1
|
Handa T, Saha A, Narayanan A, Ronzier E, Kumar P, Singla J, Tomar S. Structural Virology: The Key Determinants in Development of Antiviral Therapeutics. Viruses 2025; 17:417. [PMID: 40143346 PMCID: PMC11945554 DOI: 10.3390/v17030417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 03/28/2025] Open
Abstract
Structural virology has emerged as the foundation for the development of effective antiviral therapeutics. It is pivotal in providing crucial insights into the three-dimensional frame of viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment of viral components, including capsids, envelope proteins, replication machinery, and host interaction interfaces, is instrumental in unraveling the multiplex mechanisms of viral infection, replication, and pathogenesis. The structural elucidation of viral enzymes, including proteases, polymerases, and integrases, has been essential in combating viruses like HIV-1 and HIV-2, SARS-CoV-2, and influenza. Techniques including X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, and Cryo-electron Tomography have revolutionized the field of virology and significantly aided in the discovery of antiviral therapeutics. The ubiquity of chronic viral infections, along with the emergence and reemergence of new viral threats necessitate the development of novel antiviral strategies and agents, while the extensive structural diversity of viruses and their high mutation rates further underscore the critical need for structural analysis of viral proteins to aid antiviral development. This review highlights the significance of structure-based investigations for bridging the gap between structure and function, thus facilitating the development of effective antiviral therapeutics, vaccines, and antibodies for tackling emerging viral threats.
Collapse
Affiliation(s)
- Tanuj Handa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Ankita Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Aarthi Narayanan
- Department of Biology, College of Science, George Mason University, Fairfax, VA 22030, USA;
| | - Elsa Ronzier
- Biomedical Research Laboratory, Institute for Biohealth Innovation, George Mason University, Fairfax, VA 22030, USA;
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| |
Collapse
|
2
|
Loutan AJ, Yang B, Connolly G, Montoya A, Smiley RJ, Chatterjee AK, Götte M. Bunyaviral Cap-Snatching Endonuclease Activity and Inhibition with Baloxavir-like Inhibitors in the Context of Full-Length L Proteins. Viruses 2025; 17:420. [PMID: 40143347 PMCID: PMC11946187 DOI: 10.3390/v17030420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Revised: 03/07/2025] [Accepted: 03/09/2025] [Indexed: 03/28/2025] Open
Abstract
The Bunyavirales order includes a range of zoonotic viruses, which can cause severe disease in humans. The viral replication machinery is a logical target for the development of direct-acting antivirals. Inhibition of the cap-snatching endonuclease activity of related influenza viruses provides a proof of concept. Using the influenza B virus (IBV) RNA-dependent RNA polymerase complex as a benchmark, we conducted a comparative analysis of endonuclease activities of recombinant full-length bunyaviral L proteins using gel-based assays. The IBV complex demonstrates specific endonucleolytic cleavage and a clear preference for capped substrates. In contrast, severe fever with thrombocytopenia syndrome, Sin Nombre, and Hantaan virus L proteins readily cleave capped and uncapped RNAs to a broader spectrum of RNA fragments. Active site mutants further help to control for the potential of contaminating nucleases, exonuclease activity, and RNA hydrolysis. The influenza cap-snatching inhibitor baloxavir and derivatives have been used to validate this approach. In conclusion, the results of this study demonstrate the importance of assays with single nucleotide resolution and the use of full-length L proteins as a valuable experimental tool to identify selective endonuclease inhibitors.
Collapse
Affiliation(s)
- Arlo J. Loutan
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada (R.J.S.)
| | - Baiuyan Yang
- Calibr-Skaggs Institute for Innovation Medicines at Scripps Research, La Jolla, CA 92037, USA; (B.Y.)
| | - Gabrielle Connolly
- Calibr-Skaggs Institute for Innovation Medicines at Scripps Research, La Jolla, CA 92037, USA; (B.Y.)
| | - Adam Montoya
- Calibr-Skaggs Institute for Innovation Medicines at Scripps Research, La Jolla, CA 92037, USA; (B.Y.)
| | - Robert J. Smiley
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada (R.J.S.)
| | - Arnab K. Chatterjee
- Calibr-Skaggs Institute for Innovation Medicines at Scripps Research, La Jolla, CA 92037, USA; (B.Y.)
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada (R.J.S.)
| |
Collapse
|
3
|
Li M, Wu Y, Li H, Song W, Chen Z, Peng Y, Yang B, Xu C, Zhang J, Xing L, Weng Z, Liu Y, Liang H. Mutagenesis studies suggest a mechanism for influenza polymerase stalling during polyadenylation. Nucleic Acids Res 2025; 53:gkae1225. [PMID: 39676676 PMCID: PMC11797019 DOI: 10.1093/nar/gkae1225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 11/20/2024] [Accepted: 11/27/2024] [Indexed: 12/17/2024] Open
Abstract
Influenza polymerase (FluPol) carries out both viral transcription and replication using the same viral genome segment as a template to yield distinct end products. However, it remains largely unclear how FluPol synthesizes transcripts containing poly (A) tails during transcription termination, while producing fully complementary products during replication termination. In this study, through structural analysis combined with cell-based and biochemical assays, we identified that the PB1 Leu675/Asn676 and PB2 Arg38 residues of FluPol are critical for transcription termination and polyadenylation. During transcription termination, these three residues adopt the PB1 Leu675/Asn676down and PB2 Arg38out conformations, with their side chains positioned against the G12 and G14 residues of the RNA template at the 5' end. These steric hindrances block template translocation and facilitate FluPol 'stuttering' at U17, which is required for viral messenger RNA polyadenylation. Importantly, both structural analysis and mutational studies suggest that this specific conformation of these residues is unique to the transcription termination state. Overall, our findings provide novel insights into the mechanisms by which FluPol generates distinct 3' end products during transcription and replication termination.
Collapse
Affiliation(s)
- Minke Li
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Yixi Wu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Huanhuan Li
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Wenjun Song
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - Zhenxing Chen
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Yuzhou Peng
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Boyao Yang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Chang Xu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Jihua Zhang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Lei Xing
- School of Life Science, YunNan University, East Outer Ring Road, Chenggong District, KunMing, 650500, Yunnan, China
| | - Zhuangfeng Weng
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Yingfang Liu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| | - Huanhuan Liang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China
| |
Collapse
|
4
|
Arragain B, Krischuns T, Pelosse M, Drncova P, Blackledge M, Naffakh N, Cusack S. Structures of influenza A and B replication complexes give insight into avian to human host adaptation and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase. Nat Commun 2024; 15:6910. [PMID: 39160148 PMCID: PMC11333492 DOI: 10.1038/s41467-024-51007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024] Open
Abstract
Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal low complexity acidic region (LCAR). Here we present evidence suggesting that ANP32 is recruited to the replication complex as an electrostatic chaperone that stabilises the encapsidase moiety within apo-polymerase symmetric dimers that are distinct for influenza A and B polymerases. The ANP32 bound encapsidase, then forms the asymmetric replication complex with the replicase, which is embedded in a parental ribonucleoprotein particle (RNP). Cryo-EM structures reveal the architecture of the influenza A and B replication complexes and the likely trajectory of the nascent RNA product into the encapsidase. The cryo-EM map of the FluB replication complex shows extra density attributable to the ANP32 LCAR wrapping around and stabilising the apo-encapsidase conformation. These structures give new insight into the various mutations that adapt avian strain polymerases to use the distinct ANP32 in mammalian cells.
Collapse
Affiliation(s)
- Benoît Arragain
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology of Influenza Virus, Paris, France
- Heidelberg University, Department of Infectious Diseases, Virology, Schaller Research Group, Heidelberg, Germany
| | - Martin Pelosse
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Petra Drncova
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble-Alpes-CEA-CNRS UMR5075, Grenoble, France
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology of Influenza Virus, Paris, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France.
| |
Collapse
|
5
|
Xie J, Ouizougun-Oubari M, Wang L, Zhai G, Wu D, Lin Z, Wang M, Ludeke B, Yan X, Nilsson T, Gao L, Huang X, Fearns R, Chen S. Structural basis for dimerization of a paramyxovirus polymerase complex. Nat Commun 2024; 15:3163. [PMID: 38605025 PMCID: PMC11009304 DOI: 10.1038/s41467-024-47470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a cofactor protein, such as phosphoprotein (P). Previous studies have shown that the nsNSV polymerase can adopt a dimeric form, however, the structure of the dimer and its function are poorly understood. Here we determine a 2.7 Å cryo-EM structure of human parainfluenza virus type 3 (hPIV3) L-P complex with the connector domain (CD') of a second L built, while reconstruction of the rest of the second L-P obtains a low-resolution map of the ring-like L core region. This study reveals detailed atomic features of nsNSV polymerase active site and distinct conformation of hPIV3 L with a unique β-strand latch. Furthermore, we report the structural basis of L-L dimerization, with CD' located at the putative template entry of the adjoining L. Disruption of the L-L interface causes a defect in RNA replication that can be overcome by complementation, demonstrating that L dimerization is necessary for hPIV3 genome replication. These findings provide further insight into how nsNSV polymerases perform their functions, and suggest a new avenue for rational drug design.
