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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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Ling YH, Wang H, Han MQ, Wang D, Hu YX, Zhou K, Li Y. Nucleoporin 85 interacts with influenza A virus PB1 and PB2 to promote its replication by facilitating nuclear import of ribonucleoprotein. Front Microbiol 2022; 13:895779. [PMID: 36051755 PMCID: PMC9426659 DOI: 10.3389/fmicb.2022.895779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription and replication of the influenza A virus (IAV) genome take place in the nucleus of infected cells, which rely on host factors to aid viral ribonucleoprotein (vRNP) to cross the nuclear pore complex (NPC) and complete the bidirectional nucleocytoplasmic trafficking. Here, we showed that nucleoporin 85 (NUP85), a component of NPC, interacted with RNP subunits polymerase basic 1 (PB1) and polymerase basic 2 (PB2) in an RNA-dependent manner during IAV infection. Knockdown of NUP85 delayed the nuclear import of vRNP, PB1 and PB2, inhibiting polymerase activity and ultimately suppressing viral replication. Further analysis revealed that NUP85 assisted the binding of PB1 to nuclear transport factor Ran-binding protein 5 (RanBP5) and the binding of PB2 to nuclear transport factor importin α1 and importin α7. We also found that NUP85 expression was downregulated upon IAV infection. Together, our study demonstrated that NUP85 positively regulated IAV infection by interacting with viral PB1 and PB2, which may provide new insight into the process of vRNP nuclear import and a novel target for effective antivirals.
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Affiliation(s)
- Yue-Huan Ling
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Hao Wang
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Mei-Qing Han
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Di Wang
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Yi-Xiang Hu
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute, Zhejiang University, Sanya, Hainan, China
| | - Kun Zhou
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Yan Li
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute, Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Yan Li,
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G Protein Subunit β1 Facilitates Influenza A Virus Replication by Promoting the Nuclear Import of PB2. J Virol 2022; 96:e0049422. [PMID: 35604143 DOI: 10.1128/jvi.00494-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
G protein subunit β1 (GNB1), the beta subunit of the G protein family, plays an important role in regulating transmembrane signal transduction. Although a recent study has demonstrated that GNB1 can bind the matrix protein 1 (M1) to facilitate M1 transport to budding sites and promote the release of progeny influenza A virus (IAV), whether the GNB1 protein has other functions in IAV replication requires further study. Here, we found that GNB1 promoted IAV replication, as virus yield decreased in GNB1 knockdown or knockout cells. GNB1 interacted with polymerase subunits PB2, PB1, and PA. Overexpressed GNB1 facilitated PB2 binding to importin α3, α5, and α7 promoting the nuclear import of PB2, enhancing viral RNA synthesis and polymerase activity. Altogether, our results demonstrated that GNB1 positively regulates virus replication by interacting with polymerase subunits and facilitating the nuclear import of PB2, which provide novel insights into the molecular mechanism of IAV. IMPORTANCE Until now, there has been only one article on the role of GNB1 in IAV budding. No study has investigated the role of GNB1 in IAV replication. In this study, our research demonstrated that GNB1 could increase the interaction between PB2 and the importin α isoform and mediate the nuclear import of PB2. Therefore, GNB1 could promote viral replication and transcription. Our results provide a better understanding of the molecular mechanisms of viral replication and provide potential antiviral drug targets.
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The Influenza Virus RNA-Polymerase and the Host RNA-Polymerase II: RPB4 Is Targeted by a PB2 Domain That Is Involved in Viral Transcription. Viruses 2022; 14:v14030518. [PMID: 35336925 PMCID: PMC8950122 DOI: 10.3390/v14030518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/10/2022] Open
Abstract
Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3′-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and influenza A FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and was found to occur with the homologous domains of influenza B and C FluPols. The N-half domain of RPB4 was found to be critical in this interaction. Punctual mutants generated at conserved positions between influenza A, B, and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defects. These results suggest that FluPol interacts with several domains of Pol II (the CTD to bind Pol II), initiating host transcription and a second transcription on RPB4 to locate FluPol at the proximity of the 5′-end of nascent host mRNA.
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Strategies for fighting pandemic virus infections: Integration of virology and drug delivery. J Control Release 2022; 343:361-378. [PMID: 35122872 PMCID: PMC8810279 DOI: 10.1016/j.jconrel.2022.01.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Respiratory viruses have sometimes resulted in worldwide pandemics, with the influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) being major participants. Long-term efforts have made it possible to control the influenza virus, but seasonal influenza continues to take many lives each year, and a pandemic influenza virus sometimes emerges. Although vaccines for coronavirus disease 2019 (COVID-19) have been developed, we are not yet able to coexist with the SARS-CoV-2. To overcome such viruses, it is necessary to obtain knowledge about international surveillance systems, virology, ecology and to determine that immune responses are effective. The information must then be transferred to drugs. Delivery systems would be expected to contribute to the rational development of drugs. In this review, virologist and drug delivery system (DDS) researchers discuss drug delivery strategies, especially the use of lipid-based nanocarriers, for fighting to respiratory virus infections.
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Ogasawara S, Yamada A. RNA Editing with Viral RNA-Dependent RNA Polymerase. ACS Synth Biol 2022; 11:46-52. [PMID: 34978432 DOI: 10.1021/acssynbio.1c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNA editing is currently attracting attention as a method for editing genetic information without injury to the genome. The most common approach to edit RNA sequences involves the induction of an A-to-I change by adenosine deaminase acting on RNA (ADAR). However, this method only allows point editing. Here, we report a highly flexible RNA editing method called "RNA overwriting" that employs the influenza A virus RNA-dependent RNA polymerase (RdRp) comprising PA, PB1, and PB2 subunits. RdRp binds to the 5'-cap structure of the host mRNA and cleaves at the AG site, followed by transcription of the viral RNA; this process is called cap-snatching. We engineered a targeting snatch system wherein the target RNA is cleaved and extended at any site addressed by guide RNA (gRNA). We constructed five recombinant RdRps containing a PB2 mutant and demonstrated the editing capability of RdRp mutants by using short RNAs in vitro. PB2-480-containing RdRp exhibited good performance in both cleavage and extension assays; we succeeded in RNA overwriting using PB2-480-containing RdRp. In principle, this method allows RNA editing of any type including mutation, addition, and deletion, by changing the sequence of the template RNA to the sequence of interest; hence, the use of viral RdRp could open new avenues in RNA editing and be a powerful tool in life science.
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Affiliation(s)
- Shinzi Ogasawara
- Department of Biology, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Ai Yamada
- Department of Biology, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Pyle JD, Whelan SPJ, Bloyet LM. Structure and function of negative-strand RNA virus polymerase complexes. Enzymes 2021; 50:21-78. [PMID: 34861938 DOI: 10.1016/bs.enz.2021.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.
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Affiliation(s)
- Jesse D Pyle
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States; Ph.D. Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
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Staller E, Barclay WS. Host Cell Factors That Interact with Influenza Virus Ribonucleoproteins. Cold Spring Harb Perspect Med 2021; 11:a038307. [PMID: 32988980 PMCID: PMC8559542 DOI: 10.1101/cshperspect.a038307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza viruses hijack host cell factors at each stage of the viral life cycle. After host cell entry and endosomal escape, the influenza viral ribonucleoproteins (vRNPs) are released into the cytoplasm where the classical cellular nuclear import pathway is usurped for nuclear translocation of the vRNPs. Transcription takes place inside the nucleus at active host transcription sites, and cellular mRNA export pathways are subverted for export of viral mRNAs. Newly synthesized RNP components cycle back into the nucleus using various cellular nuclear import pathways and host-encoded chaperones. Replication of the negative-sense viral RNA (vRNA) into complementary RNA (cRNA) and back into vRNA requires complex interplay between viral and host factors. Progeny vRNPs assemble at the host chromatin and subsequently exit from the nucleus-processes orchestrated by sets of host and viral proteins. Finally, several host pathways appear to play a role in vRNP trafficking from the nuclear envelope to the plasma membrane for egress.
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Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
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Dunsing V, Petrich A, Chiantia S. Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection. eLife 2021; 10:e69687. [PMID: 34494547 PMCID: PMC8545396 DOI: 10.7554/elife.69687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023] Open
Abstract
Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.
