagy pathway during different steps of viral life cycle, from entry, replication, and maturation to release. We also provide an overview of recent progress in EV subversion of the autophagy for immune evasion.
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Affiliation(s)
- Yasir Mohamud
- a Center for Heart Lung Innovation, St. Paul' s Hospital and Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Honglin Luo
- a Center for Heart Lung Innovation, St. Paul' s Hospital and Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
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10
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A Single Point Mutation in the Rhinovirus 2B Protein Reduces the Requirement for Phosphatidylinositol 4-Kinase Class III Beta in Viral Replication. J Virol 2018; 92:JVI.01462-18. [PMID: 30209171 DOI: 10.1128/jvi.01462-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/31/2018] [Indexed: 01/31/2023] Open
Abstract
Rhinoviruses (RVs) replicate on cytoplasmic membranes derived from the Golgi apparatus. They encode membrane-targeted proteins 2B, 2C, and 3A, which control trafficking and lipid composition of the replication membrane. The virus recruits host factors for replication, such as phosphatidylinositol 4 (PI4)-kinase 3beta (PI4K3b), which boosts PI4-phosphate (PI4P) levels and drives lipid countercurrent exchange of PI4P against cholesterol at endoplasmic reticulum-Golgi membrane contact sites through the lipid shuttling protein oxysterol binding protein 1 (OSBP1). We identified a PI4K3b inhibitor-resistant RV-A16 variant with a single point mutation in the conserved 2B protein near the cytosolic carboxy terminus, isoleucine 92 to threonine (termed 2B[I92T]). The mutation did not confer resistance to cholesterol-sequestering compounds or OSBP1 inhibition, suggesting invariant dependency on the PI4P/cholesterol lipid countercurrents. In the presence of PI4K3b inhibitor, Golgi reorganization and PI4P lipid induction occurred in RV-A16 2B[I92] but not in wild-type infection. The knockout of PI4K3b abolished the replication of both the 2B[I92T] mutant and the wild type. Doxycycline-inducible expression of PI4K3b in PI4K3b knockout cells efficiently rescued the 2B[I92T] mutant and, less effectively, wild-type virus infection. Ectopic expression of 2B[I92T] or 2B was less efficient than that of 3A in recruiting PI4K3b to perinuclear membranes, suggesting a supportive rather than decisive role of 2B in recruiting PI4K3b. The data suggest that 2B tunes the recruitment of PI4K3b to the replication membrane and allows the virus to adapt to cells with low levels of PI4K3b while still maintaining the PI4P/cholesterol countercurrent for establishing Golgi-derived RV replication membranes.IMPORTANCE Human rhinoviruses (RVs) are the major cause of the common cold worldwide. They cause asthmatic exacerbations and chronic obstructive pulmonary disease. Despite recent advances, the development of antivirals and vaccines has proven difficult due to the high number and variability of RV types. The identification of critical host factors and their interactions with viral proteins and membrane lipids for the establishment of viral replication is a basis for drug development strategies. Our findings here shed new light on the interactions between nonstructural viral membrane proteins and class III phosphatidylinositol 4 kinases from the host and highlight the importance of phosphatidylinositol 4 phosphate for RV replication.
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Guan H, Tian J, Zhang C, Qin B, Cui S. Crystal structure of a soluble fragment of poliovirus 2CATPase. PLoS Pathog 2018; 14:e1007304. [PMID: 30231078 PMCID: PMC6166989 DOI: 10.1371/journal.ppat.1007304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 10/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022] Open
Abstract
Poliovirus (PV) 2CATPase is the most studied 2C protein in the Picornaviridae family. It is involved in RNA replication, encapsidation and uncoating and many inhibitors have been found that target PV 2CATPase. Despite numerous investigations to characterize its functions, a high-resolution structure of PV 2C has not yet been determined. We report here the crystal structure of a soluble fragment of PV 2CATPase to 2.55Å, containing an ATPase domain, a zinc finger and a C-terminal helical domain but missing the N-terminal domain. The ATPase domain shares the common structural features with EV71 2C and other Superfamily 3 helicases. The C-terminal cysteine-rich motif folds into a CCCC type zinc finger in which four cysteine ligands and several auxiliary residues assist in zinc binding. By comparing with the known zinc finger fold groups, we found the zinc finger of 2C proteins belong to a new fold group, which we denote the "Enterovirus 2C-like" group. The C-terminus of PV 2CATPase forms an amphipathic helix that occupies a hydrophobic pocket located on an adjacent PV 2CATPase in the crystal lattice. The C-terminus mediated PV 2C-2C interaction promotes self-oligomerization, most likely hexamerization, which is fundamental to the ATPase activity of 2C. The zinc finger is the most structurally diverse feature in 2C proteins. Available structural and virological data suggest that the zinc finger of 2C might confer the specificity of interaction with other proteins. We built a hexameric ring model of PV 2CATPase and visualized the previously identified functional motifs and drug-resistant sites, thus providing a structure framework for antiviral drug development.
