101
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Lee N, Le Sage V, Nanni AV, Snyder DJ, Cooper VS, Lakdawala SS. Genome-wide analysis of influenza viral RNA and nucleoprotein association. Nucleic Acids Res 2017; 45:8968-8977. [PMID: 28911100 PMCID: PMC5587783 DOI: 10.1093/nar/gkx584] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of ‘beads on a string’. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association. Intriguingly, both H1N1 strains have similar yet distinct NP binding profiles despite extensive sequence conservation. Peaks identified by HITS-CLIP were verified as true NP binding sites based on insensitivity to DNA antisense oligonucleotide-mediated RNase H digestion. Moreover, nucleotide content analysis of NP peaks revealed that these sites are relatively G-rich and U-poor compared to the genome-wide nucleotide content, indicating an as-yet unidentified sequence bias for NP association in vivo. Taken together, our genome-wide study of NP–vRNA interaction has implications for the understanding of influenza vRNA architecture and genome packaging.
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Affiliation(s)
- Nara Lee
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Valerie Le Sage
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Adalena V Nanni
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Dan J Snyder
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Vaughn S Cooper
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Seema S Lakdawala
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
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102
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Ma X, Xie L, Wartchow C, Warne R, Xu Y, Rivkin A, Tully D, Shia S, Uehara K, Baldwin DM, Muiru G, Zhong W, Zaror I, Bussiere DE, Leonard VHJ. Structural basis for therapeutic inhibition of influenza A polymerase PB2 subunit. Sci Rep 2017; 7:9385. [PMID: 28839261 PMCID: PMC5571044 DOI: 10.1038/s41598-017-09538-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/27/2017] [Indexed: 11/09/2022] Open
Abstract
Influenza virus uses a unique mechanism to initiate viral transcription named cap-snatching. The PB2 subunit of the viral heterotrimeric RNA polymerase binds the cap structure of cellular pre-mRNA to promote its cleavage by the PA subunit. The resulting 11-13 capped oligomer is used by the PB1 polymerase subunit to initiate transcription of viral proteins. VX-787 is an inhibitor of the influenza A virus pre-mRNA cap-binding protein PB2. This clinical stage compound was shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, the binding of this molecule in the context of an extended form of the PB2 subunit has remained elusive. Here we generated a collection of PB2 truncations to identify a PB2 protein representative of its structure in the viral heterotrimeric protein. We present the crystal structure of VX-787 bound to a PB2 construct that recapitulates VX-787's biological antiviral activity in vitro. This co-structure reveals more extensive interactions than previously identified and provides insight into the observed resistance profile, affinity, binding kinetics, and conformational rearrangements induced by VX-787.
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Affiliation(s)
- Xiaolei Ma
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
| | - Lili Xie
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Charles Wartchow
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Robert Warne
- Virology Lead Discovery, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Yongjin Xu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Alexey Rivkin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - David Tully
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Steven Shia
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Kyoko Uehara
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dianna M Baldwin
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Gladys Muiru
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Weidong Zhong
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Isabel Zaror
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dirksen E Bussiere
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
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103
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Xing W, Barauskas O, Kirschberg T, Niedziela-Majka A, Clarke M, Birkus G, Weissburg P, Liu X, Schultz BE, Sakowicz R, Kwon H, Feng JY. Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Endonuclease activity and evaluation of inhibitors. PLoS One 2017; 12:e0181969. [PMID: 28809961 PMCID: PMC5557545 DOI: 10.1371/journal.pone.0181969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza polymerase is a heterotrimer composed of polymerase acidic protein A (PA) and basic proteins 1 (PB1) and 2 (PB2). The endonuclease active site, located in the PA subunit, cleaves host mRNA to prime viral mRNA transcription, and is essential for viral replication. To date, the human influenza A endonuclease activity has only been studied on the truncated active-site containing N-terminal domain of PA (PAN) or full-length PA in the absence of PB1 or PB2. In this study, we characterized the endonuclease activity of recombinant proteins of influenza A/PR8 containing full length PA, PA/PB1 dimer, and PA/PB1/PB2 trimer, observing 8.3-, 265-, and 142-fold higher activity than PAN, respectively. Using the PA/PB1/PB2 trimer, we developed a robust endonuclease assay with a synthetic fluorogenic RNA substrate. The observed Km (150 ± 11 nM) and kcat [(1.4 ± 0.2) x 10-3s-1] values were consistent with previous reports using virion-derived replication complex. Two known influenza endonuclease phenylbutanoic acid inhibitors showed IC50 values of 10–20 nM, demonstrating the utility of this system for future high throughput screening.
