1
|
Alobaida A, Abouzied AS, Younes KM, Alzhrani RM, Alsaab HO, Huwaimel B. Analyzing energetics and dynamics of hepatitis C virus polymerase interactions with marine bacterial compounds: a computational study. Mol Divers 2024:10.1007/s11030-024-10904-x. [PMID: 38856834 DOI: 10.1007/s11030-024-10904-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
Hepatitis C Virus (HCV) is a significant health concern affecting a large portion of the global population and is a major cause of acute liver diseases, including cirrhosis. The variability in the HCV genome mainly results from the rapid replication facilitated by the NS5B polymerase, making it a prime target for anti-HCV drug development. This study explores potential compounds from marine bacteria that could inhibit the HCV NS5B polymerase by virtual screening, analyzing the energetics, and dynamic behavior of target-compound complexes. Virtual screening with the Lipinski filter was employed to select compounds from the marine bacteria database that demonstrated strong binding affinity to NS5B. The top four (CMNPD27216, CMNPD21066, CMNPD21065, and CMNPD27283) compounds, ranked by their re-docking scores, underwent additional evaluation. Molecular dynamics simulations for 200 ns were conducted to assess the dynamic stability of these complexes in a solvent environment. Furthermore, methods such as MM-GBSA, PCA, and free energy landscape analysis were used to analyze the system's energetics and identify stable conformations by locating transition states. The findings suggest that these compounds exhibit promising binding capabilities to HCV polymerase and could be considered for future experimental validation.
Collapse
Affiliation(s)
- Ahmed Alobaida
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, 81442, Ha'il, Saudi Arabia
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia.
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12311, Egypt.
| | - Kareem M Younes
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Rami M Alzhrani
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, 55473, Hail, Saudi Arabia
| |
Collapse
|
2
|
Matthaei A, Joecks S, Frauenstein A, Bruening J, Bankwitz D, Friesland M, Gerold G, Vieyres G, Kaderali L, Meissner F, Pietschmann T. Landscape of protein-protein interactions during hepatitis C virus assembly and release. Microbiol Spectr 2024; 12:e0256222. [PMID: 38230952 PMCID: PMC10846047 DOI: 10.1128/spectrum.02562-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/11/2023] [Indexed: 01/18/2024] Open
Abstract
Assembly of infectious hepatitis C virus (HCV) particles requires multiple cellular proteins including for instance apolipoprotein E (ApoE). To describe these protein-protein interactions, we performed an affinity purification mass spectrometry screen of HCV-infected cells. We used functional viral constructs with epitope-tagged envelope protein 2 (E2), protein (p) 7, or nonstructural protein 4B (NS4B) as well as cells expressing a tagged variant of ApoE. We also evaluated assembly stage-dependent remodeling of protein complexes by using viral mutants carrying point mutations abrogating particle production at distinct steps of the HCV particle production cascade. Five ApoE binding proteins, 12 p7 binders, 7 primary E2 interactors, and 24 proteins interacting with NS4B were detected. Cell-derived PREB, STT3B, and SPCS2 as well as viral NS2 interacted with both p7 and E2. Only GTF3C3 interacted with E2 and NS4B, highlighting that HCV assembly and replication complexes exhibit largely distinct interactomes. An HCV core protein mutation, preventing core protein decoration of lipid droplets, profoundly altered the E2 interactome. In cells replicating this mutant, E2 interactions with HSPA5, STT3A/B, RAD23A/B, and ZNF860 were significantly enhanced, suggesting that E2 protein interactions partly depend on core protein functions. Bioinformatic and functional studies including STRING network analyses, RNA interference, and ectopic expression support a role of Rad23A and Rad23B in facilitating HCV infectious virus production. Both Rad23A and Rad23B are involved in the endoplasmic reticulum (ER)-associated protein degradation (ERAD). Collectively, our results provide a map of host proteins interacting with HCV assembly proteins, and they give evidence for the involvement of ER protein folding machineries and the ERAD pathway in the late stages of the HCV replication cycle.IMPORTANCEHepatitis C virus (HCV) establishes chronic infections in the majority of exposed individuals. This capacity likely depends on viral immune evasion strategies. One feature likely contributing to persistence is the formation of so-called lipo-viro particles. These peculiar virions consist of viral structural proteins and cellular lipids and lipoproteins, the latter of which aid in viral attachment and cell entry and likely antibody escape. To learn about how lipo-viro particles are coined, here, we provide a comprehensive overview of protein-protein interactions in virus-producing cells. We identify numerous novel and specific HCV E2, p7, and cellular apolipoprotein E-interacting proteins. Pathway analyses of these interactors show that proteins participating in processes such as endoplasmic reticulum (ER) protein folding, ER-associated protein degradation, and glycosylation are heavily engaged in virus production. Moreover, we find that the proteome of HCV replication sites is distinct from the assembly proteome, suggesting that transport process likely shuttles viral RNA to assembly sites.
Collapse
Affiliation(s)
- Alina Matthaei
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Sebastian Joecks
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Annika Frauenstein
- RG Experimental Systems Immunology, Max-Planck Institute for Biochemistry, Planegg, Bavaria, Germany
| | - Janina Bruening
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Dorothea Bankwitz
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Martina Friesland
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Gisa Gerold
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Gabrielle Vieyres
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
- Junior Research Group “Cell Biology of RNA Viruses,” Leibniz Institute of Experimental Virology, Hamburg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Felix Meissner
- RG Experimental Systems Immunology, Max-Planck Institute for Biochemistry, Planegg, Bavaria, Germany
- Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| |
Collapse
|
3
|
Characterization of a multipurpose NS3 surface patch coordinating HCV replicase assembly and virion morphogenesis. PLoS Pathog 2022; 18:e1010895. [PMID: 36215335 PMCID: PMC9616216 DOI: 10.1371/journal.ppat.1010895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/28/2022] [Accepted: 09/25/2022] [Indexed: 11/16/2022] Open
Abstract
The hepatitis C virus (HCV) life cycle is highly regulated and characterized by a step-wise succession of interactions between viral and host cell proteins resulting in the assembly of macromolecular complexes, which catalyse genome replication and/or virus production. Non-structural (NS) protein 3, comprising a protease and a helicase domain, is involved in orchestrating these processes by undergoing protein interactions in a temporal fashion. Recently, we identified a multifunctional NS3 protease surface patch promoting pivotal protein-protein interactions required for early steps of the HCV life cycle, including NS3-mediated NS2 protease activation and interactions required for replicase assembly. In this work, we extend this knowledge by identifying further NS3 surface determinants important for NS5A hyperphosphorylation, replicase assembly or virion morphogenesis, which map to protease and helicase domain and form a contiguous NS3 surface area. Functional interrogation led to the identification of phylogenetically conserved amino acid positions exerting a critical function in virion production without affecting RNA replication. These findings illustrate that NS3 uses a multipurpose protein surface to orchestrate the step-wise assembly of functionally distinct multiprotein complexes. Taken together, our data provide a basis to dissect the temporal formation of viral multiprotein complexes required for the individual steps of the HCV life cycle.
Collapse
|
4
|
Walther T, Bruhn B, Isken O, Tautz N. A novel NS3/4A protease dependent cleavage site within pestiviral NS2. J Gen Virol 2021; 102. [PMID: 34676824 DOI: 10.1099/jgv.0.001666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pestiviruses like bovine viral diarrhoea virus (BVDV) and classical swine fever virus (CSFV) belong to the family Flaviviridae. A special feature of the Flaviviridae is the importance of nonstructural (NS) proteins for both genome replication and virion morphogenesis. The NS2-3-4A region and its regulated processing by the NS2 autoprotease and the NS3/4A protease plays a central role in the pestiviral life cycle. We report the identification and characterization of a novel internal cleavage in BVDV NS2, which is mediated by the NS3/4A protease. Further mapping using the NS2 of BVDV-1 strain NCP7 showed that cleavage occurs between L188 and G189. This cleavage site represents a novel sequence motif recognized by the NS3/4A protease and is conserved between the pestivirus species A, B and D. Inhibition of this internal NS2 cleavage by mutating the cleavage site did not cause obvious effects on RNA replication or virion morphogenesis in cultured cell lines. Accordingly, this novel internal NS2 cleavage adds an additional layer to the already complex polyprotein processing of Pestiviruses and might further extend the repertoires of the multifunctional NS2. However, unravelling of the functional relevance of this novel processing event in NS2, therefore, awaits future in vivo studies.
Collapse
Affiliation(s)
- Thomas Walther
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany.,Present address: EUROIMMUN AG, Luebeck, Germany
| | - Barbara Bruhn
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
| | - Olaf Isken
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
| | - Norbert Tautz
- University of Luebeck, Institute of Virology and Cell Biology, Luebeck, Germany
| |
Collapse
|
5
|
Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
Collapse
Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| |
Collapse
|
6
|
Zheng F, Li N, Xu Y, Zhou Y, Li YP. Adaptive mutations promote hepatitis C virus assembly by accelerating core translocation to the endoplasmic reticulum. J Biol Chem 2021; 296:100018. [PMID: 33144326 PMCID: PMC7949066 DOI: 10.1074/jbc.ra120.016010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
The envelopment of hepatitis C virus (HCV) is believed to occur primarily in the endoplasmic reticulum (ER)-associated membrane, and the translocation of viral Core protein from lipid droplets (LDs) to the ER is essential for the envelopment of viral particles. However, the factors involved are not completely understood. Herein, we identified eight adaptive mutations that enhanced virus spread and infectivity of genotype 1a clone TNcc in hepatoma Huh7 cells through long-term culture adaptation and reverse genetic study. Of eight mutations, I853V in NS2 and C2865F in NS5B were found to be minimal mutation sets that enabled an increase in virus production without apparently affecting RNA replication, thus suggesting its roles in the post-replication stage of the HCV life cycle. Using a protease K protection and confocal microscopy analysis, we demonstrated that C2865F and the combination of I853V/C2865F enhanced virus envelopment by facilitating Core translocation from the LDs to the ER. Buoyant density analysis revealed that I853V/C2865F contributed to the release of virion with a density of ∼1.10 g/ml. Moreover, we demonstrated that NS5B directly interacted with NS2 at the protease domain and that mutations I853V, C2865F, and I853V/C2865F enhanced the interaction. In addition, C2865F also enhanced the interaction between NS5B and Core. In conclusion, this study demonstrated that adaptive mutations in NS2 and NS5B promoted HCV envelopment by accelerating Core translocation from the LDs to the ER and reinforced the interaction between NS2 and NS5B. The findings facilitate our understanding of the assembly of HCV morphogenesis.
