1
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Pyle JD, Whelan SPJ, Bloyet LM. Structure and function of negative-strand RNA virus polymerase complexes. Enzymes 2021; 50:21-78. [PMID: 34861938 DOI: 10.1016/bs.enz.2021.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.
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Affiliation(s)
- Jesse D Pyle
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States; Ph.D. Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
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2
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Wang Y, Yuan C, Xu X, Chong TH, Zhang L, Cheung PPH, Huang X. The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription. Biophys Chem 2021; 277:106652. [PMID: 34237555 DOI: 10.1016/j.bpc.2021.106652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023]
Abstract
Favipiravir (T-705) has been developed as a potent anti-influenza drug and exhibited a strong inhibition effect against a broad spectrum of RNA viruses. Its active form, ribofuranosyl-triphosphate (T-705-RTP), functions as a competitive substrate for the RNA-dependent RNA polymerase (RdRp) of the influenza A virus (IAV). However, the exact inhibitory mechanisms of T-705 remain elusive and subject to a long-standing debate. Although T-705 has been proposed to inhibit transcription by acting as a chain terminator, it is also paradoxically suggested to be a mutagen towards IAV RdRp by inducing mutations due to its ambiguous base pairing of C and U. Here, we combined biochemical assay with molecular dynamics (MD) simulations to elucidate the molecular mechanism underlying the inhibitory functions exerted by T-705 in IAV RdRp. Our in vitro transcription assay illustrated that IAV RdRp could recognize T-705 as a purine analogue and incorporate it into the nascent RNA strand. Incorporating a single T-705 is incapable of inhibiting transcription as extra natural nucleotides can be progressively added. However, when two consecutive T-705 are incorporated, viral transcription is completely terminated. MD simulations reveal that the sequential appearance of two T-705 in the nascent strand destabilizes the active site and disrupts the base stacking of the nascent RNA. Altogether, our results provide a plausible explanation for the inhibitory roles of T-705 targeting IAV RdRp by integrating the computational and experimental methods. Our study also offers a comprehensive platform to investigate the inhibition effect of antivirals and a novel explanation for the designing of anti-flu drugs.
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Affiliation(s)
- Yuqing Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Congmin Yuan
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xinzhou Xu
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong; Li Ka Shing Institute of Health Sciences, Li Ka Shing Medical Sciences Building, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong; Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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3
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Rodriguez P, Marcos-Villar L, Zamarreño N, Yángüez E, Nieto A. Mutations of the segment-specific nucleotides at the 3' end of influenza virus NS segment control viral replication. Virology 2019; 539:104-113. [PMID: 31706162 DOI: 10.1016/j.virol.2019.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
The vRNAs of influenza A viruses contain 12 and 13 nucleotide-long sequences at their 3' and 5' termini respectively that are highly conserved and constitute the vRNA promoter. These sequences and the next three segment-specific nucleotides show inverted partial complementarity and are followed by several unpaired nucleotides of poorly characterized function at the 3' end. We have performed systematic point-mutations at the segment-specific nucleotides 15-18 of the 3'-end of a NS-like vRNA segment. All NS-like vRNAs containing mutations at position 15, and some at positions 16-18 showed reduced transcription/replication efficiency in a transfection/infection system. In addition, the replication of recombinant viruses containing mutations at position 15 was impaired both in single and multi-cycle experiments. This reduction was the consequence of a decreased expression of the NS segment. The data indicate that NS1 plays a role in the transcription/replication of its own segment, which elicits a global defect on virus replication.
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Affiliation(s)
- Paloma Rodriguez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Laura Marcos-Villar
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Noelia Zamarreño
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Emilio Yángüez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Amelia Nieto
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain.
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4
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Amorim MJ. A Comprehensive Review on the Interaction Between the Host GTPase Rab11 and Influenza A Virus. Front Cell Dev Biol 2019; 6:176. [PMID: 30687703 PMCID: PMC6333742 DOI: 10.3389/fcell.2018.00176] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022] Open
Abstract
This year marks the 100th anniversary of one of the deadliest pandemic outbreaks, commonly referred as the Spanish Flu, that was caused by influenza A virus (IAV). Since then, IAV has been in governmental agendas worldwide, and a lot of effort has been put into understanding the pathogen's lifecycle, predict and mitigate the emergence of the strains that provoke yearly epidemics and pandemic events. Despite decades of research and seminal contributions there is still a lot to be investigated. In particular for this review, IAV lifecycle that takes place inside the host cell is not fully understood. Two steps that need clarification include genome transport to budding sites and genome assembly, the latter a complex process challenged by the nature of IAV genome that is divided into eight distinct parts. Assembly of such segmented genome is crucial to form fully infectious viral particles but is also critical for the emergence of viruses with pandemic potential that arise when avian and human IAV strains co-infect a host. The host GTPase Rab11 was separately implicated in both steps, and, interestingly these processes are beginning to emerge as being intimately related. Rab11 was initially proposed to be involved in the budding/release of IAV virions. It was subsequently shown to transport progeny genome, and later proposed to promote assembly of viral genome, but the underlying bridging mechanism the two is far from clear. For simplicity, this Rab11-centric review provides an initial separate account of Rab11 involvement in genome transport and in assembly. IAV genome assembly is a complicated molecular biology process, and therefore earned a dedicated section on how/if the viral genome forms a genomic supramolecular complex. Both topics present intricate challenges, outstanding questions, and unique controversies. At the end of the review, I will explore possible mechanisms intertwining IAV vRNP transport and genome assembly. Importantly, Rab11 has recently emerged as a key factor subverted by evolutionary unrelated viral families (Paramyxo, Bunya, and Orthomyxoviruses, among many others) and bacteria (Salmonella and Shigella) relevant to human health. This review provides a framework to identify common biological principles among the lifecycles of these pathogens.
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Affiliation(s)
- Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
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5
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Synthesis and biological evaluation of a library of hybrid derivatives as inhibitors of influenza virus PA-PB1 interaction. Eur J Med Chem 2018; 157:743-758. [PMID: 30142611 DOI: 10.1016/j.ejmech.2018.08.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/03/2018] [Accepted: 08/11/2018] [Indexed: 11/21/2022]
Abstract
The limited treatment options against influenza virus along with the growing public health concerns regarding the continuous emergence of drug-resistant viruses make essential the development of new anti-flu agents with novel mechanisms of action. One of the most attractive targets is the interaction between two subunits of the RNA-dependent RNA polymerase, PA and PB1. Herein we report the rational design of hybrid compounds starting from a 3-cyano-4,6-diphenylpyridine scaffold recently identified as disruptor of PA-PB1 interactions. Guided by the previously reported SAR data, a library of amino acid derivatives was synthesized. The biological evaluation led to the identification of new PA-PB1 inhibitors, that do not show appreciable toxicity. Molecular modeling shed further lights on the inhibition mechanism of these compounds.