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Affiliation(s)
- Weimei Xing
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Ona Barauskas
- Gilead Sciences, Inc., Foster City, California, United States of America
| | | | | | - Michael Clarke
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Gabriel Birkus
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Perry Weissburg
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xiaohong Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Brian E. Schultz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - HyockJoo Kwon
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
| | - Joy Y. Feng
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
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104
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Desantis J, Nannetti G, Massari S, Barreca ML, Manfroni G, Cecchetti V, Palù G, Goracci L, Loregian A, Tabarrini O. Exploring the cycloheptathiophene-3-carboxamide scaffold to disrupt the interactions of the influenza polymerase subunits and obtain potent anti-influenza activity. Eur J Med Chem 2017; 138:128-139. [PMID: 28666191 DOI: 10.1016/j.ejmech.2017.06.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/13/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022]
Abstract
With the aim to identify small molecules able to disrupt PA-PB1 subunits interaction of influenza virus (flu) RNA-dependent RNA polymerase, and based on previous structural and computational information, in this paper we have designed and synthesized a new series of cycloheptathiophene-3-carboxamide (cHTC) derivatives. Their biological evaluation led to highlight important structural insights along with new interesting compounds, such as the 2-hydroxybenzamido derivatives 29, 31, and 32, and the 4-aminophenyl derivative 54, which inhibited viral growth in the low micromolar range (EC50 = 0.18-1.2 μM) at no toxic concentrations (CC50 > 250 μM). This study permitted to obtain among the most potent anti-flu compounds within the PA-PB1 interaction inhibitors, confirming the cHTC scaffold as particularly suitable to achieve innovative anti-flu agents.
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Affiliation(s)
- Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Giulio Nannetti
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | | | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Laura Goracci
- 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 Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
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105
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Hara K, Kashiwagi T, Hamada N, Watanabe H. Basic amino acids in the N-terminal half of the PB2 subunit of influenza virus RNA polymerase are involved in both transcription and replication. J Gen Virol 2017; 98:900-905. [DOI: 10.1099/jgv.0.000750] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Koyu Hara
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Takahito Kashiwagi
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Nobuyuki Hamada
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Hiroshi Watanabe
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka 830-0011, Japan
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106
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Rosenthal M, Gogrefe N, Vogel D, Reguera J, Rauschenberger B, Cusack S, Günther S, Reindl S. Structural insights into reptarenavirus cap-snatching machinery. PLoS Pathog 2017; 13:e1006400. [PMID: 28505175 PMCID: PMC5444859 DOI: 10.1371/journal.ppat.1006400] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 05/25/2017] [Accepted: 05/05/2017] [Indexed: 01/15/2023] Open
Abstract
Cap-snatching was first discovered in influenza virus. Structures of the involved domains of the influenza virus polymerase, namely the endonuclease in the PA subunit and the cap-binding domain in the PB2 subunit, have been solved. Cap-snatching endonucleases have also been demonstrated at the very N-terminus of the L proteins of mammarena-, orthobunya-, and hantaviruses. However, a cap-binding domain has not been identified in an arena- or bunyavirus L protein so far. We solved the structure of the 326 C-terminal residues of the L protein of California Academy of Sciences virus (CASV), a reptarenavirus, by X-ray crystallography. The individual domains of this 37-kDa fragment (L-Cterm) as well as the domain arrangement are structurally similar to the cap-binding and adjacent domains of influenza virus polymerase PB2 subunit, despite the absence of sequence homology, suggesting a common evolutionary origin. This enabled identification of a region in CASV L-Cterm with similarity to a cap-binding site; however, the typical sandwich of two aromatic residues was missing. Consistent with this, cap-binding to CASV L-Cterm could not be detected biochemically. In addition, we solved the crystal structure of the corresponding endonuclease in the N-terminus of CASV L protein. It shows a typical endonuclease fold with an active site configuration that is essentially identical to that of known mammarenavirus endonuclease structures. In conclusion, we provide evidence for a presumably functional cap-snatching endonuclease in the N-terminus and a degenerate cap-binding domain in the C-terminus of a reptarenavirus L protein. Implications of these findings for the cap-snatching mechanism in arenaviruses are discussed.
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Affiliation(s)
- Maria Rosenthal
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Nadja Gogrefe
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Dominik Vogel
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Juan Reguera
- Aix-Marseille Université, INSERM, CNRS, AFMB UMR 7257, Marseille, France
| | - Bianka Rauschenberger
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Sophia Reindl
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
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107
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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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108
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Elgendy EM, Arai Y, Kawashita N, Daidoji T, Takagi T, Ibrahim MS, Nakaya T, Watanabe Y. Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeons. J Gen Virol 2017; 98:6-17. [PMID: 27926816 DOI: 10.1099/jgv.0.000674] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Highly pathogenic avian influenza virus H5N1 infects a wide range of host species, with a few cases of sporadic pigeon infections reported in the Middle East and Asia. However, the role of pigeons in the ecology and evolution of H5N1 viruses remains unclear. We previously reported two H5N1 virus strains, isolated from naturally infected pigeons in Egypt, that have several unique mutations in their viral polymerase genes. Here, we investigated the effect of these mutations on H5N1 polymerase activity and viral growth and identified three mutations that affected viral polymerase activity. The results showed that the PB1-V3D mutation significantly decreased polymerase activity and viral growth in both mammalian and avian cells. In contrast, the PB2-K627E and PA-K158R mutations had moderate effects: PB2-K627E decreased and PA-K158R increased polymerase activity. Structural homology modelling indicated that the PB1-V3D residue was located in the PB1 core region that interacts with PA, predicting that the PB1 mutation would produce a stronger interaction between PB1 and PA that results in decreased replication of pigeon-derived H5N1 viruses. Our results identified several unique mutations responsible for changes in polymerase activity in H5N1 virus strains isolated from infected pigeons, emphasizing the importance of avian influenza surveillance in pigeons and in studying the possible role of pigeon-derived H5N1 viruses in avian influenza virus evolution.