Collapse
Affiliation(s)
- Fuxiang Zheng
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Ni Li
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Yi Xu
- Department of Pediatric, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, and Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China; Department of Infectious Disease, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China.
| |
Collapse
|
7
|
Shaw J, Gosain R, Kalita MM, Foster TL, Kankanala J, Mahato DR, Abas S, King BJ, Scott C, Brown E, Bentham MJ, Wetherill L, Bloy A, Samson A, Harris M, Mankouri J, Rowlands DJ, Macdonald A, Tarr AW, Fischer WB, Foster R, Griffin S. Rationally derived inhibitors of hepatitis C virus (HCV) p7 channel activity reveal prospect for bimodal antiviral therapy. eLife 2020; 9:e52555. [PMID: 33169665 PMCID: PMC7714397 DOI: 10.7554/elife.52555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
Since the 1960s, a single class of agent has been licensed targeting virus-encoded ion channels, or 'viroporins', contrasting the success of channel blocking drugs in other areas of medicine. Although resistance arose to these prototypic adamantane inhibitors of the influenza A virus (IAV) M2 proton channel, a growing number of clinically and economically important viruses are now recognised to encode essential viroporins providing potential targets for modern drug discovery. We describe the first rationally designed viroporin inhibitor with a comprehensive structure-activity relationship (SAR). This step-change in understanding not only revealed a second biological function for the p7 viroporin from hepatitis C virus (HCV) during virus entry, but also enabled the synthesis of a labelled tool compound that retained biological activity. Hence, p7 inhibitors (p7i) represent a unique class of HCV antiviral targeting both the spread and establishment of infection, as well as a precedent for future viroporin-targeted drug discovery.
Collapse
Affiliation(s)
- Joseph Shaw
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Rajendra Gosain
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Monoj Mon Kalita
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Toshana L Foster
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jayakanth Kankanala
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - D Ram Mahato
- Institute of Biophotonics, National Yang-Ming UniversityTaipeiTaiwan
| | - Sonia Abas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Barnabas J King
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | - Claire Scott
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Emma Brown
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Matthew J Bentham
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Laura Wetherill
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Abigail Bloy
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Adel Samson
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
| | - Mark Harris
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Jamel Mankouri
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Andrew Macdonald
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Alexander W Tarr
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical CentreNottinghamUnited Kingdom
| | | | - Richard Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| | - Stephen Griffin
- Leeds Institute of Medical Research, School of Medicine, Faculty of Medicine and Health, University of Leeds, St James’ University HospitalLeedsUnited Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsUnited Kingdom
| |
Collapse
|
8
|
Lee JY, Cortese M, Haselmann U, Tabata K, Romero-Brey I, Funaya C, Schieber NL, Qiang Y, Bartenschlager M, Kallis S, Ritter C, Rohr K, Schwab Y, Ruggieri A, Bartenschlager R. Spatiotemporal Coupling of the Hepatitis C Virus Replication Cycle by Creating a Lipid Droplet- Proximal Membranous Replication Compartment. Cell Rep 2020; 27:3602-3617.e5. [PMID: 31216478 DOI: 10.1016/j.celrep.2019.05.063] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/05/2019] [Accepted: 05/17/2019] [Indexed: 02/08/2023] Open
Abstract
The hepatitis C virus (HCV) is a major cause of chronic liver disease, affecting around 71 million people worldwide. Viral RNA replication occurs in a membranous compartment composed of double-membrane vesicles (DMVs), whereas virus particles are thought to form by budding into the endoplasmic reticulum (ER). It is unknown how these steps are orchestrated in space and time. Here, we established an imaging system to visualize HCV structural and replicase proteins in live cells and with high resolution. We determined the conditions for the recruitment of viral proteins to putative assembly sites and studied the dynamics of this event and the underlying ultrastructure. Most notable was the selective recruitment of ER membranes around lipid droplets where structural proteins and the viral replicase colocalize. Moreover, ER membranes wrapping lipid droplets were decorated with double membrane vesicles, providing a topological map of how HCV might coordinate the steps of viral replication and virion assembly.
Collapse
Affiliation(s)
- Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Charlotta Funaya
- Electron Microscopy Core Facility, Heidelberg University, 69120 Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yu Qiang
- Biomedical Computer Vision Group, Heidelberg University, BIOQUANT, IPMB, and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Marie Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Stephanie Kallis
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Christian Ritter
- Biomedical Computer Vision Group, Heidelberg University, BIOQUANT, IPMB, and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, Heidelberg University, BIOQUANT, IPMB, and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, Heidelberg, Germany.
| |
Collapse
|
9
|
Determination of Critical Requirements for Classical Swine Fever Virus NS2-3-Independent Virion Formation. J Virol 2019; 93:JVI.00679-19. [PMID: 31292243 DOI: 10.1128/jvi.00679-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/27/2019] [Indexed: 01/07/2023] Open
Abstract
For members of the Flaviviridae, it is known that, besides the structural proteins, nonstructural (NS) proteins also play a critical role in virion formation. Pestiviruses, such as bovine viral diarrhea virus (BVDV), rely on uncleaved NS2-3 for virion formation, while its cleavage product, NS3, is selectively active in RNA replication. This dogma was recently challenged by the selection of gain-of-function mutations in NS2 and NS3 which allowed virion formation in the absence of uncleaved NS2-3 in BVDV type 1 (BVDV-1) variants encoding either a ubiquitin (Ubi) (NS2-Ubi-NS3) or an internal ribosome entry site (IRES) (NS2-IRES-NS3) between NS2 and NS3. To determine whether the ability to adapt to NS2-3-independent virion morphogenesis is conserved among pestiviruses, we studied the corresponding NS2 and NS3 mutations (2/T444-V and 3/M132-A) in classical swine fever virus (CSFV). We observed that these mutations were capable of restoring low-level NS2-3-independent virion formation only for CSFV NS2-Ubi-NS3. Interestingly, a second NS2 mutation (V439-D), identified by selection, was essential for high-titer virion production. Similar to previous findings for BVDV-1, these mutations in NS2 and NS3 allowed for low-titer virion production only in CSFV NS2-IRES-NS3. For efficient virion morphogenesis, additional exchanges in NS4A (A48-T) and NS5B (D280-G) were required, indicating that these proteins cooperate in NS2-3-independent virion formation. Interestingly, both NS5B mutations, selected independently for NS2-IRES-NS3 variants of BVDV-1 and CSFV, are located in the fingertip region of the viral RNA-dependent RNA polymerase, classifying this structural element as a novel determinant for pestiviral NS2-3-independent virion formation. Together, these findings will stimulate further mechanistic studies on the genome packaging of pestiviruses.IMPORTANCE For Flaviviridae members, the nonstructural proteins are essential for virion formation and thus exert a dual role in RNA replication and virion morphogenesis. However, it remains unclear how these proteins are functionalized for either process. In wild-type pestiviruses, the NS3/4A complex is selectively active in RNA replication, while NS2-3/4A is essential for virion formation. Mutations recently identified in BVDV-1 rendered NS3/4A capable of supporting NS2-3-independent virion morphogenesis. A comparison of NS3/4A complexes incapable/capable of supporting virion morphogenesis revealed that changes in NS3/NS4A surface interactions are decisive for the gain of function. However, so far, the role of the NS2 mutations as well as the accessory mutations additionally required in the NS2-IRES-NS3 virus variant has not been clarified. To unravel the course of genome packaging, the additional sets of mutations obtained for a second pestivirus species (CSFV) are of significant importance to develop mechanistic models for this complex process.
Collapse
|
10
|
Endoplasmic Reticulum Detergent-Resistant Membranes Accommodate Hepatitis C Virus Proteins for Viral Assembly. Cells 2019; 8:cells8050487. [PMID: 31121874 PMCID: PMC6562800 DOI: 10.3390/cells8050487] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
During Hepatitis C virus (HCV) morphogenesis, the non-structural protein 2 (NS2) brings the envelope proteins 1 and 2 (E1, E2), NS3, and NS5A together to form a complex at the endoplasmic reticulum (ER) membrane, initiating HCV assembly. The nature of the interactions in this complex is unclear, but replication complex and structural proteins have been shown to be associated with cellular membrane structures called detergent-resistant membranes (DRMs). We investigated the role of DRMs in NS2 complex formation, using a lysis buffer combining Triton and n-octyl glucoside, which solubilized both cell membranes and DRMs. When this lysis buffer was used on HCV-infected cells and the resulting lysates were subjected to flotation gradient centrifugation, all viral proteins and DRM-resident proteins were found in soluble protein fractions. Immunoprecipitation assays demonstrated direct protein–protein interactions between NS2 and E2 and E1 proteins, and an association of NS2 with NS3 through DRMs. The well-folded E1E2 complex and NS5A were not associated, instead interacting separately with the NS2-E1-E2-NS3 complex through less stable DRMs. Core was also associated with NS2 and the E1E2 complex through these unstable DRMs. We suggest that DRMs carrying this NS2-E1-E2-NS3-4A-NS5A-core complex may play a central role in HCV assembly initiation, potentially as an assembly platform.
Collapse
|
11
|
Alazard-Dany N, Denolly S, Boson B, Cosset FL. Overview of HCV Life Cycle with a Special Focus on Current and Possible Future Antiviral Targets. Viruses 2019; 11:v11010030. [PMID: 30621318 PMCID: PMC6356578 DOI: 10.3390/v11010030] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C infection is the leading cause of liver diseases worldwide and a major health concern that affects an estimated 3% of the global population. Novel therapies available since 2014 and 2017 are very efficient and the WHO considers HCV eradication possible by the year 2030. These treatments are based on the so-called direct acting antivirals (DAAs) that have been developed through research efforts by academia and industry since the 1990s. After a brief overview of the HCV life cycle, we describe here the functions of the different targets of current DAAs, the mode of action of these DAAs and potential future inhibitors.
