1
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Bai Y, Lei H, Song W, Shin SC, Wang J, Xiao B, Koçer ZA, Song MS, Webster R, Webby RJ, Wong SS, Zanin M. Amino acids in the polymerase complex of shorebird-isolated H1N1 influenza virus impact replication and host-virus interactions in mammalian models. Emerg Microbes Infect 2024; 13:2332652. [PMID: 38517705 PMCID: PMC11018082 DOI: 10.1080/22221751.2024.2332652] [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: 11/01/2023] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
A diverse population of avian influenza A viruses (AIVs) are maintained in wild birds and ducks yet the zoonotic potential of AIVs in these environmental reservoirs and the host-virus interactions involved in mammalian infection are not well understood. In studies of a group of subtype H1N1 AIVs isolated from migratory wild birds during surveillance in North America, we previously identified eight amino acids in the polymerase genes PB2 and PB1 that were important for the transmissibility of these AIVs in a ferret model of human influenza virus transmission. In this current study we found that PB2 containing amino acids associated with transmissibility at 67, 152, 199, 508, and 649 and PB1 at 298, 642, and 667 were associated with more rapid viral replication kinetics, greater infectivity, more active polymerase complexes and greater kinetics of viral genome replication and transcription. Pathogenicity in the mouse model was also impacted, evident as greater weight loss and lung pathology associated with greater inflammatory lung cytokine expression. Further, these AIVs all contained the avian-type amino acids of PB2-E627, D701, G590, Q591 and T271. Therefore, our study provides novel insights into the role of the AIV polymerase complex in the zoonotic transmission of AIVs in mammals.
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Affiliation(s)
- Yaqin Bai
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Hui Lei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
| | - Wenjun Song
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People’s Republic of China
| | | | - Jiaqi Wang
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Biying Xiao
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Zeynep A. Koçer
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Department of Biomedicine and Health Technologies, Izmir International Biomedicine and Genome Institute, Izmir, Türkiye
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University Medical School, Chungbuk, Korea
| | - Robert Webster
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard J. Webby
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sook-San Wong
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mark Zanin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
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2
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Kwon T, Artiaga BL, McDowell CD, Whitworth KM, Wells KD, Prather RS, Delhon G, Cigan M, White SN, Retallick J, Gaudreault NN, Morozov I, Richt JA. Gene editing of pigs to control influenza A virus infections. Emerg Microbes Infect 2024; 13:2387449. [PMID: 39083026 PMCID: PMC11346336 DOI: 10.1080/22221751.2024.2387449] [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: 04/28/2024] [Revised: 06/24/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
Proteolytic activation of the haemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ubiquitous proteases, such as furin; in contrast, the monobasic HA motif is recognized and activated by trypsin-like proteases, such as the transmembrane serine protease 2 (TMPRSS2). Here, we aimed to determine the effects of TMPRSS2 on the replication of pandemic H1N1 and H3N2 subtype IAVs in the natural host, the pig. The use of the CRISPR/Cas 9 system led to the establishment of homozygous gene edited (GE) TMPRSS2 knockout (KO) pigs. Delayed IAV replication was demonstrated in primary respiratory cells of KO pigs in vitro. IAV infection in vivo resulted in a significant reduction of virus shedding in the upper respiratory tract, and lower virus titers and pathological lesions in the lower respiratory tract of TMPRSS2 KO pigs as compared to wild-type pigs. Our findings support the commercial use of GE pigs to mitigate influenza A virus infection in pigs, as an alternative approach to prevent zoonotic influenza A transmissions from pigs to humans.
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Affiliation(s)
- Taeyong Kwon
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Bianca L. Artiaga
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Kristin M. Whitworth
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Kevin D. Wells
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Randall S. Prather
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Gustavo Delhon
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Jamie Retallick
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
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3
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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.
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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.
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4
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Zhao L, Li S, Deng L, Zhang Y, Jiang C, Wei Y, Xia J, Ping J. Host-specific SRSF7 regulates polymerase activity and replication of influenza A virus. Microbes Infect 2024:105401. [PMID: 39134172 DOI: 10.1016/j.micinf.2024.105401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/19/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024]
Abstract
Avian influenza viruses crossing the host barrier to infect humans have caused great panic in human society and seriously threatened public health. Herein, we revealed that knockdown of SRSF7 significantly down-regulated influenza virus titers and viral protein expression. We further observed for the first time that human SRSF7, but not avian SRSF7, significantly inhibited polymerase activity (PB2627E). Molecular mapping demonstrated that amino acids 206 to 228 of human SRSF7 play a decisive role in regulating the polymerase activity, which contains the amino acid motif absent in avian SRSF7. Importantly, our results illustrated that the PB2627K-encoding influenza virus induces SRSF7 protein degradation more strongly via the lysosome pathway and not via the proteasome pathway. Functional enrichment analysis of SRSF7-related KEGG pathways indicated that SRSF7 is closely related to cell growth and death. Lastly, our results showed that knocking down SRSF7 interferes with normal polymerase activity. Taken together, our results advance our understanding of interspecies transmission and our findings point out new targets for the development of drugs preventing or treating influenza virus infection.
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Affiliation(s)
- Lingcai Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shengmin Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Lulu Deng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yijia Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Chenfeng Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yurong Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, 830013, China.
| | - Jun Xia
- Key Laboratory of Herbivore Disease Prevention and Control, (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, China.
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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5
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Sun J, Kuai L, Zhang L, Xie Y, Zhang Y, Li Y, Peng Q, Shao Y, Yang Q, Tian WX, Zhu J, Qi J, Shi Y, Deng T, Gao GF. NS2 induces an influenza A RNA polymerase hexamer and acts as a transcription to replication switch. EMBO Rep 2024:10.1038/s44319-024-00208-4. [PMID: 39026012 DOI: 10.1038/s44319-024-00208-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
Genome transcription and replication of influenza A virus (FluA), catalyzed by viral RNA polymerase (FluAPol), are delicately controlled across the virus life cycle. A switch from transcription to replication occurring at later stage of an infection is critical for progeny virion production and viral non-structural protein NS2 has been implicated in regulating the switch. However, the underlying regulatory mechanisms and the structure of NS2 remained elusive for years. Here, we determine the cryo-EM structure of the FluAPol-NS2 complex at ~3.0 Å resolution. Surprisingly, three domain-swapped NS2 dimers arrange three symmetrical FluPol dimers into a highly ordered barrel-like hexamer. Further structural and functional analyses demonstrate that NS2 binding not only hampers the interaction between FluAPol and the Pol II CTD because of steric conflicts, but also impairs FluAPol transcriptase activity by stalling it in the replicase conformation. Moreover, this is the first visualization of the full-length NS2 structure. Our findings uncover key molecular mechanisms of the FluA transcription-replication switch and have implications for the development of antivirals.
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Affiliation(s)
- Junqing Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, 030801, China
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Kuai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuekun Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiuxian Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen-Xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Junhao Zhu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Shi
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tao Deng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - George F Gao
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Lee CY. Exploring Potential Intermediates in the Cross-Species Transmission of Influenza A Virus to Humans. Viruses 2024; 16:1129. [PMID: 39066291 PMCID: PMC11281536 DOI: 10.3390/v16071129] [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: 06/25/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The influenza A virus (IAV) has been a major cause of several pandemics, underscoring the importance of elucidating its transmission dynamics. This review investigates potential intermediate hosts in the cross-species transmission of IAV to humans, focusing on the factors that facilitate zoonotic events. We evaluate the roles of various animal hosts, including pigs, galliformes, companion animals, minks, marine mammals, and other animals, in the spread of IAV to humans.
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Affiliation(s)
- Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea;
- Untreatable Infectious Disease Institute, Kyungpook National University, Daegu 41944, Republic of Korea
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7
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Liu X, Chen W, Li K, Sheng J. RNA N6-methyladenosine methylation in influenza A virus infection. Front Microbiol 2024; 15:1401997. [PMID: 38957616 PMCID: PMC11217485 DOI: 10.3389/fmicb.2024.1401997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Influenza A virus (IAV) is a negative-sense single-stranded RNA virus that causes acute lung injury and acute respiratory distress syndrome, posing a serious threat to both animal and human health. N6-methyladenosine (m6A), a prevalent and abundant post-transcriptional methylation of RNA in eukaryotes, plays a crucial regulatory role in IAV infection by altering viral RNA and cellular transcripts to affect viral infection and the host immune response. This review focuses on the molecular mechanisms underlying m6A modification and its regulatory function in the context of IAV infection and the host immune response. This will provide a better understanding of virus-host interactions and offer insights into potential anti-IAV strategies.
