1
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Marongiu L, Burkard M, Helling T, Biendl M, Venturelli S. Modulation of the replication of positive-sense RNA viruses by the natural plant metabolite xanthohumol and its derivatives. Crit Rev Food Sci Nutr 2023:1-15. [PMID: 37942943 DOI: 10.1080/10408398.2023.2275169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The COVID-19 pandemic has highlighted the importance of identifying new potent antiviral agents. Nutrients as well as plant-derived substances are promising candidates because they are usually well tolerated by the human body and readily available in nature, and consequently mostly cheap to produce. A variety of antiviral effects have recently been described for the hop chalcone xanthohumol (XN), and to a lesser extent for its derivatives, making these hop compounds particularly attractive for further investigation. Noteworthy, mounting evidence indicated that XN can suppress a wide range of viruses belonging to several virus families, all of which share a common reproductive cycle. As a result, the purpose of this review is to summarize the most recent research on the antiviral properties of XN and its derivatives, with a particular emphasis on the positive-sense RNA viruses human hepatitis C virus (HCV), porcine reproductive and respiratory syndrome virus (PRRSV), and severe acute respiratory syndrome corona virus (SARS-CoV-2).
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Affiliation(s)
- Luigi Marongiu
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Markus Burkard
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Thomas Helling
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Martin Biendl
- HHV Hallertauer Hopfenveredelungsgesellschaft m.b.H, Mainburg, Germany
| | - Sascha Venturelli
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
- Department of Vegetative and Clinical Physiology, University Hospital of Tuebingen, Tuebingen, Germany
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2
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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3
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Lou Z, Rao Z. The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. Annu Rev Biochem 2022; 91:381-401. [PMID: 35729072 DOI: 10.1146/annurev-biochem-052521-115653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.
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Affiliation(s)
- Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; ,
| | - Zihe Rao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; , .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangzhou Laboratory, Guangzhou, China
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4
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An overview of SARS-COV-2 epidemiology, mutant variants, vaccines, and management strategies. J Infect Public Health 2021; 14:1299-1312. [PMID: 34429257 PMCID: PMC8366110 DOI: 10.1016/j.jiph.2021.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background Over the last two decades, humanity has observed the extraordinary anomaly caused by novel, weird coronavirus strains, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). As the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has made its entry into the world, it has dramatically affected life in every domain by continuously producing new variants. The vaccine development is an ongoing process, although some vaccines got marketed. The big challenge is now whether the vaccine candidates can provide long-lasting protection or prevention against mutant variants. Methods The information was gathered from various journals, electronic searches via Internet-based information such as PubMed, Google Scholar, Science Direct, online electronic journals, WHO landscape, world meters, WHO website, and News. Results This review will present and discuss some coronavirus disease 19 (COVID-19) related aspects including: the pathophysiology, epidemiology, mutant variants vaccine candidates, vaccine efficacy, and management strategies. Due to the high death rate, continuous spread, an inadequate workforce, lack of required therapeutics, and incomplete understanding of the viral strain, it becomes crucial to build the knowledge of its biological characteristics and make available the rapid diagnostic and vital therapeutic machinery for the combat and management of an infection. Conclusion The data summarizes current research on the COVID 19 infection and therapeutic interventions, which will direct future decision-making on the effort-worthy phases of the COVID 19 and the development of critical therapeutics. The only possible solution is the vaccine development targeting against all variant strains to halt its progress; the identified theoretical and practical knowledge can eliminate the gaps to improve a better understanding of the novel coronavirus structure and its design of a vaccine. In addition, to that the long-lasting protection is another challenging objective that need to be looked into.
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5
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Roe MK, Junod NA, Young AR, Beachboard DC, Stobart CC. Targeting novel structural and functional features of coronavirus protease nsp5 (3CL pro, M pro) in the age of COVID-19. J Gen Virol 2021; 102. [PMID: 33507143 PMCID: PMC8515871 DOI: 10.1099/jgv.0.001558] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Coronavirus protease nsp5 (Mpro, 3CLpro) remains a primary target for coronavirus therapeutics due to its indispensable and conserved role in the proteolytic processing of the viral replicase polyproteins. In this review, we discuss the diversity of known coronaviruses, the role of nsp5 in coronavirus biology, and the structure and function of this protease across the diversity of known coronaviruses, and evaluate past and present efforts to develop inhibitors to the nsp5 protease with a particular emphasis on new and mostly unexplored potential targets of inhibition. With the recent emergence of pandemic SARS-CoV-2, this review provides novel and potentially innovative strategies and directions to develop effective therapeutics against the coronavirus protease nsp5.
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Affiliation(s)
- Molly K Roe
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Nathan A Junod
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Audrey R Young
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Dia C Beachboard
- Department of Biology, DeSales University, Center Valley, PA, USA
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6
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Wang Y, Grunewald M, Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol 2020; 2203:1-29. [PMID: 32833200 DOI: 10.1007/978-1-0716-0900-2_1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. CoVs cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs, and upper respiratory tract and kidney disease in chickens to lethal human respiratory infections. Most recently, the novel coronavirus, SARS-CoV-2, which was first identified in Wuhan, China in December 2019, is the cause of a catastrophic pandemic, COVID-19, with more than 8 million infections diagnosed worldwide by mid-June 2020. Here we provide a brief introduction to CoVs discussing their replication, pathogenicity, and current prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which are relevant for understanding COVID-19.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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7
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Haque SKM, Ashwaq O, Sarief A, Azad John Mohamed AK. A comprehensive review about SARS-CoV-2. Future Virol 2020; 15:625-648. [PMID: 33224265 PMCID: PMC7664148 DOI: 10.2217/fvl-2020-0124] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease (COVID-19) was first identified in China, December 2019. Since then, it has spread the length and breadth of the world at an unprecedented, alarming rate. Severe acute respiratory syndrome coronavirus (SARS-CoV)-2, which causes COVID-19, has much in common with its closest homologs, SARS-CoV and Middle East respiratory syndrome-CoV. The virus-host interaction of SARS-CoV-2 uses the same receptor, ACE2, which is similar to that of SARS-CoV, which spreads through the respiratory tract. Patients with COVID-19 report symptoms including mild-to-severe fever, cough and fatigue; very few patients report gastrointestinal infections. There are no specific antiviral strategies. A few strong medications are under investigation, so we have to focus on proposals which ought to be taken to forestall this infection in a living host.
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Affiliation(s)
- SK Manirul Haque
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Omar Ashwaq
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Abdulla Sarief
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
| | - Abdul Kalam Azad John Mohamed
- Department of Chemical & Process Engineering Technology, Jubail Industrial College, P. O. Box 10099, Jubail Industrial City 31961, Saudi Arabia
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8
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Gupta A, Kumar S, Kumar R, Choudhary AK, Kumari K, Singh P, Kumar V. COVID-19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives. ChemistrySelect 2020; 5:7521-7533. [PMID: 32835089 PMCID: PMC7361534 DOI: 10.1002/slct.202001709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023]
Abstract
Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease-2019 (COVID-19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID-19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS-CoV-2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present-day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding.
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Affiliation(s)
- Akanksha Gupta
- Department of ChemistrySri Venkateswara CollegeUniversity of DelhiIndia.
| | - Sanjay Kumar
- Department of ChemistryDeshbandhu CollegeUniversity of DelhiIndia.
| | - Ravinder Kumar
- Department of Chemistry, Gurukula Kangri VishwavidyalayaHaridwarIndia.
| | | | - Kamlesh Kumari
- Department of ZoologyDeen Dayal Upadhyaya CollegeDelhiIndia.
| | - Prashant Singh
- Department of ChemistryAtma Ram Sanatan Dharma CollegeDelhi UniversityNew DelhiIndia.
| | - Vinod Kumar
- Department of ChemistryKirori Mal CollegeUniversity of DelhiIndia
- Special Centre for Nano SciencesJawaharlal Nehru UniversityDelhiIndia
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9
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Naik B, Gupta N, Ojha R, Singh S, Prajapati VK, Prusty D. High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment. Int J Biol Macromol 2020; 160:1-17. [PMID: 32470577 PMCID: PMC7250083 DOI: 10.1016/j.ijbiomac.2020.05.184] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
The present-day world is severely suffering from the recently emerged SARS-CoV-2. The lack of prescribed drugs for the deadly virus has stressed the likely need to identify novel inhibitors to alleviate and stop the pandemic. In the present high throughput virtual screening study, we used in silico techniques like receptor-ligand docking, Molecular dynamic (MD), and ADME properties to screen natural compounds. It has been documented that many natural compounds display antiviral activities, including anti–SARS-CoV effect. The present study deals with compounds of Natural Product Activity and Species Source (NPASS) database with known biological activity that probably impedes the activity of six essential enzymes of the virus. Promising drug-like compounds were identified, demonstrating better docking score and binding energy for each druggable targets. After an extensive screening analysis, three novel multi-target natural compounds were predicted to subdue the activity of three/more major drug targets simultaneously. Concerning the utility of natural compounds in the formulation of many therapies, we propose these compounds as excellent lead candidates for the development of therapeutic drugs against SARS-CoV-2.