Collapse
Affiliation(s)
- Nathalie Alazard-Dany
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Solène Denolly
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Bertrand Boson
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| |
Collapse
|
12
|
Roder AE, Horner SM. Measuring Hepatitis C Virus Envelopment by Using a Proteinase K Protection Assay. Methods Mol Biol 2019; 1911:209-217. [PMID: 30593628 DOI: 10.1007/978-1-4939-8976-8_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The infectious virion of hepatitis C virus (HCV) is made up of the viral nucleocapsid surrounded by an envelope that contains an ER-derived membrane bilayer, cellular lipids, and the viral E1 and E2 glycoproteins. Because the infectious HCV particle contains both protein and lipid layers, selective disruption of these layers and analysis for the presence or absence of resulting virion components can be used to study the virion assembly process. This chapter describes an experimental method to measure HCV virion envelopment, which can reveal the mechanisms of how specific viral protein-protein interactions and host factors contribute to the process of HCV envelopment.
Collapse
Affiliation(s)
- Allison E Roder
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
13
|
Abstract
Viroporins are short polypeptides encoded by viruses. These small membrane proteins assemble into oligomers that can permeabilize cellular lipid bilayers, disrupting the physiology of the host to the advantage of the virus. Consequently, efforts during the last few decades have been focused towards the discovery of viroporin channel inhibitors, but in general these have not been successful to produce licensed drugs. Viroporins are also involved in viral pathogenesis by engaging in critical interactions with viral proteins, or disrupting normal host cellular pathways through coordinated interactions with host proteins. These protein-protein interactions (PPIs) may become alternative attractive drug targets for the development of antivirals. In this sense, while thus far most antiviral molecules have targeted viral proteins, focus is moving towards targeting host proteins that are essential for virus replication. In principle, this largely would overcome the problem of resistance, with the possibility of using repositioned existing drugs. The precise role of these PPIs, their strain- and host- specificities, and the structural determination of the complexes involved, are areas that will keep the fields of virology and structural biology occupied for years to come. In the present review, we provide an update of the efforts in the characterization of the main PPIs for most viroporins, as well as the role of viroporins in these PPIs interactions.
Collapse
Affiliation(s)
| | - David Bhella
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| |
Collapse
|
14
|
Boukadida C, Fritz M, Blumen B, Fogeron ML, Penin F, Martin A. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities. PLoS Pathog 2018; 14:e1006863. [PMID: 29415072 PMCID: PMC5819835 DOI: 10.1371/journal.ppat.1006863] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/20/2018] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Over the recent years, several homologues with varying degrees of genetic relatedness to hepatitis C virus (HCV) have been identified in a wide range of mammalian species. HCV infectious life cycle relies on a first critical proteolytic event of its single polyprotein, which is carried out by nonstructural protein 2 (NS2) and allows replicase assembly and genome replication. In this study, we characterized and evaluated the conservation of the proteolytic mode of action and regulatory mechanisms of NS2 across HCV and animal hepaciviruses. We first demonstrated that NS2 from equine, bat, rodent, New and Old World primate hepaciviruses also are cysteine proteases. Using tagged viral protein precursors and catalytic triad mutants, NS2 of equine NPHV and simian GBV-B, which are the most closely and distantly related viruses to HCV, respectively, were shown to function, like HCV NS2 as dimeric proteases with two composite active sites. Consistent with the reported essential role for NS3 N-terminal domain (NS3N) as HCV NS2 protease cofactor via NS3N key hydrophobic surface patch, we showed by gain/loss of function mutagenesis studies that some heterologous hepacivirus NS3N may act as cofactors for HCV NS2 provided that HCV-like hydrophobic residues are conserved. Unprecedently, however, we also observed efficient intrinsic proteolytic activity of NS2 protease in the absence of NS3 moiety in the context of C-terminal tag fusions via flexible linkers both in transiently transfected cells for all hepaciviruses studied and in the context of HCV dicistronic full-length genomes. These findings suggest that NS3N acts as a regulatory rather than essential cofactor for hepacivirus NS2 protease. Overall, unique features of NS2 including enzymatic function as dimers with two composite active sites and additional NS3-independent proteolytic activity are conserved across hepaciviruses regardless of their genetic distances, highlighting their functional significance in hepacivirus life cycle. Despite remarkable progress in the development of therapeutic options, more than 70 million individuals are chronically infected by hepatitis C virus (HCV) worldwide and major challenges in basic and translational research remain. Phylogenetically-related HCV homologues have recently been identified in the wild in several mammalian species, whose host restriction and potential for zoonosis remain largely unknown. We comparatively characterized the functions and properties of nonstructural proteins 2 (NS2) from several animal hepaciviruses and HCV. We demonstrated that NS2 from animal hepaciviruses, like HCV NS2, are cysteine proteases, which function as dimers with two composite active sites to ensure a key proteolytic event of the single viral polyprotein at the NS2/NS3 junction. In addition to the activation of HCV NS2 protease by NS3 N-terminal domain, our data revealed a novel NS3-independent substrate specificity and efficient intrinsic proteolytic activity of NS2. The conservation of its properties and peculiar mode of action among distantly related hepaciviruses supports an important regulatory role for NS2 protein in the life cycle of these viruses. It also strengthens the value of animal, notably rodent hepaciviruses for the development of surrogate, immunocompetent models of HCV infection to address HCV-associated pathogenesis and vaccine strategies.
Collapse
Affiliation(s)
- Célia Boukadida
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Matthieu Fritz
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Brigitte Blumen
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Annette Martin
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
- * E-mail:
| |
Collapse
|
15
|
Hung HM, Hang TD, Nguyen MT. Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane. Proteins 2018; 86:423-433. [PMID: 29341226 DOI: 10.1002/prot.25458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/02/2018] [Accepted: 01/11/2018] [Indexed: 12/16/2022]
Abstract
Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis, and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level. Our results indicated that protease domain of HCV NS3 protein can spontaneously bind and penetrate to an endoplasmic reticulum complex membrane containing phosphatidylinositol 4,5-bisphosphate (PIP2). An amphipathic helix α0 and loop S1 show their anchoring role to keep the protein on the membrane surface. Proper orientation of the protein domain at membrane surface was identified through measuring tilt angles of two specific vectors, wherein residue R161 plays a crucial role in its final orientation. Remarkably, PIP2 molecules were observed to bind to three main sites of the protease domain via specific electrostatic contacts and hydrogen bonds. PIP2-interaction determines the protein orientation at the membrane while both hydrophobic interplay and PIP2-interaction can stabilize the NS3 - membrane complex. Simulated results provide us with a detailed characterization of insertion, orientation and PIP2-interaction of NS3 protease domain at membrane environment, thus enhancing our understanding of structural functions and mechanism for the association of HCV non-structure 3 protein with respect to ER membranes.
Collapse
Affiliation(s)
- Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, B-3001, Belgium.,Department of Chemistry, Quy Nhon University, Quy Nhon, Vietnam
| | - Tran Dieu Hang
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, B-3001, Belgium.,Department of Chemistry, Quy Nhon University, Quy Nhon, Vietnam
| | - Minh Tho Nguyen
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, B-3001, Belgium
| |
Collapse
|
16
|
Zhao C, Shen X, Wu R, Li L, Pan Z. Classical swine fever virus nonstructural protein p7 modulates infectious virus production. Sci Rep 2017; 7:12995. [PMID: 29021567 PMCID: PMC5636883 DOI: 10.1038/s41598-017-13352-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/21/2017] [Indexed: 02/07/2023] Open
Abstract
The classical swine fever virus (CSFV) nonstructural protein p7 is crucial for virus production, yet precisely how the p7 modulates this process is unclear. In this study, we first identified the interactions of p7 with E2 and NS2. The key binding regions of both p7 and NS2 mapped to the first transmembrane (TM1) domain of two proteins. Three amino acid substitutions in the TM1 region of p7 (p7TDI18/19/20AAA, p7EVV21/22/23AAA and p7YFY25/26/30AAA) impaired infectious virus production and reduced the interaction of p7 with the NS2 protein. The E2p7 processing and mature p7, but not the E2p7 precursor, are essential for infectious virus production. Bicistronic mutants (pSM/E2/IRES) with single substitutions at residues 1 to 9 of p7 exhibited a significantly increased infectious CSFV titer compared to their counterparts in the context of pSM. Viral genomic RNA copies of the mutants exhibited similar levels compared with the wt CSFV. Our results demonstrated that CSFV p7 and its precursor E2p7 modulate viral protein interactions and infectious virus production without influencing viral RNA replication.