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Affiliation(s)
- Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
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8
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Bessonne M, Morel J, Nevers Q, Da Costa B, Ballandras-Colas A, Chenavier F, Grange M, Roussel A, Crépin T, Delmas B. Antiviral activity of intracellular nanobodies targeting the influenza virus RNA-polymerase core. PLoS Pathog 2024; 20:e1011642. [PMID: 38875296 PMCID: PMC11210859 DOI: 10.1371/journal.ppat.1011642] [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: 08/30/2023] [Revised: 06/27/2024] [Accepted: 05/15/2024] [Indexed: 06/16/2024] Open
Abstract
Influenza viruses transcribe and replicate their genome in the nucleus of the infected cells, two functions that are supported by the viral RNA-dependent RNA-polymerase (FluPol). FluPol displays structural flexibility related to distinct functional states, from an inactive form to conformations competent for replication and transcription. FluPol machinery is constituted by a structurally-invariant core comprising the PB1 subunit stabilized with PA and PB2 domains, whereas the PA endonuclease and PB2 C-domains can pack in different configurations around the core. To get insights into the functioning of FluPol, we selected single-domain nanobodies (VHHs) specific of the influenza A FluPol core. When expressed intracellularly, some of them exhibited inhibitory activity on type A FluPol, but not on the type B one. The most potent VHH (VHH16) binds PA and the PA-PB1 dimer with an affinity below the nanomolar range. Ectopic intracellular expression of VHH16 in virus permissive cells blocks multiplication of different influenza A subtypes, even when induced at late times post-infection. VHH16 was found to interfere with the transport of the PA-PB1 dimer to the nucleus, without affecting its handling by the importin β RanBP5 and subsequent steps in FluPol assembly. Using FluPol mutants selected after passaging in VHH16-expressing cells, we identified the VHH16 binding site at the interface formed by PA residues with the N-terminus of PB1, overlapping or close to binding sites of two host proteins, ANP32A and RNA-polymerase II RPB1 subunit which are critical for virus replication and transcription, respectively. These data suggest that the VHH16 neutralization is likely due to several activities, altering the import of the PA-PB1 dimer into the nucleus as well as inhibiting specifically virus transcription and replication. Thus, the VHH16 binding site represents a new Achilles' heel for FluPol and as such, a potential target for antiviral development.
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Affiliation(s)
- Mélissa Bessonne
- Unité de Virologie et Immunologie moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jessica Morel
- Unité de Virologie et Immunologie moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Quentin Nevers
- Unité de Virologie et Immunologie moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bruno Da Costa
- Unité de Virologie et Immunologie moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Florian Chenavier
- Institut de biologie structurale, CNRS, Université de Grenoble, Grenoble, France
| | - Magali Grange
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), CNRS, Université d’Aix-Marseille, Marseille, France
| | - Alain Roussel
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), CNRS, Université d’Aix-Marseille, Marseille, France
| | - Thibaut Crépin
- Institut de biologie structurale, CNRS, Université de Grenoble, Grenoble, France
| | - Bernard Delmas
- Unité de Virologie et Immunologie moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
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9
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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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10
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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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11
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Keown J, Baazaoui A, Šebesta M, Štefl R, Carrique L, Fodor E, Grimes JM. Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. J Virol 2024; 98:e0013824. [PMID: 38563748 PMCID: PMC11092357 DOI: 10.1128/jvi.00138-24] [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: 01/19/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Influenza A viruses, causing seasonal epidemics and occasional pandemics, rely on interactions with host proteins for their RNA genome transcription and replication. The viral RNA polymerase utilizes host RNA polymerase II (Pol II) and interacts with the serine 5 phosphorylated (pS5) C-terminal domain (CTD) of Pol II to initiate transcription. Our study, using single-particle electron cryomicroscopy (cryo-EM), reveals the structure of the 1918 pandemic influenza A virus polymerase bound to a synthetic pS5 CTD peptide composed of four heptad repeats mimicking the 52 heptad repeat mammalian Pol II CTD. The structure shows that the CTD peptide binds at the C-terminal domain of the PA viral polymerase subunit (PA-C) and reveals a previously unobserved position of the 627 domain of the PB2 subunit near the CTD. We identify crucial residues of the CTD peptide that mediate interactions with positively charged cavities on PA-C, explaining the preference of the viral polymerase for pS5 CTD. Functional analysis of mutants targeting the CTD-binding site within PA-C reveals reduced transcriptional function or defects in replication, highlighting the multifunctional role of PA-C in viral RNA synthesis. Our study provides insights into the structural and functional aspects of the influenza virus polymerase-host Pol II interaction and identifies a target for antiviral development.IMPORTANCEUnderstanding the intricate interactions between influenza A viruses and host proteins is crucial for developing targeted antiviral strategies. This study employs advanced imaging techniques to uncover the structural nuances of the 1918 pandemic influenza A virus polymerase bound to a specific host protein, shedding light on the vital process of viral RNA synthesis. The study identifies key amino acid residues in the influenza polymerase involved in binding host polymerase II (Pol II) and highlights their role in both viral transcription and genome replication. These findings not only deepen our understanding of the influenza virus life cycle but also pinpoint a potential target for antiviral development. By elucidating the structural and functional aspects of the influenza virus polymerase-host Pol II interaction, this research provides a foundation for designing interventions to disrupt viral replication and transcription, offering promising avenues for future antiviral therapies.
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Affiliation(s)
- Jeremy Keown
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alaa Baazaoui
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marek Šebesta
- CEITEC–Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Richard Štefl
- CEITEC–Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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12
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Yu DS, Wu XX, Weng TH, Cheng LF, Liu FM, Wu HB, Lu XY, Wu NP, Sun SL, Yao HP. Host proteins interact with viral elements and affect the life cycle of highly pathogenic avian influenza A virus H7N9. Heliyon 2024; 10:e28218. [PMID: 38560106 PMCID: PMC10981070 DOI: 10.1016/j.heliyon.2024.e28218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Host-virus interactions can significantly impact the viral life cycle and pathogenesis; however, our understanding of the specific host factors involved in highly pathogenic avian influenza A virus H7N9 (HPAI H7N9) infection is currently restricted. Herein, we designed and synthesized 65 small interfering RNAs targeting host genes potentially associated with various aspects of RNA virus life cycles. Afterward, HPAI H7N9 viruses were isolated and RNA interference was used to screen for host factors likely to be involved in the life cycle of HPAI H7N9. Moreover, the research entailed assessing the associations between host proteins and HPAI H7N9 proteins. Twelve key host proteins were identified: Annexin A (ANXA)2, ANXA5, adaptor related protein complex 2 subunit sigma 1 (AP2S1), adaptor related protein complex 3 subunit sigma 1 (AP3S1), ATP synthase F1 subunit alpha (ATP5A1), COPI coat complex subunit alpha (COP)A, COPG1, heat shock protein family A (Hsp70) member 1A (HSPA)1A, HSPA8, heat shock protein 90 alpha family class A member 1 (HSP90AA1), RAB11B, and RAB18. Co-immunoprecipitation revealed intricate interactions between viral proteins (hemagglutinin, matrix 1 protein, neuraminidase, nucleoprotein, polymerase basic 1, and polymerase basic 2) and these host proteins, presumably playing a crucial role in modulating the life cycle of HPAI H7N9. Notably, ANXA5, AP2S1, AP3S1, ATP5A1, HSP90A1, and RAB18, were identified as novel interactors with HPAI H7N9 proteins rather than other influenza A viruses (IAVs). These findings underscore the significance of host-viral protein interactions in shaping the dynamics of HPAI H7N9 infection, while highlighting subtle variations compared with other IAVs. Deeper understanding of these interactions holds promise to advance disease treatment and prevention strategies.
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Affiliation(s)
- Dong-Shan Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
- Department of Infectious Disease, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, PR China
| | - Xiao-Xin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
| | - Tian-Hao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
| | - Lin-Fang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
| | - Fu-Min Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
| | - Hai-Bo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
- Department of Infectious Disease, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, PR China
| | - Xiang-Yun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250021, PR China
| | - Shui-Lin Sun
- Department of Infectious Disease, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, PR China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310003, PR China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250021, PR China
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13
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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.