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Affiliation(s)
- Hongxin Guan
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Tian
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chu Zhang
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Qin
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sheng Cui
- MOH key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail:
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Lyoo H, Dorobantu CM, van der Schaar HM, van Kuppeveld FJM. Modulation of proteolytic polyprotein processing by coxsackievirus mutants resistant to inhibitors targeting phosphatidylinositol-4-kinase IIIβ or oxysterol binding protein. Antiviral Res 2017; 147:86-90. [PMID: 29024767 DOI: 10.1016/j.antiviral.2017.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
Abstract
Enteroviruses (e.g. poliovirus, coxsackievirus, and rhinovirus) require several host factors for genome replication. Among these host factors are phosphatidylinositol-4-kinase IIIβ (PI4KB) and oxysterol binding protein (OSBP). Enterovirus mutants resistant to inhibitors of PI4KB and OSBP were previously isolated, which demonstrated a role of single substitutions in the non-structural 3A protein in conferring resistance. Besides the 3A substitutions (i.e., 3A-I54F and 3A-H57Y) in coxsackievirus B3 (CVB3), substitution N2D in 2C was identified in each of the PI4KB-inhibitor resistant CVB3 pools, but its possible benefit has not been investigated yet. In this study, we set out to investigate the possible role of 2C-N2D in the resistance to PI4KB and OSBP inhibition. We show that 2C-N2D by itself did not confer any resistance to inhibitors of PI4KB and OSBP. However, the double mutant (i.e., 2C-N2D/3A-H57Y) showed better replication than the 3A-H57Y single mutant in the presence of inhibitors. Growing evidence suggests that alterations in lipid homeostasis affect the proteolytic processing of the poliovirus polyprotein. Therefore, we studied the effect of PI4KB or OSBP inhibition on proteolytic processing of the CVB3 polyprotein during infection as well as in a replication-independent system. We show that both PI4KB and OSBP inhibitors specifically affected the cleavage at the 3A-3B junction, and that mutation 3A-H57Y recovered impaired proteolytic processing at this junction. Although 2C-N2D enhanced replication of the 3A-H57Y single mutant, we did not detect additional effects of this substitution on polyprotein processing, which leaves the mechanism of how 2C-N2D contributes to the resistance to be revealed.
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Affiliation(s)
- Heyrhyoung Lyoo
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Cristina M Dorobantu
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Hilde M van der Schaar
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Department of Infectious Diseases & Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Chan YM, Moustafa IM, Arnold JJ, Cameron CE, Boehr DD. Long-Range Communication between Different Functional Sites in the Picornaviral 3C Protein. Structure 2016; 24:509-517. [PMID: 27050688 DOI: 10.1016/j.str.2016.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 10/22/2022]
Abstract
The 3C protein is a master regulator of the picornaviral infection cycle, responsible for both cleaving viral and host proteins, and interacting with genomic RNA replication elements. Here we use nuclear magnetic resonance spectroscopy and molecular dynamics simulations to show that 3C is conformationally dynamic across multiple timescales. Binding of peptide and RNA lead to structural dynamics changes at both the protease active site and the RNA-binding site, consistent with these sites being dynamically coupled. Indeed, binding of RNA influences protease activity, and likewise, interactions at the active site affect RNA binding. We propose that RNA and peptide binding re-shapes the conformational energy landscape of 3C to regulate subsequent functions, including formation of complexes with other viral proteins. The observed channeling of the 3C energy landscape may be important for regulation of the viral infection cycle.