Collapse
Affiliation(s)
- Cheng Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaofang Shen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ling Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zishu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
17
|
Dubrau D, Tortorici MA, Rey FA, Tautz N. A positive-strand RNA virus uses alternative protein-protein interactions within a viral protease/cofactor complex to switch between RNA replication and virion morphogenesis. PLoS Pathog 2017; 13:e1006134. [PMID: 28151973 PMCID: PMC5308820 DOI: 10.1371/journal.ppat.1006134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 02/14/2017] [Accepted: 12/16/2016] [Indexed: 01/20/2023] Open
Abstract
The viruses of the family Flaviviridae possess a positive-strand RNA genome and express a single polyprotein which is processed into functional proteins. Initially, the nonstructural (NS) proteins, which are not part of the virions, form complexes capable of genome replication. Later on, the NS proteins also play a critical role in virion formation. The molecular basis to understand how the same proteins form different complexes required in both processes is so far unknown. For pestiviruses, uncleaved NS2-3 is essential for virion morphogenesis while NS3 is required for RNA replication but is not functional in viral assembly. Recently, we identified two gain of function mutations, located in the C-terminal region of NS2 and in the serine protease domain of NS3 (NS3 residue 132), which allow NS2 and NS3 to substitute for uncleaved NS2-3 in particle assembly. We report here the crystal structure of pestivirus NS3-4A showing that the NS3 residue 132 maps to a surface patch interacting with the C-terminal region of NS4A (NS4A-kink region) suggesting a critical role of this contact in virion morphogenesis. We show that destabilization of this interaction, either by alanine exchanges at this NS3/4A-kink interface, led to a gain of function of the NS3/4A complex in particle formation. In contrast, RNA replication and thus replicase assembly requires a stable association between NS3 and the NS4A-kink region. Thus, we propose that two variants of NS3/4A complexes exist in pestivirus infected cells each representing a basic building block required for either RNA replication or virion morphogenesis. This could be further corroborated by trans-complementation studies with a replication-defective NS3/4A double mutant that was still functional in viral assembly. Our observations illustrate the presence of alternative overlapping surfaces providing different contacts between the same proteins, allowing the switch from RNA replication to virion formation. Many positive-strand RNA viruses replicate without transcribing subgenomic RNAs otherwise often used to temporally coordinate the expression of proteins involved either in genome replication (early) or virion formation (late). Instead, the RNA genomes of the Flaviviridae are translated into a single polyprotein. Their nonstructural proteins (NS), while not present in the virions, are known to be crucially involved in RNA replication and virion formation. The important question how the same proteins form specific complexes required for fundamentally different aspects of the viral replication cycle is not solved yet. For pestiviruses the mature NS3/4A complex is an essential component of the viral RNA-replicase but is incapable of participating in virion morphogenesis which in turn depends on uncleaved NS2-3 in complex with NS4A. However, a gain of function mutation in NS3 enabled the NS3/4A complex to function in virion assembly. Using structure guided mutagenesis in combination with functional studies we identified the interface between NS3 and the C-terminal NS4A region as a module critical for the decision whether a NS3/4A complex serves in RNA replication or as a packaging component. Thus, we propose that subtle changes in local protein interactions represent decisive switches in viral complex formation pathways.
Collapse
Affiliation(s)
- Danilo Dubrau
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - M. Alejandra Tortorici
- Institut Pasteur, Unité de Virologie Structurale, Paris, France
- CNRS UMR 3569 Virologie, Paris, France
| | - Félix A. Rey
- Institut Pasteur, Unité de Virologie Structurale, Paris, France
- CNRS UMR 3569 Virologie, Paris, France
| | - Norbert Tautz
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
- * E-mail:
| |
Collapse
|
18
|
Singh P, Dass JFP. A multifaceted computational report on the variants effect on KIR2DL3 and IFNL3 candidate gene in HCV clearance. Mol Biol Rep 2016; 43:1101-17. [PMID: 27461217 DOI: 10.1007/s11033-016-4044-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
HCV infection causes acute and chronic liver diseases including, cirrhosis and hepatocellular carcinoma. Following HCV infection, spontaneous clearance occurs in approximately 20 % of the population dependant upon HCV genotype. In this study, functional and non-functional variant analysis was executed for the classical and the latest HCV clearance candidate genes namely, KIR2DL3 and IFNL3. Initially, the functional effects of non-synonymous SNPs were assigned on exposing to homology based tools, SIFT, PolyPhen-2 and PROVEAN. Further, UTR and splice sites variants were scanned for the gene expression and regulation changes. Subsequently, the haplotype and CNV were also identified. The mutation H77Y of KIR2DL3 and R157Q, H156Y, S63L, R157W, F179V, H128R, T101M, R180C, and F176I of IFNL3 results in conservation, RMSD, total energy, stability, and secondary structures revealed a negative impact on the structural fitness. UTRscan and the splice site result indicate functional change, which may affect gene regulation and expression. The graphical display of selected population shows alleles like rs270779, rs2296370, rs10423751, rs12982559, rs9797797, and rs35987710 of KIR2DL3 and rs12972991, rs12980275, rs4803217, rs8109886, and rs8099917 of IFNL3 are in high LD with a measure of [Formula: see text] broadcasting its protective effect in HCV clearance. Similarly, CNV report suggests major DNA fragment loss that could have a profound impact on the gene expression affecting the overall phenotype. This roundup report specifies the effect of NK cell receptor, KIR2DL3 and IFNL3 variants that can have a better prospect in GWAS and immunogenetic studies leading to better understanding of HCV clearance and progression.
Collapse
Affiliation(s)
- Pratichi Singh
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - J Febin Prabhu Dass
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
19
|
Hung HM, Nguyen VP, Ngo ST, Nguyen MT. Theoretical study of the interactions between the first transmembrane segment of NS2 protein and a POPC lipid bilayer. Biophys Chem 2016; 217:1-7. [DOI: 10.1016/j.bpc.2016.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 07/16/2016] [Accepted: 07/16/2016] [Indexed: 01/22/2023]
|
20
|
Hung HM, Hang TD, Nguyen MT. Multiscale simulations on conformational dynamics and membrane interactions of the non-structural 2 (NS2) transmembrane domain. Biochem Biophys Res Commun 2016; 478:193-198. [DOI: 10.1016/j.bbrc.2016.07.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 07/16/2016] [Indexed: 01/08/2023]
|
21
|
Release of Infectious Hepatitis C Virus from Huh7 Cells Occurs via a trans-Golgi Network-to-Endosome Pathway Independent of Very-Low-Density Lipoprotein Secretion. J Virol 2016; 90:7159-70. [PMID: 27226379 PMCID: PMC4984645 DOI: 10.1128/jvi.00826-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/23/2016] [Indexed: 12/12/2022] Open
Abstract
The release of infectious hepatitis C virus (HCV) particles from infected cells remains poorly characterized. We previously demonstrated that virus release is dependent on the endosomal sorting complex required for transport (ESCRT). Here, we show a critical role of trans-Golgi network (TGN)-endosome trafficking during the assembly, but principally the secretion, of infectious virus. This was demonstrated by both small interfering RNA (siRNA)-mediated silencing of TGN-associated adaptor proteins and a panel of dominant negative (DN) Rab GTPases involved in TGN-endosome trafficking steps. Importantly, interfering with factors critical for HCV release did not have a concomitant effect on secretion of triglycerides, ApoB, or ApoE, indicating that particles are likely released from Huh7 cells via pathways distinct from that of very-low-density lipoprotein (VLDL). Finally, we show that HCV NS2 perturbs TGN architecture, redistributing TGN membranes to closely associate with HCV core protein residing on lipid droplets. These findings support the notion that HCV hijacks TGN-endosome trafficking to facilitate particle assembly and release. Moreover, although essential for assembly and infectivity, the trafficking of mature virions is seemingly independent of host lipoproteins. IMPORTANCE The mechanisms by which infectious hepatitis C virus particles are assembled and released from the cell are poorly understood. We show that the virus subverts host cell trafficking pathways to effect the release of virus particles and disrupts the structure of the Golgi apparatus, a key cellular organelle involved in secretion. In addition, we demonstrate that the mechanisms used by the virus to exit the cell are distinct from those used by the cell to release lipoproteins, suggesting that the virus effects a unique modification to cellular trafficking pathways.
Collapse
|
22
|
Interaction between Nonstructural Proteins NS4B and NS5A Is Essential for Proper NS5A Localization and Hepatitis C Virus RNA Replication. J Virol 2016; 90:7205-7218. [PMID: 27252526 DOI: 10.1128/jvi.00037-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/23/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The hepatitis C virus NS5A protein is tethered to cellular membranes via an amphipathic amino-terminal helix that is inserted in-plane into the outer endoplasmic reticulum (ER)-derived membrane leaflet. The charged face of the helix faces the cytoplasm and may contribute to interactions involved in replicase assembly and function. Using an aggressive charge flip mutagenesis strategy, we identified a number of essential residues for replication on the charged face of the NS5A anchor and identified a double charge face mutant that is lethal for RNA replication but generates suppressor mutations in the carboxy-terminal helix of the NS4B protein. This suppressor restores RNA replication of the NS5A helix double flip mutant (D1979K/D1982K) and, interestingly, seems to function by restoring the proper localization of NS5A to the viral replicase. These data add to our understanding of the complex organization and assembly of the viral replicase via NS4B-NS5A interactions. IMPORTANCE Information about the functional role of the cytosolic face of the NS5A anchoring helix remains obscure. In this study, we show that while the hydrophobic face of the NS5A anchor helix mediates membrane association, the polar cytosolic face of the helix plays a key role during hepatitis C virus (HCV) replication by mediating the interaction of NS5A with other HCV nonstructural proteins via NS4B. Such an interaction determines the subcellular localization of NS5A by engaging NS5A in the HCV replication process during the formation of a functional HCV replication complex. Thus, collectively, it can be stated that the findings in the present study provide further information about the interactions between the HCV nonstructural proteins during HCV RNA replication and provide a platform to gain more insights about the molecular architecture of HCV replication complexes.
Collapse
|
23
|
Champeimont R, Laine E, Hu SW, Penin F, Carbone A. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins. Sci Rep 2016; 6:26401. [PMID: 27198619 PMCID: PMC4873791 DOI: 10.1038/srep26401] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/03/2016] [Indexed: 12/20/2022] Open
Abstract
A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.
Collapse
Affiliation(s)
- Raphaël Champeimont
- Sorbonne Universités, UPMC-Univ P6, CNRS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 15 rue de l’Ecole de Médecine, 75006 Paris, France
| | - Elodie Laine
- Sorbonne Universités, UPMC-Univ P6, CNRS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 15 rue de l’Ecole de Médecine, 75006 Paris, France
| | - Shuang-Wei Hu
- Sorbonne Universités, UPMC-Univ P6, CNRS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 15 rue de l’Ecole de Médecine, 75006 Paris, France
| | - Francois Penin
- CNRS, UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, Cedex 07, F-69367 Lyon, France
- LABEX Ecofect, Université de Lyon, Lyon, France
| | - Alessandra Carbone
- Sorbonne Universités, UPMC-Univ P6, CNRS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 15 rue de l’Ecole de Médecine, 75006 Paris, France
- Institut Universitaire de France, 75005, Paris, France
| |
Collapse
|
24
|
Ceña-Díez R, Sepúlveda-Crespo D, Maly M, Muñoz-Fernández MA. Dendrimeric based microbicides against sexual transmitted infections associated to heparan sulfate. RSC Adv 2016. [DOI: 10.1039/c6ra06969j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cell surface heparan sulfate (HS) represents a common link that many sexually transmitted infections (STIs) require for infection.
