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Fellenberg J, Dubrau D, Isken O, Tautz N. Packaging defects in pestiviral NS4A can be compensated by mutations in NS2 and NS3. J Virol 2023; 97:e0057223. [PMID: 37695056 PMCID: PMC10537661 DOI: 10.1128/jvi.00572-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/18/2023] [Indexed: 09/12/2023] Open
Abstract
The non-structural (NS) proteins of the Flaviviridae members play a dual role in genome replication and virion morphogenesis. For pestiviruses, like bovine viral diarrhea virus, the NS2-3 region and its processing by the NS2 autoprotease is of particular importance. While uncleaved NS2-3 in complex with NS4A is essential for virion assembly, it cannot replace free NS3/4A in the viral replicase. Furthermore, surface interactions between NS3 and the C-terminal cytosolic domain of NS4A were shown to serve as a molecular switch between RNA replication and virion morphogenesis. To further characterize the functionality of NS4A, we performed an alanine-scanning mutagenesis of two NS4A regions, a short highly conserved cytoplasmic linker downstream of the transmembrane domain and the C-terminal domain. NS4A residues critical for polyprotein processing, RNA replication, and/or virion morphogenesis were identified. Three double-alanine mutants, two in the linker region and one close to the C-terminus of NS4A, showed a selective effect on virion assembly. All three packaging defective mutants could be rescued by a selected set of two second-site mutations, located in NS2 and NS3, respectively. This phenotype was additionally confirmed by complementation studies providing the NS2-3/4A packaging molecules containing the rescue mutations in trans. This indicates that the linker region and the cytosolic C-terminal part of NS4A are critical for the formation of protein complexes required for virion morphogenesis. The ability of the identified sets of second-site mutations in NS2-3 to compensate for diverse NS4A defects highlights a surprising functional flexibility for pestiviral NS proteins. IMPORTANCE Positive-strand RNA viruses have a limited coding capacity due to their rather small genome size. To overcome this constraint, viral proteins often exhibit multiple functions that come into play at different stages during the viral replication cycle. The molecular basis for this multifunctionality is often unknown. For the bovine viral diarrhea virus, the non-structural protein (NS) 4A functions as an NS3 protease cofactor, a replicase building block, and a component in virion morphogenesis. Here, we identified the critical amino acids of its C-terminal cytosolic region involved in those processes and show that second-site mutations in NS2 and NS3 can compensate for diverse NS4A defects in virion morphogenesis. The ability to evolve alternative functional solutions by gain-of-function mutations highlights the astounding plasticity of the pestiviral system.
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Affiliation(s)
- Jonas Fellenberg
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Danilo Dubrau
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Olaf Isken
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Norbert Tautz
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
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2
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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.
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3
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Guo R, Pyle AM. Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study. Methods Enzymol 2022; 673:39-52. [DOI: 10.1016/bs.mie.2022.03.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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4
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Klaitong P, Smith DR. Roles of Non-Structural Protein 4A in Flavivirus Infection. Viruses 2021; 13:v13102077. [PMID: 34696510 PMCID: PMC8538649 DOI: 10.3390/v13102077] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Infections with viruses in the genus Flavivirus are a worldwide public health problem. These enveloped, positive sense single stranded RNA viruses use a small complement of only 10 encoded proteins and the RNA genome itself to remodel host cells to achieve conditions favoring viral replication. A consequence of the limited viral armamentarium is that each protein exerts multiple cellular effects, in addition to any direct role in viral replication. The viruses encode four non-structural (NS) small transmembrane proteins (NS2A, NS2B, NS4A and NS4B) which collectively remain rather poorly characterized. NS4A is a 16kDa membrane associated protein and recent studies have shown that this protein plays multiple roles, including in membrane remodeling, antagonism of the host cell interferon response, and in the induction of autophagy, in addition to playing a role in viral replication. Perhaps most importantly, NS4A has been implicated as playing a critical role in fetal developmental defects seen as a consequence of Zika virus infection during pregnancy. This review provides a comprehensive overview of the multiple roles of this small but pivotal protein in mediating the pathobiology of flaviviral infections.