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6
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Haller O, Arnheiter H, Pavlovic J, Staeheli P. The Discovery of the Antiviral Resistance Gene Mx: A Story of Great Ideas, Great Failures, and Some Success. Annu Rev Virol 2018; 5:33-51. [PMID: 29958082 DOI: 10.1146/annurev-virology-092917-043525] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of the Mx gene-dependent, innate resistance of mice against influenza virus was a matter of pure chance. Although the subsequent analysis of this antiviral resistance was guided by straightforward logic, it nevertheless led us into many blind alleys and was full of surprising turns and twists. Unexpectedly, this research resulted in the identification of one of the first interferon-stimulated genes and provided a new view of interferon action. It also showed that in many species, MX proteins have activities against a broad range of viruses. To this day, Mx research continues to flourish and to provide insights into the never-ending battle between viruses and their hosts.
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Affiliation(s)
- Otto Haller
- Institute of Virology, Medical Center University of Freiburg, D-79104 Freiburg, Germany; .,Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Heinz Arnheiter
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jovan Pavlovic
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Peter Staeheli
- Institute of Virology, Medical Center University of Freiburg, D-79104 Freiburg, Germany; .,Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
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7
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Cheng K, Yu Z, Chai H, Sun W, Xin Y, Zhang Q, Huang J, Zhang K, Li X, Yang S, Wang T, Zheng X, Wang H, Qin C, Qian J, Chen H, Hua Y, Gao Y, Xia X. PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. Virology 2014; 468-470:207-213. [PMID: 25194918 DOI: 10.1016/j.virol.2014.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/09/2014] [Accepted: 08/13/2014] [Indexed: 01/08/2023]
Abstract
H6N1 avian influenza viruses (AIVs) may pose a potential human risk as suggested by the first documented naturally-acquired human H6N1 virus infection in 2013. Here, we set out to elucidate viral determinants critical to the pathogenesis of this virus using a mouse model. We found that the recombinant H6N1 viruses possessing both the PA-T97I and PB2-E627K substitutions displayed the greatest enhancement of replication in vitro and in vivo. Polymerase complexes possessing either PB2-E627K, PA-T97I, and PB2-E627K/PA-T97I displayed higher virus polymerase activity when compared to the wild-type virus, which may account for the increased replication kinetics and enhanced virulence of variant viruses. Our results demonstrate that PB2-E627K and PA-T97I enhance the ability of H6N1 virus to replicate and cause disease in mammals. Influenza surveillance efforts should include scrutiny of these regions of PB2 and PA because of their impact on the increased virulence of H6N1 AIVs in mice.
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Affiliation(s)
- Kaihui Cheng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China; Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan 250132, People׳s Republic of China
| | - Zhijun Yu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China; Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, People׳s Republic of China
| | - Hongliang Chai
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, People׳s Republic of China
| | - Weiyang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Yue Xin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Qianyi Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People׳s Republic of China
| | - Jing Huang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Kun Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Xue Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Xuexing Zheng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Hualei Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, People׳s Republic of China
| | - Jun Qian
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People׳s Republic of China
| | - Yuping Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, People׳s Republic of China.
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China.
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, PLA 666 Liuyingxi Street, Changchun 130122, People׳s Republic of China; Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, People׳s Republic of China.
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8
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An efficient screening system for influenza virus cap-dependent endonuclease inhibitors. J Virol Methods 2014; 202:8-14. [DOI: 10.1016/j.jviromet.2014.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/28/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
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9
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Lepri S, Nannetti G, Muratore G, Cruciani G, Ruzziconi R, Mercorelli B, Palù G, Loregian A, Goracci L. Optimization of Small-Molecule Inhibitors of Influenza Virus Polymerase: From Thiophene-3-Carboxamide to Polyamido Scaffolds. J Med Chem 2014; 57:4337-50. [DOI: 10.1021/jm500300r] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Susan Lepri
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Giulio Nannetti
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Giulia Muratore
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Renzo Ruzziconi
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Giorgio Palù
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Arianna Loregian
- Department
of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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10
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Maruyama J, Okamatsu M, Soda K, Sakoda Y, Kida H. Factors responsible for pathogenicity in chickens of a low-pathogenic H7N7 avian influenza virus isolated from a feral duck. Arch Virol 2013; 158:2473-8. [PMID: 23779115 DOI: 10.1007/s00705-013-1762-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/04/2013] [Indexed: 11/24/2022]
Abstract
Highly pathogenic avian influenza viruses have poly-basic amino acid sequences at the cleavage site in their hemagglutinin (HA). Although this poly-basic region is a prerequisite factor for pathogenicity in chickens, not much is known about additional factors responsible for the acquisition of pathogenicity of the duck influenza virus in chickens. Here, we introduced multiple basic amino acid residues into the HA cleavage site of the A/duck/Hokkaido/Vac-2/2004 (H7N7) strain of avian influenza virus, which has low pathogenicity in chickens; the resultant Vac2sub-P0 strain was not intravenously pathogenic in chickens. In contrast, the Vac2sub-P3 strain, which was recovered from three consecutive passages of Vac2sub-P0 in chicks, was intravenously pathogenic in chickens. Six amino acid substitutions were identified by comparison of the Vac2sub-P3 and Vac2sub-P0 genomic sequences: Lys123Glu in PB2, Asn16Asp in PB1, Glu227Gly and Ile388Thr in HA, Gly228Arg in M1, and Leu46Pro in M2. The results of intravenous inoculations of chickens with recombinant virus indicated that all six amino acid substitutions were required to varying degrees for Vac2sub-P3 pathogenicity, with Glu227Gly and Ile388Thr in HA being particularly essential. These results reveal the roles of additional viral factors in the acquisition of pathogenicity in addition to the previously characterized role of the poly-basic amino acid sequences at the HA cleavage site.
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Affiliation(s)
- Junki Maruyama
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
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11
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CHD6, a cellular repressor of influenza virus replication, is degraded in human alveolar epithelial cells and mice lungs during infection. J Virol 2013; 87:4534-44. [PMID: 23408615 DOI: 10.1128/jvi.00554-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The influenza virus polymerase associates to an important number of transcription-related proteins, including the largest subunit of the RNA polymerase II complex (RNAP II). Despite this association, degradation of the RNAP II takes place in the infected cells once viral transcription is completed. We have previously shown that the chromatin remodeler CHD6 protein interacts with the influenza virus polymerase complex, represses viral replication, and relocalizes to inactive chromatin during influenza virus infection. In this paper, we report that CHD6 acts as a negative modulator of the influenza virus polymerase activity and is also subjected to degradation through a process that includes the following characteristics: (i) the cellular proteasome is not implicated, (ii) the sole expression of the three viral polymerase subunits from its cloned cDNAs is sufficient to induce proteolysis, and (iii) degradation is also observed in vivo in lungs of infected mice and correlates with the increase of viral titers in the lungs. Collectively, the data indicate that CHD6 degradation is a general effect exerted by influenza A viruses and suggest that this viral repressor may play an important inhibitory role since degradation and accumulation into inactive chromatin occur during the infection.