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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.
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14
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Zhang M, Liu M, Chen H, Qiu T, Jin X, Fu W, Teng Q, Zhao C, Xu J, Li Z, Zhang X. PB2 residue 473 contributes to the mammalian virulence of H7N9 avian influenza virus by modulating viral polymerase activity via ANP32A. J Virol 2024; 98:e0194423. [PMID: 38421166 PMCID: PMC10949425 DOI: 10.1128/jvi.01944-23] [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: 12/14/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Since the first human infection reported in 2013, H7N9 avian influenza virus (AIV) has been regarded as a serious threat to human health. In this study, we sought to identify the virulence determinant of the H7N9 virus in mammalian hosts. By comparing the virulence of the SH/4664 H7N9 virus, a non-virulent H9N2 virus, and various H7N9-H9N2 hybrid viruses in infected mice, we first pinpointed PB2 as the primary viral factor accounting for the difference between H7N9 and H9N2 in mammalian virulence. We further analyzed the in vivo effects of individually mutating H7N9 PB2 residues different from the closely related H9N2 virus and consequently found residue 473, alongside the well-known residue 627, to be critical for the virulence of the H7N9 virus in mice and the activity of its reconstituted viral polymerase in mammalian cells. The importance of PB2-473 was further strengthened by studying reverse H7N9 substitutions in the H9N2 background. Finally, we surprisingly found that species-specific usage of ANP32A, a family member of host factors connecting with the PB2-627 polymorphism, mediates the contribution of PB2 473 residue to the mammalian adaption of AIV polymerase, as the attenuating effect of PB2 M473T on the viral polymerase activity and viral growth of the H7N9 virus could be efficiently complemented by co-expression of chicken ANP32A but not mouse ANP32A and ANP32B. Together, our studies uncovered the PB2 473 residue as a novel viral host range determinant of AIVs via species-specific co-opting of the ANP32 host factor to support viral polymerase activity.IMPORTANCEThe H7N9 avian influenza virus has been considered to have the potential to cause the next pandemic since the first case of human infection reported in 2013. In this study, we identified PB2 residue 473 as a new determinant of mouse virulence and mammalian adaptation of the viral polymerase of the H7N9 virus and its non-pathogenic H9N2 counterparts. We further demonstrated that the variation in PB2-473 is functionally linked to differential co-opting of the host ANP32A protein in supporting viral polymerase activity, which is analogous to the well-known PB2-627 polymorphism, albeit the two PB2 positions are spatially distant. By providing new mechanistic insight into the PB2-mediated host range determination of influenza A viruses, our study implicated the potential existence of multiple PB2-ANP32 interfaces that could be targets for developing new antivirals against the H7N9 virus as well as other mammalian-adapted influenza viruses.
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Affiliation(s)
- Miaomiao Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shanghai Veterinary Research Institute, Shanghai, China
| | - Mingbin Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Shanghai, China
| | - Tianyi Qiu
- Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xuanxuan Jin
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Weihui Fu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Shanghai, China
| | - Chen Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Shanghai, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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15
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Zhou Y, Li T, Zhang Y, Zhang N, Guo Y, Gao X, Peng W, Shu S, Zhao C, Cui D, Sun H, Sun Y, Liu J, Tang J, Zhang R, Pu J. BAG6 inhibits influenza A virus replication by inducing viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. PLoS Pathog 2024; 20:e1012110. [PMID: 38498560 PMCID: PMC10977894 DOI: 10.1371/journal.ppat.1012110] [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: 09/20/2023] [Revised: 03/28/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
The interaction between influenza A virus (IAV) and host proteins is an important process that greatly influences viral replication and pathogenicity. PB2 protein is a subunit of viral ribonucleoprotein (vRNP) complex playing distinct roles in viral transcription and replication. BAG6 (BCL2-associated athanogene 6) as a multifunctional host protein participates in physiological and pathological processes. Here, we identify BAG6 as a new restriction factor for IAV replication through targeting PB2. For both avian and human influenza viruses, overexpression of BAG6 reduced viral protein expression and virus titers, whereas deletion of BAG6 significantly enhanced virus replication. Moreover, BAG6-knockdown mice developed more severe clinical symptoms and higher viral loads upon IAV infection. Mechanistically, BAG6 restricted IAV transcription and replication by inhibiting the activity of viral RNA-dependent RNA polymerase (RdRp). The co-immunoprecipitation assays showed BAG6 specifically interacted with the N-terminus of PB2 and competed with PB1 for RdRp complex assembly. The ubiquitination assay indicated that BAG6 promoted PB2 ubiquitination at K189 residue and targeted PB2 for K48-linked ubiquitination degradation. The antiviral effect of BAG6 necessitated its N-terminal region containing a ubiquitin-like (UBL) domain (17-92aa) and a PB2-binding domain (124-186aa), which are synergistically responsible for viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. These findings unravel a novel antiviral mechanism via the interaction of viral PB2 and host protein BAG6 during avian or human influenza virus infection and highlight a potential application of BAG6 for antiviral drug development.
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Affiliation(s)
- Yong Zhou
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tian Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yunfan Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuxin Guo
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoyi Gao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenjing Peng
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Sicheng Shu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chuankuo Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Honglei Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yipeng Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jun Tang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rui Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Basic Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Juan Pu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Preventive Veterinary, College of Veterinary Medicine, China Agricultural University, Beijing, China
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16
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [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: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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17
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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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18
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Na L, Sun L, Yu M, Zhang Y, Zhang Y, Zhang Z, Zhang H, Qi T, Guo W, Guo X, Wang S, Wang J, Lin Y, Wang X. Avian ANP32A incorporated in avian influenza A virions promotes interspecies transmission by priming early viral replication in mammals. SCIENCE ADVANCES 2024; 10:eadj4163. [PMID: 38295177 PMCID: PMC10830118 DOI: 10.1126/sciadv.adj4163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
Species-specific differences in acidic nuclear phosphoprotein 32 family member A (ANP32A) determine the restriction of avian-signature polymerase in mammalian cells. Mutations that evade this restriction, such as PB2-E627K, are frequently acquired when avian influenza A viruses jump from avian hosts to mammalian hosts. However, the mechanism underlying this adaptation process is still unclear. Here, we report that host factor ANP32 proteins can be incorporated into influenza viral particles through combination with the viral RNA polymerase (vPol) and then transferred into targeted cells where they support virus replication. The packaging of the ANP32 proteins into influenza viruses is dependent on their affinity with the vPol. Avian ANP32A (avANP32A) delivered by avian influenza A virions primes early viral replication in mammalian cells, thereby favoring the downstream interspecies transmission event by increasing the total amount of virus carrying adaptive mutations. Our study clarifies one role of avANP32A where it is used by avian influenza virus to help counteract the restriction barrier in mammals.
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Affiliation(s)
- Lei Na
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Liuke Sun
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mengmeng Yu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yingzhi Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhenyu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Haili Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Ting Qi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wei Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xing Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Shida Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jingfei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuezhi Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiaojun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
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19
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Zhang L, Shao Y, Wang Y, Yang Q, Guo J, Gao GF, Deng T. Twenty natural amino acid substitution screening at the last residue 121 of influenza A virus NS2 protein reveals the critical role of NS2 in promoting virus genome replication by coordinating with viral polymerase. J Virol 2024; 98:e0116623. [PMID: 38054704 PMCID: PMC10804943 DOI: 10.1128/jvi.01166-23] [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: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023] Open
Abstract
Both influenza A virus genome transcription (vRNA→mRNA) and replication (vRNA→cRNA→vRNA), catalyzed by the influenza RNA polymerase (FluPol), are dynamically regulated across the virus life cycle. It has been reported that the last amino acid I121 of the viral NS2 protein plays a critical role in promoting viral genome replication in influenza mini-replicon systems. Here, we performed a 20 natural amino acid substitution screening at residue NS2-I121 in the context of virus infection. We found that the hydrophobicity of the residue 121 is essential for virus survival. Interestingly, through serial passage of the rescued mutant viruses, we further identified adaptive mutations PA-K19E and PB1-S713N on FluPol which could effectively compensate for the replication-promoting defect caused by NS2-I121 mutation in the both mini-replicon and virus infection systems. Structural analysis of different functional states of FluPol indicates that PA-K19E and PB1-S713N could stabilize the replicase conformation of FluPol. By using a cell-based NanoBiT complementary reporter assay, we further demonstrate that both wild-type NS2 and PA-K19E/PB1-S713N could enhance FluPol dimerization, which is necessary for genome replication. These results reveal the critical role NS2 plays in promoting viral genome replication by coordinating with FluPol.IMPORTANCEThe intrinsic mechanisms of influenza RNA polymerase (FluPol) in catalyzing viral genome transcription and replication have been largely resolved. However, the mechanisms of how transcription and replication are dynamically regulated remain elusive. We recently reported that the last amino acid of the viral NS2 protein plays a critical role in promoting viral genome replication in an influenza mini-replicon system. Here, we conducted a 20 amino acid substitution screening at the last residue 121 in virus rescue and serial passage. Our results demonstrate that the replication-promoting function of NS2 is important for virus survival and efficient multiplication. We further show evidence that NS2 and NS2-I121 adaptive mutations PA-K19E/PB1-S713N regulate virus genome replication by promoting FluPol dimerization. This work highlights the coordination between NS2 and FluPol in fulfilling efficient genome replication. It further advances our understanding of the regulation of viral RNA synthesis for influenza A virus.