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In Vitro Antiviral Activity of Tyrosinase from Mushroom Agaricus bisporus against Hepatitis C Virus. Pharmaceuticals (Basel) 2021; 14:ph14080759. [PMID: 34451856 PMCID: PMC8399381 DOI: 10.3390/ph14080759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Tyrosinases from a commercial Agaricus bisporus protein extract and directly isolated from white mushrooms were purified in order to obtaining the well-known tyrosinase from A. bisporus (TyrAB) of 45 kDa and a newly discovered 50 kDa tyrosinase isoform (Tyr50 kDa), and tested showing high antiviral activity against the hepatitis C virus for the first time. Cell toxicity and antiviral activity of tyrosinases were determined in cultured Huh 5-2 liver tumor cells transfected with a replicon system (a plasmid that includes all non-structural hepatitis C virus proteins and replicates autonomously). TyrAB was able to inhibit the replication of the hepatitis C virus without inducing toxicity in liver cells. In addition, the post-translational isoform Tyr50 kDa showed higher antiviral capacity than the former (up to 10 times greater), also exhibiting 10 times higher activity than the commercial drug Ribavirin®. This antiviral activity was directly proportional to the enzymatic activity of tyrosinases, as no antiviral capacity was observed in the inactive form of the enzymes. The tyrosinases approach could represent a new antiviral inhibition mechanism, through a plausible catalytic mechanism of selective hydroxylation of the key role of tyrosine residues in viral proteases.
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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.
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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
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Li HC, Yang CH, Lo SY. Hepatitis C Viral Replication Complex. Viruses 2021; 13:v13030520. [PMID: 33809897 PMCID: PMC8004249 DOI: 10.3390/v13030520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
The life cycle of the hepatitis C virus (HCV) can be divided into several stages, including viral entry, protein translation, RNA replication, viral assembly, and release. HCV genomic RNA replication occurs in the replication organelles (RO) and is tightly linked to ER membrane alterations containing replication complexes (proteins NS3 to NS5B). The amplification of HCV genomic RNA could be regulated by the RO biogenesis, the viral RNA structure (i.e., cis-acting replication elements), and both viral and cellular proteins. Studies on HCV replication have led to the development of direct-acting antivirals (DAAs) targeting the replication complex. This review article summarizes the viral and cellular factors involved in regulating HCV genomic RNA replication and the DAAs that inhibit HCV replication.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
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8
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Kumar D, Kumar A, Bhardwaj T, Giri R. Zika virus NS4A N-Terminal region (1-48) acts as a cofactor for inducing NTPase activity of NS3 helicase but not NS3 protease. Arch Biochem Biophys 2020; 695:108631. [DOI: 10.1016/j.abb.2020.108631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
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9
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Yerukhimovich MM, Marohnic CC, Frick DN. Role of the Conserved DECH-Box Cysteine in Coupling Hepatitis C Virus Helicase-Catalyzed ATP Hydrolysis to RNA Unwinding. Biochemistry 2018; 57:6247-6255. [PMID: 30281972 DOI: 10.1021/acs.biochem.8b00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DECH-box proteins are a subset of DExH/D-box superfamily 2 helicases possessing a conserved Asp-Glu-Cys-His motif in their ATP binding site. The conserved His helps position the Asp and Glu residues, which coordinate the divalent metal cation that connects the protein to ATP and activate the water molecule needed for ATP hydrolysis, but the role of the Cys is still unclear. This study uses site-directed mutants of the model DECH-box helicase encoded by the hepatitis C virus (HCV) to examine the role of the Cys in helicase action. Proteins lacking a Cys unwound DNA less efficiently than wild-type proteins did. For example, at low protein concentrations, a helicase harboring a Gly instead of the DECH-box Cys unwound DNA more slowly than the wild-type helicase did, but at higher protein concentrations, the two proteins unwound DNA at similar rates. All HCV proteins analyzed had similar affinities for ATP and nucleic acids and hydrolyzed ATP in the presence of RNA at similar rates. However, in the absence of RNA, all proteins lacking a DECH-box cysteine hydrolyzed ATP 10-15 times faster with higher Km values, and lower apparent affinities for metal ions, compared to those observed with wild-type proteins. These differences were observed with proteins isolated from HCV genotypes 2a and 1b, suggesting that this role is conserved. These data suggest the helicase needs Cys292 to bind ATP in a state where ATP is not hydrolyzed until RNA binds.