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Affiliation(s)
- Valentin Dunsing
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Annett Petrich
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Salvatore Chiantia
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
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Tano J, Ripa MB, Tondo ML, Carrau A, Petrocelli S, Rodriguez MV, Ferreira V, Siri MI, Piskulic L, Orellano EG. Light modulates important physiological features of Ralstonia pseudosolanacearum during the colonization of tomato plants. Sci Rep 2021; 11:14531. [PMID: 34267245 PMCID: PMC8282871 DOI: 10.1038/s41598-021-93871-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Ralstonia pseudosolanacearum GMI1000 (Rpso GMI1000) is a soil-borne vascular phytopathogen that infects host plants through the root system causing wilting disease in a wide range of agro-economic interest crops, producing economical losses. Several features contribute to the full bacterial virulence. In this work we study the participation of light, an important environmental factor, in the regulation of the physiological attributes and infectivity of Rpso GMI1000. In silico analysis of the Rpso genome revealed the presence of a Rsp0254 gene, which encodes a putative blue light LOV-type photoreceptor. We constructed a mutant strain of Rpso lacking the LOV protein and found that the loss of this protein and light, influenced characteristics involved in the pathogenicity process such as motility, adhesion and the biofilms development, which allows the successful host plant colonization, rendering bacterial wilt. This protein could be involved in the adaptive responses to environmental changes. We demonstrated that light sensing and the LOV protein, would be used as a location signal in the host plant, to regulate the expression of several virulence factors, in a time and tissue dependent way. Consequently, bacteria could use an external signal and Rpsolov gene to know their location within plant tissue during the colonization process.
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Affiliation(s)
- Josefina Tano
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas (IBR-FBIOyF), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario (CONICET-UNR), Suipacha 531, S2002LRK, Rosario, Argentina
| | - María Belén Ripa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas (IBR-FBIOyF), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario (CONICET-UNR), Suipacha 531, S2002LRK, Rosario, Argentina
| | - María Laura Tondo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Analía Carrau
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas (IBR-FBIOyF), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario (CONICET-UNR), Suipacha 531, S2002LRK, Rosario, Argentina
| | - Silvana Petrocelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Victoria Rodriguez
- Área Biología Vegetal, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Virginia Ferreira
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Inés Siri
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Piskulic
- Área Estadística y Procesamiento de datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elena Graciela Orellano
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas (IBR-FBIOyF), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario (CONICET-UNR), Suipacha 531, S2002LRK, Rosario, Argentina.
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Eukaryotic Translation Elongation Factor 1 Delta Inhibits the Nuclear Import of the Nucleoprotein and PA-PB1 Heterodimer of Influenza A Virus. J Virol 2020; 95:JVI.01391-20. [PMID: 33087462 DOI: 10.1128/jvi.01391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
The viral ribonucleoprotein (vRNP) of the influenza A virus (IAV) is responsible for the viral RNA transcription and replication in the nucleus, and its functions rely on host factors. Previous studies have indicated that eukaryotic translation elongation factor 1 delta (eEF1D) may associate with RNP subunits, but its roles in IAV replication are unclear. Herein, we showed that eEF1D was an inhibitor of IAV replication because knockout of eEF1D resulted in a significant increase in virus yield. eEF1D interacted with RNP subunits polymerase acidic protein (PA), polymerase basic 1 (PB1), polymerase basic 2 (PB2), and also with nucleoprotein (NP) in an RNA-dependent manner. Further studies revealed that eEF1D impeded the nuclear import of NP and PA-PB1 heterodimer of IAV, thereby suppressing the vRNP assembly, viral polymerase activity, and viral RNA synthesis. Together, our studies demonstrate eEF1D negatively regulating the IAV replication by inhibition of the nuclear import of RNP subunits, which not only uncovers a novel role of eEF1D in IAV replication but also provides new insights into the mechanisms of nuclear import of vRNP proteins.IMPORTANCE Influenza A virus is the major cause of influenza, a respiratory disease in humans and animals. Different from most other RNA viruses, the transcription and replication of IAV occur in the cell nucleus. Therefore, the vRNPs must be imported into the nucleus for viral transcription and replication, which requires participation of host proteins. However, the mechanisms of the IAV-host interactions involved in nuclear import remain poorly understood. Here, we identified eEF1D as a novel inhibitor for the influenza virus life cycle. Importantly, eEF1D impaired the interaction between NP and importin α5 and the interaction between PB1 and RanBP5, which impeded the nuclear import of vRNP. Our studies not only reveal the molecular mechanisms of the nuclear import of IAV vRNP but also provide potential anti-influenza targets for antiviral development.
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12
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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An SH, Lee CY, Choi JG, Lee YJ, Kim JH, Kwon HJ. Generation of highly productive and mammalian nonpathogenic recombinant H9N2 avian influenza viruses by optimization of 3'end promoter and NS genome. Vet Microbiol 2018; 228:213-218. [PMID: 30593370 DOI: 10.1016/j.vetmic.2018.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 01/02/2023]
Abstract
We developed A/PR/8/34 (PR8) virus-based reverse genetics system in which six internal genes of PR8 and attenuated hemagglutinin and intact neuraminidase genes of field avian influenza viruses (AIVs) have been used for the generation of highly productive recombinant vaccine strains. The 6 + 2 recombinant vaccine strains can induce protective humoral immunity against intended field AIVs; however, the epitopes of B and T cells encoded by internal genes may be important for heterosubtypic protection. Therefore, it is advantageous to use homologous internal genes of field AIVs for recombinant vaccine strains. However, the rescue of recombinant viruses having whole internal genes of field AIVs by the PR8-based reverse genetics system was unsuccessful in some cases. Although partial replacement of an internal gene has been successful for generation of highly productive and mammalian nonpathogenic recombinant viruses, complete replacement of internal genes may be more favorable. In this study, we successfully generated complete recombinant H9N2 AIVs possessing 8 genomes of H9N2 AIVs by optimal combinations of 3' end promoter sequences of polymerase genomes, and a NS genome. All the generated recombinant viruses showed highly productive and mammalian nonpathogenic traits but some of them showed much higher virus titers in embryonated chicken eggs. Additionally, we found the same mutations of NS1 gene determined pathogenicity of AIVs in chicken embryos as well as mammals. Thus, the 3' end promoter optimization, and highly productive and mammalian nonpathogenic internal genes may be useful to develop vaccines against AIVs.
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Affiliation(s)
- Se-Hee An
- Laboratory of Avian Diseases, Republic of Korea
| | | | - Jun-Gu Choi
- Avian Disease Division, Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Youn-Jeong Lee
- Avian Disease Division, Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Avian Diseases, Republic of Korea; Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea
| | - Hyuk-Joon Kwon
- Department of Farm Animal Medicine, Republic of Korea; Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea; Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, 25354, Pyeongchangdae-ro, Kangwon-do, Republic of Korea.
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14
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Kamiki H, Matsugo H, Kobayashi T, Ishida H, Takenaka-Uema A, Murakami S, Horimoto T. A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Viruses 2018; 10:v10110653. [PMID: 30463209 PMCID: PMC6266086 DOI: 10.3390/v10110653] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 01/25/2023] Open
Abstract
H9N2 avian influenza viruses are present in poultry worldwide. These viruses are considered to have pandemic potential, because recent isolates can recognize human-type receptor and several sporadic human infections have been reported. In this study, we aimed to identify mutations related to mammalian adaptation of H9N2 influenza virus. We found that mouse-adapted viruses had several mutations in hemagglutinin (HA), PB2, PA, and PB1. Among the detected mutations, PB1-K577E was a novel mutation that had not been previously reported to involve mammalian adaptation. A recombinant H9N2 virus bearing only the PB1-K577E mutation showed enhanced pathogenicity in mice, with increased virus titers in nasal turbinates compared to that in mice infected with the wild-type virus. In addition, the PB1-K577E mutation increased virus polymerase activity in human cell culture at a lower temperature. These data suggest that the PB1-K577E mutation is a novel pathogenicity determinant of H9N2 virus in mice and could be a signature for mammalian adaptation.
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Affiliation(s)
- Haruhiko Kamiki
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Hiromichi Matsugo
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Tomoya Kobayashi
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Hiroho Ishida
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Akiko Takenaka-Uema
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Shin Murakami
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Taisuke Horimoto
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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15
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Dou D, Revol R, Östbye H, Wang H, Daniels R. Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement. Front Immunol 2018; 9:1581. [PMID: 30079062 PMCID: PMC6062596 DOI: 10.3389/fimmu.2018.01581] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process.
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Affiliation(s)
- Dan Dou
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca Revol
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Henrik Östbye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hao Wang
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert Daniels
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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16
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Kaliszewski MJ, Shi X, Hou Y, Lingerak R, Kim S, Mallory P, Smith AW. Quantifying membrane protein oligomerization with fluorescence cross-correlation spectroscopy. Methods 2018; 140-141:40-51. [PMID: 29448037 DOI: 10.1016/j.ymeth.2018.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/17/2017] [Accepted: 02/07/2018] [Indexed: 01/27/2023] Open
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is an advanced fluorescence technique that can quantify protein-protein interactions in vivo. Due to the dynamic, heterogeneous nature of the membrane, special considerations must be made to interpret FCCS data accurately. In this study, we describe a method to quantify the oligomerization of membrane proteins tagged with two commonly used fluorescent probes, mCherry (mCH) and enhanced green (eGFP) fluorescent proteins. A mathematical model is described that relates the relative cross-correlation value (fc) to the degree of oligomerization. This treatment accounts for mismatch in the confocal volumes, combinatoric effects of using two fluorescent probes, and the presence of non-fluorescent probes. Using this model, we calculate a ladder of fc values which can be used to determine the oligomer state of membrane proteins from live-cell experimental data. Additionally, a probabilistic mathematical simulation is described to resolve the affinity of different dimeric and oligomeric protein controls.