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12
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Sarkar M, Chanda S, Chakrabarti S, Mazumdar J, Ganguly A, Chadha MS, Mishra AC, Chawla-Sarkar M. Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. Virol J 2012; 9:3. [PMID: 22217077 PMCID: PMC3284387 DOI: 10.1186/1743-422x-9-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/05/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Influenza A virus encodes for eleven proteins, of which HA, NA, NS1 and PB1-F2 have been implicated in viral pathogenicity and virulence. Thus, in addition to the HA and NA gene segments, monitoring diversity of NS1 and PB1-F2 is also important. METHODS 55 out of 166 circulating influenza A strains (31 H1N1 and 24 H3N2) were randomly picked during 2007-2009 and NS and PB1-F2 genes were sequenced. Phylogenetic analysis was carried out with reference to the prototype strains, concurrent vaccine strains and other reference strains isolated world wide. RESULTS Comparative analysis of both nucleotide and deduced amino acid sequences, revealed presence of NS gene with A/PR/8/34(H1N1)-like mutations (H4N, Q21R, A22V, K44R, N53D, C59R, V60A, F103S and M106I) in both RNA-binding and effector domain of NS1 protein, and G63E, the HPAI-H5N1-like mutation in NEP/NS2 of five A/H1N1 strains of 2007 and 2009. NS1 of other A/H1N1 strains clustered with concurrent A/H1N1 vaccine strains. Of 31 A/H1N1 strains, five had PB1-F2 similar to the H3N2 strains; six had non-functional PB1-F2 protein (11 amino acids) similar to the 2009 pandemic H1N1 strains and rest 20 strains had 57 amino acids PB1-F2 protein, similar to concurrent A/H1N1 vaccine strain. Interestingly, three A/H1N1 strains with H3N2-like PB1-F2 protein carried primitive PR8-like NS gene. Full gene sequencing of PB1 gene confirmed presence of H3N2-like PB1 gene in these A/H1N1 strains. CONCLUSION Overall the study highlights reassortment event involving gene segments other than HA and NA in the co-circulating A/H1N1 and A/H3N2 strains and their importance in complexity of influenza virus genetics. In contrast, NS and PB1-F2 genes of all A/H3N2 eastern India strains were highly conserved and homologous to the concurrent A/H3N2 vaccine strains suggesting that these gene segments of H3N2 viruses are evolutionarily more stable compared to H1N1 viruses.
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Affiliation(s)
- Mehuli Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, CIT, Road, Scheme XM, Beliaghata, Kolkata 700 010, West Bengal, India
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13
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Jeon YH, Lee JY, Kim S. Chemical modulators working at pharmacological interface of target proteins. Bioorg Med Chem 2011; 20:1893-901. [PMID: 22227462 DOI: 10.1016/j.bmc.2011.12.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/30/2011] [Accepted: 12/08/2011] [Indexed: 01/23/2023]
Abstract
For last few decades, the active site cleft and substrate-binding site of enzymes as well as ligand-binding site of the receptors have served as the main pharmacological space for drug discovery. However, rapid accumulation of proteome and protein network analysis data has opened a new therapeutic space that is the interface between the interacting proteins. Due to the complexity of the interaction modes and the numbers of the participating components, it is still challenging to identify the chemicals that can accurately control the protein-protein interactions at desire. Nonetheless, the number of chemical drugs and candidates working at the interface of the interacting proteins are rapidly increasing. This review addresses the current case studies and state-of-the-arts in the development of small chemical modulators controlling the interactions of the proteins that have pathological implications in various human diseases such as cancer, immune disorders, neurodegenerative and infectious diseases.
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Affiliation(s)
- Young Ho Jeon
- Korea University College of Pharmacy Sejong-ro, Jochiwon, Yeonggi-gun, Chungnam 339-700, Republic of Korea
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14
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Alfonso R, Lutz T, Rodriguez A, Chavez JP, Rodriguez P, Gutierrez S, Nieto A. CHD6 chromatin remodeler is a negative modulator of influenza virus replication that relocates to inactive chromatin upon infection. Cell Microbiol 2011; 13:1894-906. [PMID: 21899694 DOI: 10.1111/j.1462-5822.2011.01679.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The influenza virus establishes close functional and structural connections with the nucleus of the infected cell. Thus, viral ribonucleoproteins (RNPs) are closely bound to chromatin components and the main constituent of viral RNPs, the nucleoprotein (NP) protein, interacts with histone tails. Using a yeast two-hybrid screening, we previously found that the PA influenza virus polymerase subunit interacts with the CHD6 protein, a member of the CHD family of chromatin remodelers. Here we show that CHD6 also interacts with the viral polymerase complex and colocalizes with viral RNPs in the infected cells. To study the relationships between RNPs, chromatin and CHD6, we have analysed whether NP and CHD6 binds to peptides representing trimethylated lysines of histone 3 tails that mark transcriptionally active or inactive chromatin. Upon infection, NP binds to marks of repressed chromatin and, interestingly an important recruitment of CHD6 to these heterochromatin marks occurs in this situation. Silencing experiments indicate that CHD6 acts as a negative modulator of influenza virus replication. Hence, the CHD6 association with inactive chromatin could be part of a process where the influenza virus triggers modifications of chromatin-associated proteins that could contribute to the pathogenic events used by the virus to induce host cell shut-off.
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Affiliation(s)
- Roberto Alfonso
- Centro Nacional de Biotecnología. Darwin 3, Cantoblanco, 28049 Madrid, Spain
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15
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The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 2008; 454:1127-31. [PMID: 18660801 DOI: 10.1038/nature07225] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Accepted: 07/02/2008] [Indexed: 12/23/2022]
Abstract
Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. The virus reproduces rapidly, mutates frequently and occasionally crosses species barriers. The recent emergence in Asia of avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. Here we demonstrate the importance to viral replication of a subunit interface in the viral RNA polymerase, thereby providing a new set of potential drug binding sites entirely independent of surface antigen type. No current medication targets this heterotrimeric polymerase complex. All three subunits, PB1, PB2 and PA, are required for both transcription and replication. PB1 carries the polymerase active site, PB2 includes the capped-RNA recognition domain, and PA is involved in assembly of the functional complex, but so far very little structural information has been reported for any of them. We describe the crystal structure of a large fragment of one subunit (PA) of influenza A RNA polymerase bound to a fragment of another subunit (PB1). The carboxy-terminal domain of PA forms a novel fold, and forms a deep, highly hydrophobic groove into which the amino-terminal residues of PB1 can fit by forming a 3(10) helix.
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16
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Rodriguez A, Pérez-González A, Nieto A. Influenza virus infection causes specific degradation of the largest subunit of cellular RNA polymerase II. J Virol 2007; 81:5315-24. [PMID: 17344288 PMCID: PMC1900203 DOI: 10.1128/jvi.02129-06] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been described that influenza virus polymerase associates with RNA polymerase II (RNAP II). To gain information about the role of this interaction, we explored if changes in RNAP II occur during infection. Here we show that influenza virus causes the specific degradation of the hypophosphorylated form of the largest subunit of RNAP II without affecting the accumulation of its hyperphosphorylated forms. This effect is independent of the viral strain and the origin of the cells used. Analysis of synthesized mRNAs in isolated nuclei of infected cells indicated that transcription decreases concomitantly with RNAP II degradation. Moreover, this degradation correlated with the onset of viral transcription and replication. The ubiquitin-mediated proteasome pathway is not involved in virally induced RNAP II proteolysis. The expression of viral polymerase from its cloned cDNAs was sufficient to cause the degradation. Since the PA polymerase subunit has proteolytic activity, we tested its participation in the process. A recombinant virus that encodes a PA point mutant with decreased proteolytic activity and that has defects in replication delayed the effect, suggesting that PA's contribution to RNAP II degradation occurs during infection.
