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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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Carascal MB, Pavon RDN, Rivera WL. Recent Progress in Recombinant Influenza Vaccine Development Toward Heterosubtypic Immune Response. Front Immunol 2022; 13:878943. [PMID: 35663997 PMCID: PMC9162156 DOI: 10.3389/fimmu.2022.878943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Flu, a viral infection caused by the influenza virus, is still a global public health concern with potential to cause seasonal epidemics and pandemics. Vaccination is considered the most effective protective strategy against the infection. However, given the high plasticity of the virus and the suboptimal immunogenicity of existing influenza vaccines, scientists are moving toward the development of universal vaccines. An important property of universal vaccines is their ability to induce heterosubtypic immunity, i.e., a wide immune response coverage toward different influenza subtypes. With the increasing number of studies and mounting evidence on the safety and efficacy of recombinant influenza vaccines (RIVs), they have been proposed as promising platforms for the development of universal vaccines. This review highlights the current progress and advances in the development of RIVs in the context of heterosubtypic immunity induction toward universal vaccine production. In particular, this review discussed existing knowledge on influenza and vaccine development, current hemagglutinin-based RIVs in the market and in the pipeline, other potential vaccine targets for RIVs (neuraminidase, matrix 1 and 2, nucleoprotein, polymerase acidic, and basic 1 and 2 antigens), and deantigenization process. This review also provided discussion points and future perspectives in looking at RIVs as potential universal vaccine candidates for influenza.
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Affiliation(s)
- Mark B Carascal
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines.,Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Rance Derrick N Pavon
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
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Sada M, Saraya T, Ishii H, Okayama K, Hayashi Y, Tsugawa T, Nishina A, Murakami K, Kuroda M, Ryo A, Kimura H. Detailed Molecular Interactions of Favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza Virus Polymerases In Silico. Microorganisms 2020; 8:E1610. [PMID: 33092045 PMCID: PMC7589801 DOI: 10.3390/microorganisms8101610] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 12/20/2022] Open
Abstract
Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions underlying its potential impact on the coronaviruses including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) remain unclear. We performed in silico studies to elucidate detailed molecular interactions between favipiravir and the SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus RNA-dependent RNA polymerases (RdRp). As a result, no interactions between favipiravir ribofuranosyl-5'-triphosphate (F-RTP), the active form of favipiravir, and the active sites of RdRps (PB1 proteins) from influenza A (H1N1)pdm09 virus were found, yet the agent bound to the tunnel of the replication genome of PB1 protein leading to the inhibition of replicated RNA passage. In contrast, F-RTP bound to the active sites of coronavirus RdRp in the presence of the agent and RdRp. Further, the agent bound to the replicated RNA terminus in the presence of agent, magnesium ions, nucleotide triphosphate, and RdRp proteins. These results suggest that favipiravir exhibits distinct mechanisms of action against influenza virus and various coronaviruses.
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Affiliation(s)
- Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University, Shibukawa, Gunma 377-0008, Japan;
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Takeshi Saraya
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Haruyuki Ishii
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Kaori Okayama
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Yuriko Hayashi
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan;
| | - Atsuyoshi Nishina
- College of Science and Technology, Nihon University, Tokyo 101-0062, Japan;
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
| | - Hirokazu Kimura
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki, Gunma 370-0006, Japan
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Zhou Z, Liu T, Zhang J, Zhan P, Liu X. Influenza A virus polymerase: an attractive target for next-generation anti-influenza therapeutics. Drug Discov Today 2018; 23:503-518. [PMID: 29339107 DOI: 10.1016/j.drudis.2018.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/31/2017] [Accepted: 01/05/2018] [Indexed: 12/20/2022]
Abstract
The influenza RNA-dependent RNA polymerase (RdRP) is conserved among different types of influenza virus, playing an important part in transcription and replication. In this regard, influenza RdRP is an attractive target for novel anti-influenza drug discovery. Herein, we will introduce the structural and functional information of influenza polymerase; and an overview of inhibitors targeting the PA endonuclease and PB2 cap-binding site is provided, along with the approaches utilized for identification of these inhibitors. The protein-protein interactions (PPIs) of the three polymerase subunits: PA, PB1 and PB2, are described based on the published crystal structures, and inhibitors targeting the PA-PB1 interaction are introduced briefly.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Tao Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