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Affiliation(s)
- Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India.
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10
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Abstract
The recent approval by the regulatory authorities in the United States of several HIV proteinase inhibitors as therapeutics for the treatment of AIDS confirms that virus proteinases are valid molecular targets in the search for new antiviral drugs. This review summarizes the available approaches that can be taken to discover virus proteinase inhibitors and reviews the current status of our knowledge with respect to virus proteinases in viruses of clinical significance other than HIV. The major focus is on proteinases identified in the viruses that cause the common cold, hepatitis C virus and the herpesviruses.
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Affiliation(s)
- J. S. Mills
- Molecular Virology Department, Roche Research Centre, 40 Broadwater Road, Welwyn Garden City, Herts AL7 3AY, UK
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11
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Ye G, Deng F, Shen Z, Luo R, Zhao L, Xiao S, Fu ZF, Peng G. Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Virology 2016; 494:225-35. [PMID: 27128350 PMCID: PMC7111274 DOI: 10.1016/j.virol.2016.04.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/16/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CLpro), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CLpro and a molecular complex between an inactive PEDV 3CLpro variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CLpro. The dimerization of PEDV 3CLpro is similar to that of other Alphacoronavirus 3CLpros but has several differences from that of SARS-CoV 3CLpro from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CLpros, which may provide new insights into the recognition of substrates by 3CLpros in various coronavirus genera. The substrate binding mechanism of PEDV 3CLpro has been characterized. The large buried surface area is responsible for dimerization of PEDV 3CLpro. Non-conserved motifs cause different cleavage between PEDV and SARS-CoV 3CLpros.
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Affiliation(s)
- Gang Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China.
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12
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Tomar S, Johnston ML, St John SE, Osswald HL, Nyalapatla PR, Paul LN, Ghosh AK, Denison MR, Mesecar AD. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. J Biol Chem 2015; 290:19403-22. [PMID: 26055715 PMCID: PMC4528106 DOI: 10.1074/jbc.m115.651463] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/20/2022] Open
Abstract
All coronaviruses, including the recently emerged Middle East respiratory
syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the
proteolytic activity of the nsp5 protease (also known as 3C-like protease,
3CLpro) during virus replication, making it a high value target
for the development of anti-coronavirus therapeutics. Kinetic studies indicate
that in contrast to 3CLpro from other β-CoV 2c members,
including HKU4 and HKU5, MERS-CoV 3CLpro is less efficient at
processing a peptide substrate due to MERS-CoV 3CLpro being a weakly
associated dimer. Conversely, HKU4, HKU5, and SARS-CoV 3CLpro enzymes
are tightly associated dimers. Analytical ultracentrifugation studies support
that MERS-CoV 3CLpro is a weakly associated dimer
(Kd ∼52 μm) with a
slow off-rate. Peptidomimetic inhibitors of MERS-CoV 3CLpro were
synthesized and utilized in analytical ultracentrifugation experiments and
demonstrate that MERS-CoV 3CLpro undergoes significant ligand-induced
dimerization. Kinetic studies also revealed that designed reversible inhibitors
act as activators at a low compound concentration as a result of induced
dimerization. Primary sequence comparisons and x-ray structural analyses of two
MERS-CoV 3CLpro and inhibitor complexes, determined to 1.6 Å, reveal
remarkable structural similarity of the dimer interface with 3CLpro
from HKU4-CoV and HKU5-CoV. Despite this structural similarity, substantial
differences in the dimerization ability suggest that long range interactions by
the nonconserved amino acids distant from the dimer interface may control
MERS-CoV 3CLpro dimerization. Activation of MERS-CoV
3CLpro through ligand-induced dimerization appears to be unique
within the genogroup 2c and may potentially increase the complexity in the
development of MERS-CoV 3CLpro inhibitors as antiviral agents.
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Affiliation(s)
| | | | | | | | | | - Lake N Paul
- the Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, and
| | - Arun K Ghosh
- Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Mark R Denison
- the Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Andrew D Mesecar
- From the Departments of Biological Sciences and Chemistry, Purdue University, West Lafayette, Indiana 47907,
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13
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Wu A, Wang Y, Zeng C, Huang X, Xu S, Su C, Wang M, Chen Y, Guo D. Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus. Virus Res 2015; 208:56-65. [PMID: 26036787 PMCID: PMC7114542 DOI: 10.1016/j.virusres.2015.05.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/20/2022]
Abstract
Coronavirus 3C-like protease (3CLpro) is responsible for the cleavage of coronaviral polyprotein 1a/1ab (pp1a/1ab) to produce the mature non-structural proteins (nsps) of nsp4-16. The nsp5 of the newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as 3CLpro and its canonical cleavage sites (between nsps) were predicted based on sequence alignment, but the cleavability of these cleavage sites remains to be experimentally confirmed and putative non-canonical cleavage sites (inside one nsp) within the pp1a/1ab awaits further analysis. Here, we proposed a method for predicting coronaviral 3CLpro cleavage sites which balances the prediction accuracy and false positive outcomes. By applying this method to MERS-CoV, the 11 canonical cleavage sites were readily identified and verified by the biochemical assays. The Michaelis constant of the canonical cleavage sites of MERS-CoV showed that the substrate specificity of MERS-CoV 3CLpro is relatively conserved. Interestingly, nine putative non-canonical cleavage sites were predicted and three of them could be cleaved by MERS-CoV nsp5. These results pave the way for identification and functional characterization of new nsp products of coronaviruses.
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Affiliation(s)
- Andong Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Yi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Cong Zeng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Xingyu Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Shan Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Ceyang Su
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China
| | - Min Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, PR China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China.
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China; School of Basic Medical Sciences, Wuhan University, Wuhan, PR China.
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14
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Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2015. [PMID: 25720466 DOI: 10.1007/978‐1‐4939‐2438‐7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Anthony R Fehr
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Helena Jane Maier
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Erica Bickerton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Paul Britton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
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16
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Fung TS, Liu DX. Coronavirus infection, ER stress, apoptosis and innate immunity. Front Microbiol 2014; 5:296. [PMID: 24987391 PMCID: PMC4060729 DOI: 10.3389/fmicb.2014.00296] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/29/2014] [Indexed: 12/27/2022] Open
Abstract
The replication of coronavirus, a family of important animal and human pathogens, is closely associated with the cellular membrane compartments, especially the endoplasmic reticulum (ER). Coronavirus infection of cultured cells was previously shown to cause ER stress and induce the unfolded protein response (UPR), a process that aims to restore the ER homeostasis by global translation shutdown and increasing the ER folding capacity. However, under prolonged ER stress, UPR can also induce apoptotic cell death. Accumulating evidence from recent studies has shown that induction of ER stress and UPR may constitute a major aspect of coronavirus–host interaction. Activation of the three branches of UPR modulates a wide variety of signaling pathways, such as mitogen-activated protein (MAP) kinase activation, autophagy, apoptosis, and innate immune response. ER stress and UPR activation may therefore contribute significantly to the viral replication and pathogenesis during coronavirus infection. In this review, we summarize the current knowledge on coronavirus-induced ER stress and UPR activation, with emphasis on their cross-talking to apoptotic signaling.
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Affiliation(s)
- To S Fung
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| | - Ding X Liu
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore
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17
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18
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Lugari A, Betzi S, Decroly E, Bonnaud E, Hermant A, Guillemot JC, Debarnot C, Borg JP, Bouvet M, Canard B, Morelli X, Lécine P. Molecular mapping of the RNA Cap 2'-O-methyltransferase activation interface between severe acute respiratory syndrome coronavirus nsp10 and nsp16. J Biol Chem 2010; 285:33230-33241. [PMID: 20699222 PMCID: PMC2963367 DOI: 10.1074/jbc.m110.120014] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Several protein-protein interactions within the SARS-CoV proteome have been
identified, one of them being between non-structural proteins nsp10 and nsp16. In
this work, we have mapped key residues on the nsp10 surface involved in this
interaction. Alanine-scanning mutagenesis, bioinformatics, and molecular modeling
were used to identify several “hot spots,” such as Val42,
Met44, Ala71, Lys93, Gly94, and
Tyr96, forming a continuous protein-protein surface of about 830
Å2, bearing very conserved amino acids among coronaviruses.
Because nsp16 carries RNA cap 2′-O-methyltransferase
(2′O-MTase) activity only in the presence of its
interacting partner nsp10 (Bouvet, M., Debarnot, C., Imbert, I., Selisko, B.,
Snijder, E. J., Canard, B., and Decroly, E. (2010) PLoS Pathog. 6,
e1000863), functional consequences of mutations on this surface were evaluated
biochemically. Most changes that disrupted the nsp10-nsp16 interaction without
structural perturbations were shown to abrogate stimulation of nsp16 RNA cap
2′O-MTase activity. More strikingly, the Y96A mutation
abrogates stimulation of nsp16 2′O-MTase activity, whereas
Y96F overstimulates it. Thus, the nsp10-nsp16 interface may represent an attractive
target for antivirals against human and animal pathogenic coronaviruses.
