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Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X. Cryo-EM structures of Thogoto virus polymerase reveal unique RNA transcription and replication mechanisms among orthomyxoviruses. Nat Commun 2024; 15:4620. [PMID: 38816392 PMCID: PMC11139864 DOI: 10.1038/s41467-024-48848-3] [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: 11/30/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Influenza viruses and thogotoviruses account for most recognized orthomyxoviruses. Thogotoviruses, exemplified by Thogoto virus (THOV), are capable of infecting humans using ticks as vectors. THOV transcribes mRNA without the extraneous 5' end sequences derived from cap-snatching in influenza virus mRNA. Here, we report cryo-EM structures to characterize THOV polymerase RNA synthesis initiation and elongation. The structures demonstrate that THOV RNA transcription and replication are able to start with short dinucleotide primers and that the polymerase cap-snatching machinery is likely non-functional. Triggered by RNA synthesis, asymmetric THOV polymerase dimers can form without the involvement of host factors. We confirm that, distinctive from influenza viruses, THOV-polymerase RNA synthesis is weakly dependent of the host factors ANP32A/B/E in human cells. This study demonstrates varied mechanisms in RNA synthesis and host factor utilization among orthomyxoviruses, providing insights into the mechanisms behind thogotoviruses' broad-infectivity range.
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Affiliation(s)
- Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tiancai Chang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Chenchen Wang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Heyu Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mei Li
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Peng Tang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xin Wen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xichen Bao
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong, China.
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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Staller E, Carrique L, Swann OC, Fan H, Keown JR, Sheppard CM, Barclay WS, Grimes JM, Fodor E. Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation. Nat Commun 2024; 15:4123. [PMID: 38750014 PMCID: PMC11096171 DOI: 10.1038/s41467-024-48470-3] [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: 01/05/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer-the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA.
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Affiliation(s)
- Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Olivia C Swann
- Section of Molecular Virology, Imperial College London, London, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jeremy R Keown
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Carol M Sheppard
- Section of Molecular Virology, Imperial College London, London, UK
| | - Wendy S Barclay
- Section of Molecular Virology, Imperial College London, London, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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Zhirnov OP, Lvov DK. Avian flu: «for whom the bell tolls»? Vopr Virusol 2024; 69:101-118. [PMID: 38843017 DOI: 10.36233/10.36233/0507-4088-213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Indexed: 06/14/2024]
Abstract
The family Orthomyxoviridae consists of 9 genera, including Alphainfluenzavirus, which contains avian influenza viruses. In two subtypes H5 and H7 besides common low-virulent strains, a specific type of highly virulent avian virus have been described to cause more than 60% mortality among domestic birds. These variants of influenza virus are usually referred to as «avian influenza virus». The difference between high (HPAI) and low (LPAI) virulent influenza viruses is due to the structure of the arginine-containing proteolytic activation site in the hemagglutinin (HA) protein. The highly virulent avian influenza virus H5 was identified more than 100 years ago and during this time they cause outbreaks among wild and domestic birds on all continents and only a few local episodes of the disease in humans have been identified in XXI century. Currently, a sharp increase in the incidence of highly virulent virus of the H5N1 subtype (clade h2.3.4.4b) has been registered in birds on all continents, accompanied by the transmission of the virus to various species of mammals. The recorded global mortality rate among wild, domestic and agricultural birds from H5 subtype is approaching to the level of 1 billion cases. A dangerous epidemic factor is becoming more frequent outbreaks of avian influenza with high mortality among mammals, in particular seals and marine lions in North and South America, minks and fur-bearing animals in Spain and Finland, domestic and street cats in Poland. H5N1 avian influenza clade h2.3.4.4b strains isolated from mammals have genetic signatures of partial adaptation to the human body in the PB2, NP, HA, NA genes, which play a major role in regulating the aerosol transmission and the host range of the virus. The current situation poses a real threat of pre-adaptation of the virus in mammals as intermediate hosts, followed by the transition of the pre-adapted virus into the human population with catastrophic consequences.
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Affiliation(s)
- O P Zhirnov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
- The Russian-German Academy of Medical-Social and Biotechnological Sciences, Skolkovo Innovation Center
| | - D K Lvov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
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Edwards SJ, Luczo JM. Editorial: Zoonotic negative-sense RNA viruses. Front Vet Sci 2024; 11:1384858. [PMID: 38496315 PMCID: PMC10940540 DOI: 10.3389/fvets.2024.1384858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Sarah J. Edwards
- Health and Biosecurity, Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Jasmina M. Luczo
- Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
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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: 0] [Impact Index Per Article: 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.
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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.
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