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Affiliation(s)
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Yixuan Hou
- Food Animal Health Research Program, Ohio Agriculture Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Ryan Lingerak
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Paul Mallory
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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17
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Abstract
Influenza is a negative-sense single-stranded RNA virus with segmented genome. Each segment is encapsidated by a ribonucleoprotein (RNP) complex composed of RNA-dependent RNA polymerase (RdRP) and multiple copies of nucleoprotein (NP). The RNP complex plays a crucial role in viral life cycle, supporting and regulating transcription and replication of viral genome in infected cells. The structural characterization of RdRP and RNP in recent years has shed light on its functions and mechanism of action. In this review, we summarize current understanding on the structure of RNP complex, as well as the structure of each subunit. Crucial functions of RNP are also discussed.
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Affiliation(s)
- Chun-Yeung Lo
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Yun-Sang Tang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China.
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18
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Role of the PB2 627 Domain in Influenza A Virus Polymerase Function. J Virol 2017; 91:JVI.02467-16. [PMID: 28122973 PMCID: PMC5355620 DOI: 10.1128/jvi.02467-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/14/2017] [Indexed: 11/20/2022] Open
Abstract
The RNA genome of influenza A viruses is transcribed and replicated by the viral RNA-dependent RNA polymerase, composed of the subunits PA, PB1, and PB2. High-resolution structural data revealed that the polymerase assembles into a central polymerase core and several auxiliary highly flexible, protruding domains. The auxiliary PB2 cap-binding and the PA endonuclease domains are both involved in cap snatching, but the role of the auxiliary PB2 627 domain, implicated in host range restriction of influenza A viruses, is still poorly understood. In this study, we used structure-guided truncations of the PB2 subunit to show that a PB2 subunit lacking the 627 domain accumulates in the cell nucleus and assembles into a heterotrimeric polymerase with PB1 and PA. Furthermore, we showed that a recombinant viral polymerase lacking the PB2 627 domain is able to carry out cap snatching, cap-dependent transcription initiation, and cap-independent ApG dinucleotide extension in vitro, indicating that the PB2 627 domain of the influenza virus RNA polymerase is not involved in core catalytic functions of the polymerase. However, in a cellular context, the 627 domain is essential for both transcription and replication. In particular, we showed that the PB2 627 domain is essential for the accumulation of the cRNA replicative intermediate in infected cells. Together, these results further our understanding of the role of the PB2 627 domain in transcription and replication of the influenza virus RNA genome.IMPORTANCE Influenza A viruses are a major global health threat, not only causing disease in both humans and birds but also placing significant strains on economies worldwide. Avian influenza A virus polymerases typically do not function efficiently in mammalian hosts and require adaptive mutations to restore polymerase activity. These adaptations include mutations in the 627 domain of the PB2 subunit of the viral polymerase, but it still remains to be established how these mutations enable host adaptation on a molecular level. In this report, we characterize the role of the 627 domain in polymerase function and offer insights into the replication mechanism of influenza A viruses.
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19
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 458] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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20
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Swale C, Monod A, Tengo L, Labaronne A, Garzoni F, Bourhis JM, Cusack S, Schoehn G, Berger I, Ruigrok RWH, Crépin T. Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5. Sci Rep 2016; 6:24727. [PMID: 27095520 PMCID: PMC4837377 DOI: 10.1038/srep24727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 01/19/2023] Open
Abstract
The genome of influenza A virus (IAV) comprises eight RNA segments (vRNA) which are transcribed and replicated by the heterotrimeric IAV RNA-dependent RNA-polymerase (RdRp). RdRp consists of three subunits (PA, PB1 and PB2) and binds both the highly conserved 3′- and 5′-ends of the vRNA segment. The IAV RdRp is an important antiviral target, but its structural mechanism has remained largely elusive to date. By applying a polyprotein strategy, we produced RdRp complexes and define a minimal human IAV RdRp core complex. We show that PA-PB1 forms a stable heterodimeric submodule that can strongly interact with 5′-vRNA. In contrast, 3′-vRNA recognition critically depends on the PB2 N-terminal domain. Moreover, we demonstrate that PA-PB1 forms a stable and stoichiometric complex with host nuclear import factor RanBP5 that can be modelled using SAXS and we show that the PA-PB1-RanPB5 complex is no longer capable of 5′-vRNA binding. Our results provide further evidence for a step-wise assembly of IAV structural components, regulated by nuclear transport mechanisms and host factor binding.
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Affiliation(s)
- Christopher Swale
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Alexandre Monod
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France
| | - Laura Tengo
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Alice Labaronne
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Frédéric Garzoni
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,EMBL Grenoble, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France
| | - Jean-Marie Bourhis
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Stephen Cusack
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,EMBL Grenoble, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France
| | - Guy Schoehn
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Imre Berger
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,EMBL Grenoble, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,The School of Biochemistry, University of Bristol, Clifton BS8 1TD, United Kingdom
| | - Rob W H Ruigrok
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Thibaut Crépin
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,CNRS, Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble Cedex 9, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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21
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Avilov S, Magnus J, Cusack S, Naffakh N. Time-Resolved Visualisation of Nearly-Native Influenza A Virus Progeny Ribonucleoproteins and Their Individual Components in Live Infected Cells. PLoS One 2016; 11:e0149986. [PMID: 26978069 PMCID: PMC4792379 DOI: 10.1371/journal.pone.0149986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/06/2016] [Indexed: 02/02/2023] Open
Abstract
Influenza viruses are a global health concern because of the permanent threat of novel emerging strains potentially capable of causing pandemics. Viral ribonucleoproteins (vRNPs) containing genomic RNA segments, nucleoprotein oligomers, and the viral polymerase, play a central role in the viral replication cycle. Our knowledge about critical events such as vRNP assembly and interactions with other viral and cellular proteins is poor and could be substantially improved by time lapse imaging of the infected cells. However, such studies are limited by the difficulty to achieve live-cell compatible labeling of active vRNPs. Previously we designed the first unimpaired recombinant influenza WSN-PB2-GFP11 virus allowing fluorescent labeling of the PB2 subunit of the viral polymerase (Avilov et al., J.Virol. 2012). Here, we simultaneously labeled the viral PB2 protein using the above-mentioned strategy, and virus-encoded progeny RNPs through spontaneous incorporation of transiently expressed NP-mCherry fusion proteins during RNP assembly in live infected cells. This dual labeling enabled us to visualize progeny vRNPs throughout the infection cycle and to characterize independently the mobility, oligomerization status and interactions of vRNP components in the nuclei of live infected cells.
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Affiliation(s)
- Sergiy Avilov
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
- University Grenoble Alpes-CNRS-EMBL International Unit (UMI 3265) for Virus Host-Cell Interactions, UMI 3265, Grenoble, France
- * E-mail: (NN); (SA)
| | - Julie Magnus
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
- University Grenoble Alpes-CNRS-EMBL International Unit (UMI 3265) for Virus Host-Cell Interactions, UMI 3265, Grenoble, France
| | - Nadia Naffakh
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- * E-mail: (NN); (SA)
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22
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Isokane M, Walter T, Mahen R, Nijmeijer B, Hériché JK, Miura K, Maffini S, Ivanov MP, Kitajima TS, Peters JM, Ellenberg J. ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores. J Cell Biol 2016; 212:647-59. [PMID: 26953350 PMCID: PMC4792069 DOI: 10.1083/jcb.201408089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/11/2016] [Indexed: 12/15/2022] Open
Abstract
The spindle assembly checkpoint (SAC) ensures genome stability during cell division. Here, a new essential SAC factor, ARHGEF17, is characterized by quantitative imaging, biochemical, and biophysical experiments, which show that it targets the checkpoint kinase Mps1 to kinetochores. To prevent genome instability, mitotic exit is delayed until all chromosomes are properly attached to the mitotic spindle by the spindle assembly checkpoint (SAC). In this study, we characterized the function of ARHGEF17, identified in a genome-wide RNA interference screen for human mitosis genes. Through a series of quantitative imaging, biochemical, and biophysical experiments, we showed that ARHGEF17 is essential for SAC activity, because it is the major targeting factor that controls localization of the checkpoint kinase Mps1 to the kinetochore. This mitotic function is mediated by direct interaction of the central domain of ARHGEF17 with Mps1, which is autoregulated by the activity of Mps1 kinase, for which ARHGEF17 is a substrate. This mitosis-specific role is independent of ARHGEF17’s RhoGEF activity in interphase. Our study thus assigns a new mitotic function to ARHGEF17 and reveals the molecular mechanism for a key step in SAC establishment.