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Affiliation(s)
- Emad Mohamed Elgendy
- Department of Microbiology, Faculty of Veterinary Medicine, Damanhour University, Damanhur, Egypt.,Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuha Arai
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Norihito Kawashita
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuya Takagi
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Madiha Salah Ibrahim
- Department of Microbiology, Faculty of Veterinary Medicine, Damanhour University, Damanhur, Egypt.,Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yohei Watanabe
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
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109
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Pflug A, Lukarska M, Resa-Infante P, Reich S, Cusack S. Structural insights into RNA synthesis by the influenza virus transcription-replication machine. Virus Res 2017; 234:103-117. [PMID: 28115197 DOI: 10.1016/j.virusres.2017.01.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/31/2016] [Accepted: 01/13/2017] [Indexed: 12/22/2022]
Abstract
Influenza virus is a segmented, negative strand RNA virus with each genome segment being packaged in a distinct ribonucleoprotein particle (RNP). The RNP consists of the heterotrimeric viral RNA-dependent RNA polymerase bound to the conserved 5' and 3' ends of the genome segment (the viral promoter) with the rest of the viral RNA (vRNA) being covered by multiple copies of nucleoprotein. This review focusses on the new insights that recent crystal structures have given into the detailed molecular mechanisms by which the polymerase performs both transcription and replication of the vRNA genome. Promoter binding, in particular that of 5' end, is essential to allosterically activate all polymerase functions. Transcription is initiated by the hijacking of nascent, capped host transcripts by the process of 'cap-snatching', for which the viral polymerase makes an essential interaction with the C-terminal domain (CTD) of cellular RNA polymerase II. The structures allow a coherent mechanistic model of the subsequent cap-snatching, cap-dependent priming, elongation and self-polyadenylation steps of viral mRNA synthesis. During replication, the vRNA is copied without modification into complementary RNA (cRNA) which is packaged into cRNPs. A priming loop located in the polymerase active site is required for the unprimed synthesis of cRNA from vRNA, but is not required for cRNA to vRNA replication due to differences in the mode of initiation of RNA synthesis. Overall a picture emerges of influenza polymerase being a highly complex, flexible and dynamic machine. The challenge remains to understand in more detail how it functions within the RNP and how interacting host factors modulate its activity in the cellular context. Finally, these detailed insights have opened up new opportunities for structure-based antiviral drug design targeting multiple aspects of polymerase function.
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Affiliation(s)
- Alexander Pflug
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maria Lukarska
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Patricia Resa-Infante
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stefan Reich
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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110
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Structural Biology of the Arterivirus nsp11 Endoribonucleases. J Virol 2016; 91:JVI.01309-16. [PMID: 27795409 DOI: 10.1128/jvi.01309-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/01/2016] [Indexed: 12/17/2022] Open
Abstract
Endoribonuclease (NendoU) is unique and conserved as a major genetic marker in nidoviruses that infect vertebrate hosts. Arterivirus nonstructural protein 11 (nsp11) was shown to have NendoU activity and play essential roles in the viral life cycle. Here, we report three crystal structures of porcine reproductive and respiratory syndrome virus (PRRSV) and equine arteritis virus (EAV) nsp11 mutants. The structures of arterivirus nsp11 contain two conserved compact domains: the N-terminal domain (NTD) and C-terminal domain (CTD). The structures of PRRSV and EAV endoribonucleases are similar and conserved in the arterivirus, but they are greatly different from that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoV), representing important human pathogens in the Nidovirales order. The catalytic center of NendoU activity is located in the CTD, where a positively charged groove is next to the key catalytic residues conserved in nidoviruses. Although the NTD is nearly identical, the catalytic region of the arterivirus nsp11 family proteins is remarkably flexible, and the oligomerization may be concentration dependent. In summary, our structures provide new insight into this key multifunctional NendoU family of proteins and lay a foundation for better understanding of the molecular mechanism and antiviral drug development. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) and equine arteritis virus are two major members of the arterivirus family. PRRSV, a leading swine pathogen, causes reproductive failure in breeding stock and respiratory tract illness in young pigs. Due to the lack of a suitable vaccine or effective drug treatment and the quick spread of these viruses, infected animals either die quickly or must be culled. PRRSV costs the swine industry around $644 million annually in the United States and almost €1.5 billion in Europe every year. To find a way to combat these viruses, we focused on the essential viral nonstructural protein 11 (nsp11). nsp11 is associated with multiple functions, such as RNA processing and suppression of the infected host innate immunity system. The three structures solved in this study provide new insight into the molecular mechanisms of this crucial protein family and will benefit the development of new treatments against these deadly viruses.