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Affiliation(s)
- A Rodriguez
- Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049 Madrid, Spain
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17
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Pérez-González A, Rodriguez A, Huarte M, Salanueva IJ, Nieto A. hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator. J Mol Biol 2006; 362:887-900. [PMID: 16950395 DOI: 10.1016/j.jmb.2006.07.085] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 07/28/2006] [Accepted: 07/31/2006] [Indexed: 11/16/2022]
Abstract
The human protein hCLE was previously identified by its interaction with the PA subunit of influenza virus polymerase. It exhibits a sequence similarity of 38% with the yeast Spt16 component of the FACT complex, which is involved in transcriptional regulation. Therefore, we studied the possible relationship of hCLE with the transcription machinery. Here we show that hCLE and different phosphorylated forms of the RNA polymerase II (RNAP II) largest subunit, co-immunoprecipitate and colocalize by confocal microscopy analysis. Furthermore, hCLE was found in nuclear sites of active mRNA synthesis, as demonstrated by its colocalization with spots of in situ Br-UTP incorporation. Silencing of hCLE expression by RNA interference inhibited the synthesis of RNAP II transcripts around 50%. Accordingly, the expression profiling in hCLE-silenced cells studied by microarray analysis showed that, among the genes that exhibited a differential expression under hCLE silencing, more than 90% were down-regulated. Collectively these results indicate that hCLE works as a positive modulator of the RNA polymerase II activity.
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18
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Chen GW, Yang CC, Tsao KC, Huang CG, Lee LA, Yang WZ, Huang YL, Lin TY, Shih SR. Influenza A virus PB1-F2 gene in recent Taiwanese isolates. Emerg Infect Dis 2004; 10:630-6. [PMID: 15200852 PMCID: PMC3323094 DOI: 10.3201/eid1004.030412] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Influenza A virus contains eight RNA segments and encodes 10 viral proteins. However, an 11th protein, called PB1-F2, was found in A/Puerto Rico/8/34 (H1N1). This novel protein is translated from an alternative open reading frame (ORF) in the PB1 gene. We analyzed the PB1 gene of 42 recent influenza A isolates in Taiwan, including 24 H1N1 and 18 H3N2 strains. One H1N1 isolate and 17 H3N2 isolates contained the entire PB1-F2 ORF of 90 residues, three amino acids (aa) longer than the PB1-F2 of A/Puerto Rico/8/34 at the C terminal. The one remaining H3N2 isolate encoded a truncated PB1-F2 with 79 residues. The other 23 H1N1 isolates contained a truncated PB1-F2 of 57 aa. Phylogenetic analysis of both the HA and the PB1 genes showed that they shared similar clustering of these Taiwanese isolates, suggesting that no obvious reassortment occurred between the two genomic segments.
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Affiliation(s)
| | | | - Kuo-Chien Tsao
- Chang Gung University, Tao-Yuan, Taiwan
- Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Chung-Guei Huang
- Chang Gung University, Tao-Yuan, Taiwan
- Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Li-Ang Lee
- Chang Gung University, Tao-Yuan, Taiwan
- Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Wen-Zhi Yang
- Center for Disease Control and Prevention, Taipei, Taiwan
| | - Ya-Ling Huang
- Chang Gung University, Tao-Yuan, Taiwan
- Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | | | - Shin-Ru Shih
- Chang Gung University, Tao-Yuan, Taiwan
- Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
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19
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Abstract
Uncoating of influenza occurs in endosomes where the acid environment is instrumental in membrane fusion and the dissociation of the ribonucleoprotein (RNP) from matrix protein by the action of the hemagglutinin and M2 protein ion channels, respectively. Earlier studies have shown that low pH treatment results in the release of M1 protein from RNP. To obtain RNP free of M1 protein, we attempted to isolate RNP by velocity sedimentation on pH 5 glycerol gradients; however, the RNP sedimented as pellets under centrifugation conditions that had previously resolved RNP on neutral gradients. The increase in sedimentation rate occurred between pH 5.6 and 6.0 and was reversible for a portion of the RNP on raising the pH to neutrality. RNP isolated from infected cells or virions sedimented on acidification and was seen to form clumps visible by electron microscopy. If acidification preceded NP40 detergent lysis, virion RNP appeared to be released as genomic complexes. The pH threshold for viral membrane fusion was 5.8 indicating that the same pH condition also resulted in aggregation of RNP. Because exposure of virions to pH 5 occurs during uncoating in endosomes and is essential for infectivity, it is possible that low pH-induced RNP aggregation may facilitate aspects of viral uncoating such as dissociation of RNP from M1 or transport of genomes to the nucleus.
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Affiliation(s)
- Olga P Zoueva
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H 8M5.
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20
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Honda A, Endo A, Mizumoto K, Ishihama A. Differential roles of viral RNA and cRNA in functional modulation of the influenza virus RNA polymerase. J Biol Chem 2001; 276:31179-85. [PMID: 11373286 DOI: 10.1074/jbc.m102856200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-dependent RNA polymerase of influenza virus is composed of three viral P proteins (PB1, PB2, and PA) and involved in both transcription and replication of the RNA genome. For the molecular anatomy of this multifunctional enzyme, we have established a simultaneous expression of three P proteins in cultured insect cells using recombinant baculoviruses. For purification of P protein complexes, the PA protein was expressed as a fusion with a histidine tag added at its N terminus. By using affinity chromatography, a complex consisting of the three P proteins was isolated from nuclear extracts of virus-infected cells. The affinity-purified 3P complex showed the activities of capped RNA binding, capped RNA cleavage, viral model RNA binding, model RNA-directed RNA synthesis, and polyadenylation of newly synthesized RNA. We conclude that a functional form of the viral RNA polymerase with the catalytic specificity of transcriptase is formed in recombinant baculovirus-infected insect cells. Using the viral RNA-free 3P complex, we found that the capped RNA cleavage takes place in the presence of vRNA but not of cRNA, indicating that the vRNA functions as a regulatory factor for the specificity control of viral RNA polymerase as well as a template for transcription. The structural elements of RNA directing the expression of RNA polymerase functions were analyzed using variant forms of the model RNA templates.
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Affiliation(s)
- A Honda
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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21
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Jambrina E, Bárcena J, Uez O, Portela A. The three subunits of the polymerase and the nucleoprotein of influenza B virus are the minimum set of viral proteins required for expression of a model RNA template. Virology 1997; 235:209-17. [PMID: 9281500 DOI: 10.1006/viro.1997.8682] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The genes encoding the nucleoprotein, PB1, PB2, and PA proteins of the influenza virus strain B/Panamá/45/90 have been cloned under control of the T7 RNA polymerase promoter of plasmid pGEM-3. Transfection of the recombinant plasmids obtained into mammalian cells, which had been infected with a vaccinia virus encoding the T7 RNA polymerase, resulted in expression of the expected influenza B virus polypeptides. Moreover, it is shown that coexpression of the four recombinant core proteins in COS-1 cells reconstituted a functional polymerase capable of expressing a synthetic influenza B virus-like CAT RNA. By using the influenza B virus recombinant plasmids and a set of pGEM-derived plasmids encoding the homologous core proteins of the influenza A virus A/Victoria/3/75 (I. Mena et al. (1994). J. Gen. Virol. 75, 2109-2114), the capabilities of homo- and heterotypic mixtures of the four core proteins to express synthetic type A and B CAT RNAs were analyzed. Both the influenza A and B virus polymerases were active in expressing, albeit with reduced efficiencies, the heterotypic model CAT RNAs. However, none of all possible heterotypic mixtures of the core proteins reconstituted a functional polymerase. In order to fully characterize the recombinant plasmids obtained, the nucleotide sequences of the cloned genes were determined and compared to sequences of other type B virus isolates. The results obtained from these latter analyses are discussed in terms of the conservation and evolution of the influenza B virus core genes.