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Affiliation(s)
- Mayumi Isokane
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Thomas Walter
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Robert Mahen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kota Miura
- Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Miroslav Penchev Ivanov
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Tomoya S Kitajima
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jan-Michael Peters
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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23
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Codon Deletions in the Influenza A Virus PA Gene Generate Temperature-Sensitive Viruses. J Virol 2016; 90:3684-93. [PMID: 26792748 DOI: 10.1128/jvi.03101-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The influenza virus RNA-dependent RNA polymerase, which is composed of three subunits, PB1, PB2, and PA, catalyzes genome replication and transcription within the cell nucleus. The PA linker (residues 197 to 256) can be altered by nucleotide substitutions to engineer temperature-sensitive (ts), attenuated mutants that display a defect in the transport of the PA-PB1 complex to the nucleus at a restrictive temperature. In this study, we investigated the ability of the PA linker to tolerate deletion mutations for further in vitro and in vivo characterization. Four viable mutants with single-codon deletions were generated; all of them exhibited a ts phenotype that was associated with the reduced efficiency of replication/transcription of a pseudoviral reporter RNA in a minireplicon assay. Using fluorescently tagged PB1, we observed that the deletion mutants did not efficiently recruit PB1 to reach the nucleus at a restrictive temperature (39.5°C). Mouse infections showed that the four mutants were attenuated and induced antibodies that were able to protect mice from challenge with a lethal homologous wild-type virus. Serial in vitro passages of two deletion mutants at 39.5°C and 37°C did not allow the restoration of a wild-type phenotype among virus progeny. Thus, our results identify codons that can be deleted in the PA gene to engineer genetically stable ts mutants that could be used to design novel attenuated vaccines. IMPORTANCE In order to generate genetically stable live influenza A virus vaccines, we constructed viruses with single-codon deletions in a discrete domain of the RNA polymerase PA gene. The four rescued viruses exhibited a temperature-sensitive phenotype that we found was associated with a defect in the transport of the PA-PB1 dimer to the nucleus, where viral replication occurs. These ts deletion mutants were shown to be attenuated and to be able to produce antibodies in mice and to protect them from a lethal challenge. Assays to select revertants that were able to grow efficiently at a restrictive temperature failed, showing that these deletion mutants are genetically more stable than conventional substitution mutants. These results are of interest for the design of genetically stable live influenza virus vaccines.
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24
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Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S. Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains. Mol Cell 2016; 61:125-37. [PMID: 26711008 PMCID: PMC4712189 DOI: 10.1016/j.molcel.2015.11.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/13/2015] [Accepted: 11/05/2015] [Indexed: 01/26/2023]
Abstract
Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of promoter-bound polymerase, the cap-binding and endonuclease domains are configured for cap snatching, which generates capped transcription primers. Here, we present a FluB polymerase structure with a bound complementary cRNA 5' end that exhibits a major rearrangement of the subdomains within the C-terminal two-thirds of PB2 (PB2-C). Notably, the PB2 nuclear localization signal (NLS)-containing domain translocates ∼90 Å to bind to the endonuclease domain. FluA PB2-C alone and RNA-free FluC polymerase are similarly arranged. Biophysical and cap-dependent endonuclease assays show that in solution the polymerase explores different conformational distributions depending on which RNA is bound. The inherent flexibility of the polymerase allows it to adopt alternative conformations that are likely important during polymerase maturation into active progeny RNPs.
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Affiliation(s)
- Eric Thierry
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Delphine Guilligay
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Bock
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Gaudon
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Adam Round
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Alexander Pflug
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Narin Hengrung
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kamel El Omari
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Florence Baudin
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Darren J Hart
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Skalickova S, Heger Z, Krejcova L, Pekarik V, Bastl K, Janda J, Kostolansky F, Vareckova E, Zitka O, Adam V, Kizek R. Perspective of Use of Antiviral Peptides against Influenza Virus. Viruses 2015; 7:5428-42. [PMID: 26492266 PMCID: PMC4632391 DOI: 10.3390/v7102883] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/13/2023] Open
Abstract
The threat of a worldwide influenza pandemic has greatly increased over the past decade with the emergence of highly virulent avian influenza strains. The increased frequency of drug-resistant influenza strains against currently available antiviral drugs requires urgent development of new strategies for antiviral therapy, too. The research in the field of therapeutic peptides began to develop extensively in the second half of the 20(th) century. Since then, the mechanisms of action for several peptides and their antiviral prospect received large attention due to the global threat posed by viruses. Here, we discussed the therapeutic properties of peptides used in influenza treatment. Peptides with antiviral activity against influenza can be divided into three main groups. First, entry blocker peptides such as a Flupep that interact with influenza hemagglutinin, block its binding to host cells and prevent viral fusion. Second, several peptides display virucidal activity, disrupting viral envelopes, e.g., Melittin. Finally, a third set of peptides interacts with the viral polymerase complex and act as viral replication inhibitors such as PB1 derived peptides. Here, we present a review of the current literature describing the antiviral activity, mechanism and future therapeutic potential of these influenza antiviral peptides.
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Affiliation(s)
- Sylvie Skalickova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Ludmila Krejcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Vladimir Pekarik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Karel Bastl
- Wool and Knitting Research Institute, Brno, Sujanovo namesti 3, Brno CZ-602 00, Czech Republic.
| | - Jozef Janda
- Laboratory of Tumour Biology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov CZ-277 21, Czech Republic.
| | - Frantisek Kostolansky
- Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovak Republic.
| | - Eva Vareckova
- Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovak Republic.
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
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Caly L, Ghildyal R, Jans DA. Respiratory virus modulation of host nucleocytoplasmic transport; target for therapeutic intervention? Front Microbiol 2015; 6:848. [PMID: 26322040 PMCID: PMC4536372 DOI: 10.3389/fmicb.2015.00848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/03/2015] [Indexed: 01/02/2023] Open
Abstract
The respiratory diseases caused by rhinovirus, respiratory syncytial virus, and influenza virus represent a large social and financial burden on healthcare worldwide. Although all three viruses have distinctly unique properties in terms of infection and replication, they share the ability to exploit/manipulate the host-cell nucleocytoplasmic transport system in order to replicate effectively and efficiently. This review outlines the various ways in which infection by these viruses impacts on the host nucleocytoplasmic transport system, and examples where inhibition thereof in turn decreases viral replication. The highly conserved nature of the nucleocytoplasmic transport system and the viral proteins that interact with it make this virus–host interface a prime candidate for the development of specific antiviral therapeutics in the future.
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Affiliation(s)
- Leon Caly
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
| | - Reena Ghildyal
- Faculty of ESTeM, University of Canberra, Bruce, ACT Australia
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
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27
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Lasecka L, Bin-Tarif A, Bridgen A, Juleff N, Waters RA, Baron MD. Antibodies to the core proteins of Nairobi sheep disease virus/Ganjam virus reveal details of the distribution of the proteins in infected cells and tissues. PLoS One 2015; 10:e0124966. [PMID: 25905707 PMCID: PMC4407892 DOI: 10.1371/journal.pone.0124966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/19/2015] [Indexed: 12/19/2022] Open
Abstract
Nairobi sheep disease virus (NSDV; also called Ganjam virus in India) is a bunyavirus of the genus Nairovirus. It causes a haemorrhagic gastroenteritis in sheep and goats with mortality up to 90%. The virus is closely related to the human pathogen Crimean-Congo haemorrhagic fever virus (CCHFV). Little is currently known about the biology of NSDV. We have generated specific antibodies against the virus nucleocapsid protein (N) and polymerase (L) and used these to characterise NSDV in infected cells and to study its distribution during infection in a natural host. Due to its large size and the presence of a papain-like protease (the OTU-like domain) it has been suggested that the L protein of nairoviruses undergoes an autoproteolytic cleavage into polymerase and one or more accessory proteins. Specific antibodies which recognise either the N-terminus or the C-terminus of the NSDV L protein showed no evidence of L protein cleavage in NSDV-infected cells. Using the specific anti-N and anti-L antibodies, it was found that these viral proteins do not fully colocalise in infected cells; the N protein accumulated near the Golgi at early stages of infection while the L protein was distributed throughout the cytoplasm, further supporting the multifunctional nature of the L protein. These antibodies also allowed us to gain information about the organs and cell types targeted by the virus in vivo. We could detect NSDV in cryosections prepared from various tissues collected post-mortem from experimentally inoculated animals; the virus was found in the mucosal lining of the small and large intestine, in the lungs, and in mesenteric lymph nodes (MLN), where NSDV appeared to target monocytes and/or macrophages.