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111
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Yuan S, Chu H, Ye J, Singh K, Ye Z, Zhao H, Kao RYT, Chow BKC, Zhou J, Zheng BJ. Identification of a novel small-molecule compound targeting the influenza A virus polymerase PB1-PB2 interface. Antiviral Res 2016; 137:58-66. [PMID: 27840201 PMCID: PMC7113721 DOI: 10.1016/j.antiviral.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 01/06/2023]
Abstract
The PB1 C-terminal domain and PB2 N-terminal domain interaction of the influenza A polymerase, which modulates the assembly of PB1 and PB2 subunits, may serve as a valuable target for the development of novel anti-influenza therapeutics. In this study, we performed a systematic screening of a chemical library, followed by the antiviral evaluation of primary hits and their analogues. Eventually, a novel small-molecule compound PP7 that abrogated the PB1-PB2 association and impaired viral polymerase activity was identified. PP7 exhibited antiviral activities against influenza virus subtypes A (H1N1)pdm09, A(H7N9) and A(H9N2) in cell cultures and partially protected mice against lethal challenge of mouse-adapted influenza A (H1N1)pdm09 virus. Surprisingly, a panel of other subtypes of influenza virus, including A(H5N1) and A(H7N7), showed various degrees of resistance to the compound. Biochemical studies revealed a similar pattern of resistance on the impairment of polymerase activity. Molecular docking analyses suggested a PP7-binding site that appeared to be completely conserved among the subtypes of the virus mentioned above. Thus, we propose that alternative/additional binding site (s) may exist for the regulation of PB1-PB2 subunits assembly of influenza A virus. A novel small-molecule compound was identified to provide anti-influenza effect in vitro and in vivo. An RT-qPCR based assay was modified to evaluate the polymerase activity of various subtypes of influenza viruses. The PB1-PB2 assembly strategies of the trimeric polymerase complex might be stain/subtype specific.
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Affiliation(s)
- Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hin Chu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jiahui Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kailash Singh
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Ziwei Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hanjun Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Richard Y T Kao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Billy K C Chow
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China
| | - Jie Zhou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Bo-Jian Zheng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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112
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Du Y, Wu NC, Jiang L, Zhang T, Gong D, Shu S, Wu TT, Sun R. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis. mBio 2016; 7:e01801-16. [PMID: 27803181 PMCID: PMC5090041 DOI: 10.1128/mbio.01801-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/07/2016] [Indexed: 11/28/2022] Open
Abstract
Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. IMPORTANCE To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available.
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Affiliation(s)
- Yushen Du
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nicholas C Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Lin Jiang
- Department of Neurology, University of California Los Angeles, Los Angeles, California, USA
| | - Tianhao Zhang
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Sara Shu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, USA
- Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
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113
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Robb NC, Te Velthuis AJW, Wieneke R, Tampé R, Cordes T, Fodor E, Kapanidis AN. Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA. Nucleic Acids Res 2016; 44:10304-10315. [PMID: 27694620 PMCID: PMC5137447 DOI: 10.1093/nar/gkw884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 01/20/2023] Open
Abstract
Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3′ terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3′ terminus of the vRNA template in a pre-initiation state, bound on the surface of the RNAP rather than in the active site; no information is available on 3′ cRNA binding. Here, we have used single-molecule Förster resonance energy transfer (smFRET) to probe the viral RNA conformations that occur during RNAP binding and initial replication. We show that even in the absence of nucleotides, the RNAP-bound 3′ termini of both vRNA and cRNA exist in two conformations, corresponding to the pre-initiation state and an initiation conformation in which the 3′ terminus of the viral RNA is in the RNAP active site. Nucleotide addition stabilises the 3′ vRNA in the active site and results in unwinding of the duplexed region of the promoter. Our data provide insights into the dynamic motions of RNA that occur during initial influenza replication and has implications for our understanding of the replication mechanisms of similar pathogenic viruses.