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Affiliation(s)
- Yan M Chan
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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A Single Amino Acid Substitution in Poliovirus Nonstructural Protein 2CATPase Causes Conditional Defects in Encapsidation and Uncoating. J Virol 2016; 90:6174-6186. [PMID: 27076638 PMCID: PMC4936127 DOI: 10.1128/jvi.02877-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/28/2016] [Indexed: 12/11/2022] Open
Abstract
The specificity of encapsidation of C-cluster enteroviruses depends on an interaction between capsid proteins and nonstructural protein 2CATPase. In particular, residue N252 of poliovirus 2CATPase interacts with VP3 of coxsackievirus A20, in the context of a chimeric virus. Poliovirus 2CATPase has important roles both in RNA replication and encapsidation. In this study, we searched for additional sites in 2CATPase, near N252, that are required for encapsidation. Accordingly, segments adjacent to N252 were analyzed by combining triple and single alanine mutations to identify residues required for function. Two triple alanine mutants exhibited defects in RNA replication. The remaining two mutations, located in secondary structures in a predicted three-dimensional model of 2CATPase, caused lethal growth phenotypes. Most single alanine mutants, derived from the lethal variants, were either quasi-infectious and yielded variants with wild-type (wt) or temperature-sensitive (ts) growth phenotypes or had a lethal growth phenotype due to defective RNA replication. The K259A mutation, mapping to an α helix in the predicted structure of 2CATPase, resulted in a cold-sensitive virus. In vivo protein synthesis and virus production were strikingly delayed at 33°C relative to the wt, suggesting a defect in uncoating. Studies with a reporter virus indicated that this mutant is also defective in encapsidation at 33°C. Cell imaging confirmed a much-reduced production of K259A mature virus at 33°C relative to the wt. In conclusion, we have for the first time linked a cold-sensitive encapsidation defect in 2CATPase (K259A) to a subsequent delay in uncoating of the virus particle at 33°C during the next cycle of infection. IMPORTANCE Enterovirus morphogenesis, which involves the encapsidation of newly made virion RNA, is a process still poorly understood. Elucidation of this process is important for future drug development for a large variety of diseases caused by these agents. We have previously shown that the specificity of encapsidation of poliovirus and of C-cluster coxsackieviruses, which are prototypes of enteroviruses, is dependent on an interaction of capsid proteins with the multifunctional nonstructural protein 2CATPase. In this study, we have searched for residues in poliovirus 2CATPase, near a presumed capsid-interacting site, important for encapsidation. An unusual cold-sensitive mutant of 2CATPase possessed a defect in encapsidation at 37°C and subsequently in uncoating during the next cycle of infection at 33°C. These studies not only reveal a new site in 2CATPase that is involved in encapsidation but also identify a link between encapsidation and uncoating.
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Agudo R, de la Higuera I, Arias A, Grande-Pérez A, Domingo E. Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism. Virology 2016; 494:257-66. [PMID: 27136067 PMCID: PMC7111656 DOI: 10.1016/j.virol.2016.04.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 02/05/2023]
Abstract
We previously characterized a foot-and-mouth disease virus (FMDV) with three amino acid replacements in its polymerase (3D) that conferred resistance to the mutagenic nucleoside analogue ribavirin. Here we show that passage of this mutant in the presence of high ribavirin concentrations resulted in selection of viruses with the additional replacement I248T in 2C. This 2C substitution alone (even in the absence of replacements in 3D) increased FMDV fitness mainly in the presence of ribavirin, prevented an incorporation bias in favor of A and U associated with ribavirin mutagenesis, and conferred the ATPase activity of 2C decreased sensitivity to ribavirin-triphosphate. Since in previous studies we described that 2C with I248T was selected under different selective pressures, this replacement qualifies as a joker substitution in FMDV evolution. The results have identified a role of 2C in nucleotide incorporation, and have unveiled a new polymerase-independent mechanism of virus escape to lethal mutagenesis. A replacement in FMDV protein 2C confers reduced sensitivity to the mutagen ribavirin. The effect of the replacement is to prevent a mutational bias evoked by ribavirin. 2C has an effect in nucleotide incorporation by the FMDV polymerase. We describe a new molecular mechanism of escape to ribavirin-mediated extinction.