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Affiliation(s)
- E Jambrina
- Instituto de Salud Carlos III, Centro Nacional de Biología Fundamental, Majadahonda 28220, Madrid, Spain
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22
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Bárcena J, Ochoa M, de la Luna S, Melero JA, Nieto A, Ortín J, Portela A. Monoclonal antibodies against influenza virus PB2 and NP polypeptides interfere with the initiation step of viral mRNA synthesis in vitro. J Virol 1994; 68:6900-9. [PMID: 7933070 PMCID: PMC237125 DOI: 10.1128/jvi.68.11.6900-6909.1994] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two panels of monoclonal antibodies (MAbs) specific for the influenza A virus PA and PB2 polypeptides have been obtained from mice immunized with denatured proteins produced in Escherichia coli. All MAbs (13 specific for the PA polypeptide and 8 specific for the PB2 protein) reacted to the corresponding influenza virus protein in Western blotting (immunoblotting), immunoprecipitation, and immunofluorescence assays. To gain information about the roles of the nucleoprotein (NP) and PB2 and PA proteins during viral mRNA synthesis, the 21 anti-P antibodies and 3 anti-NP antibodies (J. A. López, M. Guillen, A. Sánchez-Fauquier, and J. A. Melero, J. Virol. Methods 13:255-264, 1986) were purified and tested for their ability to inhibit the transcriptase activity associated with viral cores purified from virions. Four of the antibodies (one anti-PB2 and the three anti-NP MAbs) inhibited transcription by more than 50% compared with unrelated control antibodies. The inhibitory effect was not due to a nonspecific effect of the antibody preparations, because these MAbs did not inhibit transcription when tested on influenza B virus nucleocapsids, which are not recognized by the antibodies. To determine whether the antibodies were acting on an early transcription step, transcription reactions were carried out in the presence of globin mRNA (a mixture of alpha- and beta-globin chains) and only one labeled nucleoside triphosphate (either GTP or CTP). The results obtained showed that MAbs to the PB2 and NP polypeptides interfered with the initiation step of mRNA-primed transcription. The implications of these results regarding initiation of viral mRNA synthesis are discussed.
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Affiliation(s)
- J Bárcena
- Centro Nacional de Microbiología Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Madrid, Spain
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23
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Qiu D, Tannock GA, Barry RD, Jackson DC. Western blot analysis of antibody responses to influenza virion proteins. Immunol Cell Biol 1992; 70 ( Pt 3):181-91. [PMID: 1452221 DOI: 10.1038/icb.1992.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An immunoblotting procedure was developed to detect antibody responses in mice and humans to influenza virion proteins. The technique was capable of detecting 1.5 micrograms of haemagglutinin (HA) on nitrocellulose strips at a 1:5000 dilution of a mouse serum with an initial haemagglutination inhibition titre of 20. The effects of the use of the blocking agent Tween-20 on virion proteins were also studied. The commonly used concentration of 0.05% (v/v) Tween-20, when included in blocking and incubation buffers, greatly reduced the amount of detectable matrix protein but caused no detectable loss of HA and neuraminidase/nucleoprotein proteins. If virion proteins were separated by polyacrylamide gel electrophoresis under reducing conditions, antibody bound to HA2 more strongly than to HA1. Under non-reducing conditions, more antibody bound to the uncleaved HA protein than to other proteins. IgG1 and IgG2a antibody responses in mice to each protein were stronger than IgG2b and IgG3 responses.
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Affiliation(s)
- D Qiu
- Faculty of Medicine, University of Newcastle, Callaghan, New South Wales, Australia
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24
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Nieto A, de la Luna S, Bárcena J, Portela A, Valcárcel J, Melero JA, Ortín J. Nuclear transport of influenza virus polymerase PA protein. Virus Res 1992; 24:65-75. [PMID: 1320800 DOI: 10.1016/0168-1702(92)90031-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The subcellular distribution of influenza polymerase PA subunit has been studied using a SV40-recombinant virus (SVPA76), which allows the expression and accumulation of this protein in COS-1 cells. In contrast to the complete nuclear localization observed for the PA subunit several hours after influenza virus infection, when COS-1 cells were infected with the SVPA76 recombinant, the PA protein accumulated either in the nucleus, in the cytoplasm or was distributed throughout the cell. When cells were infected with the SVPA76 recombinant and superinfected with influenza virus, a clear increase in the proportion of cells showing nuclear localization of the PA protein was observed, suggesting that some trans-factor may be required to allow complete nuclear accumulation of the protein. Double infections using SVPA76 recombinant and either SVPB1 or SVNS recombinant viruses showed a complete correlation between expression of polymerase PB1 subunit or NS1 protein and nuclear localization of polymerase PA subunit. However, no such correlation was observed in the double infections of SVPA76 and SVNP recombinants. These results suggest that polymerase PB1 subunit and the non-structural proteins could be involved in the nuclear targeting or nuclear retention of influenza polymerase PA protein.
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Affiliation(s)
- A Nieto
- Centro Nacional de Biotecnología (CSIC), Universidad Autónoma, Madrid, Spain
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25
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Kobayashi M, Tuchiya K, Nagata K, Ishihama A. Reconstitution of influenza virus RNA polymerase from three subunits expressed using recombinant baculovirus system. Virus Res 1992; 22:235-45. [PMID: 1626419 DOI: 10.1016/0168-1702(92)90055-e] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Influenza virus RNA polymerase catalyzes multiple step reactions in transcription and replication of the genome RNA. The core enzyme is composed of each one of the three P proteins, PB1, PB2 and PA (Honda et al. (1990) J. Biochem. 107, 624-628). For detailed analysis of the role of each P protein and of the functional domains on each P polypeptide, we expressed individual P proteins in cultured insect cells after infection with recombinant baculoviruses. PB1 and PB2 accumulated in cell nuclei whereas PA stayed in cytoplasm. Both the PB1 and PB2 proteins were purified from aggregates in the respective nuclear extract, and the PA was partially purified from the cytoplasm. RNA polymerase was reconstituted by mixing the three P proteins in a urea solution and then dialyzing against a reconstitution buffer. The reconstituted enzyme was able to transcribe model RNA templates. Minus-sense RNA was a better template than plus-sense RNA.