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Affiliation(s)
- Lidia Lasecka
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
- * E-mail:
| | - Abdelghani Bin-Tarif
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - Anne Bridgen
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine BT52 1SA, Northern Ireland, United Kingdom
| | - Nicholas Juleff
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - Ryan A. Waters
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - Michael D. Baron
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
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28
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Temperature-Sensitive Mutants in the Influenza A Virus RNA Polymerase: Alterations in the PA Linker Reduce Nuclear Targeting of the PB1-PA Dimer and Result in Viral Attenuation. J Virol 2015; 89:6376-90. [PMID: 25855727 DOI: 10.1128/jvi.00589-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/30/2015] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The influenza virus RNA-dependent RNA polymerase catalyzes genome replication and transcription within the cell nucleus. Efficient nuclear import and assembly of the polymerase subunits PB1, PB2, and PA are critical steps in the virus life cycle. We investigated the structure and function of the PA linker (residues 197 to 256), located between its N-terminal endonuclease domain and its C-terminal structured domain that binds PB1, the polymerase core. Circular dichroism experiments revealed that the PA linker by itself is structurally disordered. A large series of PA linker mutants exhibited a temperature-sensitive (ts) phenotype (reduced viral growth at 39.5°C versus 37°C/33°C), suggesting an alteration of folding kinetic parameters. The ts phenotype was associated with a reduced efficiency of replication/transcription of a pseudoviral reporter RNA in a minireplicon assay. Using a fluorescent-tagged PB1, we observed that ts and lethal PA mutants did not efficiently recruit PB1 to reach the nucleus at 39.5°C. A protein complementation assay using PA mutants, PB1, and β-importin IPO5 tagged with fragments of the Gaussia princeps luciferase showed that increasing the temperature negatively modulated the PA-PB1 and the PA-PB1-IPO5 interactions or complex stability. The selection of revertant viruses allowed the identification of different types of compensatory mutations located in one or the other of the three polymerase subunits. Two ts mutants were shown to be attenuated and able to induce antibodies in mice. Taken together, our results identify a PA domain critical for PB1-PA nuclear import and that is a "hot spot" to engineer ts mutants that could be used to design novel attenuated vaccines. IMPORTANCE By targeting a discrete domain of the PA polymerase subunit of influenza virus, we were able to identify a series of 9 amino acid positions that are appropriate to engineer temperature-sensitive (ts) mutants. This is the first time that a large number of ts mutations were engineered in such a short domain, demonstrating that rational design of ts mutants can be achieved. We were able to associate this phenotype with a defect of transport of the PA-PB1 complex into the nucleus. Reversion substitutions restored the ability of the complex to move to the nucleus. Two of these ts mutants were shown to be attenuated and able to produce antibodies in mice. These results are of high interest for the design of novel attenuated vaccines and to develop new antiviral drugs.
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29
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Intracellular expression of camelid single-domain antibodies specific for influenza virus nucleoprotein uncovers distinct features of its nuclear localization. J Virol 2014; 89:2792-800. [PMID: 25540369 DOI: 10.1128/jvi.02693-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Perturbation of protein-protein interactions relies mostly on genetic approaches or on chemical inhibition. Small RNA viruses, such as influenza A virus, do not easily lend themselves to the former approach, while chemical inhibition requires that the target protein be druggable. A lack of tools thus constrains the functional analysis of influenza virus-encoded proteins. We generated a panel of camelid-derived single-domain antibody fragments (VHHs) against influenza virus nucleoprotein (NP), a viral protein essential for nuclear trafficking and packaging of the influenza virus genome. We show that these VHHs can target NP in living cells and perturb NP's function during infection. Cytosolic expression of NP-specific VHHs (αNP-VHHs) disrupts virus replication at an early stage of the life cycle. Based on their specificity, these VHHs fall into two distinct groups. Both prevent nuclear import of the viral ribonucleoprotein (vRNP) complex without disrupting nuclear import of NP alone. Different stages of the virus life cycle thus rely on distinct nuclear localization motifs of NP. Their molecular characterization may afford new means of intervention in the virus life cycle. IMPORTANCE Many proteins encoded by RNA viruses are refractory to manipulation due to their essential role in replication. Thus, studying their function and determining how to disrupt said function through pharmaceutical intervention are difficult. We present a novel method based on single-domain-antibody technology that permits specific targeting and disruption of an essential influenza virus protein in the absence of genetic manipulation of influenza virus itself. Characterization of such interactions may help identify new targets for pharmaceutical intervention. This approach can be extended to study proteins encoded by other viral pathogens.
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30
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Chin AWH, Li OTW, Mok CKP, Ng MKW, Peiris M, Poon LLM. Influenza A viruses with different amino acid residues at PB2-627 display distinct replication properties in vitro and in vivo: revealing the sequence plasticity of PB2-627 position. Virology 2014; 468-470:545-555. [PMID: 25262472 DOI: 10.1016/j.virol.2014.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/23/2014] [Accepted: 09/08/2014] [Indexed: 11/26/2022]
Abstract
Sequence analyses of influenza PB2 sequences indicate that the 627 position almost exclusively contains either lysine (K) or glutamic acid (E), suggesting a high sequence constraint at this genetic marker. Here, we used a site-directed random mutagenesis method to demonstrate that PB2-627 position has a high sequence plasticity. Recombinant viruses carrying various amino acid residues at this position are viable in cell cultures. These PB2-627 mutants showed various polymerase activities and replication kinetics in mammalian and avian cells as well as pathogenicity in mice. Serially passaging these mutants in MDCK cells generated some compensatory PB2 mutations that can restore polymerase activities of the PB2-627 mutants. Of these, PB2-D309N was identified as a novel one. Besides showing that influenza virus can tolerate a wide range of amino acid residues at the PB2-627 position, this study also demonstrates a potential strategy to identify novel mutations that can enhance viral polymerase.
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Affiliation(s)
- Alex W H Chin
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Olive T W Li
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chris K P Mok
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Miko K W Ng
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Malik Peiris
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Leo L M Poon
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.
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Abstract
The influenza A virus causes a highly contagious respiratory disease that significantly impacts our economy and health. Its replication and transcription is catalyzed by the viral RNA polymerase. This enzyme is also crucial for the virus, because it is involved in the adaptation of zoonotic strains. It is thus of major interest for the development of antiviral therapies and is being intensively studied. In this article, we will discuss recent advances that have improved our knowledge of the structure of the RNA polymerase and how mutations in the polymerase help the virus to spread effectively among new hosts.
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Affiliation(s)
- Thomas M Stubbs
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK ; Babraham Institute, Brabraham Research Campus, Cambridge, CB22 3AT, UK
| | - Aartjan Jw Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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32
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Li W, Chen H, Sutton T, Obadan A, Perez DR. Interactions between the influenza A virus RNA polymerase components and retinoic acid-inducible gene I. J Virol 2014; 88:10432-47. [PMID: 24942585 PMCID: PMC4178842 DOI: 10.1128/jvi.01383-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/12/2014] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED The influenza A virus genome possesses eight negative-strand RNA segments in the form of viral ribonucleoprotein particles (vRNPs) in association with the three viral RNA polymerase subunits (PB2, PB1, and PA) and the nucleoprotein (NP). Through interactions with multiple host factors, the RNP subunits play vital roles in replication, host adaptation, interspecies transmission, and pathogenicity. In order to gain insight into the potential roles of RNP subunits in the modulation of the host's innate immune response, the interactions of each RNP subunit with retinoic acid-inducible gene I protein (RIG-I) from mammalian and avian species were investigated. Studies using coimmunoprecipitation (co-IP), bimolecular fluorescence complementation (BiFc), and colocalization using confocal microscopy provided direct evidence for the RNA-independent binding of PB2, PB1, and PA with RIG-I from various hosts (human, swine, mouse, and duck). In contrast, the binding of NP with RIG-I was found to be RNA dependent. Expression of the viral NS1 protein, which interacts with RIG-I, did not interfere with the association of RNA polymerase subunits with RIG-I. The association of each individual virus polymerase component with RIG-I failed to significantly affect the interferon (IFN) induction elicited by RIG-I and 5' triphosphate (5'ppp) RNA in reporter assays, quantitative reverse transcription-PCR (RT-PCR), and IRF3 phosphorylation tests. Taken together, these findings indicate that viral RNA polymerase components PB2, PB1, and PA directly target RIG-I, but the exact biological significance of these interactions in the replication and pathogenicity of influenza A virus needs to be further clarified. IMPORTANCE RIG-I is an important RNA sensor to elicit the innate immune response in mammals and some bird species (such as duck) upon influenza A virus infection. Although the 5'-triphosphate double-stranded RNA (dsRNA) panhandle structure at the end of viral genome RNA is responsible for the binding and subsequent activation of RIG-I, this structure is supposedly wrapped by RNA polymerase complex (PB2, PB1, and PA), which may interfere with the induction of RIG-I signaling pathway. In the present study, PB2, PB1, and PA were found to individually interact with RIG-Is from multiple mammalian and avian species in an RNA-independent manner, without significantly affecting the generation of IFN. The data suggest that although RIG-I binding by RNA polymerase complex is conserved in different species, it does not appear to play crucial role in the modulation of IFN in vitro.