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Affiliation(s)
- Adrien Lugari
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Stephane Betzi
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Emmanuel Bonnaud
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Aurélie Hermant
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Jean-Claude Guillemot
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Claire Debarnot
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Jean-Paul Borg
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Mickaël Bouvet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Xavier Morelli
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
| | - Patrick Lécine
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France.
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In vitro reconstitution of SARS-coronavirus mRNA cap methylation. PLoS Pathog 2010; 6:e1000863. [PMID: 20421945 PMCID: PMC2858705 DOI: 10.1371/journal.ppat.1000863] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 03/18/2010] [Indexed: 01/17/2023] Open
Abstract
SARS-coronavirus (SARS-CoV) genome expression depends on the synthesis of a set of mRNAs, which presumably are capped at their 5' end and direct the synthesis of all viral proteins in the infected cell. Sixteen viral non-structural proteins (nsp1 to nsp16) constitute an unusually large replicase complex, which includes two methyltransferases putatively involved in viral mRNA cap formation. The S-adenosyl-L-methionine (AdoMet)-dependent (guanine-N7)-methyltransferase (N7-MTase) activity was recently attributed to nsp14, whereas nsp16 has been predicted to be the AdoMet-dependent (nucleoside-2'O)-methyltransferase. Here, we have reconstituted complete SARS-CoV mRNA cap methylation in vitro. We show that mRNA cap methylation requires a third viral protein, nsp10, which acts as an essential trigger to complete RNA cap-1 formation. The obligate sequence of methylation events is initiated by nsp14, which first methylates capped RNA transcripts to generate cap-0 (7Me)GpppA-RNAs. The latter are then selectively 2'O-methylated by the 2'O-MTase nsp16 in complex with its activator nsp10 to give rise to cap-1 (7Me)GpppA(2'OMe)-RNAs. Furthermore, sensitive in vitro inhibition assays of both activities show that aurintricarboxylic acid, active in SARS-CoV infected cells, targets both MTases with IC(50) values in the micromolar range, providing a validated basis for anti-coronavirus drug design.
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Murine hepatitis virus nonstructural protein 4 regulates virus-induced membrane modifications and replication complex function. J Virol 2010; 84:280-90. [PMID: 19846526 DOI: 10.1128/jvi.01772-09] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Positive-strand RNA viruses induce modifications of cytoplasmic membranes to form replication complexes. For coronaviruses, replicase nonstructural protein 4 (nsp4) has been proposed to function in the formation and organization of replication complexes. Murine hepatitis virus (MHV) nsp4 is glycosylated at residues Asn176 (N176) and N237 during plasmid expression of nsp4 in cells. To test if MHV nsp4 residues N176 and N237 are glycosylated during virus replication and to determine the effects of N176 and N237 on nsp4 function and MHV replication, alanine substitutions of nsp4 N176, N237, or both were engineered into the MHV-A59 genome. The N176A, N237A, and N176A/N237A mutant viruses were viable, and N176 and N237 were glycosylated during infection of wild-type (wt) and mutant viruses. The nsp4 glycosylation mutants exhibited impaired virus growth and RNA synthesis, with the N237A and N176A/N237A mutant viruses demonstrating more profound defects in virus growth and RNA synthesis. Electron microscopic analysis of ultrastructure from infected cells demonstrated that the nsp4 mutants had aberrant morphology of virus-induced double-membrane vesicles (DMVs) compared to those infected with wt virus. The degree of altered DMV morphology directly correlated with the extent of impairment in viral RNA synthesis and virus growth of the nsp4 mutant viruses. The results indicate that nsp4 plays a critical role in the organization and stability of DMVs. The results also support the conclusion that the structure of DMVs is essential for efficient RNA synthesis and optimal replication of coronaviruses.
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Ulasli M, Verheije MH, de Haan CAM, Reggiori F. Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus. Cell Microbiol 2010; 12:844-61. [PMID: 20088951 PMCID: PMC7159092 DOI: 10.1111/j.1462-5822.2010.01437.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Coronaviruses (CoV) are enveloped positive‐strand RNA viruses that induce different membrane rearrangements in infected cells in order to efficiently replicate and assemble. The origin, the protein composition and the function of these structures are not well established. To shed further light on these structures, we have performed a time‐course experiment in which the mouse hepatitis virus (MHV)‐induced membrane rearrangements were examined qualitatively and quantitatively by (immuno)‐electron microscopy. With our approach we were able to confirm the appearance of 6, previously reported, membranous structures during the course of a complete infection cycle. These structures include the well‐characterized double‐membrane vesicles (DMVs), convoluted membranes (CMs) and virions but also the more enigmatic large virion‐containing vacuoles (LVCVs), tubular bodies (TBs) and cubic membrane structures (CMSs). We have characterized the LVCVs, TBs and CMSs, and found that the CoV‐induced structures appear in a strict order. By combining these data with quantitative analyses on viral RNA, protein synthesis and virion release, this study generates an integrated molecular and ultrastructural overview of CoV infection. In particular, it provides insights in the role of each CoV‐induced structure and reveals that LVCVs are ERGIC/Golgi compartments that expand to accommodate an increasing production of viral particles.
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Affiliation(s)
- Mustafa Ulasli
- Department of Cell Biology and Institute of Biomembranes, University Medical Centre Utrecht, The Netherlands
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22
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Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity. J Virol 2008; 82:8071-84. [PMID: 18417574 DOI: 10.1128/jvi.00407-08] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The coronavirus family of positive-strand RNA viruses includes important pathogens of livestock, companion animals, and humans, including the severe acute respiratory syndrome coronavirus that was responsible for a worldwide outbreak in 2003. The unusually complex coronavirus replicase/transcriptase is comprised of 15 or 16 virus-specific subunits that are autoproteolytically derived from two large polyproteins. In line with bioinformatics predictions, we now show that feline coronavirus (FCoV) nonstructural protein 16 (nsp16) possesses an S-adenosyl-L-methionine (AdoMet)-dependent RNA (nucleoside-2'O)-methyltransferase (2'O-MTase) activity that is capable of cap-1 formation. Purified recombinant FCoV nsp16 selectively binds to short capped RNAs. Remarkably, an N7-methyl guanosine cap ((7Me)GpppAC(3-6)) is a prerequisite for binding. High-performance liquid chromatography analysis demonstrated that nsp16 mediates methyl transfer from AdoMet to the 2'O position of the first transcribed nucleotide, thus converting (7Me)GpppAC(3-6) into (7Me)GpppA(2')(O)(Me)C(3-6). The characterization of 11 nsp16 mutants supported the previous identification of residues K45, D129, K169, and E202 as the putative K-D-K-E catalytic tetrad of the enzyme. Furthermore, residues Y29 and F173 of FCoV nsp16, which may be the functional counterparts of aromatic residues involved in substrate recognition by the vaccinia virus MTase VP39, were found to be essential for both substrate binding and 2'O-MTase activity. Finally, the weak inhibition profile of different AdoMet analogues indicates that nsp16 has evolved an atypical AdoMet binding site. Our results suggest that coronavirus mRNA carries a cap-1, onto which 2'O methylation follows an order of events in which 2'O-methyl transfer must be preceded by guanine N7 methylation, with the latter step being performed by a yet-unknown N7-specific MTase.
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23
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A novel mutation in murine hepatitis virus nsp5, the viral 3C-like proteinase, causes temperature-sensitive defects in viral growth and protein processing. J Virol 2008; 82:5999-6008. [PMID: 18385240 DOI: 10.1128/jvi.00203-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Sequencing and reversion analysis of murine hepatitis virus (MHV) temperature-sensitive (ts) viruses has identified putative ts mutations in the replicase nonstructural proteins (nsp's) of these coronaviruses. In this study, reverse transcriptase PCR sequencing of the RNA genome of an isolate of the MHV ts virus Alb ts6, referred to as Alb/ts/nsp5/V148A, identified a putative ts mutation in nsp5 (T10651C, Val148Ala), the viral 3C-like proteinase (3CLpro). The introduction of the T10651C mutation into the infectious MHV clone resulted in the recovery of a mutant virus, the nsp5/V148A virus, that demonstrated reduced growth and nsp5 proteinase activity identical to that of Alb/ts/nsp5/V148A at the nonpermissive temperature. Sequence analysis of 40 degrees C revertants of Alb/ts/nsp5/V148A identified primary reversion to Ala148Val in nsp5, as well as two independent second-site mutations resulting in Ser133Asn and His134Tyr substitutions in nsp5. The introduction of the Ser133Asn or His134Tyr substitution into the cloned nsp5/V148A mutant virus background resulted in the recovery of viruses with increased growth fitness and the partial restoration of nsp5 activity at the nonpermissive temperature. Modeling of the nsp5 structure of Alb/ts/nsp5/V148A predicted that the Val148Ala mutation alters residue 148 interactions with residues of the substrate binding S1 subsite of the nsp5 active-site cavity. This study identifies novel residues in nsp5 that may be important for regulating substrate specificity and nsp5 proteinase activity.