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Affiliation(s)
- Mark M Yerukhimovich
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| | - Christopher C Marohnic
- Abbott Laboratories , 100 Abbott Park Road , Abbott Park , Illinois 60064 , United States
| | - David N Frick
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
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10
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Sloan KE, Bohnsack MT. Unravelling the Mechanisms of RNA Helicase Regulation. Trends Biochem Sci 2018; 43:237-250. [PMID: 29486979 DOI: 10.1016/j.tibs.2018.02.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/28/2018] [Accepted: 02/01/2018] [Indexed: 12/22/2022]
Abstract
RNA helicases are critical regulators at the nexus of multiple pathways of RNA metabolism, and in the complex cellular environment, tight spatial and temporal regulation of their activity is essential. Dedicated protein cofactors play key roles in recruiting helicases to specific substrates and modulating their catalytic activity. Alongside individual RNA helicase cofactors, networks of cofactors containing evolutionarily conserved domains such as the G-patch and MIF4G domains highlight the potential for cross-regulation of different aspects of gene expression. Structural analyses of RNA helicase-cofactor complexes now provide insight into the diverse mechanisms by which cofactors can elicit specific and coordinated regulation of RNA helicase action. Furthermore, post-translational modifications (PTMs) and long non-coding RNA (lncRNA) regulators have recently emerged as novel modes of RNA helicase regulation.
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Affiliation(s)
- Katherine E Sloan
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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11
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Schwartz N, Pellach M, Glick Y, Gil R, Levy G, Avrahami D, Barbiro-Michaely E, Nahmias Y, Gerber D. Neuregulin 1 discovered as a cleavage target for the HCV NS3/4A protease by a microfluidic membrane protein array. N Biotechnol 2018; 45:113-122. [PMID: 29438748 DOI: 10.1016/j.nbt.2018.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 12/26/2022]
Abstract
The hepatitis C virus (HCV) non-structural protein 3 (NS3) is essential for HCV maturation. The NS3/4A protease is a target for several HCV treatments and is a well-known target for HCV drug discovery. The protein is membrane associated and thus probably interacts with other membrane proteins. However, the vast majority of known NS3 host partners are soluble proteins rather than membrane proteins, most likely due to lack of appropriate platforms for their discovery. Utilization of an integrated microfluidics platform enables analysis of membrane proteins in their native form. We screened over 2800 membrane proteins for interaction with NS3 and 90 previously unknown interactions were identified. Of these, several proteins were selected for validation by co-immunoprecipitation and for NS3 proteolytic activity. Bearing in mind the considerable number of interactions formed, together with the popularity of NS3/4A protease as a drug target, it was striking to note its lack of proteolytic activity. Only a single protein, Neuregulin1, was observed to be cleaved, adding to the 3 known NS3/4A cleavage targets. Neuregulin1 participates in neural proliferation. Recent studies have shown its involvement in HCV infection and hepatocellular carcinoma. We showed that NS3/4A triggers an increase in neuregulin1 mRNA levels in HCV infected cells. Despite this increase, its protein concentration is decreased due to proteolytic cleavage. Additionally, its EGF-like domain levels were increased, possibly explaining the ErbB2 and EGFR upregulation in HCV infected cells. The newly discovered protein interactions may provide insights into HCV infection mechanisms and potentially provide new therapeutic targets against HCV.