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Affiliation(s)
- Weizhong Li
- Department of Veterinary Medicine, University of Maryland, College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, USA
| | - Hongjun Chen
- Department of Veterinary Medicine, University of Maryland, College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, USA
| | - Troy Sutton
- Department of Veterinary Medicine, University of Maryland, College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, USA
| | - Adebimpe Obadan
- Department of Veterinary Medicine, University of Maryland, College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, USA
| | - Daniel R Perez
- Department of Veterinary Medicine, University of Maryland, College Park, and Virginia-Maryland Regional College of Veterinary Medicine, College Park, Maryland, USA
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33
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Recent applications of fluorescence correlation spectroscopy in live systems. FEBS Lett 2014; 588:3571-84. [PMID: 24726724 DOI: 10.1016/j.febslet.2014.03.056] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used technique in biophysics and has helped address many questions in the life sciences. It provides important advantages compared to other fluorescence and biophysical methods. Its single molecule sensitivity allows measuring proteins within biological samples at physiological concentrations without the need of overexpression. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions even in live organisms. And its reliance on simple fluorescence intensity and its fluctuations makes it widely applicable. In this review we focus on applications of FCS in live samples, with an emphasis on work in the last 5 years, in the hope to provide an overview of the present capabilities of FCS to address biologically relevant questions.
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34
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Padilla-Parra S, Audugé N, Coppey-Moisan M, Tramier M. Quantitative study of protein-protein interactions in live cell by dual-color fluorescence correlation spectroscopy. Methods Mol Biol 2014; 1076:683-698. [PMID: 24108650 DOI: 10.1007/978-1-62703-649-8_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Dual-color FCS is a powerful method to monitor protein-protein interactions in living cells. The main idea is based on the cross-correlation analysis of temporal fluorescence intensity fluctuations of two fluorescent proteins to obtain their co-diffusion and relative concentration. But, when performing these experiments, the spectral overlap in the emission of the two colors produces an artifact that corrupts the cross-correlation data: spectral bleed-through. We have shown that problems with cross talk are overcome with Fluorescence Lifetime Correlation Spectroscopy (FLCS). FLCS applied to dual-color cross-correlation, utilizing for example eGFP and mCherry fluorescent proteins, allows the determination of protein-protein interactions in living cells without the need of spectral bleed-through calibration. Here, we present in detail how this methodology can be implemented using a commercial setup (Microtime from PicoQuant, SP8 SMD from Leica or any conventional confocal with PicoQuant TCSPC module, and also with a Becker and Hickl TCSPC module). The dual-color FLCS experimental procedure where the different laser intensities do not have to be controlled during the experiment constitutes a very powerful technique to quantitatively study protein interactions in live samples.
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Affiliation(s)
- Sergi Padilla-Parra
- Institut de Génétique et Développement de Rennes, UMR 6290, CNRS, Université de Rennes 1, Rennes, France
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35
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Massari S, Nannetti G, Goracci L, Sancineto L, Muratore G, Sabatini S, Manfroni G, Mercorelli B, Cecchetti V, Facchini M, Palù G, Cruciani G, Loregian A, Tabarrini O. Structural Investigation of Cycloheptathiophene-3-carboxamide Derivatives Targeting Influenza Virus Polymerase Assembly. J Med Chem 2013; 56:10118-31. [DOI: 10.1021/jm401560v] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Serena Massari
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giulio Nannetti
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Laura Goracci
- Department
of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Luca Sancineto
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giulia Muratore
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Stefano Sabatini
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giuseppe Manfroni
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | | | - Violetta Cecchetti
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Marzia Facchini
- Department of Infectious, Parasitic, and Immunomediated Diseases,
WHO National Influenza Centre, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Gabriele Cruciani
- Department
of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Oriana Tabarrini
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
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36
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Abstract
The influenza A viruses cause yearly epidemics and occasional pandemics of respiratory disease, which constitute a serious health and economic burden. Their genome consists of eight single-stranded, negative-polarity RNAs that associate to the RNA polymerase and many nucleoprotein monomers to form ribonucleoprotein complexes (RNPs). Here, we focus on the organization of these RNPs, as well as on the structure and interactions of its constitutive elements and we discuss the mechanisms by which the RNPs transcribe and replicate the viral genome.
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Hutchinson EC, Fodor E. Transport of the influenza virus genome from nucleus to nucleus. Viruses 2013; 5:2424-46. [PMID: 24104053 PMCID: PMC3814596 DOI: 10.3390/v5102424] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 11/24/2022] Open
Abstract
The segmented genome of an influenza virus is encapsidated into ribonucleoprotein complexes (RNPs). Unusually among RNA viruses, influenza viruses replicate in the nucleus of an infected cell, and their RNPs must therefore recruit host factors to ensure transport across a number of cellular compartments during the course of an infection. Recent studies have shed new light on many of these processes, including the regulation of nuclear export, genome packaging, mechanisms of virion assembly and viral entry and, in particular, the identification of Rab11 on recycling endosomes as a key mediator of RNP transport and genome assembly. This review uses these recent gains in understanding to describe in detail the journey of an influenza A virus RNP from its synthesis in the nucleus through to its entry into the nucleus of a new host cell.
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Affiliation(s)
- Edward C Hutchinson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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38
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Gabriel G, Czudai-Matwich V, Klenk HD. Adaptive mutations in the H5N1 polymerase complex. Virus Res 2013; 178:53-62. [PMID: 23732876 DOI: 10.1016/j.virusres.2013.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 04/04/2013] [Accepted: 05/20/2013] [Indexed: 12/28/2022]
Abstract
Adaptation of the viral polymerase to host factors plays an important role in interspecies transmission of H5N1 viruses. Several adaptive mutations have been identified that, in general, determine not only host range, but also pathogenicity and transmissibility of the virus. The available evidence indicates that most of these mutations are found in the PB2 subunit of the polymerase. Particularly prominent mutations are located in the C-terminal domain of PB2 involving the amino acid exchanges E627K and D701N. Both mutations, that are also responsible for the adaptation of other avian viruses to mammalian hosts, have been described in human H5N1 isolates. In animal models, it could be demonstrated that they enhance pathogenicity in mice and induce contact transmission in guinea pigs. Mutation E627K has also been identified as a determinant of air-borne H5N1 transmission in ferrets. We are only beginning to understand the underlying mechanisms at the molecular level. Thus, mutation D701N promotes importin-α mediated nuclear transport in mammalian cells. Mutation E627K also enhances the replication rate in an importin-α dependent fashion in mammalian cells, yet without affecting nuclear entry of PB2. Numerous other adaptive mutations, some of which compensate for the lack of PB2 E627K, have been observed in PB2 as well as in the polymerase subunit PB1, the nucleoprotein NP, and the nuclear export protein NEP (NS2).
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Affiliation(s)
- Gülsah Gabriel
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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39
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Li C, Ba Q, Wu A, Zhang H, Deng T, Jiang T. A peptide derived from the C-terminus of PB1 inhibits influenza virus replication by interfering with viral polymerase assembly. FEBS J 2013; 280:1139-49. [PMID: 23279951 DOI: 10.1111/febs.12107] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/07/2012] [Accepted: 12/21/2012] [Indexed: 11/25/2022]
Abstract
Efficient assembly of the influenza virus RNA-dependent RNA polymerase, a heterotrimeric complex formed by three subunits (PA, PB1 and PB2) is critical for virus replication and pathogenicity. Therefore, interfering with the assembly of the RNA-dependent RNA polymerase complex could offer novel and effective anti-influenza therapeutics. In the present study, we show that a short peptide derived from amino acids 731-757 of PB1 (PB1(731-757)) can disrupt the interaction between the C-terminal part of PB1 (denoted as PB1c corresponding to PB1(676-757)) and the N-terminal part of PB2 (denoted as PB2n corresponding to PB2(1-40) ). We further show that PB1(731-757) is capable of inhibiting viral polymerase activity and viral replication. Interestingly, we find that PB1(731-757) interacts with PB1c rather than PB2n. Furthermore, mutational analyses show that the hydrophobic sites of PB1c play an essential role in the PB1c-PB1(731-757) interaction. The characterization of the inhibitory effect of PB1(731-757) on viral polymerase activity and viral replication could offer a potential target for anti-influenza drug development.
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Affiliation(s)
- Chunfeng Li
- Key Laboratory of Protein and Peptide Pharmaceutical, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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40
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Sasaki Y, Hagiwara K, Kakisaka M, Yamada K, Murakami T, Aida Y. Importin α3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. PLoS One 2013; 8:e55765. [PMID: 23383277 PMCID: PMC3559588 DOI: 10.1371/journal.pone.0055765] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 01/04/2013] [Indexed: 01/06/2023] Open
Abstract
The nucleoprotein (NP) of influenza A virus is transported into the nucleus via the classical importin α/β pathway, and proceeds via nuclear localization signals (NLSs) recognized by importin α molecules. Although NP binds to importin α isoforms Rch1, Qip1 and NPI-1, the role of each individual isoform during the nuclear transport of NP and replication of the influenza virus remains unknown. In this study, we examined the contribution of importin α isoforms for nuclear localization of NP and viral growth using a panel of NP mutants containing serial alanine replacements within an unconventional NLS of NP. Alanine mutation at amino acid 8 (R8A) caused a significant reduction in the nuclear localization and binding to the three importin isoforms. The R8A NP mutant virus did not generate by reverse-genetics approach. This indicates that position 8 is the main site that mediates nuclear localization via interactions with Rch1, Qip1 and NPI-1, and subsequent viral production. This was confirmed by the finding that the conservation of amino acid 8 in human- and avian-origin influenza virus NP was necessary for virus propagation. By contrast, another mutant, S9A NP, which localized in the nucleus, caused a reduction in viral growth and vRNA transcription, suggesting that the unconventional NLS within NP may be associated with nuclear transport, vRNA transcription and viral replication through independent pathways. Interestingly, the N-terminal 110-amino acid region, which contained the unconventional NLS with S9A mutation, mainly bound to Qip1. Furthermore, activities of vRNA transcription and replication of S9A NP mutants were decreased by silencing Qip1 in without changing nuclear localization, indicating that Qip1 involves in multiplication of S9A mutant virus independently of nuclear transport function. Collectively, our results demonstrate the unconventional NLS within NP might have the additional ability to regulate the viral replication that is independent of nuclear localization activity via interactions with Qip1.