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Affiliation(s)
- Nicole C Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Aartjan J W Te Velthuis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ervin Fodor
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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114
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Delaforge E, Milles S, Huang JR, Bouvier D, Jensen MR, Sattler M, Hart DJ, Blackledge M. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions. Front Mol Biosci 2016; 3:54. [PMID: 27679800 PMCID: PMC5020063 DOI: 10.3389/fmolb.2016.00054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
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Affiliation(s)
- Elise Delaforge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Sigrid Milles
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Jie-Rong Huang
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Denis Bouvier
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum MünchenNeuherberg, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR, Technische Universität MünchenGarching, Germany
| | - Darren J Hart
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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115
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Stevaert A, Naesens L. The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design. Med Res Rev 2016; 36:1127-1173. [PMID: 27569399 PMCID: PMC5108440 DOI: 10.1002/med.21401] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
Influenza viruses cause seasonal epidemics and pandemic outbreaks associated with significant morbidity and mortality, and a huge cost. Since resistance to the existing anti‐influenza drugs is rising, innovative inhibitors with a different mode of action are urgently needed. The influenza polymerase complex is widely recognized as a key drug target, given its critical role in virus replication and high degree of conservation among influenza A (of human or zoonotic origin) and B viruses. We here review the major progress that has been made in recent years in unravelling the structure and functions of this protein complex, enabling structure‐aided drug design toward the core regions of the PA endonuclease, PB1 polymerase, or cap‐binding PB2 subunit. Alternatively, inhibitors may target a protein–protein interaction site, a cellular factor involved in viral RNA synthesis, the viral RNA itself, or the nucleoprotein component of the viral ribonucleoprotein. The latest advances made for these diverse pharmacological targets have yielded agents in advanced (i.e., favipiravir and VX‐787) or early clinical testing, besides several experimental inhibitors in various stages of development, which are all covered here.
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Affiliation(s)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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116
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Naesens L, Stevaert A, Vanderlinden E. Antiviral therapies on the horizon for influenza. Curr Opin Pharmacol 2016; 30:106-115. [PMID: 27570127 DOI: 10.1016/j.coph.2016.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
Adequate response to severe influenza infections or pandemic outbreaks requires two complementary strategies: preventive vaccination and antiviral therapy. The existing influenza drugs, M2 blockers and neuraminidase inhibitors, show modest clinical efficacy and established or potential resistance. In the past three years, several new agents have entered the clinical pipeline and already yielded some promising data from Phase 2 trials. For two main categories, that is, the broadly neutralizing anti-hemagglutinin antibodies and small-molecule inhibitors of the viral polymerase complex, crystallography was instrumental to guide drug development. These structural insights also aid to expand the activity spectrum towards influenza A plus B viruses, or conceive nucleoprotein or polymerase assembly inhibitors. The practice of influenza therapy should radically change in the next decade.
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Affiliation(s)
- Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
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117
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Vidic J, Noiray M, Bagchi A, Slama-Schwok A. Identification of a Novel Complex between the Nucleoprotein and PA(1–27) of Influenza A Virus Polymerase. Biochemistry 2016; 55:4259-62. [DOI: 10.1021/acs.biochem.6b00514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jasmina Vidic
- Paris Saclay University, UR892, INRA, 78350 Jouy en Josas, France
| | - Magali Noiray
- UMS
IPSIT-Intermol, University Paris Sud, Paris Saclay University, 92296 Châtenay-Malabry, France
| | - Angshuman Bagchi
- Paris Saclay University, UR892, INRA, 78350 Jouy en Josas, France
- Department
of Biochemistry and Biophysics, University of Kalyani, Kalyani, India
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118
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Te Velthuis AJW, Fodor E. Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis. Nat Rev Microbiol 2016; 14:479-93. [PMID: 27396566 DOI: 10.1038/nrmicro.2016.87] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The genomes of influenza viruses consist of multiple segments of single-stranded negative-sense RNA. Each of these segments is bound by the heterotrimeric viral RNA-dependent RNA polymerase and multiple copies of nucleoprotein, which form viral ribonucleoprotein (vRNP) complexes. It is in the context of these vRNPs that the viral RNA polymerase carries out transcription of viral genes and replication of the viral RNA genome. In this Review, we discuss our current knowledge of the structure of the influenza virus RNA polymerase, and insights that have been gained into the molecular mechanisms of viral transcription and replication, and their regulation by viral and host factors. Furthermore, we discuss how advances in our understanding of the structure and function of polymerases could help in identifying new antiviral targets.