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Affiliation(s)
- Nika Schwartz
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Michal Pellach
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yair Glick
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Reuven Gil
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Gahl Levy
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dorit Avrahami
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Efrat Barbiro-Michaely
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel.
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12
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Riber CF, Andersen AHF, Rolskov LA, Zuwala K, Gajda P, Løvschall KB, Dagnæs-Hansen F, Banda DH, Pietschmann T, Tolstrup M, Zelikin AN. Synthetic Polymer with a Structure-Driven Hepatic Deposition and Curative Pharmacological Activity in Hepatic Cells. ACS Macro Lett 2017; 6:935-940. [PMID: 35650894 DOI: 10.1021/acsmacrolett.7b00471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthetic polymers make strong contributions as tools for delivery of biological drugs and chemotherapeutics. The most praised characteristic of polymers in these applications is complete lack of pharmacological function such as to minimize the side effects within the human body. In contrast, synthetic polymers with curative pharmacological activity are truly rare. Moreover, such activity is typically nonspecific rather than structure-defined. In this work, we present the discovery of poly(ethylacrylic acid) (PEAA) as a polymer with a suit of structure-defined, unexpected, pharmacological, and pharmacokinetic properties not observed in close structural analogues. Specifically, PEAA reveals capacity to bind to albumin with ensuing natural hepatic deposition in vivo and exhibits concurrent inhibitory activity against the hepatitis C virus and inflammation in hepatic cells. Our findings provide a view on synthetic polymers as curative, functional agents and present PEAA as a unique biomedical tool with applications related to health of the human liver.
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Affiliation(s)
- Camilla Frich Riber
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Anna Halling Folkmar Andersen
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
- Department
of Infectious Diseases, Aarhus University Hospital, Aarhus 8200, Denmark
- Department
of Clinical Medicine, Aarhus University, Aarhus 8200, Denmark
| | - Lærke Anegaard Rolskov
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Kaja Zuwala
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
- Department
of Infectious Diseases, Aarhus University Hospital, Aarhus 8200, Denmark
- Department
of Clinical Medicine, Aarhus University, Aarhus 8200, Denmark
| | - Paulina Gajda
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
- Department
of Infectious Diseases, Aarhus University Hospital, Aarhus 8200, Denmark
- Department
of Clinical Medicine, Aarhus University, Aarhus 8200, Denmark
| | - Kaja Borup Løvschall
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | | | - Dominic H. Banda
- Institute
of Experimental Virology, TWINCORE Centre for Experimental and Clinical
Infection Research, Medical School Hannover/Helmholtz Centre for Infection Research, Hannover, Germany
| | - Thomas Pietschmann
- Institute
of Experimental Virology, TWINCORE Centre for Experimental and Clinical
Infection Research, Medical School Hannover/Helmholtz Centre for Infection Research, Hannover, Germany
| | - Martin Tolstrup
- Department
of Infectious Diseases, Aarhus University Hospital, Aarhus 8200, Denmark
- Department
of Clinical Medicine, Aarhus University, Aarhus 8200, Denmark
| | - Alexander N. Zelikin
- Department
of Chemistry and iNano Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
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13
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Ablenas CJ, Liu HW, Shkriabai N, Kvaratskhelia M, Cosa G, Götte M. Dynamic Interconversions of HCV Helicase Binding Modes on the Nucleic Acid Substrate. ACS Infect Dis 2017; 3:99-109. [PMID: 28081608 DOI: 10.1021/acsinfecdis.6b00177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The dynamics involved in the interaction between hepatitis C virus nonstructural protein 3 (NS3) C-terminal helicase and its nucleic acid substrate have been the subject of interest for some time given the key role of this enzyme in viral replication. Here, we employed fluorescence-based techniques and focused on events that precede the unwinding process. Both ensemble Förster resonance energy transfer (FRET) and ensemble protein induced fluorescence enhancement (PIFE) assays show binding on the 3' single-stranded overhang of model DNA substrates (>5 nucleotides) with no preference for the single-stranded/double-stranded (ss/ds) junction. Single-molecule PIFE experiments revealed three enhancement levels that correspond to three discrete binding sites at adjacent bases. The enzyme is able to transition between binding sites in both directions without dissociating from the nucleic acid. In contrast, the NS3 mutant W501A, which is unable to engage in stacking interactions with the DNA, is severely compromised in this switching activity. Altogether our data are consistent with a model for NS3 dynamics that favors ATP-independent random binding and sliding by one and two nucleotides along the overhang of the loading strand.