Collapse
Affiliation(s)
- Jin Xie
- Roche Pharma Research and Early Development, Lead Discovery, Roche Innovation Center Shanghai, 201203, Shanghai, China
| | - Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Li Wang
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Shanghai, 201203, Shanghai, China
| | - Guanglei Zhai
- Roche Pharma Research and Early Development, Lead Discovery, Roche Innovation Center Shanghai, 201203, Shanghai, China
| | - Daitze Wu
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Shanghai, 201203, Shanghai, China
| | - Zhaohu Lin
- Roche Pharma Research and Early Development, Lead Discovery, Roche Innovation Center Shanghai, 201203, Shanghai, China
| | - Manfu Wang
- Wuxi Biortus Biosciences Co. Ltd., 214437, Jiangyin, Jiangsu, China
| | - Barbara Ludeke
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Xiaodong Yan
- Wuxi Biortus Biosciences Co. Ltd., 214437, Jiangyin, Jiangsu, China
| | - Tobias Nilsson
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, Basel, 4070, Switzerland
| | - Lu Gao
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Shanghai, 201203, Shanghai, China.
| | - Xinyi Huang
- Roche Pharma Research and Early Development, Lead Discovery, Roche Innovation Center Shanghai, 201203, Shanghai, China.
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
| | - Shuai Chen
- Roche Pharma Research and Early Development, Lead Discovery, Roche Innovation Center Shanghai, 201203, Shanghai, China.
| |
Collapse
|
6
|
Krischuns T, Arragain B, Isel C, Paisant S, Budt M, Wolff T, Cusack S, Naffakh N. The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome. Nat Commun 2024; 15:1064. [PMID: 38316757 PMCID: PMC10844641 DOI: 10.1038/s41467-024-45205-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation and activity towards transcription or replication of the viral genome, respectively. Here, we provide evidence that the FluPol-RNAP II binding interface, beyond its well-acknowledged function in cap-snatching during transcription initiation, has also a pivotal role in replication of the viral genome. Using a combination of cell-based and in vitro approaches, we show that the RNAP II C-terminal-domain, jointly with ANP32, enhances FluPol replication activity. We observe successive conformational changes to switch from a transcriptase to a replicase conformation in the presence of the bound RNPAII C-terminal domain and propose a model in which the host RNAP II is the anchor for transcription and replication of the viral genome. Our data open new perspectives on the spatial coupling of viral transcription and replication and the coordinated balance between these two activities.
Collapse
Affiliation(s)
- Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, RNA Biology of Influenza Virus, Paris, France.
| | | | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, RNA Biology of Influenza Virus, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, RNA Biology of Influenza Virus, Paris, France
| | - Matthias Budt
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Berlin, Germany
| | - Thorsten Wolff
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Berlin, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France.
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, RNA Biology of Influenza Virus, Paris, France.
| |
Collapse
|
7
|
Ghorbani A, Ngunjiri JM, Rendon G, Brooke CB, Kenney SP, Lee CW. Diversity and Complexity of Internally Deleted Viral Genomes in Influenza A Virus Subpopulations with Enhanced Interferon-Inducing Phenotypes. Viruses 2023; 15:2107. [PMID: 37896883 PMCID: PMC10612045 DOI: 10.3390/v15102107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Influenza A virus (IAV) populations harbor large subpopulations of defective-interfering particles characterized by internally deleted viral genomes. These internally deleted genomes have demonstrated the ability to suppress infectivity and boost innate immunity, rendering them promising for therapeutic and immunogenic applications. In this study, we aimed to investigate the diversity and complexity of the internally deleted IAV genomes within a panel of plaque-purified avian influenza viruses selected for their enhanced interferon-inducing phenotypes. Our findings unveiled that the abundance and diversity of internally deleted viral genomes were contingent upon the viral subculture and plaque purification processes. We observed a heightened occurrence of internally deleted genomes with distinct junctions in viral clones exhibiting enhanced interferon-inducing phenotypes, accompanied by additional truncation in the nonstructural 1 protein linker region (NS1Δ76-86). Computational analyses suggest the internally deleted IAV genomes can encode a broad range of carboxy-terminally truncated and intrinsically disordered proteins with variable lengths and amino acid composition. Further research is imperative to unravel the underlying mechanisms driving the increased diversity of internal deletions within the genomes of viral clones exhibiting enhanced interferon-inducing capacities and to explore their potential for modulating cellular processes and immunity.
Collapse
Affiliation(s)
- Amir Ghorbani
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - John M. Ngunjiri
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA (C.B.B.)
| | - Christopher B. Brooke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA (C.B.B.)
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Scott P. Kenney
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Chang-Won Lee
- Southeast Poultry Research Laboratory, US National Poultry Research Center, USDA, ARS, Athens, GA 30605, USA
| |
Collapse
|
8
|
Sheppard CM, Goldhill DH, Swann OC, Staller E, Penn R, Platt OK, Sukhova K, Baillon L, Frise R, Peacock TP, Fodor E, Barclay WS. An Influenza A virus can evolve to use human ANP32E through altering polymerase dimerization. Nat Commun 2023; 14:6135. [PMID: 37816726 PMCID: PMC10564888 DOI: 10.1038/s41467-023-41308-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/09/2023] [Indexed: 10/12/2023] Open
Abstract
Human ANP32A and ANP32B are essential but redundant host factors for influenza virus genome replication. While most influenza viruses cannot replicate in edited human cells lacking both ANP32A and ANP32B, some strains exhibit limited growth. Here, we experimentally evolve such an influenza A virus in these edited cells and unexpectedly, after 2 passages, we observe robust viral growth. We find two mutations in different subunits of the influenza polymerase that enable the mutant virus to use a novel host factor, ANP32E, an alternative family member, which is unable to support the wild type polymerase. Both mutations reside in the symmetric dimer interface between two polymerase complexes and reduce polymerase dimerization. These mutations have previously been identified as adapting influenza viruses to mice. Indeed, the evolved virus gains the ability to use suboptimal mouse ANP32 proteins and becomes more virulent in mice. We identify further mutations in the symmetric dimer interface which we predict allow influenza to adapt to use suboptimal ANP32 proteins through a similar mechanism. Overall, our results suggest a balance between asymmetric and symmetric dimers of influenza virus polymerase that is influenced by the interaction between polymerase and ANP32 host proteins.
Collapse
Affiliation(s)
- Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Olivia C Swann
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca Penn
- Department of Infectious Disease, Imperial College London, London, UK
| | - Olivia K Platt
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
| |
Collapse
|
9
|
Idoko-Akoh A, Goldhill DH, Sheppard CM, Bialy D, Quantrill JL, Sukhova K, Brown JC, Richardson S, Campbell C, Taylor L, Sherman A, Nazki S, Long JS, Skinner MA, Shelton H, Sang HM, Barclay WS, McGrew MJ. Creating resistance to avian influenza infection through genome editing of the ANP32 gene family. Nat Commun 2023; 14:6136. [PMID: 37816720 PMCID: PMC10564915 DOI: 10.1038/s41467-023-41476-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/05/2023] [Indexed: 10/12/2023] Open
Abstract
Chickens genetically resistant to avian influenza could prevent future outbreaks. In chickens, influenza A virus (IAV) relies on host protein ANP32A. Here we use CRISPR/Cas9 to generate homozygous gene edited (GE) chickens containing two ANP32A amino acid substitutions that prevent viral polymerase interaction. After IAV challenge, 9/10 edited chickens remain uninfected. Challenge with a higher dose, however, led to breakthrough infections. Breakthrough IAV virus contained IAV polymerase gene mutations that conferred adaptation to the edited chicken ANP32A. Unexpectedly, this virus also replicated in chicken embryos edited to remove the entire ANP32A gene and instead co-opted alternative ANP32 protein family members, chicken ANP32B and ANP32E. Additional genome editing for removal of ANP32B and ANP32E eliminated all viral growth in chicken cells. Our data illustrate a first proof of concept step to generate IAV-resistant chickens and show that multiple genetic modifications will be required to curtail viral escape.
Collapse
Affiliation(s)
- Alewo Idoko-Akoh
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Royal Veterinary College, London, UK
| | - Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Ciara Campbell
- Department of Infectious Disease, Imperial College London, London, UK
| | - Lorna Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | - Adrian Sherman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | | | - Jason S Long
- Department of Infectious Disease, Imperial College London, London, UK
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, UK
| | - Michael A Skinner
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Helen M Sang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Mike J McGrew
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
| |
Collapse
|
10
|
Gilbertson B, Duncan M, Subbarao K. Role of the viral polymerase during adaptation of influenza A viruses to new hosts. Curr Opin Virol 2023; 62:101363. [PMID: 37672875 DOI: 10.1016/j.coviro.2023.101363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 09/08/2023]
Abstract
As a group, influenza-A viruses (IAV) infect a wide range of animal hosts, however, they are constrained to infecting selected host species by species-specific interactions between the host and virus, that are required for efficient replication of the viral RNA genome. When IAV cross the species barrier, they acquire mutations in the viral genome to enable interactions with the new host factors, or to compensate for their loss. The viral polymerase genes polymerase basic 1, polymerase basic 2, and polymerase-acidic are important sites of host adaptation. In this review, we discuss why the viral polymerase is so vital to the process of host adaptation, look at some of the known viral mutations, and host factors involved in adaptation, particularly of avian IAV to mammalian hosts.