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Affiliation(s)
- M Kobayashi
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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26
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López-Turiso JA, Martínez C, Tanaka T, Ortín J. The synthesis of influenza virus negative-strand RNA takes place in insoluble complexes present in the nuclear matrix fraction. Virus Res 1990; 16:325-37. [PMID: 2392881 DOI: 10.1016/0168-1702(90)90056-h] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The replication of influenza virus RNA in vitro has been studied by cell fractionation of MDCK-infected cells and characterization of in vitro synthesized RNA. Analysis of the RNA product polarity by liquid hybridization to excess single-stranded DNA probes shows that only the RNP complexes present in the nuclear matrix fraction are able to synthesize negative-polarity RNA. This RNA product has been characterized as authentic vRNA by size analysis, RNase-protection by unlabelled, positive-polarity riboprobes and T1-fingerprinting. Priming the in vitro reaction with ApG stimulates preferentially the synthesis of positive-polarity RNA, while ApGpU stimulates both positive and negative-polarity RNA synthesis.
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Affiliation(s)
- J A López-Turiso
- Centro de Biologia Molecular (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
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27
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Yamashita M, Krystal M, Palese P. Comparison of the three large polymerase proteins of influenza A, B, and C viruses. Virology 1989; 171:458-66. [PMID: 2763462 DOI: 10.1016/0042-6822(89)90615-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The three large RNA segments of influenza C virus C/JJ/50 were cloned and sequenced, and the deduced amino acid sequences were compared with those of the polymerase (P) proteins of influenza A and B viruses. The coding strategy of the C virus RNA segments is the same as that for the large A and B virus segments as one long open reading frame is present in each segment. RNA segment 1 of influenza C virus encodes the equivalent of the PB2 protein; it has an approximate 25% sequence identity with the corresponding (cap binding) influenza A and B virus PB2 proteins. The PB1 protein of influenza C virus, coded for by segment 2, has an approximate 40% sequence identity with the corresponding proteins of influenza A and B viruses including the Asp-Asp sequence motif found in many RNA polymerase molecules. The PB1 polymerase is thus the most highly conserved protein among the influenza A, B, and C viruses. Although the protein coded for by RNA 3 of influenza C virus shows an approximate 25% sequence identity with the acid polymerase (PA) proteins of the A and B viruses, its sequence does not display any acid charge features at neutral pH. This protein is thus referred to as the P3 (rather than the PA) protein of influenza C virus.
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Affiliation(s)
- M Yamashita
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029
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28
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de la Luna S, Martínez C, Ortín J. Molecular cloning and sequencing of influenza virus A/Victoria/3/75 polymerase genes: sequence evolution and prediction of possible functional domains. Virus Res 1989; 13:143-55. [PMID: 2773594 DOI: 10.1016/0168-1702(89)90012-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The influenza virus A/Victoria/3/75 (H3N2) polymerase genes encoding PB1, PB2 and PA have been cloned by cDNA synthesis and insertion into bacterial vectors. The complete sequence for each polymerase gene has been obtained from random M13 subclones and compared to other influenza virus polymerase genes. A total of 45, 74 and 78 nucleotide changes were fixed in the period 1968-1975, corresponding to 10, 12 and 9 amino acid changes, for PB1, PB2 and PA genes, respectively. The amino acid sequence of PB1 polypeptide contains motifs found in a series of positive- and negative-RNA virus polymerase genes and that of PA polypeptide share invariant residues common to DNA and presumptive RNA helicases.
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Affiliation(s)
- S de la Luna
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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29
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Szewczyk B, Laver WG, Summers DF. Purification, thioredoxin renaturation, and reconstituted activity of the three subunits of the influenza A virus RNA polymerase. Proc Natl Acad Sci U S A 1988; 85:7907-11. [PMID: 3054875 PMCID: PMC282313 DOI: 10.1073/pnas.85.21.7907] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The virion-associated RNA polymerase and the structural nucleoprotein of influenza A virus were separated by sodium dodecyl sulfate/PAGE, electroblotted to a polyvinylidine membrane, and eluted with good recovery from the membrane. After renaturation by incubating with Escherichia coli thioredoxin, these proteins were active in a reconstituted in vitro transcription reaction with purified genomic RNAs. All four proteins (i.e., the three subunits of the RNA polymerase as well as the structural nucleoprotein) were required for activity. The RNA products were plus-strand, mRNA-sized species.
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Affiliation(s)
- B Szewczyk
- Department of Cellular, Viral, and Molecular Biology, University of Utah School of Medicine, Salt Lake City 84132
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30
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Donabedian AM, DeBorde DC, Maassab HF. Genetics of cold-adapted B/Ann Arbor/1/66 influenza virus reassortants: the acidic polymerase (PA) protein gene confers temperature sensitivity and attenuated virulence. Microb Pathog 1987; 3:97-108. [PMID: 3504545 DOI: 10.1016/0882-4010(87)90068-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cold-adapted B/Ann Arbor/1/66 influenza virus (ca B/AA/1/66) expresses temperature-sensitive (ts), cold-adapted (ca) and attenuation phenotypes. Reassortants which inherit one or more genes from ca B/AA/1/66 and all other genes from a virulent, wild-type influenza virus, B/Houston/1732/76, were produced and evaluated in order to identify the gene(s) responsible for the ts, ca and attenuation phenotypes. Only reassortants which inherited the PA gene from ca B/AA/1/66 expressed the ts phenotype in MDCK cells at 39 degrees C. None of the reassortants tested expressed the ca phenotype in embryonated eggs at 25 degrees C. The virulence of several reassortants was evaluated in ferrets. Inheritance of the PA gene from ca B/AA/1/66 was correlated with significant febrile attenuation and the apparent restriction of viral replication in the lower respiratory tract. Isolation of a virulent, non-ts revertant virus inheriting only the PA gene from ca B/AA/1/66 established a direct relationship between expression of the ts phenotype and attenuated virulence. Evidence for the contribution of at least one other gene from ca B/AA/1/66 to attenuation was observed. Thus, based on the methods used to determine reassortant gene compositions, these results indicate that the PA gene is primarily responsible for attenuation of ca B/AA/1/66 and its reassortants.
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Affiliation(s)
- A M Donabedian
- Department of Epidemiology, University of Michigan, Ann Arbor 48109
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31
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Meyer T, Horisberger MA. Combined action of mouse alpha and beta interferons in influenza virus-infected macrophages carrying the resistance gene Mx. J Virol 1984; 49:709-16. [PMID: 6321758 PMCID: PMC255528 DOI: 10.1128/jvi.49.3.709-716.1984] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In mice, the combined action of alpha and beta interferons (IFNs) against influenza viruses is modulated by the host gene Mx. High concentrations of IFN fail to prevent efficiently the replication of influenza A virus in cultured macrophages lacking the gene Mx, whereas cultured macrophages carrying Mx develop strong antiviral activity even at low concentrations of IFN. Several steps in the replication cycle of influenza virus were compared in Mx/Mx and +/+ mouse macrophages treated with IFN-alpha + beta. Uncoating was not affected. A twofold reduction in the accumulation of primary transcripts was observed in IFN-treated macrophages at the highest concentration of IFN regardless of the genetic constitution of the host cell. No evidence was obtained for inhibition of influenza virus translation in macrophages which lacked Mx when treated with IFN-alpha + beta. In contrast, a marked shut-off of influenza virus polypeptide synthesis occurred in Mx-bearing macrophages treated with these IFNs, although the primary transcripts were active in directing the synthesis of viral polypeptides in a cell-free system. We concluded that a specific inhibitory mechanism for influenza virus translation was induced by IFN-alpha + beta in macrophages bearing the resistance gene Mx.