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Affiliation(s)
- Aartjan J W Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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119
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Reguera J, Gerlach P, Rosenthal M, Gaudon S, Coscia F, Günther S, Cusack S. Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases. PLoS Pathog 2016; 12:e1005636. [PMID: 27304209 PMCID: PMC4909276 DOI: 10.1371/journal.ppat.1005636] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023] Open
Abstract
Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase. Segmented negative strand viruses (sNSV) such as Influenza, Lassa or Hantaan viruses are responsible for a large number of severe human infectious diseases. Currently, there are vaccines and antiviral treatments available for influenza but none for the infections caused by other sNSV. All carry out transcription by the cap-snatching mechanism, which requires the action of a metal ion dependent endonuclease (EN), a domain within their large viral polymerases. Here we provide the crystal structure of the Hantaan virus (family Bunyaviridae) and Lassa virus (family Arenaviridae) cap-snatching ENs in complex with manganese and a comparative functional study of their catalytic activity. Despite the high structural homology between the two ENs a few changes in the active site, involving a catalytic histidine, cause a different binding of the metal ions with dramatic consequences for their in vitro activity. Hantaan EN binds the metal ions as Influenza A (family Orthomyxoviridae) and LACV (family Bunyaviridae) ENs and all three are active in vitro. In contrast Lassa virus EN is inactive in the same experimental conditions. We can now classify sNSV into two functionally distinct groups (His+ and His- ENs), providing a broad view of the sNSV cap-snatching ENs properties that will be determinant for the comprehensive development of broad-spectrum antiviral drugs. These results also have implications for the viral transcription regulation in the light of recent studies on full-length sNSV polymerases.
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Affiliation(s)
- Juan Reguera
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- * E-mail: (JR); (SC)
| | - Piotr Gerlach
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Maria Rosenthal
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Gaudon
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Francesca Coscia
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- * E-mail: (JR); (SC)
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120
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New Insight into Metal Ion-Driven Catalysis of Nucleic Acids by Influenza PA-Nter. PLoS One 2016; 11:e0156972. [PMID: 27300442 PMCID: PMC4907508 DOI: 10.1371/journal.pone.0156972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/23/2016] [Indexed: 11/24/2022] Open
Abstract
PA subunit of influenza RNA-dependent RNA polymerase deserves constantly increasing attention due to its essential role in influenza life cycle. N-terminal domain of PA (PA-Nter) harbors endonuclease activity, which is indispensable in viral transcription and replication. Interestingly, existing literature reports on in vitro ion preferences of the enzyme are contradictory. Some show PA-Nter activity exclusively with Mn2+, whereas others report Mg2+ as a natural cofactor. To clarify it, we performed a series of experiments with varied ion concentrations and substrate type. We observed cleavage in the presence of both ions, with a slight preference for manganese, however PA-Nter activity highly depended on the amount of residual, co-purified ions. Furthermore, to quantify cleavage reaction rate, we applied fluorescence cross-correlation spectroscopy (FCCS), providing highly sensitive and real-time monitoring of single molecules. Using nanomolar ssDNA in the regime of enzyme excess, we estimated the maximum reaction rate at 0.81± 0.38 and 1.38± 0.34 nM/min for Mg2+ and Mn2+, respectively. However, our calculations of PA-Nter ion occupancy, based on thermodynamic data, suggest Mg2+ to be a canonical metal in PA-Nter processing of RNA in vivo. Presented studies constitute a step toward better understanding of PA-Nter ion-dependent activity, which will possibly contribute to new successful inhibitor design in the future.
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121
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RNA-Free and Ribonucleoprotein-Associated Influenza Virus Polymerases Directly Bind the Serine-5-Phosphorylated Carboxyl-Terminal Domain of Host RNA Polymerase II. J Virol 2016; 90:6014-6021. [PMID: 27099314 PMCID: PMC4907247 DOI: 10.1128/jvi.00494-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza viruses subvert the transcriptional machinery of their hosts to synthesize their own viral mRNA. Ongoing transcription by cellular RNA polymerase II (Pol II) is required for viral mRNA synthesis. By a process known as cap snatching, the virus steals short 5′ capped RNA fragments from host capped RNAs and uses them to prime viral transcription. An interaction between the influenza A virus RNA polymerase and the C-terminal domain (CTD) of the large subunit of Pol II has been established, but the molecular details of this interaction remain unknown. We show here that the influenza virus ribonucleoprotein (vRNP) complex binds to the CTD of transcriptionally engaged Pol II. Furthermore, we provide evidence that the viral polymerase binds directly to the serine-5-phosphorylated form of the Pol II CTD, both in the presence and in the absence of viral RNA, and show that this interaction is conserved in evolutionarily distant influenza viruses. We propose a model in which direct binding of the viral RNA polymerase in the context of vRNPs to Pol II early in infection facilitates cap snatching, while we suggest that binding of free viral polymerase to Pol II late in infection may trigger Pol II degradation. IMPORTANCE Influenza viruses cause yearly epidemics and occasional pandemics that pose a threat to human health, as well as represent a large economic burden to health care systems globally. Existing vaccines are not always effective, as they may not exactly match the circulating viruses. Furthermore, there are a limited number of antivirals available, and development of resistance to these is a concern. New measures to combat influenza are needed, but before they can be developed, it is necessary to better understand the molecular interactions between influenza viruses and their host cells. By providing further insights into the molecular details of how influenza viruses hijack the host transcriptional machinery, we aim to uncover novel targets for the development of antivirals.