Collapse
Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Melanie Duncan
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
11
|
Li H, Wu Y, Li M, Guo L, Gao Y, Wang Q, Zhang J, Lai Z, Zhang X, Zhu L, Lan P, Rao Z, Liu Y, Liang H. An intermediate state allows influenza polymerase to switch smoothly between transcription and replication cycles. Nat Struct Mol Biol 2023; 30:1183-1192. [PMID: 37488357 DOI: 10.1038/s41594-023-01043-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Influenza polymerase (FluPol) transcribes viral mRNA at the beginning of the viral life cycle and initiates genome replication after viral protein synthesis. However, it remains poorly understood how FluPol switches between its transcription and replication states, especially given that the structural bases of these two functions are fundamentally different. Here we propose a mechanism by which FluPol achieves functional switching between these two states through a previously unstudied conformation, termed an 'intermediate state'. Using cryo-electron microscopy, we obtained a structure of the intermediate state of H5N1 FluPol at 3.7 Å, which is characterized by a blocked cap-binding domain and a contracted core region. Structural analysis results suggest that the intermediate state may allow FluPol to transition smoothly into either the transcription or replication state. Furthermore, we show that the formation of the intermediate state is required for both the transcription and replication activities of FluPol, leading us to conclude that the transcription and replication cycles of FluPol are regulated via this intermediate state.
Collapse
Affiliation(s)
- Huanhuan Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yixi Wu
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Minke Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Lu Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yaqi Gao
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Quan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jihua Zhang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Zhaohua Lai
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Xing Zhang
- Departments of Biophysics and Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
| | - Lixin Zhu
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Lan
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zihe Rao
- Laboratory of Structural Biology, Tsinghua University, Beijing, China
| | - Yingfang Liu
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
- Department of General Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Huanhuan Liang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
| |
Collapse
|
12
|
Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. In vivo secondary structural analysis of Influenza A virus genomic RNA. Cell Mol Life Sci 2023; 80:136. [PMID: 37131079 PMCID: PMC10153785 DOI: 10.1007/s00018-023-04764-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 05/04/2023]
Abstract
Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
Collapse
Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Dagny Lorent
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| |
Collapse
|
13
|
Liu L, Madhugiri R, Saul VV, Bacher S, Kracht M, Pleschka S, Schmitz ML. Phosphorylation of the PA subunit of influenza polymerase at Y393 prevents binding of the 5'-termini of RNA and polymerase function. Sci Rep 2023; 13:7042. [PMID: 37120635 PMCID: PMC10148841 DOI: 10.1038/s41598-023-34285-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
The influenza A virus (IAV) polymerase is a multifunctional machine that can adopt alternative configurations to perform transcription and replication of the viral RNA genome in a temporally ordered manner. Although the structure of polymerase is well understood, our knowledge of its regulation by phosphorylation is still incomplete. The heterotrimeric polymerase can be regulated by posttranslational modifications, but the endogenously occurring phosphorylations at the PA and PB2 subunits of the IAV polymerase have not been studied. Mutation of phosphosites in PB2 and PA subunits revealed that PA mutants resembling constitutive phosphorylation have a partial (S395) or complete (Y393) defect in the ability to synthesize mRNA and cRNA. As PA phosphorylation at Y393 prevents binding of the 5' promoter of the genomic RNA, recombinant viruses harboring such a mutation could not be rescued. These data show the functional relevance of PA phosphorylations to control the activity of viral polymerase during the influenza infectious cycle.
Collapse
Affiliation(s)
- Lu Liu
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Vera Vivian Saul
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Susanne Bacher
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany.
| |
Collapse
|
14
|
A structural understanding of influenza virus genome replication. Trends Microbiol 2023; 31:308-319. [PMID: 36336541 DOI: 10.1016/j.tim.2022.09.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Influenza virus contains a single-stranded negative-sense RNA genome. Replication of the genome is carried out by the viral RNA-dependent RNA polymerase in the context of the viral ribonucleoprotein (RNP) complex, through a positive-sense complementary RNA intermediate. Genome replication is tightly controlled through interactions with accessory viral and host factors. Propelled by developments in recombinant protein expression, and technical improvements in X-ray crystallography and cryo-electron microscopy, snapshots of the replication process have been captured. Here, we review how recent structural data shed light on the molecular mechanisms of influenza virus genome replication, in particular, encapsidation of nascent RNA, de novo RNP assembly, and regulation of replication initiation through interactions with host and viral cues.
Collapse
|
15
|
Potential Role of Superoxide Dismutase 3 (SOD3) in Resistance to Influenza A Virus Infection. Antioxidants (Basel) 2023; 12:antiox12020354. [PMID: 36829913 PMCID: PMC9952479 DOI: 10.3390/antiox12020354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Influenza A virus infection induces the production of excessive reactive oxygen species (ROS). Overproduction of ROS can overwhelm the antioxidant defense system, leading to increasing intensive oxidative stress. However, antioxidant defense against oxidative damage induced by influenza A virus infection, and in particular the significance of the SOD3 response in the pathogenesis of influenza virus infection, has not been well characterized. Here, we investigated the potential role of SOD3 in resistance to influenza A virus infection. In this study, SOD3, as an important antioxidant enzyme, was shown to be highly elevated in A549 cells following influenza A virus infection. Furthermore, inhibition of SOD3 impacted viral replication and virulence. We found that SOD3 disrupts IAV replication by impairing the synthesis of vRNA, whereas it did not affect viral ribonucleoprotein nuclear export. In addition, overexpression of SOD3 greatly reduced the levels of ROS caused by influenza A virus infection, regulated the inflammatory response to virus infection by inhibiting the phosphorylation of p65 of the NF-κB signaling pathway, and inhibited virus-induced apoptosis to a certain extent. Taken together, these findings indicate that SOD3 is actively involved in influenza A virus replication. Pharmacological modulation or targeting of SOD3 may pave the way for a novel therapeutic approach to combating influenza A virus infection.
Collapse
|
16
|
Morichaud Z, Trapani S, Vishwakarma RK, Chaloin L, Lionne C, Lai-Kee-Him J, Bron P, Brodolin K. Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Nat Commun 2023; 14:484. [PMID: 36717560 PMCID: PMC9886945 DOI: 10.1038/s41467-023-36113-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σB factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σB is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation.
Collapse
Affiliation(s)
- Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France
| | - Stefano Trapani
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Rishi K Vishwakarma
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France.,Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France
| | - Corinne Lionne
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Patrick Bron
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France. .,INSERM, Montpellier, France.
| |
Collapse
|
17
|
Krischuns T, Isel C, Drncova P, Lukarska M, Pflug A, Paisant S, Navratil V, Cusack S, Naffakh N. Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD. PLoS Pathog 2022; 18:e1010328. [PMID: 35605026 PMCID: PMC9242477 DOI: 10.1371/journal.ppat.1010328] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/29/2022] [Accepted: 04/09/2022] [Indexed: 01/05/2023] Open
Abstract
During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results suggest that the CTD-binding modes of IAV and IBV may represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery.
Collapse
Affiliation(s)
- Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Petra Drncova
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Maria Lukarska
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Alexander Pflug
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
- * E-mail: (SC); (NN)
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
- * E-mail: (SC); (NN)
| |
Collapse
|
18
|
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: 2.0] [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.
Collapse
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.
| |
Collapse
|
19
|
Dupré G, Hoede C, Figueroa T, Bessière P, Bertagnoli S, Ducatez M, Gaspin C, Volmer R. Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses. Virus Evol 2021; 7:veab093. [PMID: 35299790 PMCID: PMC8923263 DOI: 10.1093/ve/veab093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/07/2021] [Accepted: 10/29/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.
Collapse
Affiliation(s)
- Gabriel Dupré
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Claire Hoede
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Thomas Figueroa
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Pierre Bessière
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Stéphane Bertagnoli
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Mariette Ducatez
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Christine Gaspin
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Romain Volmer
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| |
Collapse
|
20
|
Staller E, Barclay WS. Host Cell Factors That Interact with Influenza Virus Ribonucleoproteins. Cold Spring Harb Perspect Med 2021; 11:a038307. [PMID: 32988980 PMCID: PMC8559542 DOI: 10.1101/cshperspect.a038307] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza viruses hijack host cell factors at each stage of the viral life cycle. After host cell entry and endosomal escape, the influenza viral ribonucleoproteins (vRNPs) are released into the cytoplasm where the classical cellular nuclear import pathway is usurped for nuclear translocation of the vRNPs. Transcription takes place inside the nucleus at active host transcription sites, and cellular mRNA export pathways are subverted for export of viral mRNAs. Newly synthesized RNP components cycle back into the nucleus using various cellular nuclear import pathways and host-encoded chaperones. Replication of the negative-sense viral RNA (vRNA) into complementary RNA (cRNA) and back into vRNA requires complex interplay between viral and host factors. Progeny vRNPs assemble at the host chromatin and subsequently exit from the nucleus-processes orchestrated by sets of host and viral proteins. Finally, several host pathways appear to play a role in vRNP trafficking from the nuclear envelope to the plasma membrane for egress.