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Affiliation(s)
- Yutaka Sasaki
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
| | - Kyoji Hagiwara
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
| | | | - Kazunori Yamada
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, Japan
| | - Tomoyuki Murakami
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, Japan
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama, Japan
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, Japan
- * E-mail:
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41
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Avilov SV, Moisy D, Naffakh N, Cusack S. Influenza A virus progeny vRNP trafficking in live infected cells studied with the virus-encoded fluorescently tagged PB2 protein. Vaccine 2012; 30:7411-7. [DOI: 10.1016/j.vaccine.2012.09.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 04/26/2012] [Accepted: 09/28/2012] [Indexed: 10/27/2022]
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42
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Cellular protein HAX1 interacts with the influenza A virus PA polymerase subunit and impedes its nuclear translocation. J Virol 2012; 87:110-23. [PMID: 23055567 DOI: 10.1128/jvi.00939-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Transcription and replication of the influenza A virus RNA genome occur in the nucleus through the viral RNA-dependent RNA polymerase consisting of PB1, PB2, and PA. Cellular factors that associate with the viral polymerase complex play important roles in these processes. To look for cellular factors that could associate with influenza A virus PA protein, we have carried out a yeast two-hybrid screen using a HeLa cell cDNA library. We identified six cellular proteins that may interact with PA. We focused our study on one of the new PA-interacting proteins, HAX1, a protein with antiapoptotic function. By using glutathione S-transferase pulldown and coimmunoprecipitation assays, we demonstrate that HAX1 specifically interacts with PA in vitro and in vivo and that HAX1 interacts with the nuclear localization signal domain of PA. Nuclear accumulation of PA was increased in HAX1-knockdown cells, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can impede nuclear transport of PA. As a consequence, knockdown of HAX1 resulted in a significant increase in virus yield and polymerase activity in a minigenome assay, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can inhibit influenza A virus propagation. Together, these results not only provide insight into the mechanism underlying nuclear transport of PA but also identify an intrinsic host factor that restricts influenza A virus infection.
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43
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Hutchinson EC, Fodor E. Nuclear import of the influenza A virus transcriptional machinery. Vaccine 2012; 30:7353-8. [PMID: 22652398 DOI: 10.1016/j.vaccine.2012.04.085] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/24/2012] [Indexed: 11/18/2022]
Abstract
Unusually for an RNA virus, influenza A viruses transcribe and replicate their genomes in the nuclei of infected cells. As a result the viral ribonucleoprotein complexes (RNPs), and their newly synthesised protein subunits, must interact with the host nuclear import machinery. In this review we discuss how the virus exploits nuclear import pathways to allow regulated and chaperoned assembly of RNPs in the nucleus, and describe how the import machinery itself can be a determinant of host tropism.
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Affiliation(s)
- E C Hutchinson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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44
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Bacia K, Petrášek Z, Schwille P. Correcting for spectral cross-talk in dual-color fluorescence cross-correlation spectroscopy. Chemphyschem 2012; 13:1221-31. [PMID: 22344749 PMCID: PMC3495304 DOI: 10.1002/cphc.201100801] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/29/2011] [Indexed: 11/07/2022]
Abstract
Dual-color fluorescence cross-correlation spectroscopy (dcFCCS) allows one to quantitatively assess the interactions of mobile molecules labeled with distinct fluorophores. The technique is widely applied to both reconstituted and live-cell biological systems. A major drawback of dcFCCS is the risk of an artifactual false-positive or overestimated cross-correlation amplitude arising from spectral cross-talk. Cross-talk can be reduced or prevented by fast alternating excitation, but the technology is not easily implemented in standard commercial setups. An experimental strategy is devised that does not require specialized hardware and software for recognizing and correcting for cross-talk in standard dcFCCS. The dependence of the cross-talk on particle concentrations and brightnesses is quantitatively confirmed. Moreover, it is straightforward to quantitatively correct for cross-talk using quickly accessible parameters, that is, the measured (apparent) fluorescence count rates and correlation amplitudes. Only the bleed-through ratio needs to be determined in a calibration measurement. Finally, the limitations of cross-talk correction and its influence on experimental error are explored.
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Affiliation(s)
- Kirsten Bacia
- HALOmem, University of Halle, Kurt-Mothes-Str. 3, 06120 Halle, Germany.
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45
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Factors affecting the quantification of biomolecular interactions by fluorescence cross-correlation spectroscopy. Biophys J 2012; 102:1174-83. [PMID: 22404940 DOI: 10.1016/j.bpj.2012.01.040] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 01/13/2012] [Accepted: 01/23/2012] [Indexed: 01/11/2023] Open
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is used to determine interactions and dissociation constants (K(d)s) of biomolecules. The determination of a K(d) depends on the accurate measurement of the auto- and cross-correlation function (ACF and CCF) amplitudes. In the case of complete binding, the ratio of the CCF/ACF amplitudes is expected to be 1. However, measurements performed on tandem fluorescent proteins (FPs), in which two different FPs are linked, yield CCF/ACF amplitude ratios of ~0.5 or less for different FCCS schemes. We use single wavelength FCCS and pulsed interleaved excitation FCCS to measure various tandem FPs constituted of different red and green FPs and determine the causes for this suboptimal ratio. The main causes for the reduced CCF/ACF amplitude ratio are differences in observation volumes for the different labels, the existence of dark FPs due to maturation problems, photobleaching, and to a lesser extent Förster (or fluorescence) resonance energy transfer between the labels. We deduce the fraction of nonfluorescent proteins for EGFP, mRFP, and mCherry as well as the differences in observation volumes. We use this information to correct FCCS measurements of the interaction of Cdc42, a small Rho-GTPase, with its effector IQGAP1 in live cell measurements to obtain a label-independent value for the K(d).
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46
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MacDonald LA, Aggarwal S, Bussey KA, Desmet EA, Kim B, Takimoto T. Molecular interactions and trafficking of influenza A virus polymerase proteins analyzed by specific monoclonal antibodies. Virology 2012; 426:51-9. [PMID: 22325937 DOI: 10.1016/j.virol.2012.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 01/04/2012] [Accepted: 01/17/2012] [Indexed: 12/21/2022]
Abstract
The influenza polymerase complex composed of PA, PB1 and PB2, plays a key role in viral replication and pathogenicity. Newly synthesized components must be translocated to the nucleus, where replication and transcription of viral genomes take place. Previous studies suggest that while PB2 is translocated to the nucleus independently, PA and PB1 subunits could not localize to the nucleus unless in a PA-PB1 complex. To further determine the molecular interactions between the components, we created a panel of 16 hybridoma cell lines, which produce monoclonal antibodies (mAbs) against each polymerase component. We showed that, although PB1 interacts with both PA and PB2 individually, nuclear localization of PB1 is enhanced only when co-expressed with PA. Interestingly, one of the anti-PA mAbs reacted much more strongly with PA when co-expressed with PB1. These results suggest that PA-PB1 interactions induce a conformational change in PA, which could be required for its nuclear translocation.
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Affiliation(s)
- Leslie A MacDonald
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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47
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Human-like PB2 627K influenza virus polymerase activity is regulated by importin-α1 and -α7. PLoS Pathog 2012; 8:e1002488. [PMID: 22275867 PMCID: PMC3262014 DOI: 10.1371/journal.ppat.1002488] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 12/02/2011] [Indexed: 11/19/2022] Open
Abstract
Influenza A viruses may cross species barriers and transmit to humans with the potential to cause pandemics. Interplay of human- (PB2 627K) and avian-like (PB2 627E) influenza polymerase complexes with unknown host factors have been postulated to play a key role in interspecies transmission. Here, we have identified human importin-α isoforms (α1 and α7) as positive regulators of human- but not avian-like polymerase activity. Human-like polymerase activity correlated with efficient recruitment of α1 and α7 to viral ribonucleoprotein complexes (vRNPs) without affecting subcellular localization. We also observed that human-like influenza virus growth was impaired in α1 and α7 downregulated human lung cells. Mice lacking α7 were less susceptible to human- but not avian-like influenza virus infection. Thus, α1 and α7 are positive regulators of human-like polymerase activity and pathogenicity beyond their role in nuclear transport. Adaptive mutations in the polymerase complex, such as PB2 E627K and PB2 D701N play a crucial role in influenza virus interspecies transmission. We have shown earlier that PB2 D701N promotes nuclear entry of PB2 by enhanced importin-α binding in mammalian cells (Gabriel et al., PLoS Pathogens 2008; Gabriel et al., Nat. Commun. 2011). In this study, we show that the adaptive mutation PB2 E627K involves an interaction with importin-α by a novel mechanism that does not mediate nuclear transport of viral factors. We found that human importin-α1 and -α7 are required for efficient human- (PB2 627K) but not avian-like (PB2 627E) polymerase activity. Further, human-like polymerase activity correlated with enhanced importin-α1 and -α7 binding to viral ribonucleoprotein complexes (vRNP). Mice lacking importin-α7 were less susceptible to human-like but not avian-like influenza virus infection. Our findings strongly suggest that importin-α isoforms possess functions beyond their primary role in nuclear transport facilitating PB2 E627K mediated host adaptation and pathogenicity.