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Affiliation(s)
- Lei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- />Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuekun Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qiuxian Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Deng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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20
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Rashid MU, Coombs KM. Chloride Intracellular Channel Protein 1 (CLIC1) Is a Critical Host Cellular Factor for Influenza A Virus Replication. Viruses 2024; 16:129. [PMID: 38257829 PMCID: PMC10819074 DOI: 10.3390/v16010129] [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: 11/25/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
(1) Background: Influenza A Virus (IAV) uses host cellular proteins during replication in host cells. IAV infection causes elevated expression of chloride intracellular channel protein 1 (CLIC1) in lung epithelial cells, but the importance of this protein in IAV replication is unknown. (2) In this study, we determined the role of CLIC1 in IAV replication by investigating the effects of CLIC1 knockdown (KD) on IAV viral protein translation, genomic RNA transcription, and host cellular proteome dysregulation. (3) Results: CLIC1 KD in A549 human lung epithelial cells resulted in a significant decrease in progeny supernatant IAV, but virus protein expression was unaffected. However, a significantly larger number of viral RNAs accumulated in CLIC1 KD cells. Treatment with a CLIC1 inhibitor also caused a significant reduction in IAV replication, suggesting that CLIC1 is an important host factor in IAV replication. SomaScan®, which measures 1322 proteins, identified IAV-induced dysregulated proteins in wild-type cells and in CLIC1 KD cells. The expression of 116 and 149 proteins was significantly altered in wild-type and in CLIC1 KD cells, respectively. A large number of the dysregulated proteins in CLIC1 KD cells were associated with cellular transcription and predicted to be inhibited during IAV replication. (4) Conclusions: This study suggests that CLIC1 is involved in later stages of IAV replication. Further investigation should clarify mechanism(s) for the development of anti-IAV drugs targeting CLIC1 protein.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, Room 513, John Buhler Research Centre, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
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21
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Kwon T, Artiaga BL, McDowell CD, Whitworth KM, Wells KD, Prather RS, Delhon G, Cigan M, White SN, Retallick J, Gaudreault NN, Morozov I, Richt JA. Gene editing of pigs to control influenza A virus infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575771. [PMID: 38293027 PMCID: PMC10827075 DOI: 10.1101/2024.01.15.575771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Proteolytic activation of the hemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ubiquitous proteases, such as furin; in contrast, the monobasic HA motif is recognized and activated by trypsin-like proteases, such as the transmembrane serine protease 2 (TMPRSS2). Here, we aimed to determine the effects of TMPRSS2 on the replication of pandemic H1N1 and H3N2 subtype IAVs in the natural host, the pig. The use of the CRISPR/Cas 9 system led to the establishment of homozygous gene edited (GE) TMPRSS2 knockout (KO) pigs. Delayed IAV replication was demonstrated in primary respiratory cells of KO pigs in vitro. IAV infection in vivo resulted in significant reduction of virus shedding in the upper respiratory tract, and lower virus titers and pathological lesions in the lower respiratory tract of TMPRSS2 KO pigs as compared to WT pigs. Our findings could support the commercial use of GE pigs to minimize (i) the economic losses caused by IAV infection in pigs, and (ii) the emergence of novel IAVs with pandemic potential through genetic reassortment in the "mixing vessel", the pig.
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Affiliation(s)
- Taeyong Kwon
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Bianca L. Artiaga
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Kristin M. Whitworth
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, Columbia, MO 65211, USA
| | - Kevin D. Wells
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, Columbia, MO 65211, USA
| | - Randall S. Prather
- Division of Animal Science & National Swine Resource and Research Center, College of Agriculture Food and Natural Resources, University of Missouri, Columbia, Columbia, MO 65211, USA
| | - Gustavo Delhon
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | | | | | - Jamie Retallick
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
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22
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Li X, Ye Z, Plant EP. 5' copyback defective viral genomes are major component in clinical and non-clinical influenza samples. Virus Res 2024; 339:199274. [PMID: 37981214 PMCID: PMC10701078 DOI: 10.1016/j.virusres.2023.199274] [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: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Clinical samples from people with influenza disease have been analyzed to assess the presence and abundance of Defective Viral Genomes (DVGs), but these have not been assessed using the same bioinformatic pipeline. The type of DVG most described for influenza infections (deletion DVGs) differs from the most commonly described DVGs from non-segmented negative stranded viruses (5' copyback). This could be attributed to either differences between viruses or the tools used to detect and characterize DVGs. Here we analyze several NGS datasets from people infected with different types of influenza virus using the same bioinformatic pipeline. We observe that 5' copyback DVGs are prevalent in all human clinical samples but not in the cultured samples. To address this discrepancy between clinical and laboratory cultures, we infected cell culture and ferrets with an H5N8 influenza A virus (FLUAV) and analyzed the DVG composition. The results demonstrate that the DVG population is skewed toward 5' copyback DVGs in the in vivo infections and deletion DVGs in the in vitro infections. This demonstrates that there are differences in vivo genome production and in vitro genome production, and this has implications for how the role of DVGs in clinical disease is studied. We also investigate the role the host cofactor ANP32B has in DVG production.
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Affiliation(s)
- Xing Li
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Ewan P Plant
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA.
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23
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Sänger L, Williams HM, Yu D, Vogel D, Kosinski J, Rosenthal M, Uetrecht C. RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment. J Am Chem Soc 2023; 145:27958-27974. [PMID: 38104324 PMCID: PMC10755698 DOI: 10.1021/jacs.3c07325] [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: 07/10/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Lassa virus is a negative-strand RNA virus with only four structural proteins that causes periodic outbreaks in West Africa. The nucleoprotein (NP) encapsidates the viral genome, forming ribonucleoprotein complexes (RNPs) together with the viral RNA and the L protein. RNPs must be continuously restructured during viral genome replication and transcription. The Z protein is important for membrane recruitment of RNPs, viral particle assembly, and budding and has also been shown to interact with the L protein. However, the interaction of NP, viral RNA, and Z is poorly understood. Here, we characterize the interactions between Lassa virus NP, Z, and RNA using structural mass spectrometry. We identify the presence of RNA as the driver for the disassembly of ring-like NP trimers, a storage form, into monomers to subsequently form higher order RNA-bound NP assemblies. We locate the interaction site of Z and NP and demonstrate that while NP binds Z independently of the presence of RNA, this interaction is pH-dependent. These data improve our understanding of RNP assembly, recruitment, and release in Lassa virus.
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Affiliation(s)
- Lennart Sänger
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Harry M. Williams
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
| | - Dingquan Yu
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
| | - Dominik Vogel
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Jan Kosinski
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Maria Rosenthal
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
- Faculty
V: School of Life Sciences, University of
Siegen, Am Eichenhang 50, 57076 Siegen, Germany
- Deutsches
Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
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24
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Sabsay KR, te Velthuis AJW. Negative and ambisense RNA virus ribonucleocapsids: more than protective armor. Microbiol Mol Biol Rev 2023; 87:e0008223. [PMID: 37750733 PMCID: PMC10732063 DOI: 10.1128/mmbr.00082-23] [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] [Indexed: 09/27/2023] Open
Abstract
SUMMARYNegative and ambisense RNA viruses are the causative agents of important human diseases such as influenza, measles, Lassa fever, and Ebola hemorrhagic fever. The viral genome of these RNA viruses consists of one or more single-stranded RNA molecules that are encapsidated by viral nucleocapsid proteins to form a ribonucleoprotein complex (RNP). This RNP acts as protection, as a scaffold for RNA folding, and as the context for viral replication and transcription by a viral RNA polymerase. However, the roles of the viral nucleoproteins extend beyond these functions during the viral infection cycle. Recent advances in structural biology techniques and analysis methods have provided new insights into the formation, function, dynamics, and evolution of negative sense virus nucleocapsid proteins, as well as the role that they play in host innate immune responses against viral infection. In this review, we discuss the various roles of nucleocapsid proteins, both in the context of RNPs and in RNA-free states, as well as the open questions that remain.