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Affiliation(s)
- Rubén Agudo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Ignacio de la Higuera
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Armando Arias
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
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Abstract
The Picornaviridae represent a large family of small plus-strand RNA viruses that cause a bewildering array of important human and animal diseases. Morphogenesis is the least-understood step in the life cycle of these viruses, and this process is difficult to study because encapsidation is tightly coupled to genome translation and RNA replication. Although the basic steps of assembly have been known for some time, very few details are available about the mechanism and factors that regulate this process. Most of the information available has been derived from studies of enteroviruses, in particular poliovirus, where recent evidence has shown that, surprisingly, the specificity of encapsidation is governed by a viral protein-protein interaction that does not involve an RNA packaging signal. In this review, we make an attempt to summarize what is currently known about the following topics: (i) encapsidation intermediates, (ii) the specificity of encapsidation (iii), viral and cellular factors that are required for encapsidation, (iv) inhibitors of encapsidation, and (v) a model of enterovirus encapsidation. Finally, we compare some features of picornavirus morphogenesis with those of other plus-strand RNA viruses.
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Wang C, Ma HC, Wimmer E, Jiang P, Paul AV. A C-terminal, cysteine-rich site in poliovirus 2C(ATPase) is required for morphogenesis. J Gen Virol 2014; 95:1255-1265. [PMID: 24558221 DOI: 10.1099/vir.0.062497-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The morphogenesis of viruses belonging to the genus Enterovirus in the family Picornaviridae is still poorly understood despite decades-long investigations. However, we recently provided evidence that 2C(ATPase) gives specificity to poliovirus encapsidation through an interaction with capsid protein VP3. The polypeptide 2C(ATPase) is a highly conserved non-structural protein of enteroviruses with important roles in RNA replication, encapsidation and uncoating. We have identified a site (K279/R280) near the C terminus of the polypeptide that is required for morphogenesis. The aim of the current project was to search for additional functional sites near the C terminus of the 2C(ATPase) polypeptide, with particular interest in those that are required for encapsidation. We selected for analysis a cysteine-rich site of the polypeptide and constructed four mutants in which cysteines or a histidine was changed to an alanine. The RNA transcripts were transfected into HeLa cells yielding two lethal, one temperature-sensitive and one quasi-infectious mutants. All four mutants exhibited normal protein translation in vitro and three of them possessed severe RNA replication defects. The quasi-infectious mutant (C286A) yielded variants with a pseudo-reversion at the original site (A286D), but some also contained one additional mutation: A138V or M293V. The temperature-sensitive mutant (C272A/H273A) exhibited an encapsidation and possibly also an uncoating defect at 37 °C. Variants of this mutant revealed suppressor mutations at three different sites in the 2C(ATPase) polypeptide: A138V, M293V and K295R. We concluded that the cysteine-rich site near the C terminus of 2C(ATPase) is involved in encapsidation, possibly through an interaction with an upstream segment located between boxes A and B of the nucleotide-binding domain.
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Affiliation(s)
- Chunling Wang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hsin-Chieh Ma
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aniko V Paul
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
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18
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Springer CL, Huntoon HP, Peersen OB. Polyprotein context regulates the activity of poliovirus 2CATPase bound to bilayer nanodiscs. J Virol 2013; 87:5994-6004. [PMID: 23514879 PMCID: PMC3648184 DOI: 10.1128/jvi.03491-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/11/2013] [Indexed: 12/26/2022] Open
Abstract
Positive-strand RNA viruses generally replicate in large membrane-associated complexes. For poliovirus, these replication complexes are anchored to the membrane via the viral 2B, 2C, and 3A proteins. 2C is an AAA+ family ATPase that plays a key role in host cell membrane rearrangement, is a putative helicase, and is implicated in virion assembly and packaging. However, the membrane-binding characteristics of all of these viral proteins have made it difficult to elucidate their exact roles in virus replication. We show here that small lipid bilayers known as nanodiscs can be used to chaperone the in vitro expression of soluble poliovirus 2C, 2BC, and 2BC3AB polyproteins in a membrane-bound form. ATPase assays on these proteins show that the activity of the core 2C domain is stimulated ~0-fold compared to the larger 2BC3AB polyprotein, with most of this stimulation occurring upon removal of 2B. The proteins are active over a wide range of salt concentrations, exhibit slight lipid headgroup dependence, and show significant stimulation by acetate. Our data lead to a model wherein the replication complex can be assembled with a minimally active form of 2C that then becomes fully activated by proteolytic cleavage from the adjacent 2B viroporin domain.