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Screening for Novel Small-Molecule Inhibitors Targeting the Assembly of Influenza Virus Polymerase Complex by a Bimolecular Luminescence Complementation-Based Reporter System. J Virol 2017; 91:JVI.02282-16. [PMID: 28031371 DOI: 10.1128/jvi.02282-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza virus RNA-dependent RNA polymerase consists of three viral protein subunits: PA, PB1, and PB2. Protein-protein interactions (PPIs) of these subunits play pivotal roles in assembling the functional polymerase complex, which is essential for the replication and transcription of influenza virus RNA. Here we developed a highly specific and robust bimolecular luminescence complementation (BiLC) reporter system to facilitate the investigation of influenza virus polymerase complex formation. Furthermore, by combining computational modeling and the BiLC reporter assay, we identified several novel small-molecule compounds that selectively inhibited PB1-PB2 interaction. Function of one such lead compound was confirmed by its activity in suppressing influenza virus replication. In addition, our studies also revealed that PA plays a critical role in enhancing interactions between PB1 and PB2, which could be important in targeting sites for anti-influenza intervention. Collectively, these findings not only aid the development of novel inhibitors targeting the formation of influenza virus polymerase complex but also present a new tool to investigate the exquisite mechanism of PPIs. IMPORTANCE Formation of the functional influenza virus polymerase involves complex protein-protein interactions (PPIs) of PA, PB1, and PB2 subunits. In this work, we developed a novel BiLC assay system which is sensitive and specific to quantify both strong and weak PPIs between influenza virus polymerase subunits. More importantly, by combining in silico modeling and our BiLC assay, we identified a small molecule that can suppress influenza virus replication by disrupting the polymerase assembly. Thus, we developed an innovative method to investigate PPIs of multisubunit complexes effectively and to identify new molecules inhibiting influenza virus polymerase assembly.
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Du Y, Wu NC, Jiang L, Zhang T, Gong D, Shu S, Wu TT, Sun R. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis. mBio 2016; 7:e01801-16. [PMID: 27803181 PMCID: PMC5090041 DOI: 10.1128/mbio.01801-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/07/2016] [Indexed: 11/28/2022] Open
Abstract
Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. IMPORTANCE To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available.
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Affiliation(s)
- Yushen Du
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nicholas C Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Lin Jiang
- Department of Neurology, University of California Los Angeles, Los Angeles, California, USA
| | - Tianhao Zhang
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Sara Shu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
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Functional Genomics Reveals Linkers Critical for Influenza Virus Polymerase. J Virol 2015; 90:2938-47. [PMID: 26719244 DOI: 10.1128/jvi.02400-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/22/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED Influenza virus mRNA synthesis by the RNA-dependent RNA polymerase involves binding and cleavage of capped cellular mRNA by the PB2 and PA subunits, respectively, and extension of viral mRNA by PB1. However, the mechanism for such a dynamic process is unclear. Using high-throughput mutagenesis and sequencing analysis, we have not only generated a comprehensive functional map for the microdomains of individual subunits but also have revealed the PA linker to be critical for polymerase activity. This PA linker binds to PB1 and also forms ionic interactions with the PA C-terminal channel. Nearly all mutants with five-amino-acid insertions in the linker were nonviable. Our model further suggests that the PA linker plays an important role in the conformational changes that occur between stages that favor capped mRNA binding and cleavage and those associated with viral mRNA synthesis. IMPORTANCE The RNA-dependent RNA polymerase of influenza virus consists of the PB1, PB2, and PA subunits. By combining genome-wide mutagenesis analysis with the recently discovered crystal structure of the influenza polymerase heterotrimer, we generated a comprehensive functional map of the entire influenza polymerase complex. We identified the microdomains of individual subunits, including the catalytic domains, the interaction interfaces between subunits, and nine linkers interconnecting different domains. Interestingly, we found that mutants with five-amino-acid insertions in individual linkers were nonviable, suggesting the critical roles these linkers play in coordinating spatial relationships between the subunits. We further identified an extended PA linker that binds to PB1 and also forms ionic interactions with the PA C-terminal channel.
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Beagle dogs have low susceptibility to BJ94-like H9N2 avian influenza virus. INFECTION GENETICS AND EVOLUTION 2015; 31:216-20. [DOI: 10.1016/j.meegid.2015.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/07/2023]
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