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122
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te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E. The role of the priming loop in Influenza A virus RNA synthesis. Nat Microbiol 2016; 1:16029. [PMID: 27274864 PMCID: PMC4888940 DOI: 10.1038/nmicrobiol.2016.29] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/10/2016] [Indexed: 12/16/2022]
Abstract
RNA-dependent RNA polymerases (RdRps) are used by RNA viruses to replicate and transcribe their RNA genomes1. They adopt a closed, right-handed fold with conserved subdomains called palm, fingers, and thumb1,2. Conserved RdRp motifs A-F coordinate the viral RNA template, NTPs, and magnesium ions to facilitate nucleotide condensation1. For the initiation of RNA synthesis, most RdRps use either a primer-dependent or de novo mechanism3. The Influenza A virus RdRp in contrast, uses a capped RNA oligonucleotide to initiate transcription, and a combination of terminal and internal de novo initiation for replication4. To understand how the Influenza A virus RdRp coordinates these processes, we analysed the function of a thumb subdomain β-hairpin using initiation, elongation, and single-molecule FRET assays. Our data shows that this β-hairpin is essential for terminal initiation during replication, but auxiliary for internal initiation and transcription. Analysis of individual residues in the tip of the β-hairpin shows that PB1 proline 651 is critical for efficient RNA synthesis in vitro and in cell culture. Overall, this work advances our understanding of Influenza A virus RNA synthesis and identifies the initiation platform of viral replication.
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Affiliation(s)
- Aartjan J.W. te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, United Kingdom
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, United Kingdom
| | - Nicole C. Robb
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, United Kingdom
| | - Achillefs N. Kapanidis
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, United Kingdom
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123
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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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124
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Massari S, Goracci L, Desantis J, Tabarrini O. Polymerase Acidic Protein-Basic Protein 1 (PA-PB1) Protein-Protein Interaction as a Target for Next-Generation Anti-influenza Therapeutics. J Med Chem 2016; 59:7699-718. [PMID: 27046062 DOI: 10.1021/acs.jmedchem.5b01474] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The limited therapeutic options against the influenza virus (flu) and increasing challenges in drug resistance make the search for next-generation agents imperative. In this context, heterotrimeric viral PA/PB1/PB2 RNA-dependent RNA polymerase is an attractive target for a challenging but strategic protein-protein interaction (PPI) inhibition approach. Since 2012, the inhibition of the polymerase PA-PB1 subunit interface has become an active field of research following the publication of PA-PB1 crystal structures. In this Perspective, we briefly discuss the validity of flu polymerase as a drug target and its inhibition through a PPI inhibition strategy, including a comprehensive analysis of available PA-PB1 structures. An overview of all of the reported PA-PB1 complex formation inhibitors is provided, and approaches used for identification of the inhibitors, the hit-to-lead studies, and the emerged structure-activity relationship are described. In addition to highlighting the strengths and weaknesses of all of the PA-PB1 heterodimerization inhibitors, we analyze their hypothesized binding modes and alignment with a pharmacophore model that we have developed.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia , 06123 Perugia, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
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125
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Momose F, Morikawa Y. Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence. Front Microbiol 2016; 7:288. [PMID: 27014212 PMCID: PMC4782009 DOI: 10.3389/fmicb.2016.00288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/23/2016] [Indexed: 01/07/2023] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) of influenza A virus consists of three subunits, PB2, PB1, and PA, and catalyses both viral RNA genome replication and transcription. Cotransfection of four monocistronic expression vectors for these subunits and nucleoprotein with an expression vector for viral RNA reconstitutes functional viral ribonucleoprotein complex (vRNP). However, the specific activity of reconstituted RdRp is usually very low since the expression level and the ratio of the three subunits by transfection are uncontrollable at single-cell levels. For efficient reconstitution of RdRp and vRNP, their levels need to be at least comparable. We constructed polycistronic expression vectors in which the coding sequences of the three subunits were joined with the 2A-like self-processing sequence of Thosea asigna virus (TaV2A) in various orders. The level of PB1 protein, even when it was placed at the most downstream, was comparable with that expressed from the monocistronic PB1 vector. In contrast, the levels of PB2 and PA were very low, the latter of which was most likely due to proteasomal degradation caused by the TaV2A-derived sequences attached to the amino- and/or carboxyl-terminal ends in this expression system. Interestingly, two of the constructs, in which the PB1 coding sequence was placed at the most upstream, showed much higher reporter activity in a luciferase-based mini-genome assay than that observed by cotransfection of the monocistronic vectors. When the coding sequence of selective antibiotic marker was further placed at the most downstream of the PB1-PA-PB2 open reading frame, stable cells expressing RdRp were easily established, indicating that acquisition of antibiotic resistance assured the expression of upstream RdRp. The addition of an affinity tag to the carboxyl-terminal end of PB2 allowed us to isolate reconstituted vRNP. Taken together, the polycistronic expression system for influenza virus RdRp may be available for functional and structural studies on vRNP.