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Affiliation(s)
- Kimberly R. Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Aartjan J. W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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25
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Arragain B, Pelosse M, Thompson A, Cusack S. Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Nat Commun 2023; 14:8145. [PMID: 38066000 PMCID: PMC10709604 DOI: 10.1038/s41467-023-44044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated.
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Affiliation(s)
- Benoit Arragain
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Martin Pelosse
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Albert Thompson
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
- The Francis Crick Institute, London, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.
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26
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Liang Y. Pathogenicity and virulence of influenza. Virulence 2023; 14:2223057. [PMID: 37339323 DOI: 10.1080/21505594.2023.2223057] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
Influenza viruses, including four major types (A, B, C, and D), can cause mild-to-severe and lethal diseases in humans and animals. Influenza viruses evolve rapidly through antigenic drift (mutation) and shift (reassortment of the segmented viral genome). New variants, strains, and subtypes have emerged frequently, causing epidemic, zoonotic, and pandemic infections, despite currently available vaccines and antiviral drugs. In recent years, avian influenza viruses, such as H5 and H7 subtypes, have caused hundreds to thousands of zoonotic infections in humans with high case fatality rates. The likelihood of these animal influenza viruses acquiring airborne transmission in humans through viral evolution poses great concern for the next pandemic. Severe influenza viral disease is caused by both direct viral cytopathic effects and exacerbated host immune response against high viral loads. Studies have identified various mutations in viral genes that increase viral replication and transmission, alter tissue tropism or species specificity, and evade antivirals or pre-existing immunity. Significant progress has also been made in identifying and characterizing the host components that mediate antiviral responses, pro-viral functions, or immunopathogenesis following influenza viral infections. This review summarizes the current knowledge on viral determinants of influenza virulence and pathogenicity, protective and immunopathogenic aspects of host innate and adaptive immune responses, and antiviral and pro-viral roles of host factors and cellular signalling pathways. Understanding the molecular mechanisms of viral virulence factors and virus-host interactions is critical for the development of preventive and therapeutic measures against influenza diseases.
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Affiliation(s)
- Yuying Liang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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27
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Zhu Z, Fan H, Fodor E. Defining the minimal components of the influenza A virus replication machinery via an in vitro reconstitution system. PLoS Biol 2023; 21:e3002370. [PMID: 37943954 PMCID: PMC10662765 DOI: 10.1371/journal.pbio.3002370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
During influenza A virus infection, the viral RNA polymerase transcribes the viral negative-sense segmented RNA genome and replicates it in a two-step process via complementary RNA within viral ribonucleoprotein (vRNP) complexes. While numerous viral and host factors involved in vRNP functions have been identified, dissecting the roles of individual factors remains challenging due to the complex cellular environment in which vRNP activity has been studied. To overcome this challenge, we reconstituted viral transcription and a full cycle of replication in a test tube using vRNPs isolated from virions and recombinant factors essential for these processes. This novel system uncovers the minimal components required for influenza virus replication and also reveals new roles of regulatory factors in viral replication. Moreover, it sheds light on the molecular interplay underlying the temporal regulation of viral transcription and replication. Our highly robust in vitro system enables systematic functional analysis of factors modulating influenza virus vRNP activity and paves the way for imaging key steps of viral transcription and replication.
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Affiliation(s)
- Zihan Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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28
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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: 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: 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.
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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.
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29
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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: 7] [Impact Index Per Article: 7.0] [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.
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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.
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30
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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: 2.0] [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.
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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.
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31
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Pekarek MJ, Weaver EA. Existing Evidence for Influenza B Virus Adaptations to Drive Replication in Humans as the Primary Host. Viruses 2023; 15:2032. [PMID: 37896807 PMCID: PMC10612074 DOI: 10.3390/v15102032] [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: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Influenza B virus (IBV) is one of the two major types of influenza viruses that circulate each year. Unlike influenza A viruses, IBV does not harbor pandemic potential due to its lack of historical circulation in non-human hosts. Many studies and reviews have highlighted important factors for host determination of influenza A viruses. However, much less is known about the factors driving IBV replication in humans. We hypothesize that similar factors influence the host restriction of IBV. Here, we compile and review the current understanding of host factors crucial for the various stages of the IBV viral replication cycle. While we discovered the research in this area of IBV is limited, we review known host factors that may indicate possible host restriction of IBV to humans. These factors include the IBV hemagglutinin (HA) protein, host nuclear factors, and viral immune evasion proteins. Our review frames the current understanding of IBV adaptations to replication in humans. However, this review is limited by the amount of research previously completed on IBV host determinants and would benefit from additional future research in this area.
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Affiliation(s)
| | - Eric A. Weaver
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
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32
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Abstract
The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.
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Affiliation(s)
- Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
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33
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Camacho-Zarco AR, Yu L, Krischuns T, Dedeoglu S, Maurin D, Bouvignies G, Crépin T, Ruigrok RWH, Cusack S, Naffakh N, Blackledge M. Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation. J Am Chem Soc 2023; 145:20985-21001. [PMID: 37707433 PMCID: PMC10540212 DOI: 10.1021/jacs.3c06965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Indexed: 09/15/2023]
Abstract
Adaptation of avian influenza RNA polymerase (FluPol) to human cells requires mutations on the 627-NLS domains of the PB2 subunit. The E627K adaptive mutation compensates a 33-amino-acid deletion in the acidic intrinsically disordered domain of the host transcription regulator ANP32A, a deletion that restricts FluPol activity in mammalian cells. The function of ANP32A in the replication transcription complex and in particular its role in host restriction remains poorly understood. Here we characterize ternary complexes formed between ANP32A, FluPol, and the viral nucleoprotein, NP, supporting the putative role of ANP32A in shuttling NP to the replicase complex. We demonstrate that while FluPol and NP can simultaneously bind distinct linear motifs on avian ANP32A, the deletion in the shorter human ANP32A blocks this mode of colocalization. NMR reveals that NP and human-adapted FluPol, containing the E627 K mutation, simultaneously bind the identical extended linear motif on human ANP32A in an electrostatically driven, highly dynamic and multivalent ternary complex. This study reveals a probable molecular mechanism underlying host adaptation, whereby E627K, which enhances the basic surface of the 627 domain, is selected to confer the necessary multivalent properties to allow ANP32A to colocalize NP and FluPol in human cells.
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Affiliation(s)
- Aldo R. Camacho-Zarco
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Lefan Yu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Tim Krischuns
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Selin Dedeoglu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire
des Biomolécules, Département de Chimie, École
Normale Supérieur, UPMC Université Paris 06, CNRS, PSL Research University, 24 rue Lhomond, 75005 Paris, France
| | - Thibaut Crépin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Rob W. H. Ruigrok
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Stephan Cusack
- European
Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Nadia Naffakh
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Martin Blackledge
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
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34
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Zhang Z, Lu C, Mo B, Bai K, Ge XY, Deng L, Peng Y. Prediction of mammalian virus cross-species transmission based on host proteins. Microbiol Spectr 2023; 11:e0536822. [PMID: 37754753 PMCID: PMC10581197 DOI: 10.1128/spectrum.05368-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Most emerging viruses are spilled over from mammals. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of newly emerging viruses. This study systematically investigated the host proteins associated with the cross-species transmission of mammalian viruses based on 1,271 pairs of virus-mammal interactions including 382 viruses from 33 viral families and 73 mammal species from 11 orders. Numerous host proteins were found to contribute to the cross-species transmission of mammalian viruses. Host proteins potentially contributing to virus cross-species transmission are specific to viral families, and few overlaps of such host proteins are observed in different viral families. Based on these host proteins, the random-forest (RF) models were built to predict the cross-species transmission potential of mammalian viruses. Moderate performance was obtained when using all viruses together. However, when modeling by viral family, the performance of the RF models varied much among viral families. In 13 viral families such as Flaviviridae, Retroviridae, and Poxviridae, the AUC of the RF model was greater than 0.8. Finally, the contribution of virus receptors to cross-species transmission was evaluated, and the virus receptor was found to have a minor effect in predicting the cross-species transmission of mammalian viruses. The study deepens our understanding of the mechanism of virus cross-species transmission and provides a framework for predicting the cross-species transmission of mammalian viruses. IMPORTANCE Emerging viruses pose serious threats to humans. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of emerging viruses. This study systematically identified host factors associated with cross-species transmission of mammalian viruses and further built machine-learning models for predicting cross-species transmission of the viruses based on host factors including virus receptors. The study not only deepens our understanding of the mechanism of virus cross-species transmission but also provides a framework for predicting the cross-species transmission of mammalian viruses based on host factors.