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24
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Clementz MA, Kanjanahaluethai A, O'Brien TE, Baker SC. Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles. Virology 2008; 375:118-29. [PMID: 18295294 PMCID: PMC2443636 DOI: 10.1016/j.virol.2008.01.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 11/15/2007] [Accepted: 01/12/2008] [Indexed: 02/08/2023]
Abstract
Coronaviruses are positive-strand RNA viruses that replicate in the cytoplasm of infected cells by generating a membrane-associated replicase complex. The replicase complex assembles on double membrane vesicles (DMVs). Here, we studied the role of a putative replicase anchor, nonstructural protein 4 (nsp4), in the assembly of murine coronavirus DMVs. We used reverse genetics to generate infectious clone viruses (icv) with an alanine substitution at nsp4 glycosylation site N176 or N237, or an asparagine to threonine substitution (nsp4-N258T), which is proposed to confer a temperature sensitive phenotype. We found that nsp4-N237A is lethal and nsp4-N258T generated a virus (designated Alb ts6 icv) that is temperature sensitive for viral replication. Analysis of Alb ts6 icv-infected cells revealed that there was a dramatic reduction in DMVs and that both nsp4 and nsp3 partially localized to mitochondria when cells were incubated at the non-permissive temperature. These results reveal a critical role of nsp4 in directing coronavirus DMV assembly.
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Affiliation(s)
- Mark A Clementz
- Department of Microbiology and Immunology, Loyola University Stritch School of Medicine, Maywood, IL 60153 USA
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25
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Oostra M, te Lintelo EG, Deijs M, Verheije MH, Rottier PJM, de Haan CAM. Localization and membrane topology of coronavirus nonstructural protein 4: involvement of the early secretory pathway in replication. J Virol 2007; 81:12323-36. [PMID: 17855519 PMCID: PMC2168994 DOI: 10.1128/jvi.01506-07] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The coronavirus nonstructural proteins (nsp's) derived from the replicase polyproteins collectively constitute the viral replication complexes, which are anchored to double-membrane vesicles. Little is known about the biogenesis of these complexes, the membrane anchoring of which is probably mediated by nsp3, nsp4, and nsp6, as they contain several putative transmembrane domains. As a first step to getting more insight into the formation of the coronavirus replication complex, the membrane topology, processing, and subcellular localization of nsp4 of the mouse hepatitis virus (MHV) and severe acute respiratory syndrome-associated coronavirus (SARS-CoV) were elucidated in this study. Both nsp4 proteins became N glycosylated, while their amino and carboxy termini were localized to the cytoplasm. These observations imply nsp4 to assemble in the membrane as a tetraspanning transmembrane protein with a Nendo/Cendo topology. The amino terminus of SARS-CoV nsp4, but not that of MHV nsp4, was shown to be (partially) processed by signal peptidase. nsp4 localized to the endoplasmic reticulum (ER) when expressed alone but was recruited to the replication complexes in infected cells. nsp4 present in these complexes did not colocalize with markers of the ER or Golgi apparatus, while the susceptibility of its sugars to endoglycosidase H indicated that the protein had also not traveled trough the latter compartment. The important role of the early secretory pathway in formation of the replication complexes was also demonstrated by the inhibition of coronaviral replication when the ER export machinery was blocked by use of the kinase inhibitor H89 or by expression of a mutant, Sar1[H79G].
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Affiliation(s)
- M Oostra
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
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26
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Sparks JS, Lu X, Denison MR. Genetic analysis of Murine hepatitis virus nsp4 in virus replication. J Virol 2007; 81:12554-63. [PMID: 17855548 PMCID: PMC2169011 DOI: 10.1128/jvi.01257-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronavirus replicase polyproteins are translated from the genomic positive-strand RNA and are proteolytically processed by three viral proteases to yield 16 mature nonstructural proteins (nsp1 to nsp16). nsp4 contains four predicted transmembrane-spanning regions (TM1, -2, -3, and -4), demonstrates characteristics of an integral membrane protein, and is thought to be essential for the formation and function of viral replication complexes on cellular membranes. To determine the requirement of nsp4 for murine hepatitis virus (MHV) infection in culture, engineered deletions and mutations in TMs and intervening soluble regions were analyzed for effects on virus recovery, growth, RNA synthesis, protein expression, and intracellular membrane modifications. In-frame partial or complete deletions of nsp4; deletions of TM1, -2, and -3; and alanine substitutions of multiple conserved, clustered, charged residues in nsp4 resulted in viruses that were nonrecoverable, viruses highly impaired in growth and RNA synthesis, and viruses that were nearly wild type in replication. The results indicate that nsp4 is required for MHV replication and that while putative TM1, -2, and -3 and specific charged residues may be essential for productive virus infection, putative TM4 and the carboxy-terminal amino acids K(398) through T(492) of nsp4 are dispensable. Together, the experiments identify important residues and regions for studies of nsp4 topology, function, and interactions.
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Affiliation(s)
- Jennifer S Sparks
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2581, USA
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27
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Deming DJ, Graham RL, Denison MR, Baric RS. Processing of open reading frame 1a replicase proteins nsp7 to nsp10 in murine hepatitis virus strain A59 replication. J Virol 2007; 81:10280-91. [PMID: 17634238 PMCID: PMC2045455 DOI: 10.1128/jvi.00017-07] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Coronaviruses express open reading frame 1a (ORF1a) and ORF1b polyproteins from which 16 nonstructural proteins (nsp) are derived. The highly conserved region at the carboxy terminus of ORF1a is processed by the nsp5 proteinase (Mpro) into mature products, including nsp7, nsp8, nsp9, and nsp10, proteins with predicted or identified activities involved in RNA synthesis. Although continuous translation and proteolytic processing of ORF1ab by Mpro is required for replication, it is unknown whether specific cleavage events within the polyprotein are dispensable. We determined the requirement for the nsp7 to nsp10 proteins and their processing during murine hepatitis virus (MHV) replication. Through use of an MHV reverse genetics system, in-frame deletions of the coding sequences for nsp7 to nsp10, or ablation of their flanking Mpro cleavage sites, were made and the effects upon replication were determined. Viable viruses were characterized by analysis of Mpro processing, RNA transcription, and growth fitness. Deletion of any of the regions encoding nsp7 to nsp10 was lethal. Disruption of the cleavage sites was lethal with the exception of that of the nsp9-nsp10 site, which resulted in a mutant virus with attenuated replication. Passage of the attenuated nsp9-nsp10 cleavage mutant increased fitness to near-wild-type kinetics without reversion to a virus capable of processing nsp9-nsp10. We also confirmed the presence of a second cleavage site between nsp7 and nsp8. In order to determine whether a distinct function could be attributed to preprocessed forms of the polyprotein, including nsp7 to nsp10, the genes encoding nsp7 and nsp8 were rearranged. The mutant virus was not viable, suggesting that the uncleaved protein may be essential for replication or proteolytic processing.
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Affiliation(s)
- Damon J Deming
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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Abstract
Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly.
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Affiliation(s)
- Paul S Masters
- Wadsworth Center, New York State Department of Health, Albany, 12201, USA
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29
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Smits SL, Snijder EJ, de Groot RJ. Characterization of a torovirus main proteinase. J Virol 2006; 80:4157-67. [PMID: 16571831 PMCID: PMC1440467 DOI: 10.1128/jvi.80.8.4157-4167.2006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 02/02/2006] [Indexed: 11/20/2022] Open
Abstract
Viruses of the order Nidovirales encode huge replicase polyproteins. These are processed primarily by the chymotrypsin-like main proteinases (M(pro)s). So far, M(pro)s have been studied only for corona-, arteri-, and roniviruses. Here, we report the characterization of the M(pro) of toroviruses, the fourth main Nidovirus branch. Comparative sequence analysis of polyprotein 1a of equine torovirus (EToV) strain Berne, identified a serine proteinase domain, flanked by hydrophobic regions. Heterologous expression of this domain resulted in autoprocessing at flanking cleavage sites. N-terminal sequence analysis of cleavage products tentatively identified FxxQ downward arrow(S, A) as the substrate consensus sequence. EToV M(pro) combines several traits of its closest relatives. It has a predicted three-domain structure, with two catalytic beta-barrel domains and an additional C-terminal domain of unknown function. With respect to substrate specificity, the EToV M(pro) resembles its coronavirus homologue in its preference for P1-Gln, but its substrate-binding subsite, S1, more closely resembles that of arteri- and ronivirus M(pro)s, which prefer P1-Glu. Surprisingly, in contrast to the M(pro)s of corona- and roniviruses, but like that of arterivirus, the torovirus M(pro) uses serine instead of cysteine as its principal nucleophile. Under the premise that the M(pro)s of corona- and toroviruses are more closely related to each other than to those of arteri- and roniviruses, the transition from serine- to cysteine-based proteolytic catalysis (or vice versa) must have happened more than once in the course of nidovirus evolution. In this respect, it is of interest that a mutant EToV M(pro) with a Ser165-->Cys substitution retained partial enzymatic activity.