Collapse
Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| |
Collapse
|
21
|
Staller E, Sheppard CM, Baillon L, Frise R, Peacock TP, Sancho-Shimizu V, Barclay WS. A natural variant in ANP32B impairs influenza virus replication in human cells. J Gen Virol 2021; 102:001664. [PMID: 34524075 PMCID: PMC8567425 DOI: 10.1099/jgv.0.001664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
Viruses require host factors to support their replication, and genetic variation in such factors can affect susceptibility to infectious disease. Influenza virus replication in human cells relies on ANP32 proteins, which are involved in assembly of replication-competent dimeric influenza virus polymerase (FluPol) complexes. Here, we investigate naturally occurring single nucleotide variants (SNV) in the human Anp32A and Anp32B genes. We note that variant rs182096718 in Anp32B is found at a higher frequency than other variants in either gene. This SNV results in a D130A substitution in ANP32B, which is less able to support FluPol activity than wild-type ANP32B and binds FluPol with lower affinity. Interestingly, ANP32B-D130A exerts a dominant negative effect over wild-type ANP32B and interferes with the functionally redundant paralogue ANP32A. FluPol activity and virus replication are attenuated in CRISPR-edited cells expressing wild-type ANP32A and mutant ANP32B-D130A. We propose a model in which the D130A mutation impairs FluPol dimer formation, thus resulting in compromised replication. We suggest that both homozygous and heterozygous carriers of rs182096718 may have some genetic protection against influenza viruses.
Collapse
Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Present address: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Carol M. Sheppard
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Laury Baillon
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Thomas P. Peacock
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | | | - Wendy S. Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| |
Collapse
|
22
|
Abstract
Influenza polymerase (FluPol) plays a key role in the viral infection cycle by transcribing and replicating the viral genome. FluPol is a multifunctional, heterotrimeric enzyme with cap-binding, endonuclease, RNA-dependent RNA polymerase and polyadenylation activities. It performs its functions in the context of the viral ribonucleoprotein particle (RNP), wherein the template viral RNA is coated by multiple copies of viral nucleoprotein. Moreover, it interacts with a number of host proteins that are essential cofactors and, consequently, adaptive mutations in the polymerase are required for crossing the avian-human species barrier. In this review, we show how mechanistic understanding of how FluPol performs its multiple functions has greatly advanced over the last decade through determination of high-resolution structures by X-ray crystallography and cryo-electron microscopy. These have revealed not only the detailed architecture of FluPol but highlighted the remarkably conformational flexibility that is inherent to its functioning as a dynamic RNA synthesis machine. Structural studies are also underpinning current attempts to develop next-generation anti-influenza drugs that directly target FluPol.
Collapse
Affiliation(s)
- Joanna M Wandzik
- European Molecular Biology Laboratory, Grenoble 38042-Cedex 9, France
| | - Tomas Kouba
- European Molecular Biology Laboratory, Grenoble 38042-Cedex 9, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble 38042-Cedex 9, France
| |
Collapse
|
23
|
Synergistic Effect between 3'-Terminal Noncoding and Adjacent Coding Regions of the Influenza A Virus Hemagglutinin Segment on Template Preference. J Virol 2021; 95:e0087821. [PMID: 34190596 DOI: 10.1128/jvi.00878-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influenza A virus genome is comprised of eight single-stranded negative-sense viral RNA (vRNA) segments. Each of the eight vRNA segments contains segment-specific nonconserved noncoding regions (NCRs) of similar sequence and length in different influenza A virus strains. However, in the subtype-determinant segments, encoding hemagglutinin (HA) and neuraminidase (NA), the segment-specific noncoding regions are subtype specific, varying significantly in sequence and length at both the 3' and 5' termini among different subtypes. The significance of these subtype-specific noncoding regions (ssNCR) in the influenza virus replication cycle is not fully understood. In this study, we show that truncations of the 3'-end H1-subtype-specific noncoding region (H1-ssNCR) resulted in recombinant viruses with decreased HA vRNA replication and attenuated growth phenotype, although the vRNA replication was not affected in single-template RNP reconstitution assays. The attenuated viruses were unstable, and point mutations at nucleotide position 76 or 56 in the adjacent coding region of HA vRNA were found after serial passage. The mutations restored the HA vRNA replication and reversed the attenuated virus growth phenotype. We propose that the terminal noncoding and adjacent coding regions act synergistically to ensure optimal levels of HA vRNA replication in a multisegment environment. These results provide novel insights into the role of the 3'-end nonconserved noncoding regions and adjacent coding regions on template preference in multiple-segmented negative-strand RNA viruses. IMPORTANCE While most influenza A virus vRNA segments contain segment-specific nonconserved noncoding regions of similar length and sequence, these regions vary considerably both in length and sequence in the segments encoding HA and NA, the two major antigenic determinants of influenza A viruses. In this study, we investigated the function of the 3'-end H1-ssNCR and observed a synergistic effect between the 3'-end H1-ssNCR nucleotides and adjacent coding nucleotide(s) of the HA segment on template preference in a multisegment environment. The results unravel an additional level of complexity in the regulation of RNA replication in multiple-segmented negative-strand RNA viruses.
Collapse
|
24
|
Jochheim FA, Tegunov D, Hillen HS, Schmitzová J, Kokic G, Dienemann C, Cramer P. The structure of a dimeric form of SARS-CoV-2 polymerase. Commun Biol 2021; 4:999. [PMID: 34429502 PMCID: PMC8385044 DOI: 10.1038/s42003-021-02529-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/28/2021] [Indexed: 01/18/2023] Open
Abstract
The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic subunit nsp12, two copies of subunit nsp8, and one copy of subunit nsp7. Here we report an alternative, dimeric form of the enzyme and resolve its structure at 5.5 Å resolution. In this structure, the two RdRps contain only one copy of nsp8 each and dimerize via their nsp7 subunits to adopt an antiparallel arrangement. We speculate that the RdRp dimer facilitates template switching during production of sub-genomic RNAs.
Collapse
Affiliation(s)
- Florian A Jochheim
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Dimitry Tegunov
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Hauke S Hillen
- Max Planck Institute for Biophysical Chemistry, Research Group Structure and Function of Molecular Machines, Göttingen, Germany
- University Medical Center Göttingen, Department of Cellular Biochemistry, Göttingen, Germany
| | - Jana Schmitzová
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Goran Kokic
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
| |
Collapse
|
25
|
Kang H, Cong J, Wang C, Ji W, Xin Y, Qian Y, Li X, Chen Y, Rao Z. Structural basis for recognition and regulation of arenavirus polymerase L by Z protein. Nat Commun 2021; 12:4134. [PMID: 34226547 PMCID: PMC8257661 DOI: 10.1038/s41467-021-24458-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and transcribes the genome of JUNV, and its regulator Z protein should provide critical clues to identify therapeutic targets for disrupting the life cycle of JUNV. Here we report the 3.54 Å cryo-EM structure of the JUNV L protein complexed with regulator Z protein. JUNV L structure reveals a conserved architecture containing signature motifs found in other L proteins. Structural analysis shows that L protein is regulated by binding of Z protein at the RNA product exit site. Based on these findings, we propose a model for the role of Z protein as a switch to turn on/off the viral RNA synthesis via its interaction with L protein. Our work unveils the mechanism of JUNV transcription, replication and regulation, which provides a framework for the rational design of antivirals for combating viral infections. Junin virus (JUNV) causes Argentine hemorrhagic fever and encodes the large protein (L) of the RNA dependent RNA polymerase (RdRp) and its regulator, the matrix zinc-binding protein (Z). Here, the authors present the 3.54 Å cryo-EM structure of the complex of JUNV L with Z, and they propose a model of how JUNV L is regulated by Z during the viral life cycle and RNA synthesis.
Collapse
Affiliation(s)
- Huiling Kang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China
| | - Jingyuan Cong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chenlong Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenxin Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuhui Xin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Qian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
26
|
Waters K, Wan HJ, Han L, Xue J, Ykema M, Tao YJ, Wan XF. Variations outside the conserved motifs of PB1 catalytic active site may affect replication efficiency of the RNP complex of influenza A virus. Virology 2021; 559:145-155. [PMID: 33887645 PMCID: PMC8579824 DOI: 10.1016/j.virol.2021.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/24/2022]
Abstract
PB1 functions as the catalytic subunit of influenza virus RNA polymerase complex and plays an essential role in viral RNA transcription and replication. To determine plasticity in the PB1 enzymatic site and map catalytically important residues, 658 mutants were constructed, each with one to seven mutations in the enzymatic site of PB1. The polymerase activities of these mutants were quantified using a minigenome assay, and polymerase activity-associated residues were identified using sparse learning. Results showed that polymerase activities are affected by the residues not only within the conserved motifs, but also across the inter-motif regions of PB1, and the latter are primarily located at the base of the palm domain, a region that is conserved in avian PB1 but with high sequence diversity in swine PB1. Our results suggest that mutations outside the PB1 conserved motifs may affect RNA replication and could be associated with influenza virus host adaptation.
Collapse
Affiliation(s)
- Kaitlyn Waters
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Hamilton J Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Jianli Xue
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Matthew Ykema
- Department of BioSciences, Rice University, Houston, TX, 77251, USA
| | - Yizhi J Tao
- Department of BioSciences, Rice University, Houston, TX, 77251, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39762, USA; Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
27
|
Te Velthuis AJW, Grimes JM, Fodor E. Structural insights into RNA polymerases of negative-sense RNA viruses. Nat Rev Microbiol 2021; 19:303-318. [PMID: 33495561 PMCID: PMC7832423 DOI: 10.1038/s41579-020-00501-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 01/29/2023]
Abstract
RNA viruses include many important human and animal pathogens, such as the influenza viruses, respiratory syncytial virus, Ebola virus, measles virus and rabies virus. The genomes of these viruses consist of single or multiple RNA segments that assemble with oligomeric viral nucleoprotein into ribonucleoprotein complexes. Replication and transcription of the viral genome is performed by ~250-450 kDa viral RNA-dependent RNA polymerases that also contain capping or cap-snatching activity. In this Review, we compare recent high-resolution X-ray and cryoelectron microscopy structures of RNA polymerases of negative-sense RNA viruses with segmented and non-segmented genomes, including orthomyxoviruses, peribunyaviruses, phenuiviruses, arenaviruses, rhabdoviruses, pneumoviruses and paramyxoviruses. In addition, we discuss how structural insights into these enzymes contribute to our understanding of the molecular mechanisms of viral transcription and replication, and how we can use these insights to identify targets for antiviral drug design.