Collapse
Affiliation(s)
- Rafael Ceña-Díez
- Laboratorio InmunoBiología Molecular
- Hospital General Universitario Gregorio Marañón
- 28007 Madrid
- Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)
| | - Daniel Sepúlveda-Crespo
- Laboratorio InmunoBiología Molecular
- Hospital General Universitario Gregorio Marañón
- 28007 Madrid
- Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)
| | - Marek Maly
- Department of Innovative Technologies
- University of Applied Science of Southern Switzerland
- Switzerland
- Faculty of Science
- J. E. Purkinje University
| | - Mª Angeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular
- Hospital General Universitario Gregorio Marañón
- 28007 Madrid
- Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)
| |
Collapse
|
25
|
Characterization of the Determinants of NS2-3-Independent Virion Morphogenesis of Pestiviruses. J Virol 2015; 89:11668-80. [PMID: 26355097 DOI: 10.1128/jvi.01646-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/04/2015] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED A peculiarity of the Flaviviridae is the critical function of nonstructural (NS) proteins for virus particle formation. For pestiviruses, like bovine viral diarrhea virus (BVDV), uncleaved NS2-3 represents an essential factor for virion morphogenesis, while NS3 is an essential component of the viral replicase. Accordingly, in natural pestivirus isolates, processing at the NS2-3 cleavage site is not complete, to allow for virion morphogenesis. Virion morphogenesis of the related hepatitis C virus (HCV) shows a major deviation from that of pestiviruses: while RNA replication also requires free NS3, virion formation does not depend on uncleaved NS2-NS3. Recently, we described a BVDV-1 chimera based on strain NCP7 encompassing the NS2-4B*-coding region of strain Osloss (E. Lattwein, O. Klemens, S. Schwindt, P. Becher, and N. Tautz, J Virol 86:427-437, 2012, doi:10.1128/JVI.06133-11). This chimera allowed for the production of infectious virus particles in the absence of uncleaved NS2-3. The Osloss sequence deviates in the NS2-4B* part from NCP7 in 48 amino acids and also has a ubiquitin insertion between NS2 and NS3. The present study demonstrates that in the NCP7 backbone, only two amino acid exchanges in NS2 (E1576V) and NS3 (V1721A) are sufficient and necessary to allow for efficient NS2-3-independent virion morphogenesis. The adaptation of a bicistronic virus encompassing an internal ribosomal entry site element between the NS2 and NS3 coding sequences to efficient virion morphogenesis led to the identification of additional amino acids in E2, NS2, and NS5B that are critically involved in this process. The surprisingly small requirements for approximating the packaging schemes of pestiviruses and HCV with respect to the NS2-3 region is in favor of a common mechanism in an ancestral virus. IMPORTANCE For positive-strand RNA viruses, the processing products of the viral polyprotein serve in RNA replication as well as virion morphogenesis. For bovine viral diarrhea virus, nonstructural protein NS2-3 is of critical importance to switch between these processes. While free NS3 is essential for RNA replication, uncleaved NS2-3, which accumulates over time in the infected cell, is required for virion morphogenesis. In contrast, the virion morphogenesis of the related hepatitis C virus is independent from uncleaved NS2-NS3. Here, we demonstrate that pestiviruses can adapt to virion morphogenesis in the absence of uncleaved NS2-3 by just two amino acid exchanges. While the mechanism behind this gain of function remains elusive, the fact that it can be achieved by such minor changes is in line with the assumption that an ancestral virus already used this mechanism but lost it in the course of adapting to a new host/infection strategy.
Collapse
|
26
|
Fogeron ML, Paul D, Jirasko V, Montserret R, Lacabanne D, Molle J, Badillo A, Boukadida C, Georgeault S, Roingeard P, Martin A, Bartenschlager R, Penin F, Böckmann A. Functional expression, purification, characterization, and membrane reconstitution of non-structural protein 2 from hepatitis C virus. Protein Expr Purif 2015; 116:1-6. [PMID: 26325423 DOI: 10.1016/j.pep.2015.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 01/14/2023]
Abstract
Non-structural protein 2 (NS2) of the hepatitis C virus (HCV) is an integral membrane protein that contains a cysteine protease and that plays a central organizing role in assembly of infectious progeny virions. While the crystal structure of the protease domain has been solved, the NS2 full-length form remains biochemically and structurally uncharacterized because recombinant NS2 could not be prepared in sufficient quantities from cell-based systems. We show here that functional NS2 in the context of the NS2-NS3pro precursor protein, ensuring NS2-NS3 cleavage, can be efficiently expressed by using a wheat germ cell-free expression system. In this same system, we subsequently successfully produce and purify milligram amounts of a detergent-solubilized form of full-length NS2 exhibiting the expected secondary structure content. Furthermore, immuno-electron microscopy analyses of reconstituted proteoliposomes demonstrate NS2 association with model membranes.
Collapse
Affiliation(s)
- Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Vlastimil Jirasko
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Denis Lacabanne
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Jennifer Molle
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France; RD-Biotech, Recombinant Protein Unit, Besançon, France
| | - Célia Boukadida
- Institut Pasteur, Unit of Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université Paris Diderot - Sorbonne Paris Cité, Paris, France
| | - Sonia Georgeault
- Plate-Forme RIO des Microscopies, PPF ASB, Université François Rabelais and CHRU de Tours, Tours, France
| | - Philippe Roingeard
- Plate-Forme RIO des Microscopies, PPF ASB, Université François Rabelais and CHRU de Tours, Tours, France; INSERM U966, Universite François Rabelais and CHRU de Tours, Tours, France
| | - Annette Martin
- Institut Pasteur, Unit of Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université Paris Diderot - Sorbonne Paris Cité, Paris, France
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France.
| |
Collapse
|
27
|
"Too little, too late?" Will inhibitors of the hepatitis C virus p7 ion channel ever be used in the clinic? Future Med Chem 2015; 6:1893-907. [PMID: 25495983 DOI: 10.4155/fmc.14.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is a virus-coded ion channel, or 'viroporin'. p7 is an essential HCV protein, promoting infectious virion production, and this process can be blocked by prototypic p7 inhibitors. However, prototype potency is weak and effects in clinical trials are unsatisfactory. Nevertheless, recent structural studies render p7 amenable to modern drug discovery, with studies supporting that effective drug-like molecules should be achievable. However, burgeoning HCV therapies clear infection in the majority of treated patients. This perspective summarizes current understanding of p7 channel function and structure, pertaining to the development of improved p7 inhibitors. We ask, 'is this too little, too late', or could p7 inhibitors play a role in the long-term management of HCV disease?
Collapse
|
28
|
Structural and Functional Properties of the Hepatitis C Virus p7 Viroporin. Viruses 2015; 7:4461-81. [PMID: 26258788 PMCID: PMC4576187 DOI: 10.3390/v7082826] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
The high prevalence of hepatitis C virus (HCV) infection in the human population has triggered intensive research efforts that have led to the development of curative antiviral therapy. Moreover, HCV has become a role model to study fundamental principles that govern the replication cycle of a positive strand RNA virus. In fact, for most HCV proteins high-resolution X-ray and NMR (Nuclear Magnetic Resonance)-based structures have been established and profound insights into their biochemical and biological properties have been gained. One example is p7, a small hydrophobic protein that is dispensable for RNA replication, but crucial for the production and release of infectious HCV particles from infected cells. Owing to its ability to insert into membranes and assemble into homo-oligomeric complexes that function as minimalistic ion channels, HCV p7 is a member of the viroporin family. This review compiles the most recent findings related to the structure and dual pore/ion channel activity of p7 of different HCV genotypes. The alternative conformations and topologies proposed for HCV p7 in its monomeric and oligomeric state are described and discussed in detail. We also summarize the different roles p7 might play in the HCV replication cycle and highlight both the ion channel/pore-like function and the additional roles of p7 unrelated to its channel activity. Finally, we discuss possibilities to utilize viroporin inhibitors for antagonizing p7 ion channel/pore-like activity.
Collapse
|
29
|
Li L, Wu R, Zheng F, Zhao C, Pan Z. The N-terminus of classical swine fever virus (CSFV) nonstructural protein 2 modulates viral genome RNA replication. Virus Res 2015; 210:90-9. [PMID: 26232654 DOI: 10.1016/j.virusres.2015.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/17/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
Pestivirus nonstructural protein 2 (NS2) is a multifunctional, hydrophobic protein with an important but poorly understood role in viral RNA replication and infectious virus production. In the present study, based on sequence analysis, we mutated several representative conserved residues within the N-terminus of NS2 of classical swine fever virus (CSFV) and investigated how these mutations affected viral RNA replication and infectious virus production. Our results demonstrated that the mutation of two aspartic acids, NS2/D60A or NS2/D60K and NS2/D78K, in the N-terminus of NS2 abolished infectious virus production and that the substitution of arginine for alanine at position 100 (NS2/R100A) resulted in significantly decreased viral titer. The serial passage of cells containing viral genomic RNA molecules generated the revertants NS2/A60D, NS2/K60D and NS2/K78D, leading to the recovery of infectious virus. In the context of the NS2/R100A mutant, the NS2/I90L mutation compensated for infectious virus production. The regulatory roles of the indicated amino acid residues were identified to occur at the viral RNA replication level. These results revealed a novel function for the NS2 N-terminus of CSFV in modulating viral RNA replication.