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Affiliation(s)
- Courtney L Springer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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Selective serotonin reuptake inhibitor fluoxetine inhibits replication of human enteroviruses B and D by targeting viral protein 2C. Antimicrob Agents Chemother 2013; 57:1952-6. [PMID: 23335743 DOI: 10.1128/aac.02084-12] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although the genus Enterovirus contains many important human pathogens, there is no licensed drug for either the treatment or the prophylaxis of enterovirus infections. We report that fluoxetine (Prozac)--a selective serotonin reuptake inhibitor--inhibits the replication of human enterovirus B (HEV-B) and HEV-D but does not affect the replication of HEV-A and HEV-C or human rhinovirus A or B. We show that fluoxetine interferes with viral RNA replication, and we identified viral protein 2C as the target of this compound.
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Alanine scanning of poliovirus 2CATPase reveals new genetic evidence that capsid protein/2CATPase interactions are essential for morphogenesis. J Virol 2012; 86:9964-75. [PMID: 22761387 DOI: 10.1128/jvi.00914-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polypeptide 2C(ATPase) is one of the most thoroughly studied but least understood proteins in the life cycle of poliovirus. Within the protein, multiple functional domains important for uncoating, host cell membrane alterations, and RNA replication and encapsidation have previously been identified. In this study, charged to alanine-scanning mutagenesis was used to generate conditional-lethal mutations in hitherto-uncharacterized domains of the 2C(ATPase) polypeptide, particularly those involved in morphogenesis. Adjacent or clustered charged amino acids (2 to 4), scattered along the 2C(ATPase) coding sequence, were replaced with alanines. RNA transcripts of mutant poliovirus cDNA clones were transfected into HeLa cells. Subsequently, 10 lethal, 1 severely temperature-sensitive, 2 quasi-infectious, and 3 wild type-like mutants were identified. Using a luciferase-containing reporter virus, we demonstrated RNA replication defects in all lethal and quasi-infectious mutants. Temperature-sensitive mutants were defective in RNA replication only at the restricted temperatures. Furthermore, we characterized a quasi-infectious mutant (K(6)A/K(7)A) that produced a suppressor mutation (G(1)R) and a novel 2B^2C(ATPase) cleavage site (Q^R). Surprisingly, this cleavage site mutation did not interfere with normal processing of the polyprotein. These mutants have led to the identification of several new sites within the 2C(ATPase) polypeptide that are required for RNA replication. In addition, analysis of the suppressor mutants has revealed a new domain near the C terminus of 2C(ATPase) that is involved in encapsidation, possibly achieved through interaction with an amino acid sequence between NTP binding motifs A and B of 2C(ATPase). Most importantly, the identification of suppressor mutations in both 2C(ATPase) and the capsid domains (VP1 and VP3) of poliovirus has confirmed that an interaction between 2C(ATPase) and capsid proteins is involved in viral morphogenesis.
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Analysis of poliovirus protein 3A interactions with viral and cellular proteins in infected cells. J Virol 2011; 85:4284-96. [PMID: 21345960 DOI: 10.1128/jvi.02398-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poliovirus proteins 3A and 3AB are small, membrane-binding proteins that play multiple roles in viral RNA replication complex formation and function. In the infected cell, these proteins associate with other viral and cellular proteins as part of a supramolecular complex whose structure and composition are unknown. We isolated viable viruses with three different epitope tags (FLAG, hemagglutinin [HA], and c-myc) inserted into the N-terminal region of protein 3A. These viruses exhibited growth properties and characteristics very similar to those of the wild-type, untagged virus. Extracts prepared from the infected cells were subjected to immunoaffinity purification of the tagged proteins by adsorption to commercial antibody-linked beads and examined after elution for cellular and other viral proteins that remained bound to 3A sequences during purification. Viral proteins 2C, 2BC, 3D, and 3CD were detected in all three immunopurified 3A samples. Among the cellular proteins previously reported to interact with 3A either directly or indirectly, neither LIS1 nor phosphoinositol-4 kinase (PI4K) were detected in any of the purified tagged 3A samples. However, the guanine nucleotide exchange factor GBF1, which is a key regulator of membrane trafficking in the cellular protein secretory pathway and which has been shown previously to bind enteroviral protein 3A and to be required for viral RNA replication, was readily recovered along with immunoaffinity-purified 3A-FLAG. Surprisingly, we failed to cocapture GBF1 with 3A-HA or 3A-myc proteins. A model for variable binding of these 3A mutant proteins to GBF1 based on amino acid sequence motifs and the resulting practical and functional consequences thereof are discussed.