Collapse
Affiliation(s)
- Aartjan J W Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
28
|
Weis S, te Velthuis AJW. Influenza Virus RNA Synthesis and the Innate Immune Response. Viruses 2021; 13:v13050780. [PMID: 33924859 PMCID: PMC8146608 DOI: 10.3390/v13050780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 12/25/2022] Open
Abstract
Infection with influenza A and B viruses results in a mild to severe respiratory tract infection. It is widely accepted that many factors affect the severity of influenza disease, including viral replication, host adaptation, innate immune signalling, pre-existing immunity, and secondary infections. In this review, we will focus on the interplay between influenza virus RNA synthesis and the detection of influenza virus RNA by our innate immune system. Specifically, we will discuss the generation of various RNA species, host pathogen receptors, and host shut-off. In addition, we will also address outstanding questions that currently limit our knowledge of influenza virus replication and host adaption. Understanding the molecular mechanisms underlying these factors is essential for assessing the pandemic potential of future influenza virus outbreaks.
Collapse
|
29
|
PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. J Virol 2020; 95:JVI.01582-20. [PMID: 33028722 PMCID: PMC7737735 DOI: 10.1128/jvi.01582-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022] Open
Abstract
Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and have caused the highest number of human H5N1 influenza cases worldwide, presenting a serious global public health threat. These viruses may have the greatest evolutionary potential for adaptation from avian hosts to human hosts. Using a comprehensive phylogenetic approach, we identified several novel clade 2.2.1 virus polymerase mutations that increased viral replication in vitro in human cells and in vivo in mice. These mutations were in the polymerase PA subunit and acted cooperatively with the E627K mutation in the PB2 polymerase subunit to provide higher replication in contemporary clade 2.2.1.2 viruses than in ancestral clade 2.2.1 viruses. These data indicated that ongoing clade 2.2.1 dissemination in the field has driven PA mutations to modify viral replication to enable host range expansion, with a higher public health risk for humans. Adaptive mutations and/or reassortments in avian influenza virus polymerase subunits PA, PB1, and PB2 are one of the major factors enabling the virus to overcome the species barrier to infect humans. The majority of human adaptation polymerase mutations have been identified in PB2; fewer adaptation mutations have been characterized in PA and PB1. Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and generally carry the human adaptation PB2-E627K substitution during their dissemination in nature. In this study, we identified other human adaptation polymerase mutations by analyzing phylogeny-associated PA mutations that H5N1 clade 2.2.1 viruses have accumulated during their evolution in the field. This analysis identified several PA mutations that produced increased replication by contemporary clade 2.2.1.2 viruses in vitro in human cells and in vivo in mice compared to ancestral clade 2.2.1 viruses. The PA mutations acted cooperatively to increase viral polymerase activity and replication in both avian and human cells, with the effect being more prominent in human cells at 33°C than at 37°C. These results indicated that PA mutations have a role in establishing contemporary clade 2.2.1.2 virus infections in poultry and in adaptation to infect mammals. Our study provided data on the mechanism for PA mutations to accumulate during avian influenza virus evolution and extend the viral host range. IMPORTANCE Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and have caused the highest number of human H5N1 influenza cases worldwide, presenting a serious global public health threat. These viruses may have the greatest evolutionary potential for adaptation from avian hosts to human hosts. Using a comprehensive phylogenetic approach, we identified several novel clade 2.2.1 virus polymerase mutations that increased viral replication in vitro in human cells and in vivo in mice. These mutations were in the polymerase PA subunit and acted cooperatively with the E627K mutation in the PB2 polymerase subunit to provide higher replication in contemporary clade 2.2.1.2 viruses than in ancestral clade 2.2.1 viruses. These data indicated that ongoing clade 2.2.1 dissemination in the field has driven PA mutations to modify viral replication to enable host range expansion, with a higher public health risk for humans.
Collapse
|
30
|
Carrique L, Fan H, Walker AP, Keown JR, Sharps J, Staller E, Barclay WS, Fodor E, Grimes JM. Host ANP32A mediates the assembly of the influenza virus replicase. Nature 2020; 587:638-643. [PMID: 33208942 PMCID: PMC7116770 DOI: 10.1038/s41586-020-2927-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
Aquatic birds represent a vast reservoir from which new pandemic influenza A viruses can emerge1. Influenza viruses contain a negative-sense segmented RNA genome that is transcribed and replicated by the viral heterotrimeric RNA polymerase (FluPol) in the context of viral ribonucleoprotein complexes2,3. RNA polymerases of avian influenza A viruses (FluPolA) replicate viral RNA inefficiently in human cells because of species-specific differences in acidic nuclear phosphoprotein 32 (ANP32), a family of essential host proteins for FluPol activity4. Host-adaptive mutations, particularly a glutamic-acid-to-lysine mutation at amino acid residue 627 (E627K) in the 627 domain of the PB2 subunit, enable avian FluPolA to overcome this restriction and efficiently replicate viral RNA in the presence of human ANP32 proteins. However, the molecular mechanisms of genome replication and the interplay with ANP32 proteins remain largely unknown. Here we report cryo-electron microscopy structures of influenza C virus polymerase (FluPolC) in complex with human and chicken ANP32A. In both structures, two FluPolC molecules form an asymmetric dimer bridged by the N-terminal leucine-rich repeat domain of ANP32A. The C-terminal low-complexity acidic region of ANP32A inserts between the two juxtaposed PB2 627 domains of the asymmetric FluPolA dimer, suggesting a mechanism for how the adaptive PB2(E627K) mutation enables the replication of viral RNA in mammalian hosts. We propose that this complex represents a replication platform for the viral RNA genome, in which one of the FluPol molecules acts as a replicase while the other initiates the assembly of the nascent replication product into a viral ribonucleoprotein complex.
Collapse
Affiliation(s)
- Loïc Carrique
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Jeremy R Keown
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ecco Staller
- Section of Molecular Virology, Imperial College London, London, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Section of Molecular Virology, Imperial College London, London, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Jonathan M Grimes
- Division of Structural Biology, University of Oxford, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.
| |
Collapse
|
31
|
Lee BW, Ha TKQ, Cho HM, An JP, Kim SK, Kim CS, Kim E, Oh WK. Antiviral activity of furanocoumarins isolated from Angelica dahurica against influenza a viruses H1N1 and H9N2. JOURNAL OF ETHNOPHARMACOLOGY 2020; 259:112945. [PMID: 32389854 DOI: 10.1016/j.jep.2020.112945] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/16/2020] [Accepted: 05/01/2020] [Indexed: 05/25/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav. (Umbelliferae family) is an herbaceous, perennial plant native to northern and eastern Asia. The root of A. dahurica has traditionally been used under the name "Bai Zhi" as a medicinal plant for colds, dizziness, ulcers, and rheumatism. Moreover, it is also an important ingredient of various prescriptions, such as Gumiganghwal-Tang, for the common cold and influenza. AIM OF THE STUDY Even though various biological activities of the root of A. dahurica have been reported along with its chemical components, the detailed mechanism of how it exerts anti-influenza activity at the compound level has not been studied. Therefore, we investigated the anti-influenza properties of furanocoumarins purified by bioactivity-guided isolation. MATERIALS AND METHODS Bioactivity-guided isolation from a 70% EtOH extract of the root of A. dahurica was performed to produce four active furanocoumarins. The inhibition of cytopathic effects (CPEs) was evaluated to ascertain the antiviral activity of these compounds against influenza A (H1N1 and H9N2) viruses. The most potent compound was subjected to detailed mechanistic studies such as the inhibition of viral protein synthesis, CPE inhibition in different phases of the viral replication cycle, neuraminidase (NA) inhibition, antiapoptotic activity using flow cytometry, and immunofluorescence. RESULTS The bioactivity-guided isolation produced four active furanocoumarins, isoimperatorin (1), oxypeucedanin (2), oxypeucedanin hydrate (3) and imperatorin (4) from the n-BuOH fraction. Among them, compound 2 (followed by compounds 1, 4 and 3) showed a significant CPE inhibition effect, which was stronger than that of the positive control ribavirin, against both H1N1 and H9N2 with an EC50 (μM) of 5.98 ± 0.71 and 4.52 ± 0.39, respectively. Compound 2 inhibited the synthesis of NA and nucleoprotein (NP) in a dose-dependent manner. In the time course assays, the cytopathic effects of influenza A-infected MDCK cells were reduced by 80-90% when treated with compound 2 for 1 and 2 h after infection and declined drastically 3 h after infection. The level of viral NA and NP production was markedly reduced to less than 20% for both proteins in compound 2 (20 μM)-treated cells compared to untreated cells at 2 h after infection. In the molecular docking analysis, compound 2 showed a stronger binding affinity for the C-terminus of polymerase acidic protein (PAC; -36.28 kcal/mol) than the other two polymerase subunits. Compound 2 also exerted an antiapoptotic effect on virus infected cells and significantly inhibited the mRNA expression of caspase-3 and Bax. CONCLUSION Our results suggest that compound 2 might exert anti-influenza A activity via the inhibition of the early phase of the viral replication cycle, not direct neutralization of surface proteins, such as hemagglutinin and NA, and abnormal apoptosis induced by virus infection. Taken together, these findings suggest that furanocoumarins predominant in A. dahurica play a pivotal role in its antiviral activity. These findings can also explain the reasons for the ethnopharmacological uses of this plant as an important ingredient in many antiviral prescriptions in traditional Chinese medicine (TCM).