Collapse
Affiliation(s)
- Ling Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Rui Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fengwei Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Cheng Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zishu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
30
|
Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
Collapse
Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| |
Collapse
|
31
|
Abstract
Pestiviruses are among the economically most important pathogens of livestock. The biology of these viruses is characterized by unique and interesting features that are both crucial for their success as pathogens and challenging from a scientific point of view. Elucidation of these features at the molecular level has made striking progress during recent years. The analyses revealed that major aspects of pestivirus biology show significant similarity to the biology of human hepatitis C virus (HCV). The detailed molecular analyses conducted for pestiviruses and HCV supported and complemented each other during the last three decades resulting in elucidation of the functions of viral proteins and RNA elements in replication and virus-host interaction. For pestiviruses, the analyses also helped to shed light on the molecular basis of persistent infection, a special strategy these viruses have evolved to be maintained within their host population. The results of these investigations are summarized in this chapter.
Collapse
Affiliation(s)
- Norbert Tautz
- Institute for Virology and Cell Biology, University of Lübeck, Lübeck, Germany
| | - Birke Andrea Tews
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
| |
Collapse
|
32
|
Abstract
The Picornaviridae represent a large family of small plus-strand RNA viruses that cause a bewildering array of important human and animal diseases. Morphogenesis is the least-understood step in the life cycle of these viruses, and this process is difficult to study because encapsidation is tightly coupled to genome translation and RNA replication. Although the basic steps of assembly have been known for some time, very few details are available about the mechanism and factors that regulate this process. Most of the information available has been derived from studies of enteroviruses, in particular poliovirus, where recent evidence has shown that, surprisingly, the specificity of encapsidation is governed by a viral protein-protein interaction that does not involve an RNA packaging signal. In this review, we make an attempt to summarize what is currently known about the following topics: (i) encapsidation intermediates, (ii) the specificity of encapsidation (iii), viral and cellular factors that are required for encapsidation, (iv) inhibitors of encapsidation, and (v) a model of enterovirus encapsidation. Finally, we compare some features of picornavirus morphogenesis with those of other plus-strand RNA viruses.
Collapse
|
33
|
Isken O, Langerwisch U, Jirasko V, Rehders D, Redecke L, Ramanathan H, Lindenbach BD, Bartenschlager R, Tautz N. A conserved NS3 surface patch orchestrates NS2 protease stimulation, NS5A hyperphosphorylation and HCV genome replication. PLoS Pathog 2015; 11:e1004736. [PMID: 25774920 PMCID: PMC4361677 DOI: 10.1371/journal.ppat.1004736] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/06/2015] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a leading cause of liver disease worldwide. The HCV RNA genome is translated into a single polyprotein. Most of the cleavage sites in the non-structural (NS) polyprotein region are processed by the NS3/NS4A serine protease. The vital NS2-NS3 cleavage is catalyzed by the NS2 autoprotease. For efficient processing at the NS2/NS3 site, the NS2 cysteine protease depends on the NS3 serine protease domain. Despite its importance for the viral life cycle, the molecular details of the NS2 autoprotease activation by NS3 are poorly understood. Here, we report the identification of a conserved hydrophobic NS3 surface patch that is essential for NS2 protease activation. One residue within this surface region is also critical for RNA replication and NS5A hyperphosphorylation, two processes known to depend on functional replicase assembly. This dual function of the NS3 surface patch prompted us to reinvestigate the impact of the NS2-NS3 cleavage on NS5A hyperphosphorylation. Interestingly, NS2-NS3 cleavage turned out to be a prerequisite for NS5A hyperphosphorylation, indicating that this cleavage has to occur prior to replicase assembly. Based on our data, we propose a sequential cascade of molecular events: in uncleaved NS2-NS3, the hydrophobic NS3 surface patch promotes NS2 protease stimulation; upon NS2-NS3 cleavage, this surface region becomes available for functional replicase assembly. This model explains why efficient NS2-3 cleavage is pivotal for HCV RNA replication. According to our model, the hydrophobic surface patch on NS3 represents a module critically involved in the temporal coordination of HCV replicase assembly.
Collapse
Affiliation(s)
- Olaf Isken
- Institute of Virology and Cell Biology, University of Lübeck, Germany
| | | | - Vlastimil Jirasko
- Department of Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Dirk Rehders
- Joint Laboratory for Structural Biology of Infection and Inflammation of the University of Hamburg and the University of Lübeck, DESY, Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation of the University of Hamburg and the University of Lübeck, DESY, Hamburg, Germany
| | - Harish Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Norbert Tautz
- Institute of Virology and Cell Biology, University of Lübeck, Germany
- * E-mail:
| |
Collapse
|
34
|
Poenisch M, Metz P, Blankenburg H, Ruggieri A, Lee JY, Rupp D, Rebhan I, Diederich K, Kaderali L, Domingues FS, Albrecht M, Lohmann V, Erfle H, Bartenschlager R. Identification of HNRNPK as regulator of hepatitis C virus particle production. PLoS Pathog 2015; 11:e1004573. [PMID: 25569684 PMCID: PMC4287573 DOI: 10.1371/journal.ppat.1004573] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/12/2014] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease affecting around 130 million people worldwide. While great progress has been made to define the principle steps of the viral life cycle, detailed knowledge how HCV interacts with its host cells is still limited. To overcome this limitation we conducted a comprehensive whole-virus RNA interference-based screen and identified 40 host dependency and 16 host restriction factors involved in HCV entry/replication or assembly/release. Of these factors, heterogeneous nuclear ribonucleoprotein K (HNRNPK) was found to suppress HCV particle production without affecting viral RNA replication. This suppression of virus production was specific to HCV, independent from assembly competence and genotype, and not found with the related Dengue virus. By using a knock-down rescue approach we identified the domains within HNRNPK required for suppression of HCV particle production. Importantly, HNRNPK was found to interact specifically with HCV RNA and this interaction was impaired by mutations that also reduced the ability to suppress HCV particle production. Finally, we found that in HCV-infected cells, subcellular distribution of HNRNPK was altered; the protein was recruited to sites in close proximity of lipid droplets and colocalized with core protein as well as HCV plus-strand RNA, which was not the case with HNRNPK variants unable to suppress HCV virion formation. These results suggest that HNRNPK might determine efficiency of HCV particle production by limiting the availability of viral RNA for incorporation into virions. This study adds a new function to HNRNPK that acts as central hub in the replication cycle of multiple other viruses.
Collapse
Affiliation(s)
- Marion Poenisch
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Philippe Metz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hagen Blankenburg
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Daniel Rupp
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ilka Rebhan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Kathrin Diederich
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Lars Kaderali
- ViroQuant Research Group Modeling, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Francisco S. Domingues
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Mario Albrecht
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Holger Erfle
- ViroQuant-CellNetworks RNAi Screening Facility, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
35
|
Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection. Cell Mol Immunol 2014; 13:11-35. [PMID: 25544499 PMCID: PMC4712384 DOI: 10.1038/cmi.2014.127] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/21/2014] [Accepted: 11/22/2014] [Indexed: 12/14/2022] Open
Abstract
Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed.
Collapse
|
36
|
Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection. Cell Mol Immunol 2014; 11:218-20. [PMID: 25544499 DOI: 10.1038/cmi.2014.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 12/16/2022] Open
Abstract
Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed.
Collapse
|
37
|
Phosphatidylserine-specific phospholipase A1 involved in hepatitis C virus assembly through NS2 complex formation. J Virol 2014; 89:2367-77. [PMID: 25505071 DOI: 10.1128/jvi.02982-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Several members of the phospholipase family have been reported to be involved in hepatitis C virus (HCV) replication. Here, we identified another phospholipase, phosphatidylserine-specific phospholipase A1 (PLA1A), as a host factor involved in HCV assembly. PLA1A was upregulated by HCV infection, and PLA1A knockdown significantly reduced J399EM (genotype 2a) HCV propagation at the assembly step but not the entry, RNA replication, and protein translation steps of the life cycle. Protein localization and interaction analysis further revealed a role of PLA1A in the interaction of NS2-E2 and NS2-NS5A, as the formation of the NS2-E2 and NS2-NS5A complexes was weakened in the absence of PLA1A. In addition, PLA1A stabilized the NS2/NS5A dotted structure during infection. These data suggest that PLA1A plays an important role in bridging the membrane-associated NS2-E2 complex and the NS5A-associated replication complex via its interaction with E2, NS2, and NS5A, which leads to a coordinating interaction between the structural and nonstructural proteins and facilitates viral assembly. IMPORTANCE Hepatitis C virus (HCV) genomic replication is driven by the replication complex and occurs at the membranous web, while the lipid droplet is the organelle in which virion assembly is initiated. In this study, we identified phosphatidylserine-specific phospholipase A1 (PLA1A), a member of phospholipase A 1 family, as a novel host factor involved in the assembly process of HCV. PLA1A, which is induced by HCV infection at a late infection stage, interacts with HCV E2, NS2, and NS5A proteins and enhances and stabilizes the NS2-E2 and NS2-NS5A complex formation, which is essential for viral assembly. Thus, PLA1A is an important host factor which is involved in the initiation of the viral assembly in close proximity to Core-decorated lipid droplets through bringing together the HCV replication complex and envelope complex.
Collapse
|
38
|
A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. mBio 2014; 5:e01469-14. [PMID: 25271282 PMCID: PMC4196222 DOI: 10.1128/mbio.01469-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains. Our insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale.
Collapse
|
39
|
Bentham MJ, Marraiki N, McCormick CJ, Rowlands DJ, Griffin S. NS2 is dispensable for efficient assembly of hepatitis C virus-like particles in a bipartite trans-encapsidation system. J Gen Virol 2014; 95:2427-2441. [PMID: 25024280 PMCID: PMC4202265 DOI: 10.1099/vir.0.068932-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Infectious hepatitis C virus (HCV) particle production in the genotype 2a JFH-1-based cell culture system involves non-structural proteins in addition to canonical virion components. NS2 has been proposed to act as a protein adaptor, co-ordinating the early stages of virion assembly. However, other studies have identified late-acting roles for this protein, making its precise involvement in infectious particle production unclear. Using a robust, bipartite trans-encapsidation system based upon baculovirus expression of HCV structural proteins, we have generated HCV-like particles (HCV-LP) in the absence of NS2 with overt similarity to wild-type virions. HCV-LP could transduce naive cells with trans-encapsidated subgenomic replicon RNAs and shared similar biochemical and biophysical properties with JFH-1 HCV. Both genotype 1b and JFH-1 intracellular HCV-LP were produced in the absence of NS2, whereas restoring NS2 to the JFH-1 system dramatically enhanced secreted infectivity, consistent with a late-acting role. Our system recapitulated authentic HCV particle assembly via trans-complementation of bicistronic, NS2-deleted, chimeric HCV, which is otherwise deficient in particle production. This closely resembled replicon-mediated NS2 trans-complementation, confirming that baculovirus expression of HCV proteins did not unduly affect particle production. Furthermore, this suggests that separation of structural protein expression from replicating HCV RNAs that are destined to be packaged alleviates an early stage requirement for NS2 during particle formation. This highlights our current lack of understanding of how NS2 mediates assembly, yet comparison of full-length and bipartite systems may provide further insight into this process.