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Affiliation(s)
- Zheng Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Bocheng Mo
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Kehan Bai
- Hunan Juyoubiotech Co., Ltd, Changsha, Hunan, China
| | - Xing-Yi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Li Deng
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, Hunan, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
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35
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Briggs K, Kapczynski DR. Comparative analysis of PB2 residue 627E/K/V in H5 subtypes of avian influenza viruses isolated from birds and mammals. Front Vet Sci 2023; 10:1250952. [PMID: 37720472 PMCID: PMC10502342 DOI: 10.3389/fvets.2023.1250952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Avian influenza viruses (AIVs) are naturally found in wild birds, primarily in migratory waterfowl. Although species barriers exist, many AIVs have demonstrated the ability to jump from bird species to mammalian species. A key contributor to this jump is the adaption of the viral RNA polymerase complex to a new host for efficient replication of its RNA genome. The AIV PB2 gene appears to be essential in this conversion, as key residues have been discovered at amino acid position 627 that interact with the host cellular protein, acidic nuclear phosphoprotein 32 family member A (ANP32A). In particular, the conversion of glutamic acid (E) to lysine (K) is frequently observed at this position following isolation in mammals. The focus of this report was to compare the distribution of PB2 627 residues from different lineages and origins of H5 AIV, determine the prevalence between historical and contemporary sequences, and investigate the ratio of amino acids in avian vs. mammalian AIV sequences. Results demonstrate a low prevalence of E627K in H5 non-Goose/Guangdong/1996-lineage (Gs/GD) AIV samples, with a low number of mammalian sequences in general. In contrast, the H5-Gs/GD lineage sequences had an increased prevalence of the E627K mutation and contained more mammalian sequences. An approximate 40% conversion of E to K was observed in human sequences of H5 AIV, suggesting a non-exclusive requirement. Taken together, these results expand our understanding of the distribution of these residues within different subtypes of AIV and aid in our knowledge of PB2 mutations in different species.
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Affiliation(s)
| | - Darrell R. Kapczynski
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, Athens, GA, United States
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36
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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: 5] [Impact Index Per Article: 5.0] [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.
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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.
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37
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Sun L, Kong H, Yu M, Zhang Z, Zhang H, Na L, Qu Y, Zhang Y, Chen H, Wang X. The SUMO-interacting motif in NS2 promotes adaptation of avian influenza virus to mammals. SCIENCE ADVANCES 2023; 9:eadg5175. [PMID: 37436988 DOI: 10.1126/sciadv.adg5175] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Species differences in the host factor ANP32A/B result in the restriction of avian influenza virus polymerase (vPol) in mammalian cells. Efficient replication of avian influenza viruses in mammalian cells often requires adaptive mutations, such as PB2-E627K, to enable the virus to use mammalian ANP32A/B. However, the molecular basis for the productive replication of avian influenza viruses without prior adaptation in mammals remains poorly understood. We show that avian influenza virus NS2 protein help to overcome mammalian ANP32A/B-mediated restriction to avian vPol activity by promoting avian vRNP assembly and enhancing mammalian ANP32A/B-vRNP interactions. A conserved SUMO-interacting motif (SIM) in NS2 is required for its avian polymerase-enhancing properties. We also demonstrate that disrupting SIM integrity in NS2 impairs avian influenza virus replication and pathogenicity in mammalian hosts, but not in avian hosts. Our results identify NS2 as a cofactor in the adaptation process of avian influenza virus to mammals.
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Affiliation(s)
- Liuke Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Huihui Kong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mengmeng Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhenyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Haili Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lei Na
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuxing Qu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China
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38
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Kleinehr J, Schöfbänker M, Daniel K, Günl F, Mohamed FF, Janowski J, Brunotte L, Boergeling Y, Liebmann M, Behrens M, Gerdemann A, Klotz L, Esselen M, Humpf HU, Ludwig S, Hrincius ER. Glycolytic interference blocks influenza A virus propagation by impairing viral polymerase-driven synthesis of genomic vRNA. PLoS Pathog 2023; 19:e1010986. [PMID: 37440521 DOI: 10.1371/journal.ppat.1010986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/10/2023] [Indexed: 07/15/2023] Open
Abstract
Influenza A virus (IAV), like any other virus, provokes considerable modifications of its host cell's metabolism. This includes a substantial increase in the uptake as well as the metabolization of glucose. Although it is known for quite some time that suppression of glucose metabolism restricts virus replication, the exact molecular impact on the viral life cycle remained enigmatic so far. Using 2-deoxy-d-glucose (2-DG) we examined how well inhibition of glycolysis is tolerated by host cells and which step of the IAV life cycle is affected. We observed that effects induced by 2-DG are reversible and that cells can cope with relatively high concentrations of the inhibitor by compensating the loss of glycolytic activity by upregulating other metabolic pathways. Moreover, mass spectrometry data provided information on various metabolic modifications induced by either the virus or agents interfering with glycolysis. In the presence of 2-DG viral titers were significantly reduced in a dose-dependent manner. The supplementation of direct or indirect glycolysis metabolites led to a partial or almost complete reversion of the inhibitory effect of 2-DG on viral growth and demonstrated that indeed the inhibition of glycolysis and not of N-linked glycosylation was responsible for the observed phenotype. Importantly, we could show via conventional and strand-specific qPCR that the treatment with 2-DG led to a prolonged phase of viral mRNA synthesis while the accumulation of genomic vRNA was strongly reduced. At the same time, minigenome assays showed no signs of a general reduction of replicative capacity of the viral polymerase. Therefore, our data suggest that the significant reduction in IAV replication by glycolytic interference occurs mainly due to an impairment of the dynamic regulation of the viral polymerase which conveys the transition of the enzyme's function from transcription to replication.