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Affiliation(s)
| | - Hsiao-Wei Liu
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gonzalo Cosa
- Department of Chemistry and the Centre for Self-Assembled Chemical
Structures (CSACS/CRMAA), McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
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14
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The excluded DNA strand is SEW important for hexameric helicase unwinding. Methods 2016; 108:79-91. [DOI: 10.1016/j.ymeth.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/04/2023] Open
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15
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Neufeldt CJ, Joyce MA, Van Buuren N, Levin A, Kirkegaard K, Gale Jr. M, Tyrrell DLJ, Wozniak RW. The Hepatitis C Virus-Induced Membranous Web and Associated Nuclear Transport Machinery Limit Access of Pattern Recognition Receptors to Viral Replication Sites. PLoS Pathog 2016; 12:e1005428. [PMID: 26863439 PMCID: PMC4749181 DOI: 10.1371/journal.ppat.1005428] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Hepatitis C virus (HCV) is a positive-strand RNA virus of the Flaviviridae family and a major cause of liver disease worldwide. HCV replicates in the cytoplasm, and the synthesis of viral proteins induces extensive rearrangements of host cell membranes producing structures, collectively termed the membranous web (MW). The MW contains the sites of viral replication and assembly, and we have identified distinct membrane fractions derived from HCV-infected cells that contain replication and assembly complexes enriched for viral RNA and infectious virus, respectively. The complex membrane structure of the MW is thought to protect the viral genome limiting its interactions with cytoplasmic pattern recognition receptors (PRRs) and thereby preventing activation of cellular innate immune responses. Here we show that PRRs, including RIG-I and MDA5, and ribosomes are excluded from viral replication and assembly centers within the MW. Furthermore, we present evidence that components of the nuclear transport machinery regulate access of proteins to MW compartments. We show that the restricted assess of RIG-I to the MW can be overcome by the addition of a nuclear localization signal sequence, and that expression of a NLS-RIG-I construct leads to increased immune activation and the inhibition of viral replication. Hepatitis C virus (HCV) is a positive-strand RNA virus and it is a major cause of liver disease worldwide affecting more than 170 million individuals. Infection of cells with HCV leads to rearrangement of cytoplasmic host cell membranes and the formation of the membranous web (MW) containing viral replication and assembly complexes. The MW is thought to function in concentrating viral components, regulating virus replication, and immune evasion. Our analysis has provided new insight into the organization of the MW and the mechanisms that contribute to the formation and maintenance of distinct compartments within the MW. We show that the MW limits access of host cell innate immune receptors to sites of viral replication and assembly. Moreover, we show that components of the nuclear transport machinery, normally involved in regulating traffic between the cytoplasm and the nucleus, have a role in limiting immune receptor access to compartments within the MW. These findings provide important insights in how HCV, and likely other positive-strand RNA viruses, organize their replication factories and evaded recognition by host cell immune receptors.
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Affiliation(s)
- Christopher J. Neufeldt
- Department of Cell Biology University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
| | - Michael A. Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
| | - Nicholas Van Buuren
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Aviad Levin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
| | - Karla Kirkegaard
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael Gale Jr.