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den Boon JA, Ahlquist P. Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories. Annu Rev Microbiol 2010; 64:241-56. [PMID: 20825348 DOI: 10.1146/annurev.micro.112408.134012] [Citation(s) in RCA: 326] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Positive-strand RNA virus genome replication is invariably associated with extensively rearranged intracellular membranes. Recent biochemical and electron microscopy analyses, including three-dimensional electron microscope tomographic imaging, have fundamentally advanced our understanding of the ultrastructure and function of organelle-like RNA replication factories. Notably, for a range of positive-strand RNA viruses embodying many major differences, independent studies have revealed multiple common principles. These principles include that RNA replication often occurs inside numerous virus-induced vesicles invaginated or otherwise elaborated from a continuous, often endoplasmic reticulum-derived membrane network. Where analyzed, each such vesicle typically contains only one or a few genome replication intermediates in conjunction with many copies of viral nonstructural proteins. In addition, these genome replication compartments often are closely associated with sites of virion assembly and budding. Our understanding of these complexes is growing, providing substantial new insights into the organization, coordination, and potential control of crucial processes in virus replication.
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Affiliation(s)
- Johan A den Boon
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
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23
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Gangaramani DR, Eden EL, Shah M, Destefano JJ. The twenty-nine amino acid C-terminal cytoplasmic domain of poliovirus 3AB is critical for nucleic acid chaperone activity. RNA Biol 2010; 7:820-9. [PMID: 21045553 DOI: 10.4161/rna.7.6.13781] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Poliovirus 3AB protein is the first picornavirus protein demonstrated to have nucleic acid chaperone activity. Further characterization of 3AB demonstrates that the C-terminal 22 amino acids (3B region (also referred to as VPg), amino acid 88-109) of the protein is required for chaperone activity, as mutations in this region abrogate nucleic acid binding and chaperone function. Protein 3B alone has no chaperone activity as determined by established assays that include the ability to stimulate nucleic acid hybridization in a primer-template annealing assay, helix-destabilization in a nucleic acid unwinding assay, or aggregation of nucleic acids. In contrast, the putative 3AB C-terminal cytoplasmic domain (C terminal amino acids 81-109, 3B + the last 7 C-terminal amino acids of 3A, termed 3B+7 in this report) possesses strong activity in these assays, albeit at much higher concentrations than 3AB. The characteristics of several mutations in 3B+7 are described here, as well as a model proposing that 3B+7 is the site of the "intrinsic" chaperone activity of 3AB while the 3A N-terminal region (amino acids 1-58) and/or membrane anchor domain (amino acids 59-80) serve to increase the effective concentration of the 3B+7 region leading to the potent chaperone activity of 3AB.
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Affiliation(s)
- Divya R Gangaramani
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
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24
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Abstract
Many viruses that replicate in the cytoplasm compartmentalize their genome replication and transcription in organelle-like structures that enhance replication efficiency and protection from host defenses. In particular, recent studies with diverse positive-strand RNA viruses have further elucidated the ultrastructure of membrane-bound RNA replication complexes and how these complexes function in close coordination with virion assembly and budding. The structure, function, and assembly of some positive-strand RNA virus replication complexes have parallels and potential evolutionary links with the replicative cores of double-strand RNA virus and retrovirus virions and more general similarities with the replication factories of cytoplasmic DNA viruses.
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25
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Arias A, Perales C, Escarmís C, Domingo E. Deletion mutants of VPg reveal new cytopathology determinants in a picornavirus. PLoS One 2010; 5:e10735. [PMID: 20505767 PMCID: PMC2873979 DOI: 10.1371/journal.pone.0010735] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 04/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background Success of a viral infection requires that each infected cell delivers a sufficient number of infectious particles to allow new rounds of infection. In picornaviruses, viral replication is initiated by the viral polymerase and a viral-coded protein, termed VPg, that primes RNA synthesis. Foot-and-mouth disease virus (FMDV) is exceptional among picornaviruses in that its genome encodes 3 copies of VPg. Why FMDV encodes three VPgs is unknown. Methodology and Principal Findings We have constructed four mutant FMDVs that encode only one VPg: either VPg1, VPg3, or two chimeric versions containing part of VPg1 and VPg3. All mutants, except that encoding only VPg1, were replication-competent. Unexpectedly, despite being replication-competent, the mutants did not form plaques on BHK-21 cell monolayers. The one-VPg mutant FMDVs released lower amounts of encapsidated viral RNA to the extracellular environment than wild type FMDV, suggesting that deficient plaque formation was associated with insufficient release of infectious progeny. Mutant FMDVs subjected to serial passages in BHK-21 cells regained plaque-forming capacity without modification of the number of copies of VPg. Substitutions in non-structural proteins 2C, 3A and VPg were associated with restoration of plaque formation. Specifically, replacement R55W in 2C was repeatedly found in several mutant viruses that had regained competence in plaque development. The effect of R55W in 2C was to mediate an increase in the extracellular viral RNA release without a detectable increase of total viral RNA that correlated with an enhanced capacity to alter and detach BHK-21 cells from the monolayer, the first stage of cell killing. Conclusions The results link the VPg copies in the FMDV genome with the cytopathology capacity of the virus, and have unveiled yet another function of 2C: modulation of picornavirus cell-to-cell transmission. Implications for picornaviruses pathogenesis are discussed.