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Affiliation(s)
- Jens Kleinehr
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Michael Schöfbänker
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Katharina Daniel
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Franziska Günl
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Fakry Fahmy Mohamed
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt
| | - Josua Janowski
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Linda Brunotte
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Yvonne Boergeling
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Marie Liebmann
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, Muenster, Germany
| | - Matthias Behrens
- Institute of Food Chemistry, Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Andrea Gerdemann
- Institute of Food Chemistry, Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, Muenster, Germany
| | - Melanie Esselen
- Institute of Food Chemistry, Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
| | - Eike R Hrincius
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Muenster, Germany
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Peacock TP, Sheppard CM, Lister MG, Staller E, Frise R, Swann OC, Goldhill DH, Long JS, Barclay WS. Mammalian ANP32A and ANP32B Proteins Drive Differential Polymerase Adaptations in Avian Influenza Virus. J Virol 2023; 97:e0021323. [PMID: 37074204 PMCID: PMC10231198 DOI: 10.1128/jvi.00213-23] [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: 02/08/2023] [Accepted: 03/14/2023] [Indexed: 04/20/2023] Open
Abstract
ANP32 proteins, which act as influenza polymerase cofactors, vary between birds and mammals. In mammals, ANP32A and ANP32B have been reported to serve essential but redundant roles to support influenza polymerase activity. The well-known mammalian adaptation PB2-E627K enables influenza polymerase to use mammalian ANP32 proteins. However, some mammalian-adapted influenza viruses do not harbor this substitution. Here, we show that alternative PB2 adaptations, Q591R and D701N, also allow influenza polymerase to use mammalian ANP32 proteins, whereas other PB2 mutations, G158E, T271A, and D740N, increase polymerase activity in the presence of avian ANP32 proteins as well. Furthermore, PB2-E627K strongly favors use of mammalian ANP32B proteins, whereas D701N shows no such bias. Accordingly, PB2-E627K adaptation emerges in species with strong pro-viral ANP32B proteins, such as humans and mice, while D701N is more commonly seen in isolates from swine, dogs, and horses, where ANP32A proteins are the preferred cofactor. Using an experimental evolution approach, we show that the passage of viruses containing avian polymerases in human cells drove acquisition of PB2-E627K, but not in the absence of ANP32B. Finally, we show that the strong pro-viral support of ANP32B for PB2-E627K maps to the low-complexity acidic region (LCAR) tail of ANP32B. IMPORTANCE Influenza viruses naturally reside in wild aquatic birds. However, the high mutation rate of influenza viruses allows them to rapidly and frequently adapt to new hosts, including mammals. Viruses that succeed in these zoonotic jumps pose a pandemic threat whereby the virus adapts sufficiently to efficiently transmit human-to-human. The influenza virus polymerase is central to viral replication and restriction of polymerase activity is a major barrier to species jumps. ANP32 proteins are essential for influenza polymerase activity. In this study, we describe how avian influenza viruses can adapt in several different ways to use mammalian ANP32 proteins. We further show that differences between mammalian ANP32 proteins can select different adaptive changes and are responsible for some of the typical mutations that arise in mammalian-adapted influenza polymerases. These different adaptive mutations may determine the relative zoonotic potential of influenza viruses and thus help assess their pandemic risk.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Carol M. Sheppard
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Margaret G. Lister
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ecco Staller
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Olivia C. Swann
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Daniel H. Goldhill
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jason S. Long
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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40
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Arcos S, Han AX, te Velthuis AJW, Russell CA, Lauring AS. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. Virus Evol 2023; 9:vead037. [PMID: 37325086 PMCID: PMC10263469 DOI: 10.1093/ve/vead037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
The influenza A virus (IAV) RNA polymerase is an essential driver of IAV evolution. Mutations that the polymerase introduces into viral genome segments during replication are the ultimate source of genetic variation, including within the three subunits of the IAV polymerase (polymerase basic protein 2, polymerase basic protein 1, and polymerase acidic protein). Evolutionary analysis of the IAV polymerase is complicated, because changes in mutation rate, replication speed, and drug resistance involve epistatic interactions among its subunits. In order to study the evolution of the human seasonal H3N2 polymerase since the 1968 pandemic, we identified pairwise evolutionary relationships among ∼7000 H3N2 polymerase sequences using mutual information (MI), which measures the information gained about the identity of one residue when a second residue is known. To account for uneven sampling of viral sequences over time, we developed a weighted MI (wMI) metric and demonstrate that wMI outperforms raw MI through simulations using a well-sampled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dataset. We then constructed wMI networks of the H3N2 polymerase to extend the inherently pairwise wMI statistic to encompass relationships among larger groups of residues. We included hemagglutinin (HA) in the wMI network to distinguish between functional wMI relationships within the polymerase and those potentially due to hitch-hiking on antigenic changes in HA. The wMI networks reveal coevolutionary relationships among residues with roles in replication and encapsidation. Inclusion of HA highlighted polymerase-only subgraphs containing residues with roles in the enzymatic functions of the polymerase and host adaptability. This work provides insight into the factors that drive and constrain the rapid evolution of influenza viruses.
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41
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Hao B, Li J, Sun C, Huang J. Label-free proteomics analysis on the envelope of budded viruses of Bombyx mori nucleopolyhedrovirus harboring differential localized GP64. Virus Genes 2023; 59:260-275. [PMID: 36512182 DOI: 10.1007/s11262-022-01961-1] [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: 09/04/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) GP64 is the key membrane fusion protein that mediates budded virus (BV) infection. We recently reported that BmNPV GP64's n-region of signal peptide (SP) blocked the SP-cleavage and mediated GP64 localization on the plasma membrane (PM); n-region (SP∆nGP64) absence caused GP64 intracellular localization, however, SP∆nGP64 was still incorporated into virion to generate BVs with lower infectivity. To better understand the biogenesis of the envelope of BmNPV BV, we conducted a label-free ESI mass spectrometry analysis of the envelope of purified BVs harboring PM localized GP64 or intracellular localized SP∆nGP64. The results indicated that 31 viral proteins were identified on the envelope, among which 15 were reported in other viruses. The other 16 proteins were first reported in BmNPV BV, including the BmNPV-specific protein BRO-A and proteins associated with vesicle transportation. Six proteins with significant intensity differences were detected in virions with differential localized GP64, and five specific proteins were identified in virions with GP64. Meanwhile, we identified 81 host proteins on the envelope, and seven lipoproteins were first identified in baculovirus virion; other 74 proteins are involved in the cytoskeleton, DNA-binding, vesicle transport, etc. In the meantime, eight and five specific host proteins were, respectively, identified in GP64 and SP∆nGP64's virions. The two virions shared 68 common host proteins, and 8 proteins were identified on their envelopes with a significant difference. This study provides new insight into the protein composition of BmNPV BV and a clue for further investigation of the budding mechanism of BmNPV.
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Affiliation(s)
- Bifang Hao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People's Republic of China
- Key Laboratory of Genetic Improvement of Sericulture in the Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, People's Republic of China
| | - Jingfeng Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People's Republic of China
| | - Congcong Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People's Republic of China
| | - Jinshan Huang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People's Republic of China.
- Key Laboratory of Genetic Improvement of Sericulture in the Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, People's Republic of China.
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42
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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: 16] [Impact Index Per Article: 16.0] [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.
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43
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Siegers JY, Ferreri L, Eggink D, Veldhuis Kroeze EJB, te Velthuis AJW, van de Bildt M, Leijten L, van Run P, de Meulder D, Bestebroer T, Richard M, Kuiken T, Lowen AC, Herfst S, van Riel D. Evolution of highly pathogenic H5N1 influenza A virus in the central nervous system of ferrets. PLoS Pathog 2023; 19:e1011214. [PMID: 36897923 PMCID: PMC10032531 DOI: 10.1371/journal.ppat.1011214] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/22/2023] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
Central nervous system (CNS) disease is the most common extra-respiratory tract complication of influenza A virus infections in humans. Remarkably, zoonotic highly pathogenic avian influenza (HPAI) H5N1 virus infections are more often associated with CNS disease than infections with seasonal influenza viruses. Evolution of avian influenza viruses has been extensively studied in the context of respiratory infections, but evolutionary processes in CNS infections remain poorly understood. We have previously observed that the ability of HPAI A/Indonesia/5/2005 (H5N1) virus to replicate in and spread throughout the CNS varies widely between individual ferrets. Based on these observations, we sought to understand the impact of entrance into and replication within the CNS on the evolutionary dynamics of virus populations. First, we identified and characterized three substitutions-PB1 E177G and A652T and NP I119M - detected in the CNS of a ferret infected with influenza A/Indonesia/5/2005 (H5N1) virus that developed a severe meningo-encephalitis. We found that some of these substitutions, individually or collectively, resulted in increased polymerase activity in vitro. Nevertheless, in vivo, the virus bearing the CNS-associated mutations retained its capacity to infect the CNS but showed reduced dispersion to other anatomical sites. Analyses of viral diversity in the nasal turbinate and olfactory bulb revealed the lack of a genetic bottleneck acting on virus populations accessing the CNS via this route. Furthermore, virus populations bearing the CNS-associated mutations showed signs of positive selection in the brainstem. These features of dispersion to the CNS are consistent with the action of selective processes, underlining the potential for H5N1 viruses to adapt to the CNS.