Collapse
Affiliation(s)
- Ba Wool Lee
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Thi Kim Quy Ha
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea; College of Natural Sciences, Cantho University, Campus II, Cantho City, Viet Nam
| | - Hyo Moon Cho
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Pyo An
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seong Kyun Kim
- Choong Ang Vaccine Laboratory, 1476-37, Yuseong-daero, Yuseong-gu, Daejeon, 34055, Republic of Korea
| | - Choong-Sik Kim
- Choong Ang Vaccine Laboratory, 1476-37, Yuseong-daero, Yuseong-gu, Daejeon, 34055, Republic of Korea
| | - Eunhee Kim
- Choong Ang Vaccine Laboratory, 1476-37, Yuseong-daero, Yuseong-gu, Daejeon, 34055, Republic of Korea
| | - Won Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
32
|
Dawson AR, Wilson GM, Freiberger EC, Mondal A, Coon JJ, Mehle A. Phosphorylation controls RNA binding and transcription by the influenza virus polymerase. PLoS Pathog 2020; 16:e1008841. [PMID: 32881973 PMCID: PMC7494117 DOI: 10.1371/journal.ppat.1008841] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/16/2020] [Accepted: 07/25/2020] [Indexed: 12/03/2022] Open
Abstract
The influenza virus polymerase transcribes and replicates the viral genome. The proper timing and balance of polymerase activity is important for successful replication. Genome replication is controlled in part by phosphorylation of NP that regulates assembly of the replication machinery. However, it remains unclear whether phosphorylation directly regulated polymerase activity. Here we identified polymerase phosphosites that control its function. Mutating phosphosites in the catalytic subunit PB1 altered polymerase activity and virus replication. Biochemical analyses revealed phosphorylation events that disrupted global polymerase function by blocking the NTP entry channel or preventing RNA binding. We also identified a regulatory site that split polymerase function by specifically suppressing transcription. These experiments show that host kinases phospho-regulate viral RNA synthesis directly by modulating polymerase activity and indirectly by controlling assembly of replication machinery. Further, they suggest polymerase phosphorylation may bias replication versus transcription at discrete times or locations during the infectious cycle. The influenza virus polymerase is a multifunctional enzyme directing viral gene expression and genome replication. Immediately following infection, the polymerase primarily performs transcription to make the viral mRNAs that program the replication cycle. The polymerase then shifts output to produce more copies of the viral genome at later stages of infection. The balance between transcription and replication is critical for successful infection. Here we identify phosphorylation sites within the viral polymerase and describe how these post-translational modifications control polymerase activity. Cellular kinases modify the viral polymerase. We identified a phosphorylation site in the catalytic subunit PB1 that selectively disables transcription, but not replication. We also describe a phosphorylation site in PB1 that disrupts binding to viral RNAs, disabling all activities of the polymerase. These modifications may establish polymerases with specialized function, and help regulate the balance between transcription and replication throughout the viral life cycle.
Collapse
Affiliation(s)
- Anthony R. Dawson
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Gary M. Wilson
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Elyse C. Freiberger
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Arindam Mondal
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
- * E-mail:
| |
Collapse
|
33
|
Fodor E, Te Velthuis AJW. Structure and Function of the Influenza Virus Transcription and Replication Machinery. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038398. [PMID: 31871230 DOI: 10.1101/cshperspect.a038398] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transcription and replication of the influenza virus RNA genome is catalyzed by the viral heterotrimeric RNA-dependent RNA polymerase in the context of viral ribonucleoprotein (vRNP) complexes. Atomic resolution structures of the viral RNA synthesis machinery have offered insights into the initiation mechanisms of viral transcription and genome replication, and the interaction of the viral RNA polymerase with host RNA polymerase II, which is required for the initiation of viral transcription. Replication of the viral RNA genome by the viral RNA polymerase depends on host ANP32A, and host-specific sequence differences in ANP32A underlie the poor activity of avian influenza virus polymerases in mammalian cells. A failure to faithfully copy the viral genome segments can lead to the production of aberrant viral RNA products, such as defective interfering (DI) RNAs and mini viral RNAs (mvRNAs). Both aberrant RNA types have been implicated in innate immune responses against influenza virus infection. This review discusses recent insights into the structure-function relationship of the viral RNA polymerase and its role in determining host range and virulence.
Collapse
Affiliation(s)
- Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Aartjan J W Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 2QQ, United Kingdom
| |
Collapse
|
34
|
Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation. Nat Microbiol 2020; 5:864-871. [PMID: 32341479 DOI: 10.1038/s41564-020-0712-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as primers of transcription, and catalyse RNA synthesis. Here, we report the full-length structure of the severe fever with thrombocytopaenia syndrome virus (SFTSV) L protein, as determined by cryogenic electron microscopy at 3.4 Å, leading to an atomic model harbouring three functional parts (an endonuclease, an RNA-dependent RNA polymerase and a cap-binding domain) and two structural domains (an arm domain with a blocker motif and a carboxy-terminal lariat domain). The SFTSV L protein has a compact architecture in which its cap-binding pocket is surprisingly occupied by an Arg finger of the blocker motif, and the endonuclease active centre faces back towards the cap-binding pocket, suggesting that domain rearrangements are necessary to acquire the pre-initiation state of the active site. Our results provide insight into the complete architecture of sNSRV-encoded L protein and further the understanding of sNSRV transcription initiation.
Collapse
|
35
|
Isel C, Chen KY, Naffakh N. La dimérisation, une nouvelle propriété de l’ARN polymérase des virus influenza. Med Sci (Paris) 2020; 36:332-335. [DOI: 10.1051/medsci/2020053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
Wang F, Liu G, Lu Y, Hlasny M, Liu Q, Zhou Y. Acquisition of Avian-Origin PB1 Facilitates Viral RNA Synthesis by the 2009 Pandemic H1N1 Virus Polymerase. Viruses 2020; 12:v12030266. [PMID: 32121117 PMCID: PMC7150768 DOI: 10.3390/v12030266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
The constant crosstalk between the large avian reservoir of influenza A viruses (IAV) and its mammalian hosts drives viral evolution and facilitates their host switching. Direct adaptation of an avian strain to human or reassortment between avian-origin gene segments with that of human strains are the two mechanisms for the emergence of pandemic viruses. While it was suggested that the 1918 pandemic virus is of avian origin, reassortment of 1918 human isolates and avian influenza viruses led to the generation of 1957 and 1968 pandemic viruses. Interestingly, the avian PB1 segment, which encodes the catalytic subunit of IAV polymerase, is present in the 1957 and 1968 pandemic viruses. The biological consequence and molecular basis of such gene exchange remain less well understood. Using the 2009 pandemic H1N1 virus as a model, whose polymerase contains a human-origin PB1 subunit, we demonstrate that the acquisition of an avian PB1 markedly enhances viral RNA synthesis. This enhancement is also effective in the absence of PB2 adaptive mutations, which are key determinants of host switching. Mechanistically, the avian-origin PB1 does not appear to affect polymerase assembly but imparts the reassorted pandemic polymerase-augmented viral primary transcription and replication. Moreover, compared to the parental pandemic polymerase, the reassorted polymerase displays comparable complementary RNA (cRNA)-stabilizing activity but is specifically enhanced in progeny viral RNA (vRNA) synthesis from cRNA in a trans-activating manner. Overall, our results provide the first insight into the mechanism via which avian-origin PB1 enhances viral RNA synthesis of the 2009 pandemic virus polymerase.
Collapse
Affiliation(s)
- Fangzheng Wang
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Guanqun Liu
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
| | - Yao Lu
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
| | - Magda Hlasny
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
| | - Qiang Liu
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (F.W.); (G.L.); (Y.L.); (M.H.); (Q.L.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Correspondence: ; Tel.: +1-306-966-7716
| |
Collapse
|
37
|
Kumar S, Yeo D, Harur Muralidharan N, Lai SK, Tong C, Tan BH, Sugrue RJ. Impaired Nuclear Export of the Ribonucleoprotein Complex and Virus-Induced Cytotoxicity Combine to Restrict Propagation of the A/Duck/Malaysia/02/2001 (H9N2) Virus in Human Airway Cells. Cells 2020; 9:cells9020355. [PMID: 32028682 PMCID: PMC7072679 DOI: 10.3390/cells9020355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 01/02/2023] Open
Abstract
In humans, (A549) cells impaired H9N2 virus nuclear export of the ribonucleoprotein (RNP) complex contrasted with the early and efficient nuclear export of the H1N1/WSN and pH1N1 virus RNP complexes. Although nuclear export of the RNP complex occurred via the nuclear pore complex, H9N2 virus infection also induced modifications in the nuclear envelope and induced cell cytotoxicity. Reduced PA protein levels in H9N2 virus-infected A549 cells occurred, and this phenomenon was independent of virus infection. Silencing the H1N1/WSN PA protein expression leads to impaired nuclear export of RNP complexes, suggesting that the impaired nuclear export of the H9N2 virus RNP complex may be one of the consequences of reduced PA protein levels. Early and efficient export of the RNP complex occurred in H9N2 virus-infected avian (CEF) cells, although structural changes in the nuclear envelope also occurred. Collectively our data suggest that a combination of delayed nuclear export and virus-induced cell cytotoxicity restricts H9N2 virus transmission in A549 cells. However, the early and efficient export of the RNP complex mitigated the effects of virus-induced cytotoxicity on H9N2 virus transmission in CEF cells. Our findings highlight the multi-factorial nature of host-adaptation of the polymerase proteins of avian influenza viruses in non-avian cell environments.