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Affiliation(s)
- Armando Arias
- Departamento de Virología y Microbiología, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Departamento de Virología y Microbiología, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Cristina Escarmís
- Departamento de Virología y Microbiología, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- Departamento de Virología y Microbiología, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- * E-mail:
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26
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Ishikawa K, Sasaki J, Taniguchi K. Overall linkage map of the nonstructural proteins of Aichi virus. Virus Res 2009; 147:77-84. [PMID: 19879907 DOI: 10.1016/j.virusres.2009.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 10/08/2009] [Accepted: 10/17/2009] [Indexed: 11/16/2022]
Abstract
Aichi virus (AiV), which is associated with acute gastroenteritis in humans, is a member of the genus Kobuvirus of the family Picornaviridae. Picornavirus genome replication occurs in replication complexes that include viral nonstructural proteins, host proteins and viral RNA. In poliovirus, all nonstructural proteins are found in the replication complexes, suggesting the ability of the viral nonstructural proteins to interact with each other. In this study, we examined the interactions between the AiV nonstructural proteins using a mammalian two-hybrid system. The results showed that all of the tested proteins could interact with more than one protein. We observed homodimerization of five proteins, bidirectional heterodimerization of six protein pairs, and unidirectional heterodimerization of eighteen protein pairs. Among the interactions detected in this study, the 2A-2BC, 2A-2BC, 2A-2C, 2BC-3CD, 2BC-3C, 2C-3C, 2C-3CD and 3AB-3C interactions have not been observed in the previous two-hybrid studies with other picornaviruses. The strongest interaction was observed between 2A and 3CD. AiV 2A has already been shown to be involved in genome replication. Domain mapping of the 2A and 3CD interaction in mammalian two-hybrid analysis revealed that the C-terminal quarter of 2A is not required for the interaction with 3CD.
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Affiliation(s)
- Kumiko Ishikawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Dengakugakubo 1-98, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
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27
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Adams P, Kandiah E, Effantin G, Steven AC, Ehrenfeld E. Poliovirus 2C protein forms homo-oligomeric structures required for ATPase activity. J Biol Chem 2009; 284:22012-22021. [PMID: 19520852 DOI: 10.1074/jbc.m109.031807] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The poliovirus protein 2C plays an essential role in viral RNA replication, although its precise biochemical activities or structural requirements have not been elucidated. The protein has several distinctive properties, including ATPase activity and membrane and RNA binding, that are conserved among orthologs of many positive-strand RNA viruses. Sequence alignments have placed these proteins in the SF3 helicase family, a subset of the AAA+ ATPase superfamily. A feature common to AAA+ proteins is the formation of oligomeric rings that are essential for their catalytic functions. Here we show that a recombinant protein, MBP-2C, in which maltose-binding protein was fused to 2C, formed soluble oligomers and that ATPase activity was restricted to oligomer-containing fractions from gel-filtration chromatography. The active fraction was visualized by negative-staining electron microscopy as ring-like particles composed of 5-8 protomers. This conclusion was confirmed by mass measurements obtained by scanning transmission electron microscopy. Mutation of amino acid residues in the 2C nucleotide-binding domain demonstrated that loss of the ability to bind or hydrolyze ATP did not affect oligomerization. Co-expression of active MBP-2C and inactive mutant proteins generated mixed oligomers that exhibited little ATPase activity, suggesting that incorporation of inactive subunits eliminates the function of the entire particle. Finally, deletion of the N-terminal 38 amino acids blocked oligomerization of the fusion protein and eliminated ATPase activity, despite retention of an unaltered nucleotide-binding domain.