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Affiliation(s)
- Jurre Y. Siegers
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Lucas Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | | | - Aartjan J. W. te Velthuis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | | | - Lonneke Leijten
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Theo Bestebroer
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Sander Herfst
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Debby van Riel
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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Avian Influenza A Virus Polymerase Can Utilize Human ANP32 Proteins To Support cRNA but Not vRNA Synthesis. mBio 2023; 14:e0339922. [PMID: 36645303 PMCID: PMC9973007 DOI: 10.1128/mbio.03399-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Host restriction limits the emergence of novel pandemic strains from the influenza A virus avian reservoir. For efficient replication in mammalian cells, the avian influenza RNA-dependent RNA polymerase must adapt to use human orthologues of the host factor ANP32, which lack a 33-amino-acid insertion relative to avian ANP32A. Here, we find that influenza polymerase requires ANP32 proteins to support both steps of genome replication: cRNA and vRNA synthesis. However, avian strains are only restricted in vRNA synthesis in human cells. Therefore, avian influenza polymerase can use human ANP32 orthologues to support cRNA synthesis, without acquiring mammalian adaptations. This implies a fundamental difference in the mechanism by which ANP32 proteins support cRNA versus vRNA synthesis. IMPORTANCE To infect humans and cause a pandemic, avian influenza must first adapt to use human versions of the proteins the virus hijacks for replication, instead of the avian orthologues found in bird cells. One critical host protein is ANP32. Understanding the details of how host proteins such as ANP32 support viral activity may allow the design of new antiviral strategies that disrupt these interactions. Here, we use cells that lack ANP32 to unambiguously demonstrate ANP32 is needed for both steps of influenza genome replication. Unexpectedly, however, we found that avian influenza can use human ANP32 proteins for the first step of replication, to copy a complementary strand, without adaptation but can only utilize avian ANP32 for the second step of replication that generates new genomes. This suggests ANP32 may have a distinct role in supporting the second step of replication, and it is this activity that is specifically blocked when avian influenza infects human cells.
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45
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Arcos S, Han AX, Te Velthuis AJW, Russell CA, Lauring AS. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528850. [PMID: 36824962 PMCID: PMC9949103 DOI: 10.1101/2023.02.16.528850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The influenza A (IAV) RNA polymerase is an essential driver of IAV evolution. Mutations that the polymerase introduces into viral genome segments during replication are the ultimate source of genetic variation, including within the three subunits of the IAV polymerase (PB2, PB1, and PA). Evolutionary analysis of the IAV polymerase is complicated, because changes in mutation rate, replication speed, and drug resistance involve epistatic interactions among its subunits. In order to study the evolution of the human seasonal H3N2 polymerase since the 1968 pandemic, we identified pairwise evolutionary relationships among ∼7000 H3N2 polymerase sequences using mutual information (MI), which measures the information gained about the identity of one residue when a second residue is known. To account for uneven sampling of viral sequences over time, we developed a weighted MI metric (wMI) and demonstrate that wMI outperforms raw MI through simulations using a well-sampled SARS-CoV-2 dataset. We then constructed wMI networks of the H3N2 polymerase to extend the inherently pairwise wMI statistic to encompass relationships among larger groups of residues. We included HA in the wMI network to distinguish between functional wMI relationships within the polymerase and those potentially due to hitchhiking on antigenic changes in HA. The wMI networks reveal coevolutionary relationships among residues with roles in replication and encapsidation. Inclusion of HA highlighted polymerase-only subgraphs containing residues with roles in the enzymatic functions of the polymerase and host adaptability. This work provides insight into the factors that drive and constrain the rapid evolution of influenza viruses.
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46
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Knockout of Noxa with CRISPR/Cas9 Increases Host Resistance to Influenza Virus Infection. Cell Microbiol 2023. [DOI: 10.1155/2023/3877614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The influenza virus induces cellular apoptosis during viral propagation, and controlling this virus-induced apoptosis process has been shown to have significant antiviral effects. The proapoptotic BH3-only protein Noxa is a strong inducer of apoptosis that can be activated by this virus, suggesting that Noxa has the potential as an anti-influenza target. To assess the value of Noxa as an antiviral target, we utilized CRISPR/Cas9 technology to produce a Noxa-knockout cell line. We found that the knockout of Noxa resulted in a dramatic reduction in the cytopathic effect induced by the influenza virus. Moreover, Noxa knockout decreased the expression of influenza viral proteins (NP, M2, HA, and NS2). In addition, Noxa deficiency triggered a complete autophagic flux to weaken influenza virus-induced autophagosome accumulation, indicating that Noxa may be a promising antiviral target for controlling influenza virus infections.
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47
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The ubiquitination landscape of the influenza A virus polymerase. Nat Commun 2023; 14:787. [PMID: 36774438 PMCID: PMC9922279 DOI: 10.1038/s41467-023-36389-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/30/2023] [Indexed: 02/13/2023] Open
Abstract
During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitination landscape of the IAV polymerase proteins during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG (di-glycyl)-remnant-bearing peptides. We have identified 59 modified lysines across the three subunits, PB2, PB1 and PA of the viral polymerase of which 17 distinctively affect mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, further functional and in silico analysis indicate that ubiquitination at K578 in the PB1 thumb domain is mechanistically linked to dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R differentially affect the generation of recombinant viruses by impeding cRNA and vRNA synthesis, NP binding as well as polymerase dimerization. Collectively, our results demonstrate that the ubiquitin-mediated charge neutralization at PB1-K578 disrupts the interaction to an unstructured loop in the PB2 N-terminus that is required to coordinate polymerase dimerization and facilitate vRNA replication. This provides evidence that IAV exploits the cellular ubiquitin system to modulate the activity of the viral polymerase for viral replication.
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48
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Roy P, Veesler D, Rey F. Virus structures and molecular biology exchange glances. Structure 2023; 31:S0969-2126(23)00034-5. [PMID: 36841235 DOI: 10.1016/j.str.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
The definition of structure as the arrangement of and relations between the parts of something complex has always been a challenge in virology. The balance required for a virus to be sufficiently stable to allow transmission yet also be primed for disassembly on contact with a permissive cell is precarious and seemingly difficult to attain. Add to this that virus structural components often have multiple functions such as receptor binding, fusion, and cleavage, and the puzzle deepens. It also has consequences: virus yields may be compromised, vaccine shelf-life may be limited, and the ability to quickly evolve away from an intervention may be underestimated. Progress in understanding virus structure and the ways in which it might be exploited were the subject of the latest International Virus Assembly Symposium. Whole viruses, individual components, and transient intermediates were revealed at sufficiently high resolution to deduce the mechanisms concerned.
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Affiliation(s)
- Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Felix Rey
- Structural Virology Unit Virology Department and CNRS UMR3569 Institut Pasteur, Paris, France
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49
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Functional Importance of the Hydrophobic Residue 362 in Influenza A PB1 Subunit. Viruses 2023; 15:v15020396. [PMID: 36851609 PMCID: PMC9967172 DOI: 10.3390/v15020396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
PB1, acting as the catalytic subunit of the influenza polymerase, has numerous sequentially and structurally conserved regions. It has been observed that the slight modification of residues in PB1 would greatly affect the polymerase activity and even host adaptation ability. Here, we identified a critical residue, 362M, on the polymerase activity and virus replication. By means of the minireplicon assay, we assured the importance of the hydrophobicity of PB1 362, and the possibility that the size and charge of the side chain might directly interfere with the polymerase function. We also proposed a hydrophobic core between the PA-arch and the PB1 β-hairpin motifs and showed the importance of the core to the polymerase function.
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50
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Mettier J, Prompt C, Bruder E, Da Costa B, Chevalier C, Le Goffic R. Comparison of PB1-F2 Proximity Interactomes Reveals Functional Differences between a Human and an Avian Influenza Virus. Viruses 2023; 15:v15020328. [PMID: 36851542 PMCID: PMC9961899 DOI: 10.3390/v15020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Most influenza viruses express the PB1-F2 protein which is regarded as a virulence factor. However, PB1-F2 behaves differently in avian and mammalian hosts, suggesting that this protein may be involved in the species barrier crossings regularly observed in influenza viruses. To better understand the functions associated with this viral protein, we decided to compare the BioID2-derived proximity interactome of a human PB1-F2 from an H3N2 virus with that of an avian PB1-F2 from an H7N1 strain. The results obtained reveal that the two proteins share only a few interactors and thus common functions. The human virus protein is mainly involved in signaling by Rho GTPases while the avian virus protein is mainly involved in ribonucleoprotein complex biogenesis. PB1-F2 H3N2 interactors include several members of the 14-3-3 protein family, a family of regulatory proteins involved in many signaling pathways. We then validated the interaction with 14-3-3 proteins and were able to show that the association of H3N2-PB1-F2 with YWHAH increased the activity of the antiviral sensor MDA5, while H7N1-PB1-F2 had no effect. Collectively, these results show that PB1-F2 can associate with a large range of protein complexes and exert a wide variety of functions. Furthermore, PB1-F2 interactome differs according to the avian or human origin of the protein.
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