Collapse
Affiliation(s)
- Matthew J Bentham
- Leeds Institute of Cancer & Pathology (LICAP), and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, UK
| | - Najat Marraiki
- School of Molecular & Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Mount Preston Street, Leeds, West Yorkshire LS2 9JT, UK
| | - Christopher J McCormick
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - David J Rowlands
- School of Molecular & Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Mount Preston Street, Leeds, West Yorkshire LS2 9JT, UK
| | - Stephen Griffin
- School of Molecular & Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Mount Preston Street, Leeds, West Yorkshire LS2 9JT, UK.,Leeds Institute of Cancer & Pathology (LICAP), and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, UK
| |
Collapse
|
40
|
Atoom AM, Taylor NGA, Russell RS. The elusive function of the hepatitis C virus p7 protein. Virology 2014; 462-463:377-87. [PMID: 25001174 PMCID: PMC7112009 DOI: 10.1016/j.virol.2014.04.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) is a major global health burden with 2–3% of the world׳s population being chronically infected. Persistent infection can lead to cirrhosis and hepatocellular carcinoma. Recently available treatment options show enhanced efficacy of virus clearance, but are associated with resistance and significant side effects. This warrants further research into the basic understanding of viral proteins and their pathophysiology. The p7 protein of HCV is an integral membrane protein that forms an ion-channel. The role of p7 in the HCV life cycle is presently uncertain, but most of the research performed to date highlights its role in the virus assembly process. The aim of this review is to provide an overview of the literature investigating p7, its structural and functional details, and to summarize the developments to date regarding potential anti-p7 compounds. A better understanding of this protein may lead to development of a new and effective therapy. This review paper provides an overview of the literature investigating HCV. The content focuses on p7 structural and functional details. We summarize the developments to date regarding potential anti-p7 compounds.
Collapse
Affiliation(s)
- Ali M Atoom
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada
| | - Nathan G A Taylor
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada
| | - Rodney S Russell
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University, Newfoundland, St. John׳s, Canada.
| |
Collapse
|
41
|
Madan V, Paul D, Lohmann V, Bartenschlager R. Inhibition of HCV replication by cyclophilin antagonists is linked to replication fitness and occurs by inhibition of membranous web formation. Gastroenterology 2014; 146:1361-72.e1-9. [PMID: 24486951 DOI: 10.1053/j.gastro.2014.01.055] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 01/13/2014] [Accepted: 01/22/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Replication of hepatitis C virus (HCV) requires host cell factors, such as cyclophilin A (CypA). CypA binds to HCV's nonstructural protein (NS)5A to promote replication of viral RNA. CypA antagonists, such as cyclosporines, are potent inhibitors of HCV replication. NS2 modulates sensitivity of HCV to cyclosporines. We investigated why cyclosporines require NS2 to increase their inhibitory effect and how they block HCV replication. METHODS We determined replication fitness and sensitivity of various HCV replicons, containing or lacking NS2, to cyclosporine and other direct-acting antiviral agents. We also analyzed the effects of cyclosporine on membranous web formation by electron microscopy. RESULTS NS2-5B replicons of genotype 2a (JFH1), but not genotype 1b, had increased sensitivity to cyclosporine. This difference was lost with replication-attenuated NS3-5B JFH1 RNAs, showing that cyclosporine sensitivity is linked to reduced replication fitness of NS2-containing HCV RNAs. Fitness also determined sensitivity to a nucleoside analogue and an NS5A inhibitor, but not to telaprevir. Cyclosporine blocked de novo formation of the membranous web, but had little effect on established membranous replication factories. This block was prevented by cyclosporine resistance mutations in NS5A. CONCLUSIONS Cleavage at the NS2/3 junction is a rate-limiting step in replication of particular HCV isolates and determines their sensitivity to CypA inhibitors. These drugs target de novo formation of the membranous web and RNA replication.
Collapse
Affiliation(s)
- Vanesa Madan
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - David Paul
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Volker Lohmann
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Center for Infection Research, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
42
|
NS2 proteins of GB virus B and hepatitis C virus share common protease activities and membrane topologies. J Virol 2014; 88:7426-44. [PMID: 24741107 DOI: 10.1128/jvi.00656-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED GB virus B (GBV-B), which is hepatotropic in experimentally infected small New World primates, is a member of the Hepacivirus genus but phylogenetically relatively distant from hepatitis C virus (HCV). To gain insights into the role and specificity of hepaciviral nonstructural protein 2 (NS2), which is required for HCV polyprotein processing and particle morphogenesis, we investigated whether NS2 structural and functional features are conserved between HCV and GBV-B. We found that GBV-B NS2, like HCV NS2, has cysteine protease activity responsible for cleavage at the NS2/NS3 junction, and we experimentally confirmed the location of this junction within the viral polyprotein. A model for GBV-B NS2 membrane topology was experimentally established by determining the membrane association properties of NS2 segments fused to green fluorescent protein (GFP) and their nuclear magnetic resonance structures using synthetic peptides as well as by applying an N-glycosylation scanning approach. Similar glycosylation studies confirmed the HCV NS2 organization. Together, our data show that despite limited amino acid sequence similarity, GBV-B and HCV NS2 proteins share a membrane topology with 3 N-terminal transmembrane segments, which is also predicted to apply to other recently discovered hepaciviruses. Based on these data and using trans-complementation systems, we found that intragenotypic hybrid NS2 proteins with heterologous N-terminal membrane segments were able to efficiently trans-complement an assembly-deficient HCV mutant with a point mutation in the NS2 C-terminal domain, while GBV-B/HCV or intergenotypic NS2 chimeras were not. These studies indicate that virus- and genotype-specific intramolecular interactions between N- and C-terminal domains of NS2 are critically involved in HCV morphogenesis. IMPORTANCE Nonstructural protein 2 (NS2) of hepatitis C virus (HCV) is a multifunctional protein critically involved in polyprotein processing and virion morphogenesis. To gain insights into NS2 mechanisms of action, we investigated whether NS2 structural and functional features are conserved between HCV and GB virus B (GBV-B), a phylogenetically relatively distant primate hepacivirus. We showed that GBV-B NS2, like HCV NS2, carries cysteine protease activity. We experimentally established a model for GBV-B NS2 membrane topology and demonstrated that despite limited sequence similarity, GBV-B and HCV NS2 share an organization with three N-terminal transmembrane segments. We found that the role of HCV NS2 in particle assembly is genotype specific and relies on critical interactions between its N- and C-terminal domains. This first comparative analysis of NS2 proteins from two hepaciviruses and our structural predictions of NS2 from other newly identified mammal hepaciviruses highlight conserved key features of the hepaciviral life cycle.
Collapse
|
43
|
Incorporation of hepatitis C virus E1 and E2 glycoproteins: the keystones on a peculiar virion. Viruses 2014; 6:1149-87. [PMID: 24618856 PMCID: PMC3970144 DOI: 10.3390/v6031149] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/21/2014] [Accepted: 02/27/2014] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) encodes two envelope glycoproteins, E1 and E2. Their structure and mode of fusion remain unknown, and so does the virion architecture. The organization of the HCV envelope shell in particular is subject to discussion as it incorporates or associates with host-derived lipoproteins, to an extent that the biophysical properties of the virion resemble more very-low-density lipoproteins than of any virus known so far. The recent development of novel cell culture systems for HCV has provided new insights on the assembly of this atypical viral particle. Hence, the extensive E1E2 characterization accomplished for the last two decades in heterologous expression systems can now be brought into the context of a productive HCV infection. This review describes the biogenesis and maturation of HCV envelope glycoproteins, as well as the interplay between viral and host factors required for their incorporation in the viral envelope, in a way that allows efficient entry into target cells and evasion of the host immune response.
Collapse
|
44
|
CD81-receptor associations--impact for hepatitis C virus entry and antiviral therapies. Viruses 2014; 6:875-92. [PMID: 24553110 PMCID: PMC3939486 DOI: 10.3390/v6020875] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 02/07/2023] Open
Abstract
Tetraspanins are integral transmembrane proteins organized in microdomains displaying specific and direct interactions with other tetraspanins and molecular partners. Among them, CD81 has been implicated in a variety of physiological and pathological processes. CD81 also plays a crucial role in pathogen entry into host cells, including hepatitis C virus (HCV) entry into hepatocytes. HCV is a major cause of liver cirrhosis and hepatocellular carcinoma. HCV entry into hepatocytes is a complex process that requires the coordinated interaction of viral and host factors for the initiation of infection, including CD81, scavenger receptor BI, claudin-1, occludin, membrane-bound host cell kinases, Niemann-Pick C1 Like 1, Harvey rat sarcoma viral oncogene homolog (HRas), CD63 and transferrin receptor 1. Furthermore, recent data in HCV model systems have demonstrated that targeting critical components of tetraspanins and associated cell membrane proteins open new avenues to prevent and treat viral infection.