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Affiliation(s)
| | | | - Grégory Effantin
- NIAMS, National Institutes of Health, Bethesda, Maryland 20892-8011
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28
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Mutations in the nonstructural protein 3A confer resistance to the novel enterovirus replication inhibitor TTP-8307. Antimicrob Agents Chemother 2009; 53:1850-7. [PMID: 19237651 DOI: 10.1128/aac.00934-08] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A novel compound, TTP-8307, was identified as a potent inhibitor of the replication of several rhino- and enteroviruses. TTP-8307 inhibits viral RNA synthesis in a dose-dependent manner, without affecting polyprotein synthesis and/or processing. Drug-resistant variants of coxsackievirus B3 were all shown to carry at least one amino acid mutation in the nonstructural protein 3A. In particular, three mutations located in a nonstructured region preceding the hydrophobic domain (V45A, I54F, and H57Y) appeared to contribute to the drug-resistant phenotype. This region has previously been identified as a hot sport for mutations that resulted in resistance to enviroxime, the sole 3A-targeting enterovirus inhibitor reported thus far. This was corroborated by the fact that TTP-8307 and enviroxime proved cross-resistant. It is hypothesized that TTP-8307 and enviroxime disrupt proper interactions of 3A(B) with other viral or cellular proteins that are required for efficient replication.
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29
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Belov GA, Feng Q, Nikovics K, Jackson CL, Ehrenfeld E. A critical role of a cellular membrane traffic protein in poliovirus RNA replication. PLoS Pathog 2008; 4:e1000216. [PMID: 19023417 PMCID: PMC2581890 DOI: 10.1371/journal.ppat.1000216] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 10/23/2008] [Indexed: 12/12/2022] Open
Abstract
Replication of many RNA viruses is accompanied by extensive remodeling of intracellular membranes. In poliovirus-infected cells, ER and Golgi stacks disappear, while new clusters of vesicle-like structures form sites for viral RNA synthesis. Virus replication is inhibited by brefeldin A (BFA), implicating some components(s) of the cellular secretory pathway in virus growth. Formation of characteristic vesicles induced by expression of viral proteins was not inhibited by BFA, but they were functionally deficient. GBF1, a guanine nucleotide exchange factor for the small cellular GTPases, Arf, is responsible for the sensitivity of virus infection to BFA, and is required for virus replication. Knockdown of GBF1 expression inhibited virus replication, which was rescued by catalytically active protein with an intact N-terminal sequence. We identified a mutation in GBF1 that allows growth of poliovirus in the presence of BFA. Interaction between GBF1 and viral protein 3A determined the outcome of infection in the presence of BFA.
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Affiliation(s)
- George A. Belov
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Qian Feng
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Krisztina Nikovics
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France
| | - Catherine L. Jackson
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France
| | - Ellie Ehrenfeld
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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30
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Bessaud M, Autret A, Jegouic S, Balanant J, Joffret ML, Delpeyroux F. Development of a Taqman RT-PCR assay for the detection and quantification of negatively stranded RNA of human enteroviruses: evidence for false-priming and improvement by tagged RT-PCR. J Virol Methods 2008; 153:182-9. [PMID: 18706930 DOI: 10.1016/j.jviromet.2008.07.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 07/09/2008] [Accepted: 07/17/2008] [Indexed: 11/28/2022]
Abstract
Human enteroviruses are among the most common viruses infecting humans. These viruses are known to be able to infect a wide range of tissues and are believed to establish persistent infections. Enteroviruses are positive-sense single-stranded RNA viruses whose replication involves the synthesis of negative strand intermediates. Therefore, the specific detection of negatively stranded viral RNA in tissues or cells is a reliable marker of active enteroviral replication. The present report presents the development of a real-time RT-PCR allowing the specific detection and quantification of negatively stranded viral RNA. Since it was known that specific amplification of single-stranded RNA can be made difficult by false-priming events leading to false-positive or overestimated results, the assay was developed by using a tagged RT primer. This tagged RT-PCR was shown to be able to amplify specifically negative RNA of enteroviruses grown in cell cultures by preventing the amplification of cDNAs generated by false-priming.
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Affiliation(s)
- Maël Bessaud
- Unité postulante de biologie des virus entériques, Institut Pasteur, 25 rue du Dr Roux, 75 015 Paris, France.
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