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Affiliation(s)
- Saskia L Smits
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
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30
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Putics Á, Gorbalenya AE, Ziebuhr J. Identification of protease and ADP-ribose 1''-monophosphatase activities associated with transmissible gastroenteritis virus non-structural protein 3. J Gen Virol 2006; 87:651-656. [PMID: 16476987 DOI: 10.1099/vir.0.81596-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The replicase polyproteins, pp1a and pp1ab, of porcine Transmissible gastroenteritis virus (TGEV) have been predicted to be cleaved by viral proteases into 16 non-structural proteins (nsp). Here, enzymic activities residing in the amino-proximal region of nsp3, the largest TGEV replicase processing product, were characterized. It was shown, by in vitro translation experiments and protein sequencing, that the papain-like protease 1, PL1(pro), but not a mutant derivative containing a substitution of the presumed active-site nucleophile, Cys(1093), cleaves the nsp2|nsp3 site at (879)Gly|Gly(880). By using an antiserum raised against the pp1a/pp1ab residues 526-713, the upstream processing product, nsp2, was identified as an 85 kDa protein in TGEV-infected cells. Furthermore, PL1(pro) was confirmed to be flanked at its C terminus by a domain (called X) that mediates ADP-ribose 1''-phosphatase activity. Expression and characterization of a range of bacterially expressed forms of this enzyme suggest that the active X domain comprises pp1a/pp1ab residues Asp(1320)-Ser(1486).
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Affiliation(s)
- Ákos Putics
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Alexander E Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
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Sawicki SG, Sawicki DL, Younker D, Meyer Y, Thiel V, Stokes H, Siddell SG. Functional and genetic analysis of coronavirus replicase-transcriptase proteins. PLoS Pathog 2005; 1:e39. [PMID: 16341254 PMCID: PMC1298938 DOI: 10.1371/journal.ppat.0010039] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 11/01/2005] [Indexed: 12/15/2022] Open
Abstract
The coronavirus replicase-transcriptase complex is an assembly of viral and cellular proteins that mediate the synthesis of genome and subgenome-sized mRNAs in the virus-infected cell. Here, we report a genetic and functional analysis of 19 temperature-sensitive (ts) mutants of Murine hepatitis virus MHV-A59 that are unable to synthesize viral RNA when the infection is initiated and maintained at the non-permissive temperature. Both classical and biochemical complementation analysis leads us to predict that the majority of MHV-A59 ORF1a replicase gene products (non-structural proteins nsp1-nsp11) form a single complementation group (cistron1) while the replicase gene products encoded in ORF1b (non-structural proteins nsp12-nsp16) are able to function in trans and comprise at least three, and possibly five, further complementation groups (cistrons II-VI). Also, we have identified mutations in the non-structural proteins nsp 4, nsp5, nsp10, nsp12, nsp14, and nsp16 that are responsible for the ts phenotype of eight MHV-A59 mutants, which allows us to conclude that these proteins are essential for the assembly of a functional replicase-transcriptase complex. Finally, our analysis of viral RNA synthesis in ts mutant virus-infected cells allows us to discriminate three phenotypes with regard to the inability of specific mutants to synthesize viral RNA at the non-permissive temperature. Mutant LA ts6 appeared to be defective in continuing negative-strand synthesis, mutant Alb ts16 appeared to form negative strands but these were not utilized for positive-strand RNA synthesis, and mutant Alb ts22 was defective in the elongation of both positive- and negative-strand RNA. On the basis of these results, we propose a model that describes a pathway for viral RNA synthesis in MHV-A59-infected cells. Further biochemical analysis of these mutants should allow us to identify intermediates in this pathway and elucidate the precise function(s) of the viral replicase proteins involved.
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Affiliation(s)
- Stanley G Sawicki
- Department of Medical Microbiology and Immunology, Medical University of Ohio, Toledo, Ohio, United States of America
| | - Dorothea L Sawicki
- Department of Medical Microbiology and Immunology, Medical University of Ohio, Toledo, Ohio, United States of America
| | - Diane Younker
- Department of Medical Microbiology and Immunology, Medical University of Ohio, Toledo, Ohio, United States of America
| | - Yvonne Meyer
- Institute of Virology, University of Würzburg, Würzburg, Germany
| | - Volker Thiel
- Institute of Virology, University of Würzburg, Würzburg, Germany
| | - Helen Stokes
- Department of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Stuart G Siddell
- Department of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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32
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Brockway SM, Denison MR. Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication. Virology 2005; 340:209-23. [PMID: 16051301 PMCID: PMC7111834 DOI: 10.1016/j.virol.2005.06.035] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 06/21/2005] [Accepted: 06/25/2005] [Indexed: 11/24/2022]
Abstract
Despite ongoing research investigating mechanisms of coronavirus replication, functions of many viral nonstructural proteins (nsps) remain unknown. In the current study, a reverse genetic approach was used to define the role of the 28-kDa amino-terminal product (nsp1) of the gene 1 polyprotein during replication of the coronavirus murine hepatitis virus (MHV) in cell culture. To determine whether nsp1 is required for MHV replication and to identify residues critical for protein function, mutant viruses that contained deletions or point mutations within the nsp1-coding region were generated and assayed for defects in viral replication, viral protein expression, protein localization, and RNA synthesis. The results demonstrated that the carboxy-terminal half of nsp1 (residues K124 through L241) was dispensable for virus replication in culture but was required for efficient proteolytic cleavage of nsp1 from the gene 1 polyprotein and for optimal viral replication. Furthermore, whereas deletion of nsp1 residues amino-terminal to K124 failed to produce infectious virus, point mutagenesis of the nsp1 amino-terminus allowed recovery of several mutants with altered replication and RNA synthesis. This study identifies nsp1 residues important for protein processing, viral RNA synthesis, and viral replication.
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Affiliation(s)
- Sarah M. Brockway
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mark R. Denison
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Corresponding author. Lamb Center for Pediatric Research, D7235 MCN, Vanderbilt University School of Medicine, Nashville, TN 37232-2581, USA. Fax: +1 615 343 9723.
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33
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Graham RL, Sims AC, Brockway SM, Baric RS, Denison MR. The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication. J Virol 2005; 79:13399-411. [PMID: 16227261 PMCID: PMC1262610 DOI: 10.1128/jvi.79.21.13399-13411.2005] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Accepted: 08/09/2005] [Indexed: 01/09/2023] Open
Abstract
The positive-stranded RNA genome of the coronaviruses is translated from ORF1 to yield polyproteins that are proteolytically processed into intermediate and mature nonstructural proteins (nsps). Murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) polyproteins incorporate 16 protein domains (nsps), with nsp1 and nsp2 being the most variable among the coronaviruses and having no experimentally confirmed or predicted functions in replication. To determine if nsp2 is essential for viral replication, MHV and SARS-CoV genome RNA was generated with deletions of the nsp2 coding sequence (MHVDeltansp2 and SARSDeltansp2, respectively). Infectious MHVDeltansp2 and SARSDeltansp2 viruses recovered from electroporated cells had 0.5 to 1 log10 reductions in peak titers in single-cycle growth assays, as well as a reduction in viral RNA synthesis that was not specific for any positive-stranded RNA species. The Deltansp2 mutant viruses lacked expression of both nsp2 and an nsp2-nsp3 precursor, but cleaved the engineered chimeric nsp1-nsp3 cleavage site as efficiently as the native nsp1-nsp2 cleavage site. Replication complexes in MHVDeltansp2-infected cells lacked nsp2 but were morphologically indistinguishable from those of wild-type MHV by immunofluorescence. nsp2 expressed in cells by stable retroviral transduction was specifically recruited to viral replication complexes upon infection with MHVDeltansp2. These results demonstrate that while nsp2 of MHV and SARS-CoV is dispensable for viral replication in cell culture, deletion of the nsp2 coding sequence attenuates viral growth and RNA synthesis. These findings also provide a system for the study of determinants of nsp targeting and function.
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Affiliation(s)
- Rachel L Graham
- Department of Pediatrics, Vanderbilt University Medical Center, D6217 MCN, Nashville, TN 37232-2581, USA
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Abstract
As the largest RNA virus, coronavirus replication employs complex mechanisms and involves various viral and cellular proteins. The first open reading frame of the coronavirus genome encodes a large polyprotein, which is processed into a number of viral proteins required for viral replication directly or indirectly. These proteins include the RNA-dependent RNA polymerase (RdRp), RNA helicase, proteases, metal-binding proteins, and a number of other proteins of unknown function. Genetic studies suggest that most of these proteins are involved in viral RNA replication. In addition to viral proteins, several cellular proteins, such as heterogeneous nuclear ribonucleoprotein (hnRNP) A1, polypyrimidine-tract-binding (PTB) protein, poly(A)-binding protein (PABP), and mitochondrial aconitase (m-aconitase), have been identified to interact with the critical cis-acting elements of coronavirus replication. Like many other RNA viruses, coronavirus may subvert these cellular proteins from cellular RNA processing or translation machineries to play a role in viral replication.