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32
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Romanos MA, Hay AJ. Identification of the influenza virus transcriptase by affinity-labeling with pyridoxal 5'-phosphate. Virology 1984; 132:110-7. [PMID: 6198801 DOI: 10.1016/0042-6822(84)90095-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pyridoxal 5'-phosphate (PLP), a reversible inhibitor of in vitro transcription by fowl plaque virus, has been used to identify the transcriptase. Kinetic analyses showed that PLP competitively inhibits the addition of each nucleoside triphosphate in ApG-primed reactions, suggesting that both initiation and elongation are affected. The irreversible inhibition by PLP following reduction with borohydride was prevented by preincubation with the first substrate: GTP in unprimed reactions or CTP in the presence of ApG. On reaction of FPV proteins with PLP and [3H]borohydride the core protein PB1 was preferentially labeled and the labeling was selectively blocked by GTP or ApG + CTP. These data suggest that PB1 has the nucleotide-binding site of the transcriptase, is responsible for both initiation and elongation, and is apparently associated with the 3' ends of template RNAs in virions.
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33
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Braam J, Ulmanen I, Krug RM. Molecular model of a eucaryotic transcription complex: functions and movements of influenza P proteins during capped RNA-primed transcription. Cell 1983; 34:609-18. [PMID: 6616622 DOI: 10.1016/0092-8674(83)90393-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present a model for the functions and movements of the influenza virus P proteins (PB1, PB2, and PA) as they transcribe the virion RNAs (vRNAs) into messenger RNAs (mRNAs). Using ultraviolet-light-induced crosslinking, we show that the P proteins as a complex move from the 3' ends of the vRNA templates down the elongating mRNAs. PB2 binds the cap 1 structure of heterologous RNAs, which are cleaved to generate capped primer fragments. PB1, initially found at the first residue added onto the primer, moves to the 3' ends of the growing mRNA chains, indicating that it most likely catalyzes each nucleotide addition. PA and PB2 move down the growing chains in concert with PB1. PB2 is also associated with the cap during the first 11-15 nucleotides of chain growth, but then dissociates from the cap as the P protein complex moves further down the mRNA chains.
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34
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35
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Jones KL, Huddleston JA, Brownlee GG. The sequence of RNA segment 1 of influenza virus A/NT/60/68 and its comparison with the corresponding segment of strains A/PR/8/34 and A/WSN/33. Nucleic Acids Res 1983; 11:1555-66. [PMID: 6828387 PMCID: PMC325815 DOI: 10.1093/nar/11.5.1555] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The complete nucleotide sequence of RNA segment 1 of influenza virus A/NT/60/68, corresponding to the PB2 protein, has been determined. It is 2341 nucleotides long, encoding a predicted product of 759 amino acids with a net charge of +27 1/2 at neutral pH. The predicted amino acid sequence has been compared to the equivalent sequences in influenza viruses A/PR/8/34 and A/WSN/33. Evolutionary divergence, assuming a direct lineage from A/PR/8/34 and allowing for "laboratory drift", is 0.08% per year. The alignment of RNA segment 10 of A/NT/60/68 with segments 1 and 3 is completed, confirming that it is a mosaic of regions from these two segments.
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36
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Strauss EG, Strauss JH. Replication strategies of the single stranded RNA viruses of eukaryotes. Curr Top Microbiol Immunol 1983; 105:1-98. [PMID: 6354610 DOI: 10.1007/978-3-642-69159-1_1] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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37
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Ulmanen I, Broni B, Krug RM. Influenza virus temperature-sensitive cap (m7GpppNm)-dependent endonuclease. J Virol 1983; 45:27-35. [PMID: 6823015 PMCID: PMC256383 DOI: 10.1128/jvi.45.1.27-35.1983] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The first step in influenza viral mRNA synthesis is the endonucleolytic cleavage of heterologous RNAs containing cap 1 (m(7)GpppNm) structures to generate capped primers that are 10 to 13 nucleotides long, which are then elongated to form the viral mRNA chains. We examined the temperature sensitivity of these steps in vitro by using two WSN virus temperature-sensitive mutants, ts1 and ts6, which have a defect in the genome RNA segment coding for the viral PB2 protein. For these experiments, it was necessary to employ purified viral cores rather than detergent-treated virions to catalyze transcription, as preparations of detergent-treated virions contain destabilizing or inhibitory activities which render even the transcription catalyzed by wild-type virus temperature sensitive. Using purified wild-type viral cores, we found that the rates of endonucleolytic cleavage of capped primers and of overall transcription were similar at 39.5 and 33 degrees C, the in vivo nonpermissive and permissive temperatures, respectively. In contrast, the activities of the cap-dependent endonucleases of ts1 and ts6 viral cores at 39.5 degrees C were only about 15% of those at 33 degrees C. The steps in transcription after endonucleolytic cleavage of the capped RNA primer were largely, if not totally, temperature insensitive, indicating that the mutations in the PB2 protein found in ts1 and ts6 virions affect only the endonuclease step. The temperature-sensitive defect is most likely in the recognition of the 5'-terminal cap 1 structure that occurs as a required first step in the endonuclease reaction: the cap-dependent binding of a specific capped primer fragment to ts1 viral cores was temperature sensitive under conditions in which binding to wild-type viral cores was not affected by increasing the temperature from 33 to 39.5 degrees C. Thus, our results establish that the viral PB2 protein functions in cap recognition during the endonuclease reaction.
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38
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Anderson NG. High-resolution protein separation and identification methods applicable to virology. Curr Top Microbiol Immunol 1983; 104:197-217. [PMID: 6347533 DOI: 10.1007/978-3-642-68949-9_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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39
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Sivasubramanian N, Nayak DP. Sequence analysis of the polymerase 1 gene and the secondary structure prediction of polymerase 1 protein of human influenza virus A/WSN/33. J Virol 1982; 44:321-9. [PMID: 7143569 PMCID: PMC256267 DOI: 10.1128/jvi.44.1.321-329.1982] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The nucleotide sequence of polymerase 1 (P1) gene of a human influenza virus (A/WSN/33) has been determined by using cDNA clones, except for the last 83 nucleotides, which were obtained by primer extension. The WSN P1 gene contains 2,341 nucleotides and codes for a protein of 757 amino acids (Mr = 86,500). P1 gene possesses a striking tandem repeat of 12 nucleotides (nucleotide position 2,188 to 2,199, 2,200 to 2,211) and a corresponding tandem repeat of tetrapeptide in the P1 protein. The deduced sequence of P1 protein is enriched in basic amino acids, particularly arginine. In addition, it also contains clusters of basic amino acids which may provide sites for the interaction with the template virion RNA capped primer as well as with other proteins involved in viral replication and transcription. A secondary structure prediction, using Chou and Fasman analyses (Annu. Rev. Biochem. 47:251-276, 1978), shows that the P1 protein possesses some unique features, viz., one "four-helical supersecondary structure" and four "polypeptide double helices" (antiparallel beta-pleated sheets) which are considered important in RNA binding.