Collapse
|
45
|
Atkins E, Tatineni R, Li H, Gretch D, Harris M, Griffin S. The stability of secreted, acid-labile H77/JFH-1 hepatitis C virus (HCV) particles is altered by patient isolate genotype 1a p7 sequences. Virology 2014; 448:117-24. [PMID: 24314642 PMCID: PMC7615703 DOI: 10.1016/j.virol.2013.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/05/2013] [Accepted: 10/03/2013] [Indexed: 12/17/2022]
Abstract
Secreted infectious particles generated by the genotype 2a JFH-1 hepatitis C virus infectious clone are resistant to acidic pH, whereas intracellular virions remain acid-labile. Thus, JFH-1 particles are thought to undergo pH maturation as they are secreted from the cell. Here, we demonstrate that both infectious intracellular and secreted genotype 1a (H77)/JFH-1 chimaeric particles display enhanced acid sensitivity compared with JFH-1, although pH maturation still occurs upon release. Introduction of p7 sequences from genotype 1a infected HCV patients into the H77/JFH-1 background yielded variable effects on infectious particle production and sensitivity to small molecule inhibitors. However, two selected patient p7 sequences increased the acid stability of secreted, but not intracellular H77/JFH-1 particles, suggesting that p7 directly influences particle pH maturation via an as yet undefined mechanism. We propose that HCV particles vary in acid stability, and that this may be dictated by variations in both canonical structural proteins and p7.
Collapse
Affiliation(s)
- Elizabeth Atkins
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
| | - Ranjitha Tatineni
- Leeds Institute of Cancer & Pathology (LICAP) and Leeds Cancer Research UK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, United Kingdom
| | - Hui Li
- Department of Laboratory Medicine, University of Washington School of Medicine, Harborview Medical Centre, Ninth & Jefferson Building, 908 Jefferson Street, Seattle, WA 98104, USA
| | - David Gretch
- Department of Laboratory Medicine, University of Washington School of Medicine, Harborview Medical Centre, Ninth & Jefferson Building, 908 Jefferson Street, Seattle, WA 98104, USA
| | - Mark Harris
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
| | - Stephen Griffin
- School of Molecular & Cellular Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, United Kingdom
- Leeds Institute of Cancer & Pathology (LICAP) and Leeds Cancer Research UK Clinical Centre, Faculty of Medicine and Health, St James’ University Hospital, University of Leeds, Beckett St., Leeds, West Yorkshire LS9 7TF, United Kingdom
| |
Collapse
|
46
|
Hundt J, Li Z, Liu Q. Post-translational modifications of hepatitis C viral proteins and their biological significance. World J Gastroenterol 2013; 19:8929-8939. [PMID: 24379618 PMCID: PMC3870546 DOI: 10.3748/wjg.v19.i47.8929] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023] Open
Abstract
Replication of hepatitis C virus (HCV) depends on the interaction of viral proteins with various host cellular proteins and signalling pathways. Similar to cellular proteins, post-translational modifications (PTMs) of HCV proteins are essential for proper protein function and regulation, thus, directly affecting viral life cycle and the generation of infectious virus particles. Cleavage of the HCV polyprotein by cellular and viral proteases into more than 10 proteins represents an early protein modification step after translation of the HCV positive-stranded RNA genome. The key modifications include the regulated intramembranous proteolytic cleavage of core protein, disulfide bond formation of core, glycosylation of HCV envelope proteins E1 and E2, methylation of nonstructural protein 3 (NS3), biotinylation of NS4A, ubiquitination of NS5B and phosphorylation of core and NS5B. Other modifications like ubiquitination of core and palmitoylation of core and NS4B proteins have been reported as well. For some modifications such as phosphorylation of NS3 and NS5A and acetylation of NS3, we have limited understanding of their effects on HCV replication and pathogenesis while the impact of other modifications is far from clear. In this review, we summarize the available information on PTMs of HCV proteins and discuss their relevance to HCV replication and pathogenesis.
Collapse
|
47
|
Abstract
The hepatitis C virus nonstructural NS5A protein has roles in genome replication, virus assembly, and modulation of host pathways. NS5A is a phosphoprotein, and it has been proposed that differential phosphorylation could regulate the various roles of the protein. By SDS-PAGE, two forms of NS5A with distinct apparent molecular weights can be observed, referred to as basally phosphorylated and hyperphosphorylated species. However, the sites of phosphorylation on these two species have not been unequivocally identified, hampering our understanding of the function and regulation of NS5A. To address this, we purified tagged NS5A from cells harboring a replicating subgenomic replicon and analyzed the purified protein by mass spectrometry. We identified six peptide fragments containing 12 phosphorylated residues and were able to assign four of these to serines 146, 222, and 225 and threonine 348. A serine-rich peptide fragment spanning residues 221 to 240 was highly phosphorylated. Using mutagenesis, we identified roles for a subset of these phosphoacceptors in virus genome replication. We further showed that phosphorylation at S146 regulates hyperphosphorylation, and by generating a phospho-specific antibody targeted to pS222, we identified that S222 phosphorylation predominates in the hyperphosphorylated species. Last, by introducing phosphomimetic mutations across residues 221 to 240, we demonstrated changes in the mobility of the basally phosphorylated species suggestive of a sequential phosphorylation cascade within this serine-rich cluster. We propose that this regulation could drive a conformational switch between the dimeric structures of NS5A and could also explain the different functions of the protein in the virus life cycle.
Collapse
|
48
|
Characterization of hepatitis C virus intra- and intergenotypic chimeras reveals a role of the glycoproteins in virus envelopment. J Virol 2013; 87:13297-306. [PMID: 24089562 DOI: 10.1128/jvi.01708-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Hepatitis C virus (HCV) is highly variable and associated with chronic liver disease. Viral isolates are grouped into seven genotypes (GTs). Accumulating evidence indicates that viral determinants in the core to NS2 proteins modulate the efficiency of virus production. However, the role of the glycoproteins E1 and E2 in this process is currently poorly defined. Therefore, we constructed chimeric viral genomes to explore the role of E1 and E2 in HCV assembly. Comparison of the kinetics and efficiency of particle production by intragenotypic chimeras highlighted core and p7 as crucial determinants for efficient virion release. Glycoprotein sequences, however, had only a minimal impact on this process. In contrast, in the context of intergenotypic HCV chimeras, HCV assembly was profoundly influenced by glycoprotein genes. On the one hand, insertion of GT1a-derived (H77) E1-E2 sequences into a chimeric GT2a virus (Jc1) strongly suppressed virus production. On the other hand, replacement of H77 glycoproteins within the GT1a-GT2a chimeric genome H77/C3 by GT2a-derived (Jc1) E1-E2 increased infectious particle production. Thus, within intergenotypic chimeras, glycoprotein features strongly modulate virus production. Replacement of Jc1 glycoprotein genes by H77-derived E1-E2 did not grossly affect subcellular localization of core, E2, and NS2. However, it caused an accumulation of nonenveloped core protein and increased abundance of nonenveloped core protein structures with slow sedimentation. These findings reveal an important role for the HCV glycoproteins E1 and E2 in membrane envelopment, which likely depends on a genotype-specific interplay with additional viral factors.
Collapse
|
49
|
Lindenbach BD, Rice CM. The ins and outs of hepatitis C virus entry and assembly. Nat Rev Microbiol 2013; 11:688-700. [PMID: 24018384 DOI: 10.1038/nrmicro3098] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus, a major human pathogen, produces infectious virus particles with several unique features, such as an ability to interact with serum lipoproteins, a dizzyingly complicated process of virus entry, and a pathway of virus assembly and release that is closely linked to lipoprotein secretion. Here, we review these unique features, with an emphasis on recent discoveries concerning virus particle structure, virus entry and virus particle assembly and release.
Collapse
Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06536, USA
| | | |
Collapse
|
50
|
Suzuki R, Matsuda M, Watashi K, Aizaki H, Matsuura Y, Wakita T, Suzuki T. Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2. PLoS Pathog 2013; 9:e1003589. [PMID: 24009510 PMCID: PMC3757040 DOI: 10.1371/journal.ppat.1003589] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 07/19/2013] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) nonstructural protein 2 (NS2) is a hydrophobic, transmembrane protein that is required not only for NS2-NS3 cleavage, but also for infectious virus production. To identify cellular factors that interact with NS2 and are important for HCV propagation, we screened a human liver cDNA library by split-ubiquitin membrane yeast two-hybrid assay using full-length NS2 as a bait, and identified signal peptidase complex subunit 1 (SPCS1), which is a component of the microsomal signal peptidase complex. Silencing of endogenous SPCS1 resulted in markedly reduced production of infectious HCV, whereas neither processing of structural proteins, cell entry, RNA replication, nor release of virus from the cells was impaired. Propagation of Japanese encephalitis virus was not affected by knockdown of SPCS1, suggesting that SPCS1 does not widely modulate the viral lifecycles of the Flaviviridae family. SPCS1 was found to interact with both NS2 and E2. A complex of NS2, E2, and SPCS1 was formed in cells as demonstrated by co-immunoprecipitation assays. Knockdown of SPCS1 impaired interaction of NS2 with E2. Our findings suggest that SPCS1 plays a key role in the formation of the membrane-associated NS2-E2 complex via its interaction with NS2 and E2, which leads to a coordinating interaction between the structural and non-structural proteins and facilitates the early step of assembly of infectious particles. Viruses hijack host cells and utilize host-derived proteins for viral propagation. In the case of hepatitis C virus (HCV), many host factors have been identified that are required for genome replication; however, only a little is known about cellular proteins that interact with HCV proteins and are important for the viral assembly process. The C-terminal half of nonstructural protein 2 (NS2), and the N-terminal third of NS3, form the NS2-3 protease that cleaves the NS2/3 junction. NS2 also plays a key role in the viral assembly process independently of the protease activity. We performed split-ubiquitin yeast two-hybrid screening and identified signal peptidase complex subunit 1 (SPCS1), which is a subunit of the microsomal signal peptidase complex. In this study, we provide evidence that SPCS1 interacts with both NS2 and E2, resulting in E2-SPCS1-NS2 complex formation, and has a critical role in the assembly of infectious HCV particles. To our knowledge, SPCS1 is the first NS2-interacting cellular factor that is involved in regulation of the HCV lifecycle.
Collapse
Affiliation(s)
- Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (RS); (TS)
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiharu Matsuura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Suzuki
- Department of Infectious Diseases, Hamamatsu University School of Medicine, Shizuoka, Japan
- * E-mail: (RS); (TS)
| |
Collapse
|