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Affiliation(s)
- Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Campus Universidad Autónoma, Cantoblanco, 38049 Madrid, Spain
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35
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Chen CJ, Sugiyama K, Kubo H, Huang C, Makino S. Murine coronavirus nonstructural protein p28 arrests cell cycle in G0/G1 phase. J Virol 2004; 78:10410-9. [PMID: 15367607 PMCID: PMC516409 DOI: 10.1128/jvi.78.19.10410-10419.2004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Murine coronavirus mouse hepatitis virus (MHV) gene 1 encodes several nonstructural proteins. The functions are unknown for most of these nonstructural proteins, including p28, which is encoded at the 5' end of the MHV genome. Transient expression of cloned p28 in several different cultured cells inhibited cell growth, indicating that p28 expression suppressed cell proliferation. Expressed p28 was exclusively localized in the cytoplasm. Cell cycle analysis by flow cytometry demonstrated that p28 expression induced G(0)/G(1) cell cycle arrest. Characterization of various cellular proteins that are involved in regulating cell cycle progression demonstrated that p28 expression resulted in an accumulation of hypophosphorylated retinoblastoma protein (pRb), tumor suppressor p53, and cyclin-dependent kinase (Cdk) inhibitor p21(Cip1). Expression of p28 did not alter the amount of p53 transcripts yet increased the amount of p21(Cip1) transcripts, suggesting that p28 expression increased p53 stability and that p21(Cip1) was transcriptionally activated in a p53-dependent manner. Our present data suggest the following model of p28-induced G(0)/G(1) cell cycle arrest. Expressed cytoplasmic p28 induces the stabilization of p53, and accumulated p53 causes transcriptional upregulation of p21(Cip1). The increased amount of p21(Cip1) suppresses cyclin E/Cdk2 activity, resulting in the inhibition of pRb hyperphosphorylation. Accumulation of hypophosphorylated pRb thus prevents cell cycle progression from G(0)/G(1) to S phase.
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Affiliation(s)
- Chun-Jen Chen
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555-1019, USA
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36
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St-Jean JR, Jacomy H, Desforges M, Vabret A, Freymuth F, Talbot PJ. Human respiratory coronavirus OC43: genetic stability and neuroinvasion. J Virol 2004; 78:8824-34. [PMID: 15280490 PMCID: PMC479063 DOI: 10.1128/jvi.78.16.8824-8834.2004] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The complete genome sequences of the human coronavirus OC43 (HCoV-OC43) laboratory strain from the American Type Culture Collection (ATCC), and a HCoV-OC43 clinical isolate, designated Paris, were obtained. Both genomes are 30,713 nucleotides long, excluding the poly(A) tail, and only differ by 6 nucleotides. These six mutations are scattered throughout the genome and give rise to only two amino acid substitutions: one in the spike protein gene (I958F) and the other in the nucleocapsid protein gene (V81A). Furthermore, the two variants were shown to reach the central nervous system (CNS) after intranasal inoculation in BALB/c mice, demonstrating neuroinvasive properties. Even though the ATCC strain could penetrate the CNS more effectively than the Paris 2001 isolate, these results suggest that intrinsic neuroinvasive properties already existed for the HCoV-OC43 ATCC human respiratory isolate from the 1960s before it was propagated in newborn mouse brains. It also demonstrates that the molecular structure of HCoV-OC43 is very stable in the environment (the two variants were isolated ca. 40 years apart) despite virus shedding and chances of persistence in the host. The genomes of the two HCoV-OC43 variants display 71, 53.1, and 51.2% identity with those of mouse hepatitis virus A59, severe acute respiratory syndrome human coronavirus Tor2 strain (SARS-HCoV Tor2), and human coronavirus 229E (HCoV-229E), respectively. HCoV-OC43 also possesses well-conserved motifs with regard to the genome sequence of the SARS-HCoV Tor2, especially in open reading frame 1b. These results suggest that HCoV-OC43 and SARS-HCoV may share several important functional properties and that HCoV-OC43 may be used as a model to study the biology of SARS-HCoV without the need for level three biological facilities.
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Affiliation(s)
- Julien R St-Jean
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7 Quebec, Canada
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37
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Prentice E, Jerome WG, Yoshimori T, Mizushima N, Denison MR. Coronavirus replication complex formation utilizes components of cellular autophagy. J Biol Chem 2004; 279:10136-41. [PMID: 14699140 PMCID: PMC7957857 DOI: 10.1074/jbc.m306124200] [Citation(s) in RCA: 361] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2003] [Revised: 12/11/2003] [Indexed: 01/27/2023] Open
Abstract
The coronavirus mouse hepatitis virus (MHV) performs RNA replication on double membrane vesicles (DMVs) in the cytoplasm of the host cell. However, the mechanism by which these DMVs form has not been determined. Using genetic, biochemical, and cell imaging approaches, the role of autophagy in DMV formation and MHV replication was investigated. The results demonstrated that replication complexes co-localize with the autophagy proteins, microtubule-associated protein light-chain 3 and Apg12. MHV infection induces autophagy by a mechanism that is resistant to 3-methyladenine inhibition. MHV replication is impaired in autophagy knockout, APG5-/-, embryonic stem cell lines, but wild-type levels of MHV replication are restored by expression of Apg5 in the APG5-/-cells. In MHV-infected APG5-/-cells, DMVs were not detected; rather, the rough endoplasmic reticulum was dramatically swollen. The results of this study suggest that autophagy is required for formation of double membrane-bound MHV replication complexes and that DMV formation significantly enhances the efficiency of replication. Furthermore, the rough endoplasmic reticulum is implicated as the possible source of membranes for replication complexes.
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Affiliation(s)
- Erik Prentice
- Department of Microbiology and Immunology, Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee 37221, USA
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Kanjanahaluethai A, Jukneliene D, Baker SC. Identification of the murine coronavirus MP1 cleavage site recognized by papain-like proteinase 2. J Virol 2003; 77:7376-82. [PMID: 12805436 PMCID: PMC164800 DOI: 10.1128/jvi.77.13.7376-7382.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The replicase polyprotein of murine coronavirus is extensively processed by three proteinases, two papain-like proteinases (PLPs), termed PLP1 and PLP2, and a picornavirus 3C-like proteinase (3CLpro). Previously, we established a trans-cleavage assay and showed that PLP2 cleaves the replicase polyprotein between p210 and membrane protein 1 (MP1) (A. Kanjanahaluethai and S. C. Baker, J. Virol. 74:7911-7921, 2000). Here, we report the results of our studies identifying and characterizing this cleavage site. To determine the approximate position of the cleavage site, we expressed constructs that extended various distances upstream from the previously defined C-terminal end of MP1. We found that the construct extending from the putative PLP2 cleavage site at glycine 2840-alanine 2841 was most similar in size to the processed MP1 replicase product generated in a trans-cleavage assay. To determine which amino acids are critical for PLP2 recognition and processing, we generated 14 constructs with amino acid substitutions upstream and downstream of the putative cleavage site and assessed the effects of the mutations in the PLP2 trans-cleavage assay. We found that substitutions at phenylalanine 2835, glycine 2839, or glycine 2840 resulted in a reduction in cleavage of MP1. Finally, to unequivocally identify this cleavage site, we isolated radiolabeled MP1 protein and determined the position of [(35)S]methionine residues released by Edman degradation reaction. We found that the amino-terminal residue of MP1 corresponds to alanine 2841. Therefore, murine coronavirus PLP2 cleaves the replicase polyprotein between glycine 2840 and alanine 2841, and the critical determinants for PLP2 recognition and processing occupy the P6, P2, and P1 positions of the cleavage site. This study is the first report of the identification and characterization of a cleavage site recognized by murine coronavirus PLP2 activity.
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Affiliation(s)
- Amornrat Kanjanahaluethai
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153, USA
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Xu Z, Zhang H, Tian X, Ji J, Li W, Li Y, Tian W, Han Y, Wang L, Zhang Z, Xu J, Wei W, Zhu J, Sun H, Zhang X, Zhou J, Li S, Wang J, Wang J, Bi S, Yang H. The R protein of SARS-CoV: analyses of structure and function based on four complete genome sequences of isolates BJ01-BJ04. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:155-65. [PMID: 15626345 PMCID: PMC5172245 DOI: 10.1016/s1672-0229(03)01019-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS.