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40
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Blaas D, Patzelt E, Kuechler E. Identification of the cap binding protein of influenza virus. Nucleic Acids Res 1982; 10:4803-12. [PMID: 7133998 PMCID: PMC321130 DOI: 10.1093/nar/10.15.4803] [Citation(s) in RCA: 108] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The presence of a cap binding protein in influenza virus PR8 has recently been demonstrated by photoaffinity labelling with the cap-analogue (gamma [3 2P]-[4-(benzoylphenyl)methylamido]-7-methylguanosine 5'-triphosphate). This paper describes the identification of the labelled protein using two-dimensional gel electrophoresis. The protein is shown to be PB2, the smaller of the two basic P proteins in the polymerase complex.
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41
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Horisberger MA. Identification of a catalytic activity of the large basic P polypeptide of influenza virus. Virology 1982; 120:279-86. [PMID: 7101728 DOI: 10.1016/0042-6822(82)90030-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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42
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Bishop DH, Jones KL, Huddleston JA, Brownlee GG. Influenza A virus evolution: complete sequences of influenza A/NT/60/68 RNA segment 3 and its predicted acidic P polypeptide compared with those of influenza A/PR/8/34. Virology 1982; 120:481-9. [PMID: 7101732 DOI: 10.1016/0042-6822(82)90049-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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43
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Kaptein JS, Nayak DP. Complete nucleotide sequence of the polymerase 3 gene of human influenza virus A/WSN/33. J Virol 1982; 42:55-63. [PMID: 7045393 PMCID: PMC256044 DOI: 10.1128/jvi.42.1.55-63.1982] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The complete nucleotide sequence of polymerase 3 (P3) gene of a human influenza virus (A/WSN/33) has been determined using cDNA clones except for the last 11 nucleotides which were obtained by direct RNA sequencing. The WSN P3 gene contains 2,341 nucleotides and codes for a protein of 759 amino acids (molecular weight 85,800). The WSN P3 protein, as deduced from the plus-strand DNA sequence, is basic and enriched in positively charged amino acids. In addition, it contains clusters of basic amino acids which may provide sites for the interaction of P3 protein with the capped primer, template, and/or other polymerase proteins during the transcriptive and replicative processes of influenza viral RNA.
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44
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Abstract
The nucleotide sequence of RNA segment 2 of human influenza strain A/PR/8/34 has been determined. Segment 2 in 2341 nucleotides long and encodes a protein of 757 amino acids (86,500 daltons molecular weight) which is involved in RNA synthesis. Although segment 2 is identical in size to segment 1, which encodes a protein of related function, neither the nucleotide sequences of these two RNA segments nor the amino acid sequences of the encoded proteins appear to be homologous. The sequence of segment 2 completes the sequence of the virus (total 13,588 nucleotides).
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45
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Bishop DH, Huddleston JA, Brownlee GG. The complete sequence of RNA segment 2 of influenza A/NT/60/68 P1 protein. Nucleic Acids Res 1982; 10:1335-43. [PMID: 7041090 PMCID: PMC320529 DOI: 10.1093/nar/10.4.1335] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A DNA copy of influenza A/NT/60/68 viral RNA segment 2, corresponding to protein P1, has been cloned in the E.coli plasmid pBr322. The clone is 2341 nucleotides long and represents a full-length copy of the viral RNA. In the viral complementary (plus sense) strand there is an open reading frame that is 2271 nucleotides long. The predicted primary gene product is a basic 86,300 dalton protein with a net charge at neutral pH of +23. A 29 amino acid stretch of the protein (coded by nucleotide residues 583-669) is highly basic and contains 7 lysine and 8 arginine residues. Other smaller clusters of basic amino acids are also present in the protein.
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46
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Fields S, Winter G. Nucleotide sequences of influenza virus segments 1 and 3 reveal mosaic structure of a small viral RNA segment. Cell 1982; 28:303-13. [PMID: 7060132 DOI: 10.1016/0092-8674(82)90348-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Defective interfering RNAs of influenza virus are small segments derived from viral segments 1, 2 and 3. We present here the complete nucleotide sequences of segments 1 and 3 from the human influenza strain A/PR/8/34 and deduce that the sequence of a small RNA segment from A/NT/60/68, apparently a defective interfering RNA, is derived from five separate regions in segment 3 and from one region in segment 1. These regions, which are located near the terminal of the two parental segments, are arranged in the small RNA segment in an alternating fashion: thus a region derived from near 5' terminus is adjacent to a region derived from near a 3' terminus. We propose that the small segment is generated during positive strand synthesis as a result of the viral polymerase pausing at uridine-rich sequences in the template and reinitiating synthesis at another site.
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47
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Ulmanen I, Broni BA, Krug RM. Role of two of the influenza virus core P proteins in recognizing cap 1 structures (m7GpppNm) on RNAs and in initiating viral RNA transcription. Proc Natl Acad Sci U S A 1981; 78:7355-9. [PMID: 6950380 PMCID: PMC349265 DOI: 10.1073/pnas.78.12.7355] [Citation(s) in RCA: 178] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Purified influenza viral cores catalyze the entire process of viral RNA transcription, which includes the endonucleolytic cleavage of heterologous RNAs containing cap 1 (m(7)GpppNm) structures to generate capped primers 10-13 nucleotides long, the initiation of transcription via the incorporation of a guanosine residue onto the primers, and elongation of the viral mRNAs [Plotch, S. J., Bouloy, M., Ulmanen, L & Krug, R. M. (1980) Cell 23, 847-858]. To identify which viral core protein (nucleocapsid protein, P1, P2, or P3) recognizes the cap 1 structure on the RNA primer, we irradiated (UV) endonuclease reactions carried out by viral cores in the absence of ribonucleoside triphosphates, with a primer RNA labeled in its cap 1 structure with (32)P. The labeled cap was crosslinked to a protein that had a mobility similar to that of the P3 protein, the smaller of the two basic P proteins, in both one- and two-dimensional gel electrophoresis. This strongly suggests that this crosslinked protein is the viral P3 protein. Competition experiments with unlabeled RNAs containing or lacking a cap 1 structure established that this protein recognizes the cap 1 structure on RNAs. This protein remained associated with the cap throughout the transcription reaction, even after the viral mRNA molecules were elongated. To identify the viral core protein that catalyzes the initiation of transcription via the incorporation of a guanosine residue onto primer fragments, we irradiated transcription reactions carried out by viral cores in the presence of [alpha-(32)P]GTP as the only ribonucleoside triphosphate with an unlabeled primer RNA. A labeled guanosine residue was crosslinked to a protein that had a mobility similar to that of the P1 protein, the larger of the two basic P proteins, in both one-and two-dimensional gel electrophoresis. The transcription reaction conditions required to bring this protein in close association with a labeled guanosine residue so that crosslinking could occur indicated that this association most likely occurred coincident with the guanosine residue's being incorporated onto the primer. These results suggest that the viral P1 protein catalyzes this incorporation and hence initiates transcription.
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48
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Horisberger MA, Staritzky C. Two-dimensional gel analysis of the influenza B proteins of the transcriptase complex. FEMS Microbiol Lett 1981. [DOI: 10.1111/j.1574-6968.1981.tb07619.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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