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Affiliation(s)
- Fumitaka Momose
- Laboratory of Viral Infection II, Kitasato Institute for Life Sciences, Kitasato University Tokyo, Japan
| | - Yuko Morikawa
- Laboratory of Viral Infection II, Kitasato Institute for Life Sciences, Kitasato University Tokyo, Japan
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126
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Abstract
Continued discovery and development of new antiviral medications are paramount for global human health, particularly as new pathogens emerge and old ones evolve to evade current therapeutic agents. Great success has been achieved in developing effective therapies to suppress human immunodeficiency virus (HIV) and hepatitis B virus (HBV); however, the therapies are not curative and therefore current efforts in HIV and HBV drug discovery are directed toward longer-acting therapies and/or developing new mechanisms of action that could potentially lead to cure, or eradication, of the virus. Recently, exciting early clinical data have been reported for novel antivirals targeting respiratory syncytial virus (RSV) and influenza (flu). Preclinical data suggest that these new approaches may be effective in treating high-risk patients afflicted with serious RSV or flu infections. In this review, we highlight new directions in antiviral approaches for HIV, HBV, and acute respiratory virus infections.
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Affiliation(s)
- Wade Blair
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania, 19438, USA
| | - Christopher Cox
- Department of Discovery Chemistry, Merck Research Laboratories, West Point, Pennsylvania, 19438, USA
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127
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Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases. Curr Opin Struct Biol 2016; 36:75-84. [PMID: 26826467 DOI: 10.1016/j.sbi.2016.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/05/2016] [Indexed: 01/23/2023]
Abstract
Negative strand RNA viruses (NSVs), which may have segmented (sNSV) or non-segmented genomes (nsNSV) are responsible for numerous serious human infections such as Influenza, Measles, Rabies, Ebola, Crimean Congo Haemorrhagic Fever and Lassa Fever. Their RNA-dependent RNA polymerases transcribe and replicate the nucleoprotein coated viral genome within the context of a ribonucleoprotein particle. We review the first high resolution crystal and cryo-EM structures of representative NSV polymerases. The heterotrimeric Influenza and single-chain La Crosse orthobunyavirus polymerase structures (sNSV) show how specific recognition of both genome ends is achieved and is required for polymerase activation and how the sNSV specific 'cap-snatching' mechanism of transcription priming works. Vesicular Stomatitis Virus (nsNSV) polymerase shows a similar core architecture but has different flexibly linked C-terminal domains which perform mRNA cap synthesis. These structures pave the way for a more complete understanding of these complex, multifunctional machines which are also targets for anti-viral drug design.
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128
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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: 112] [Impact Index Per Article: 14.0] [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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129
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Highly flexible influenza polymerase. Nat Rev Microbiol 2015. [DOI: 10.1038/nrmicro3593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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130
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Paesen GC, Collet A, Sallamand C, Debart F, Vasseur JJ, Canard B, Decroly E, Grimes JM. X-ray structure and activities of an essential Mononegavirales L-protein domain. Nat Commun 2015; 6:8749. [PMID: 26549102 PMCID: PMC4659945 DOI: 10.1038/ncomms9749] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022] Open
Abstract
The L protein of mononegaviruses harbours all catalytic activities for genome replication and transcription. It contains six conserved domains (CR-I to -VI; Fig. 1a). CR-III has been linked to polymerase and polyadenylation activity, CR-V to mRNA capping and CR-VI to cap methylation. However, how these activities are choreographed is poorly understood. Here we present the 2.2-Å X-ray structure and activities of CR-VI+, a portion of human Metapneumovirus L consisting of CR-VI and the poorly conserved region at its C terminus, the +domain. The CR-VI domain has a methyltransferase fold, which besides the typical S-adenosylmethionine-binding site ((SAM)P) also contains a novel pocket ((NS)P) that can accommodate a nucleoside. CR-VI lacks an obvious cap-binding site, and the (SAM)P-adjoining site holding the nucleotides undergoing methylation ((SUB)P) is unusually narrow because of the overhanging +domain. CR-VI+ sequentially methylates caps at their 2'O and N7 positions, and also displays nucleotide triphosphatase activity.
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Affiliation(s)
- Guido C. Paesen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN UK
| | - Axelle Collet
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, Marseille, 13288 France
| | - Corinne Sallamand
- Department of Nucleic Acids, IBMM, UMR 5247, CNRS, Université Montpellier, ENSCM, Campus Triolet, Place E. Bataillon, Montpellier, 34095 France
| | - Françoise Debart
- Department of Nucleic Acids, IBMM, UMR 5247, CNRS, Université Montpellier, ENSCM, Campus Triolet, Place E. Bataillon, Montpellier, 34095 France
| | - Jean-Jacques Vasseur
- Department of Nucleic Acids, IBMM, UMR 5247, CNRS, Université Montpellier, ENSCM, Campus Triolet, Place E. Bataillon, Montpellier, 34095 France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, Marseille, 13288 France
| | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, Marseille, 13288 France
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK
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