Collapse
Affiliation(s)
- Sriram Kumar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Dawn Yeo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore;
| | - Nisha Harur Muralidharan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Cathlyn Tong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore;
| | - Richard J. Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
- Correspondence:
| |
Collapse
|
38
|
Long JS, Mistry B, Haslam SM, Barclay WS. Host and viral determinants of influenza A virus species specificity. Nat Rev Microbiol 2020; 17:67-81. [PMID: 30487536 DOI: 10.1038/s41579-018-0115-z] [Citation(s) in RCA: 395] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza A viruses cause pandemics when they cross between species and an antigenically novel virus acquires the ability to infect and transmit between these new hosts. The timing of pandemics is currently unpredictable but depends on ecological and virological factors. The host range of an influenza A virus is determined by species-specific interactions between virus and host cell factors. These include the ability to bind and enter cells, to replicate the viral RNA genome within the host cell nucleus, to evade host restriction factors and innate immune responses and to transmit between individuals. In this Review, we examine the host barriers that influenza A viruses of animals, especially birds, must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host. This knowledge is used to inform risk assessments for future pandemics and to identify virus-host interactions that could be targeted by novel intervention strategies.
Collapse
Affiliation(s)
- Jason S Long
- Department of Medicine, Imperial College London, London, UK
| | - Bhakti Mistry
- Department of Medicine, Imperial College London, London, UK
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Medicine, Imperial College London, London, UK.
| |
Collapse
|
39
|
Suttie A, Deng YM, Greenhill AR, Dussart P, Horwood PF, Karlsson EA. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019; 55:739-768. [PMID: 31428925 PMCID: PMC6831541 DOI: 10.1007/s11262-019-01700-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.
Collapse
Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
- School of Health and Life Sciences, Federation University, Churchill, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yi-Mo Deng
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew R Greenhill
- School of Health and Life Sciences, Federation University, Churchill, Australia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Erik A Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia.
| |
Collapse
|
40
|
Chen KY, Santos Afonso ED, Enouf V, Isel C, Naffakh N. Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. PLoS Pathog 2019; 15:e1008034. [PMID: 31581279 PMCID: PMC6776259 DOI: 10.1371/journal.ppat.1008034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022] Open
Abstract
The influenza A virus RNA-dependent RNA polymerase complex consists in three subunits, PB2, PB1 and PA, that perform transcription and replication of the viral genome through very distinct mechanisms. Biochemical and structural studies have revealed that the polymerase can adopt multiple conformations and form oligomers. However so far it remained unclear whether the available oligomeric crystal structures represent a functional state of the polymerase. Here we gained new insights into this question, by investigating the incompatibility between non-cognate subunits of influenza polymerase brought together through genetic reassortment. We observed that a 7:1 reassortant virus whose PB2 segment derives from the A/WSN/33 (WSN) virus in an otherwise A/PR/8/34 (PR8) backbone is attenuated, despite a 97% identity between the PR8-PB2 and WSN-PB2 proteins. Independent serial passages led to the selection of phenotypic revertants bearing distinct second-site mutations on PA, PB1 and/or PB2. The constellation of mutations present on one revertant virus was studied extensively using reverse genetics and cell-based reconstitution of the viral polymerase. The PA-E349K mutation appeared to play a major role in correcting the initial defect in replication (cRNA -> vRNA) of the PR8xWSN-PB2 reassortant. Strikingly the PA-E349K mutation, and also the PB2-G74R and PB1-K577G mutations present on other revertants, are located at a dimerization interface of the polymerase. All three restore wild-type-like polymerase activity in a minigenome assay while decreasing the level of polymerase dimerization. Overall, our data show that the polymerase subunits co-evolve to ensure not only optimal inter-subunit interactions within the heterotrimer, but also proper levels of dimerization of the heterotrimer which appears to be essential for efficient viral RNA replication. Our findings point to influenza polymerase dimerization as a feature that is controlled by a complex interplay of genetic determinants, can restrict genetic reassortment, and could become a target for antiviral drug development.
Collapse
Affiliation(s)
- Kuang-Yu Chen
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Vincent Enouf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Centre National de Référence des Virus des Infections Respiratoires, Institut Pasteur, Paris, France
- Pasteur International Bioresources network (PIBnet), Plateforme de Microbiologie Mutualisée (P2M), Institut Pasteur, Paris, France
| | - Catherine Isel
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, UMR 3569 CNRS, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail:
| |
Collapse
|
41
|
Ghorbani A, Ngunjiri JM, Lee CW. Influenza A Virus Subpopulations and Their Implication in Pathogenesis and Vaccine Development. Annu Rev Anim Biosci 2019; 8:247-267. [PMID: 31479617 DOI: 10.1146/annurev-animal-021419-083756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The concept of influenza A virus (IAV) subpopulations emerged approximately 75 years ago, when Preben von Magnus described "incomplete" virus particles that interfere with the replication of infectious virus. It is now widely accepted that infectious particles constitute only a minor portion of biologically active IAV subpopulations. The IAV quasispecies is an extremely diverse swarm of biologically and genetically heterogeneous particle subpopulations that collectively influence the evolutionary fitness of the virus. This review summarizes the current knowledge of IAV subpopulations, focusing on their biologic and genomic diversity. It also discusses the potential roles IAV subpopulations play in virus pathogenesis and live attenuated influenza vaccine development.
Collapse
Affiliation(s)
- Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , ,
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA; , , .,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
42
|
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E. Structures of influenza A virus RNA polymerase offer insight into viral genome replication. Nature 2019; 573:287-290. [PMID: 31485076 PMCID: PMC6795553 DOI: 10.1038/s41586-019-1530-7] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022]
Abstract
Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans1,2. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPolA) composed of PB1, PB2 and PA subunits3-5. Although the high-resolution crystal structure of FluPolA of bat influenza A virus has previously been reported6, there are no complete structures available for human and avian FluPolA. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase7-10-remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPolA from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPolA forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPolA bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPolA dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPolA dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPolA, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPolA that could be targeted in the development of antiviral drugs.
Collapse
Affiliation(s)
- Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Itziar Serna Martin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Narin Hengrung
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Didcot, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
43
|
Naskar S, Joshi H, Chakraborty B, Seeman NC, Maiti PK. Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. NANOSCALE 2019; 11:14863-14878. [PMID: 31355845 DOI: 10.1039/c9nr00786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
Collapse
Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | | | | | | | | |
Collapse
|
44
|
Structural insight into RNA synthesis by influenza D polymerase. Nat Microbiol 2019; 4:1750-1759. [PMID: 31209309 DOI: 10.1038/s41564-019-0487-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/13/2019] [Indexed: 01/03/2023]
Abstract
The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design.
Collapse
|
45
|
Abstract
Atomic structures of the polymerase–endonuclease complex of the orthomyxovirus influenza and the orthobunyavirus La Crosse—two distinct segmented negative-sense (SNS) RNA viruses—demonstrate that binding of the genomic 5′ RNA rearranges the catalytic residues of the RNA-dependent RNA-polymerase (RdRP). Working with the arenavirus, Machupo, we demonstrate that 5′ RNAs from the genomic and antigenomic copies of both segments activate the RdRP in conjunction with a specific promoter. This study builds upon structural studies with two different SNS RNA viruses to reveal a previously unappreciated mechanism of RNA-guided promoter-specific polymerase regulation in SNS RNA viruses. The conservation of activating RNA elements among the polymerase–endonuclease complexes of SNS RNA viruses suggests new avenues for developing antiviral therapeutics. Segmented negative-sense (SNS) RNA viruses initiate infection by delivering into cells a suite of genomic RNA segments, each sheathed by the viral nucleocapsid protein and bound by the RNA-dependent RNA-polymerase (RdRP). For the orthomyxovirus influenza and the bunyavirus La Crosse, the 5′ end of the genomic RNA binds as a hook-like structure proximal to the active site of the RdRP. Using an in vitro assay for the RNA-dependent RNA-polymerase (RdRP) of the arenavirus Machupo (MACV), we demonstrate that the 5′ genomic and antigenomic RNAs of both small and large genome segments stimulate activity in a promoter-specific manner. Functional probing of the activating RNAs identifies intramolecular base-pairing between positions +1 and +7 and a pseudotemplated 5′ terminal guanine residue as key for activation. Binding of structured 5′ RNAs is a conserved feature of all SNS RNA virus polymerases, implying that promoter-specific RdRP activation extends beyond the arenaviruses. The 5′ RNAs and the RNA binding pocket itself represent targets for therapeutic intervention.