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Affiliation(s)
- Zuyuan Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Haiqing Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiangjun Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
- Medical College, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Lili Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Zizhang Zhang
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Wei
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jingui Zhu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Haiyan Sun
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaowei Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Zhou
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Shengli Bi
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
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40
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Yount B, Denison MR, Weiss SR, Baric RS. Systematic assembly of a full-length infectious cDNA of mouse hepatitis virus strain A59. J Virol 2002; 76:11065-78. [PMID: 12368349 PMCID: PMC136593 DOI: 10.1128/jvi.76.21.11065-11078.2002] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A novel method was developed to assemble a full-length infectious cDNA of the group II coronavirus mouse hepatitis virus strain A59 (MHV-A59). Seven contiguous cDNA clones that spanned the 31.5-kb MHV genome were isolated. The ends of the cDNAs were engineered with unique junctions and assembled with only the adjacent cDNA subclones, resulting in an intact MHV-A59 cDNA construct of approximately 31.5 kb in length. The interconnecting restriction site junctions that are located at the ends of each cDNA are systematically removed during the assembly of the complete full-length cDNA product, allowing reassembly without the introduction of nucleotide changes. RNA transcripts derived from the full-length MHV-A59 construct were infectious, although transfection frequencies were enhanced 10- to 15-fold in the presence of transcripts encoding the nucleocapsid protein N. Plaque-purified virus derived from the infectious construct replicated efficiently and displayed similar growth kinetics, plaque morphology, and cytopathology in murine cells as did wild-type MHV-A59. Molecularly cloned viruses recognized the MHV receptor (MHVR) for docking and entry, and pretreatment of cells with monoclonal antibodies against MHVR blocked virus entry and replication. Cells infected with molecularly cloned MHV-A59 virus expressed replicase (gene 1) proteins identical to those of laboratory MHV-A59. Importantly, the molecularly cloned viruses contained three marker mutations that had been derived from the engineered component clones. Full-length infectious constructs of MHV-A59 will permit genetic modifications of the entire coronavirus genome, particularly in the replicase gene. The method has the potential to be used to construct viral, microbial, or eukaryotic genomes approaching several million base pairs in length and used to insert restriction sites at any given nucleotide in a microbial genome.
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Affiliation(s)
- Boyd Yount
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435, USA
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Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J 2002; 21:3213-24. [PMID: 12093723 PMCID: PMC126080 DOI: 10.1093/emboj/cdf327] [Citation(s) in RCA: 472] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The key enzyme in coronavirus polyprotein processing is the viral main proteinase, M(pro), a protein with extremely low sequence similarity to other viral and cellular proteinases. Here, the crystal structure of the 33.1 kDa transmissible gastroenteritis (corona)virus M(pro) is reported. The structure was refined to 1.96 A resolution and revealed three dimers in the asymmetric unit. The mutual arrangement of the protomers in each of the dimers suggests that M(pro) self-processing occurs in trans. The active site, comprised of Cys144 and His41, is part of a chymotrypsin-like fold that is connected by a 16 residue loop to an extra domain featuring a novel alpha-helical fold. Molecular modelling and mutagenesis data implicate the loop in substrate binding and elucidate S1 and S2 subsites suitable to accommodate the side chains of the P1 glutamine and P2 leucine residues of M(pro) substrates. Interactions involving the N-terminus and the alpha-helical domain stabilize the loop in the orientation required for trans-cleavage activity. The study illustrates that RNA viruses have evolved unprecedented variations of the classical chymotrypsin fold.
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Affiliation(s)
| | | | | | - Stuart G. Siddell
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
| | - John Ziebuhr
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
| | - Rolf Hilgenfeld
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
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42
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Ng LFP, Liu DX. Membrane association and dimerization of a cysteine-rich, 16-kilodalton polypeptide released from the C-terminal region of the coronavirus infectious bronchitis virus 1a polyprotein. J Virol 2002; 76:6257-67. [PMID: 12021359 PMCID: PMC136229 DOI: 10.1128/jvi.76.12.6257-6267.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than 10 mature proteins processed from coronavirus gene 1-encoded polyproteins have been identified in virus-infected cells. Here, we report the identification of the most C-terminal cleavage product of the 1a polyprotein as a 16-kDa protein in infectious bronchitis virus-infected Vero cells. Indirect immunofluorescence demonstrated that the protein exhibits a distinct perinuclear punctate staining pattern, suggesting that it is associated with cellular membranes. Positive staining observed on nonpermeabilized cells indicates that the protein may get transported to the cell surface, but no secretion of the protein out of the cells was observed. Treatment of the membrane fraction prepared from cells expressing the 16-kDa protein with Triton X-100, a high pH, and a high concentration of salts showed that the protein may be tightly associated with intracellular membranes. Dual-labeling experiments demonstrated that the 16-kDa protein colocalized with the 5'-bromouridine 5'-triphosphate-labeled viral RNA, suggesting that it may be associated with the viral replication machinery. Sequence comparison of the 16-kDa protein with the equivalent products of other coronaviruses showed multiple conserved cysteine residues, and site-directed mutagenesis studies revealed that these conserved residues may contribute to dimerization of the 16-kDa protein. Furthermore, increased accumulation of the 16-kDa protein upon stimulation with epidermal growth factor was observed, providing preliminary evidence that the protein might be involved in the growth factor signaling pathway.
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Affiliation(s)
- Lisa F P Ng
- Institute of Molecular Agrobiology, The National University of Singapore, Singapore 117604
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43
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de Vries AAF, Horzinek MC, Rottier PJM, de Groot RJ. The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses. ACTA ACUST UNITED AC 2002; 8:33-47. [PMID: 32288441 PMCID: PMC7128191 DOI: 10.1006/smvy.1997.0104] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viruses in the families Arteriviridae and Coronaviridae have enveloped virions which contain nonsegmented, positive-stranded RNA, but the constituent genera differ markedly in genetic complexity and virion structure. Nevertheless, there are striking resemblances among the viruses in the organization and expression of their genomes, and sequence conservation among the polymerase polyproteins strongly suggests that they have a common ancestry. On this basis, the International Committee on Taxonomy of Viruses recently established a new order, Nidovirales, to contain the two families. Here, the common traits and distinguishing features of the Nidovirales are reviewed.
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Affiliation(s)
- Antoine A F de Vries
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Marian C Horzinek
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Peter J M Rottier
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Raoul J de Groot
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
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44
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Gosert R, Kanjanahaluethai A, Egger D, Bienz K, Baker SC. RNA replication of mouse hepatitis virus takes place at double-membrane vesicles. J Virol 2002; 76:3697-708. [PMID: 11907209 PMCID: PMC136101 DOI: 10.1128/jvi.76.8.3697-3708.2002] [Citation(s) in RCA: 337] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The replication complexes (RCs) of positive-stranded RNA viruses are intimately associated with cellular membranes. To investigate membrane alterations and to characterize the RC of mouse hepatitis virus (MHV), we performed biochemical and ultrastructural studies using MHV-infected cells. Biochemical fractionation showed that all 10 of the MHV gene 1 polyprotein products examined pelleted with the membrane fraction, consistent with membrane association of the RC. Furthermore, MHV gene 1 products p290, p210, and p150 and the p150 cleavage product membrane protein 1 (MP1, also called p44) were resistant to extraction with Triton X-114, indicating that they are integral membrane proteins. The ultrastructural analysis revealed double-membrane vesicles (DMVs) in the cytoplasm of MHV-infected cells. The DMVs were found either as separate entities or as small clusters of vesicles. To determine whether MHV proteins and viral RNA were associated with the DMVs, we performed immunocytochemistry electron microscopy (IEM). We found that the DMVs were labeled using an antiserum directed against proteins derived from open reading frame 1a of MHV. By electron microscopy in situ hybridization (ISH) using MHV-specific RNA probes, DMVs were highly labeled for both gene 1 and gene 7 sequences. By combined ISH and IEM, positive-stranded RNA and viral proteins localized to the same DMVs. Finally, viral RNA synthesis was detected by labeling with 5-bromouridine 5'-triphosphate. Newly synthesized viral RNA was found to be associated with the DMVs. We conclude from these data that the DMVs carry the MHV RNA replication complex and are the site of MHV RNA synthesis.
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Affiliation(s)
- Rainer Gosert
- Institute for Medical Microbiology, University of Basel, Basel, Switzerland
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45
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Hegyi A, Friebe A, Gorbalenya AE, Ziebuhr J. Mutational analysis of the active centre of coronavirus 3C-like proteases. J Gen Virol 2002; 83:581-593. [PMID: 11842253 DOI: 10.1099/0022-1317-83-3-581] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.