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48
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Liang Y, Danzy S, Dao LD, Parslow TG, Liang Y. Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. PLoS One 2012; 7:e29485. [PMID: 22238617 PMCID: PMC3253111 DOI: 10.1371/journal.pone.0029485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 11/29/2011] [Indexed: 11/19/2022] Open
Abstract
Influenza A viral polymerase is a heterotrimeric complex that consists of PA, PB1, and PB2 subunits. We previously reported that a di-codon substitution mutation (G507A-R508A), denoted J10, in the C-terminal half of PA had no apparent effect on viral RNA synthesis but prevented infectious virus production, indicating that PA may have a novel role independent of its polymerase activity. To further examine the roles of PA in the viral life cycle, we have now generated and characterized additional mutations in regions flanking the J10 site from residues 497 to 518. All tested di-codon mutations completely abolished or significantly reduced viral infectivity, but they did so through disparate mechanisms. Several showed effects resembling those of J10, in that the mutant polymerase supported normal levels of viral RNA synthesis but nonetheless failed to generate infectious viral particles. Others eliminated polymerase activity, in most cases by perturbing the normal nuclear localization of PA protein in cells. We also engineered single-codon mutations that were predicted to pack near the J10 site in the crystal structure of PA, and found that altering residues K378 or D478 each produced a J10-like phenotype. In further studies of J10 itself, we found that this mutation does not affect the formation and release of virion-like particles per se, but instead impairs the ability of those particles to incorporate each of the eight essential RNA segments (vRNAs) that make up the viral genome. Taken together, our analysis identifies mutations in the C-terminal region of PA that differentially affect at least three distinct activities: protein nuclear localization, viral RNA synthesis, and a trans-acting function that is required for efficient packaging of all eight vRNAs.
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Affiliation(s)
- Yuhong Liang
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Shamika Danzy
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Luan Danh Dao
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Tristram G. Parslow
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Yuying Liang
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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49
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Replication-competent influenza A virus that encodes a split-green fluorescent protein-tagged PB2 polymerase subunit allows live-cell imaging of the virus life cycle. J Virol 2011; 86:1433-48. [PMID: 22114331 DOI: 10.1128/jvi.05820-11] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Studies on the intracellular trafficking of influenza virus ribonucleoproteins are currently limited by the lack of a method enabling their visualization during infection in single cells. This is largely due to the difficulty of encoding fluorescent fusion proteins within the viral genome. To circumvent this limitation, we used the split-green fluorescent protein (split-GFP) system (S. Cabantous, T. C. Terwilliger, and G. S. Waldo, Nat. Biotechnol. 23:102-107, 2005) to produce a quasi-wild-type recombinant A/WSN/33/influenza virus which allows expression of individually fluorescent PB2 polymerase subunits in infected cells. The viral PB2 proteins were fused to the 16 C-terminal amino acids of the GFP, whereas the large transcomplementing GFP fragment was supplied by transient or stable expression in cultured cells that were permissive to infection. This system was used to characterize the intranuclear dynamics of PB2 by fluorescence correlation spectroscopy and to visualize the trafficking of viral ribonucleoproteins (vRNPs) by dynamic light microscopy in live infected cells. Following nuclear export, vRNPs showed a transient pericentriolar accumulation and intermittent rapid (∼1 μm/s), directional movements in the cytoplasm, dependent on both microtubules and actin filaments. Our data establish the potential of split-GFP-based recombinant viruses for the tracking of viral proteins during a quasi-wild-type infection. This new virus, or adaptations of it, will be of use in elucidating many aspects of influenza virus host cell interactions as well as in screening for new antiviral compounds. Furthermore, the existence of cell lines stably expressing the complementing GFP fragment will facilitate applications to many other viral and nonviral systems.
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50
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Landeras-Bueno S, Jorba N, Pérez-Cidoncha M, Ortín J. The splicing factor proline-glutamine rich (SFPQ/PSF) is involved in influenza virus transcription. PLoS Pathog 2011; 7:e1002397. [PMID: 22114566 PMCID: PMC3219729 DOI: 10.1371/journal.ppat.1002397] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 10/10/2011] [Indexed: 01/15/2023] Open
Abstract
The influenza A virus RNA polymerase is a heterotrimeric complex responsible for viral genome transcription and replication in the nucleus of infected cells. We recently carried out a proteomic analysis of purified polymerase expressed in human cells and identified a number of polymerase-associated cellular proteins. Here we characterise the role of one such host factors, SFPQ/PSF, during virus infection. Down-regulation of SFPQ/PSF by silencing with two independent siRNAs reduced the virus yield by 2–5 log in low-multiplicity infections, while the replication of unrelated viruses as VSV or Adenovirus was almost unaffected. As the SFPQ/PSF protein is frequently associated to NonO/p54, we tested the potential implication of the latter in influenza virus replication. However, down-regulation of NonO/p54 by silencing with two independent siRNAs did not affect virus yields. Down-regulation of SFPQ/PSF by siRNA silencing led to a reduction and delay of influenza virus gene expression. Immunofluorescence analyses showed a good correlation between SFPQ/PSF and NP levels in infected cells. Analysis of virus RNA accumulation in silenced cells showed that production of mRNA, cRNA and vRNA is reduced by more than 5-fold but splicing is not affected. Likewise, the accumulation of viral mRNA in cicloheximide-treated cells was reduced by 3-fold. In contrast, down-regulation of SFPQ/PSF in a recombinant virus replicon system indicated that, while the accumulation of viral mRNA is reduced by 5-fold, vRNA levels are slightly increased. In vitro transcription of recombinant RNPs generated in SFPQ/PSF-silenced cells indicated a 4–5-fold reduction in polyadenylation but no alteration in cap snatching. These results indicate that SFPQ/PSF is a host factor essential for influenza virus transcription that increases the efficiency of viral mRNA polyadenylation and open the possibility to develop new antivirals targeting the accumulation of primary transcripts, a very early step during infection. The influenza A viruses cause annual epidemics and occasional pandemics of respiratory infections that may be life threatening. The viral genome contains 8 RNA molecules forming ribonucleoproteins that replicate and transcribe in the nucleus of infected cells. Influenza viruses are intracellular parasites that need the host cell machinery to replicate. To better understand this virus-cell interplay we purified the viral RNA polymerase expressed in human cells and identified several specifically associated cellular proteins. Here we characterise the role of one of them, the proline-glutamine rich splicing factor (SFPQ/PSF). Down-regulation of SFPQ/PSF indicated that it is essential for virus multiplication. Specifically, the accumulation of messenger and genomic virus-specific RNAs was reduced by SFPQ/PSF silencing in infected cells. Furthermore, transcription of parental ribonucleoproteins was affected by SFPQ/PSF down-regulation. The consequences of silencing SFPQ/PSF on the transcription and replication of a viral recombinant replicon indicated that it is required for virus transcription but not for virus RNA replication. In vitro transcription experiments indicated that SFPQ/PSF increases the efficiency of virus mRNA polyadenylation. This is the first description of a cellular factor essential for influenza virus transcription and opens the possibility to identify inhibitors that target this host-virus interaction and block virus gene expression.
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Affiliation(s)
- Sara Landeras-Bueno
- Centro Nacional de Biotecnología (CSIC), Campus de Cantoblanco, Madrid, Spain
- CIBER de Enfermedades Respiratorias, ISCIII, Bunyola, Mallorca, Spain
| | - Núria Jorba
- Centro Nacional de Biotecnología (CSIC), Campus de Cantoblanco, Madrid, Spain
- CIBER de Enfermedades Respiratorias, ISCIII, Bunyola, Mallorca, Spain
| | - Maite Pérez-Cidoncha
- Centro Nacional de Biotecnología (CSIC), Campus de Cantoblanco, Madrid, Spain
- CIBER de Enfermedades Respiratorias, ISCIII, Bunyola, Mallorca, Spain
| | - Juan Ortín
- Centro Nacional de Biotecnología (CSIC), Campus de Cantoblanco, Madrid, Spain
- CIBER de Enfermedades Respiratorias, ISCIII, Bunyola, Mallorca, Spain
- * E-mail:
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