Collapse
|
46
|
Loureiro ME, D'Antuono A, López N. Virus⁻Host Interactions Involved in Lassa Virus Entry and Genome Replication. Pathogens 2019; 8:pathogens8010017. [PMID: 30699976 PMCID: PMC6470645 DOI: 10.3390/pathogens8010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 01/08/2023] Open
Abstract
Lassa virus (LASV) is the causative agent of Lassa fever, a human hemorrhagic disease associated with high mortality and morbidity rates, particularly prevalent in West Africa. Over the past few years, a significant amount of novel information has been provided on cellular factors that are determinant elements playing a role in arenavirus multiplication. In this review, we focus on host proteins that intersect with the initial steps of the LASV replication cycle: virus entry and genome replication. A better understanding of relevant virus⁻host interactions essential for sustaining these critical steps may help to identify possible targets for the rational design of novel therapeutic approaches against LASV and other arenaviruses that cause severe human disease.
Collapse
Affiliation(s)
- María Eugenia Loureiro
- Centro de Virología Animal (CEVAN), CONICET-SENASA, Av Sir Alexander Fleming 1653, Martínez, Provincia de Buenos Aires B1640CSI, Argentina.
| | - Alejandra D'Antuono
- Centro de Virología Animal (CEVAN), CONICET-SENASA, Av Sir Alexander Fleming 1653, Martínez, Provincia de Buenos Aires B1640CSI, Argentina.
| | - Nora López
- Centro de Virología Animal (CEVAN), CONICET-SENASA, Av Sir Alexander Fleming 1653, Martínez, Provincia de Buenos Aires B1640CSI, Argentina.
| |
Collapse
|
47
|
The Surface-Exposed PA 51-72-Loop of the Influenza A Virus Polymerase Is Required for Viral Genome Replication. J Virol 2018; 92:JVI.00687-18. [PMID: 29875249 PMCID: PMC6069170 DOI: 10.1128/jvi.00687-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/29/2018] [Indexed: 12/30/2022] Open
Abstract
Influenza A viruses are a major global health threat, not only causing significant morbidity and mortality every year but also having the potential to cause severe pandemic outbreaks like the 1918 influenza pandemic. The viral polymerase is a protein complex which is responsible for transcription and replication of the viral genome and therefore is an attractive target for antiviral drug development. For that purpose it is important to understand the mechanisms of how the virus replicates its genome and how the viral polymerase works on a molecular level. In this report, we characterize the role of the flexible surface-exposed PA51-72-loop in polymerase function and offer new insights into the replication mechanism of influenza A viruses. The heterotrimeric influenza A virus RNA-dependent RNA polymerase complex, composed of PB1, PB2, and PA subunits, is responsible for transcribing and replicating the viral RNA genome. The N-terminal endonuclease domain of the PA subunit performs endonucleolytic cleavage of capped host RNAs to generate capped RNA primers for viral transcription. A surface-exposed flexible loop (PA51-72-loop) in the PA endonuclease domain has been shown to be dispensable for endonuclease activity. Interestingly, the PA51-72-loop was found to form different intramolecular interactions depending on the conformational arrangement of the polymerase. In this study, we show that a PA subunit lacking the PA51-72-loop assembles into a heterotrimeric polymerase with PB1 and PB2. We demonstrate that in a cellular context, the PA51-72-loop is required for RNA replication but not transcription by the viral polymerase. In agreement, recombinant viral polymerase lacking the PA51-72-loop is able to carry out cap-dependent transcription but is inhibited in de novo replication initiation in vitro. Furthermore, viral RNA (vRNA) synthesis is also restricted during ApG-primed extension, indicating that the PA51-72-loop is required not only for replication initiation but also for elongation on a cRNA template. We propose that the PA51-72-loop plays a role in the stabilization of the replicase conformation of the polymerase. Together, these results further our understanding of influenza virus RNA genome replication in general and highlight a role of the PA endonuclease domain in polymerase function in particular. IMPORTANCE Influenza A viruses are a major global health threat, not only causing significant morbidity and mortality every year but also having the potential to cause severe pandemic outbreaks like the 1918 influenza pandemic. The viral polymerase is a protein complex which is responsible for transcription and replication of the viral genome and therefore is an attractive target for antiviral drug development. For that purpose it is important to understand the mechanisms of how the virus replicates its genome and how the viral polymerase works on a molecular level. In this report, we characterize the role of the flexible surface-exposed PA51-72-loop in polymerase function and offer new insights into the replication mechanism of influenza A viruses.
Collapse
|
48
|
Slaine PD, MacRae C, Kleer M, Lamoureux E, McAlpine S, Warhuus M, Comeau AM, McCormick C, Hatchette T, Khaperskyy DA. Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Viruses 2018; 10:E272. [PMID: 29783694 PMCID: PMC5977265 DOI: 10.3390/v10050272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 12/16/2022] Open
Abstract
Mice are not natural hosts for influenza A viruses (IAVs), but they are useful models for studying antiviral immune responses and pathogenesis. Serial passage of IAV in mice invariably causes the emergence of adaptive mutations and increased virulence. Here, we report the adaptation of IAV reference strain A/California/07/2009(H1N1) (also known as CA/07) in outbred Swiss Webster mice. Serial passage led to increased virulence and lung titers, and dissemination of the virus to brains. We adapted a deep-sequencing protocol to identify and enumerate adaptive mutations across all genome segments. Among mutations that emerged during mouse-adaptation, we focused on amino acid substitutions in polymerase subunits: polymerase basic-1 (PB1) T156A and F740L and polymerase acidic (PA) E349G. These mutations were evaluated singly and in combination in minigenome replicon assays, which revealed that PA E349G increased polymerase activity. By selectively engineering three PB1 and PA mutations into the parental CA/07 strain, we demonstrated that these mutations in polymerase subunits decreased the production of defective viral genome segments with internal deletions and dramatically increased the release of infectious virions from mouse cells. Together, these findings increase our understanding of the contribution of polymerase subunits to successful host adaptation.
Collapse
MESH Headings
- Adaptation, Physiological/genetics
- Amino Acid Substitution
- Animals
- Animals, Outbred Strains
- Cells, Cultured
- Disease Models, Animal
- Dogs
- Female
- Genome, Viral
- Humans
- Influenza A Virus, H1N1 Subtype/enzymology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/virology
- Mice
- Mutation, Missense
- Protein Conformation
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Serial Passage
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virion/metabolism
- Virulence
- Virus Replication
Collapse
Affiliation(s)
- Patrick D Slaine
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Cara MacRae
- The Hospital for Sick Children, University Health Network, Toronto, ON M5G 2C4, Canada.
| | - Mariel Kleer
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Emily Lamoureux
- CGEB-Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Sarah McAlpine
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - Michelle Warhuus
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - André M Comeau
- CGEB-Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Todd Hatchette
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - Denys A Khaperskyy
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| |
Collapse
|
49
|
Melinek BJ, Dessoy S, Wright B, Bracewell DG, Mukhopadhyay TK. Ultra scale-down approaches to study the centrifugal harvest for viral vaccine production. Biotechnol Bioeng 2018; 115:1226-1238. [PMID: 29315484 DOI: 10.1002/bit.26546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023]
Abstract
Large scale continuous cell-line cultures promise greater reproducibility and efficacy for the production of influenza vaccines, and adenovirus for gene therapy. This paper seeks to use an existing validated ultra scale-down tool, which is designed to mimic the commercial scale process environment using only milliliters of material, to provide some initial insight into the performance of the harvest step for these processes. The performance of industrial scale centrifugation and subsequent downstream process units is significantly affected by shear. The properties of these cells, in particular their shear sensitivity, may be changed considerably by production of a viral product, but literature on this is limited to date. In addition, the scale-down tool used here has not previously been applied to the clarification of virus production processes. The results indicate that virus infected cells do not actually show any increase in sensitivity to shear, and may indeed become less shear sensitive, in a similar manner to that previously observed in old or dead cell cultures. Clarification may be most significantly dependent on the virus release mechanism, with the budding influenza virus producing a much greater decrease in clarification than the lytic, non-enveloped adenovirus. A good match was also demonstrated to the industrial scale performance in terms of clarification, protein release, and impurity profile.
Collapse
Affiliation(s)
- Beatrice J Melinek
- Department of Biochemical Engineering, Bernard Katz building, University College London, London, UK
| | | | - Bernice Wright
- Department of Biochemical Engineering, Bernard Katz building, University College London, London, UK
| | - Dan G Bracewell
- Department of Biochemical Engineering, Bernard Katz building, University College London, London, UK
| | - Tarit K Mukhopadhyay
- Department of Biochemical Engineering, Bernard Katz building, University College London, London, UK
| |
Collapse
|
50
|
The amyloidogenicity of the influenza virus PB1-derived peptide sheds light on its antiviral activity. Biophys Chem 2018; 234:16-23. [PMID: 29328990 DOI: 10.1016/j.bpc.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 01/08/2023]
Abstract
The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6-13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures. In this paper, it was shown that PB1(6-13) peptide is prone to form the amyloid-like fibrillar aggregates. The peptide homo-oligomerization kinetics were examined, and the affinity and characteristic interaction time of PB1(6-13) peptide monomers and the influenza virus polymerase complex PB1 subunit N-terminal region were evaluated by the SPR and TR-SAXS methods. Based on the data obtained, a hypothesis about the PB1(6-13) peptide mechanism of action was proposed: the peptide in its monomeric form is capable of altering the conformation of the PB1 subunit N-terminal region, causing a change from an alpha helix to a beta structure. This conformational change disrupts PB1 and PA subunit interaction and, by that mechanism, the peptide displays antiviral activity.
Collapse
|