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Affiliation(s)
- Annette Hegyi
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| | - Agnes Friebe
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| | - Alexander E Gorbalenya
- Advanced Biomedical Computing Center, 430 Miller Dr. Rm 228, SAIC/NCI-Frederick, Frederick, MD 21702-1201, USA2
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
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46
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Abstract
The key enzyme in coronavirus replicase polyprotein processing is the coronavirus main protease, 3CL(pro). The substrate specificities of five coronavirus main proteases, including the prototypic enzymes from the coronavirus groups I, II and III, were characterized. Recombinant main proteases of human coronavirus (HCoV), transmissible gastroenteritis virus (TGEV), feline infectious peritonitis virus, avian infectious bronchitis virus and mouse hepatitis virus (MHV) were tested in peptide-based trans-cleavage assays. The determination of relative rate constants for a set of corresponding HCoV, TGEV and MHV 3CL(pro) cleavage sites revealed a conserved ranking of these sites. Furthermore, a synthetic peptide representing the N-terminal HCoV 3CL(pro) cleavage site was shown to be effectively hydrolysed by noncognate main proteases. The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead us to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.
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Affiliation(s)
- Annette Hegyi
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
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47
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Kanjanahaluethai A, Baker SC. Identification of mouse hepatitis virus papain-like proteinase 2 activity. J Virol 2000; 74:7911-21. [PMID: 10933699 PMCID: PMC112322 DOI: 10.1128/jvi.74.17.7911-7921.2000] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2000] [Accepted: 06/08/2000] [Indexed: 11/20/2022] Open
Abstract
Mouse hepatitis virus (MHV) is a 31-kb positive-strand RNA virus that is replicated in the cytoplasm of infected cells by a viral RNA-dependent RNA polymerase, termed the replicase. The replicase is encoded in the 5'-most 22 kb of the genomic RNA, which is translated to produce a polyprotein of >800 kDa. The replicase polyprotein is extensively processed by viral and perhaps cellular proteinases to give rise to a functional replicase complex. To date, two of the MHV replicase-encoded proteinases, papain-like proteinase 1 (PLP1) and the poliovirus 3C-like proteinase (3CLpro), have been shown to process the replicase polyprotein. In this report, we describe the cloning, expression, and activity of the third MHV proteinase domain, PLP2. We show that PLP2 cleaves a substrate encoding the first predicted membrane-spanning domain (MP1) of the replicase polyprotein. Cleavage of MP1 and release of a 150-kDa intermediate, p150, are likely to be important for embedding the replicase complex in cellular membranes. Using an antiserum (anti-D11) directed against the C terminus of the MP1 domain, we verified that p150 encompasses the MP1 domain and identified a 44-kDa protein (p44) as a processed product of p150. Pulse-chase experiments showed that p150 is rapidly generated in MHV-infected cells and that p44 is processed from the p150 precursor. Protease inhibitor studies revealed that unlike 3CLpro activity, PLP2 activity is not sensitive to cysteine protease inhibitor E64d. Furthermore, coexpression studies using the PLP2 domain and a substrate encoding the MP1 cleavage site showed that PLP2 acts efficiently in trans. Site-directed mutagenesis studies confirmed the identification of cysteine 1715 as a catalytic residue of PLP2. This study is the first to report enzymatic activity of the PLP2 domain and to demonstrate that three distinct viral proteinase activities process the MHV replicase polyprotein.
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Affiliation(s)
- A Kanjanahaluethai
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153, USA
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48
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Ng LF, Liu DX. Further characterization of the coronavirus infectious bronchitis virus 3C-like proteinase and determination of a new cleavage site. Virology 2000; 272:27-39. [PMID: 10873746 PMCID: PMC7131205 DOI: 10.1006/viro.2000.0330] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/1999] [Revised: 03/14/2000] [Accepted: 03/29/2000] [Indexed: 11/29/2022]
Abstract
Coronavirus infectious bronchitis virus (IBV) encodes a trypsin-like proteinase (3C-like proteinase) by ORF 1a, which has been demonstrated to play a pivotal role in proteolytic processing of gene 1-encoded polyproteins. In our previous studies, the proteinase was identified as a 33-kDa protein in IBV-infected cells, and its catalytic center was shown to consist of H(2820) and C(2922) residues. It is released from the 1a and 1a/1b polyproteins by autoprocessing at two Q-S dipeptide bonds (Q(2779)-S(2780) and Q(3086)-S(3087)). In this report, further characterization of the two cleavage sites demonstrates that the N-terminal Q(2779)-S(2780) site is tolerant to mutations at the P1 position. Deletion of the C-terminal region of the proteinase shows that a significant amount of the enzymatic activity is maintained upon deletion of up to 67 amino acids, suggesting that the extreme C-terminal region may be dispensable for the proteolytic activity of the proteinase. Analysis of the autoprocessing kinetics in vitro reveals that proteolysis at the Q(2779)-S(2780) site is the first cleavage event mediated by this proteinase. This is followed by cleavage at the Q(3086)-S(3087) site. The occurrence of both cleavage events in intact cells is potentially rapid and efficient, as no intermediate cleavage products covering the proteinase were detected in either IBV-infected or transfected cells. Immunofluorescence microscopy and subcellular fractionation studies further show differential subcellular localization of the proteinase in IBV-infected cells and in cells expressing the 3C-like proteinase alone, indicating that additional roles in viral replication might be played by this protein. Finally, a Q-A (Q(3379)-A(3380)) dipeptide bond encoded by nucleotides 10,663 to 10,668 was demonstrated to be a cleavage site of the proteinase.
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Affiliation(s)
- L F Ng
- Institute of Molecular Agrobiology, The National University of Singapore, 1 Research Link, 117604, Singapore
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49
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Sims AC, Ostermann J, Denison MR. Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes. J Virol 2000; 74:5647-54. [PMID: 10823872 PMCID: PMC112052 DOI: 10.1128/jvi.74.12.5647-5654.2000] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/1999] [Accepted: 03/23/2000] [Indexed: 11/20/2022] Open
Abstract
The coronavirus replicase gene (gene 1) is translated into two co-amino-terminal polyproteins that are proteolytically processed to yield more than 15 mature proteins. Several gene 1 proteins have been shown to localize at sites of viral RNA synthesis in the infected cell cytoplasm, notably on late endosomes at early times of infection. However, both immunofluorescence and electron microscopic studies have also detected gene 1 proteins at sites distinct from the putative sites of viral RNA synthesis or virus assembly. In this study, mouse hepatitis virus (MHV)-infected cells were fractionated and analyzed to determine if gene 1 proteins segregated to more than one membrane population. Following differential centrifugation of lysates of MHV-infected DBT cells, gene 1 proteins as well as the structural N and M proteins were detected almost exclusively in a high-speed small membrane pellet. Following fractionation of the small membrane pellet on an iodixanol density gradient, the gene 1 proteins p28 and helicase cofractionated with dense membranes (1.12 to 1.13 g/ml) that also contained peak concentrations of N. In contrast, p65 and p1a-22 were detected in a distinct population of less dense membranes (1.05 to 1.09 g/ml). Viral RNA was detected in membrane fractions containing helicase, p28, and N but not in the fractions containing p65 and p1a-22. LAMP-1, a marker for late endosomes and lysosomes, was detected in both membrane populations. These results demonstrate that multiple gene 1 proteins segregate into two biochemically distinct but tightly associated membrane populations and that only one of these populations appears to be a site for viral RNA synthesis. The results further suggest that p28 is a component of the viral replication complex whereas the gene 1 proteins p1a-22 and p65 may serve roles during infection that are distinct from viral RNA transcription or replication.
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Affiliation(s)
- A C Sims
- Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA
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50
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Bost AG, Carnahan RH, Lu XT, Denison MR. Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly. J Virol 2000; 74:3379-87. [PMID: 10708455 PMCID: PMC111839 DOI: 10.1128/jvi.74.7.3379-3387.2000] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The replicase gene (gene 1) of the coronavirus mouse hepatitis virus (MHV) encodes two co-amino-terminal polyproteins presumed to incorporate all the virus-encoded proteins necessary for viral RNA synthesis. The polyproteins are cotranslationally processed by viral proteinases into at least 15 mature proteins, including four predicted cleavage products of less than 25 kDa that together would comprise the final 59 kDa of protein translated from open reading frame 1a. Monospecific antibodies directed against the four distinct domains detected proteins of 10, 12, and 15 kDa (p1a-10, p1a-12, and p1a-15) in MHV-A59-infected DBT cells, in addition to a previously identified 22-kDa protein (p1a-22). When infected cells were probed by immunofluorescence laser confocal microscopy, p1a-10, -22, -12, and -15 were detected in discrete foci that were prominent in the perinuclear region but were widely distributed throughout the cytoplasm as well. Dual-labeling experiments demonstrated colocalization of the majority of p1a-22 in replication complexes with the helicase, nucleocapsid, and 3C-like proteinase, as well as with p1a-10, -12, and -15. p1a-22 was also detected in separate foci adjacent to the replication complexes. The majority of complexes containing the gene 1 proteins were distinct from sites of accumulation of the M assembly protein. However, in perinuclear regions the gene 1 proteins and nucleocapsid were intercalated with sites of M protein localization. These results demonstrate that the complexes known to be involved in RNA synthesis contain multiple gene 1 proteins and are closely associated with structural proteins at presumed sites of virion assembly.
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Affiliation(s)
- A G Bost
- Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA
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