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
| | - D. Lorne J. Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
- * E-mail: (RWW); (DLJT)
| | - Richard W. Wozniak
- Department of Cell Biology University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
- * E-mail: (RWW); (DLJT)
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Ndjomou J, Corby MJ, Sweeney NL, Hanson AM, Aydin C, Ali A, Schiffer CA, Li K, Frankowski KJ, Schoenen FJ, Frick DN. Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy. ACS Chem Biol 2015; 10:1887-96. [PMID: 25961497 PMCID: PMC4546510 DOI: 10.1021/acschembio.5b00101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study examines the specificity and mechanism of action of a recently reported hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase-protease inhibitor (HPI), and the interaction of HPI with the NS3 protease inhibitors telaprevir, boceprevir, danoprevir, and grazoprevir. HPI most effectively reduced cellular levels of subgenomic genotype 4a replicons, followed by genotypes 3a and 1b replicons. HPI had no effect on HCV genotype 2a or dengue virus replicon levels. Resistance evolved more slowly to HPI than telaprevir, and HPI inhibited telaprevir-resistant replicons. Molecular modeling and analysis of the ability of HPI to inhibit peptide hydrolysis catalyzed by a variety of wildtype and mutant NS3 proteins suggested that HPI forms a bridge between the NS3 RNA-binding cleft and an allosteric site previously shown to bind other protease inhibitors. In most combinations, the antiviral effect of HPI was additive with telaprevir and boceprevir, minor synergy was observed with danoprevir, and modest synergy was observed with grazoprevir.
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Affiliation(s)
- Jean Ndjomou
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - M. Josie Corby
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Noreena L. Sweeney
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Alicia M. Hanson
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Cihan Aydin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Kelin Li
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Kevin J. Frankowski
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Frank J. Schoenen
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - David N. Frick
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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Kazakov T, Yang F, Ramanathan HN, Kohlway A, Diamond MS, Lindenbach BD. Hepatitis C virus RNA replication depends on specific cis- and trans-acting activities of viral nonstructural proteins. PLoS Pathog 2015; 11:e1004817. [PMID: 25875808 PMCID: PMC4395149 DOI: 10.1371/journal.ppat.1004817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/18/2015] [Indexed: 02/07/2023] Open
Abstract
Many positive-strand RNA viruses encode genes that can function in trans, whereas other genes are required in cis for genome replication. The mechanisms underlying trans- and cis-preferences are not fully understood. Here, we evaluate this concept for hepatitis C virus (HCV), an important cause of chronic liver disease and member of the Flaviviridae family. HCV encodes five nonstructural (NS) genes that are required for RNA replication. To date, only two of these genes, NS4B and NS5A, have been trans-complemented, leading to suggestions that other replicase genes work only in cis. We describe a new quantitative system to measure the cis- and trans-requirements for HCV NS gene function in RNA replication and identify several lethal mutations in the NS3, NS4A, NS4B, NS5A, and NS5B genes that can be complemented in trans, alone or in combination, by expressing the NS3-5B polyprotein from a synthetic mRNA. Although NS5B RNA binding and polymerase activities can be supplied in trans, NS5B protein expression was required in cis, indicating that NS5B has a cis-acting role in replicase assembly distinct from its known enzymatic activity. Furthermore, the RNA binding and NTPase activities of the NS3 helicase domain were required in cis, suggesting that these activities play an essential role in RNA template selection. A comprehensive complementation group analysis revealed functional linkages between NS3-4A and NS4B and between NS5B and the upstream NS3-5A genes. Finally, NS5B polymerase activity segregated with a daclatasvir-sensitive NS5A activity, which could explain the synergy of this antiviral compound with nucleoside analogs in patients. Together, these studies define several new aspects of HCV replicase structure-function, help to explain the potency of HCV-specific combination therapies, and provide an experimental framework for the study of cis- and trans-acting activities in positive-strand RNA virus replication more generally.
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Affiliation(s)
- Teymur Kazakov
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Feng Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Harish N. Ramanathan
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Michael S. Diamond
- Departments of Medicine, Molecular Microbiology, and Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
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Nonstructural protein 5A (NS5A) and human replication protein A increase the processivity of hepatitis C virus NS5B polymerase activity in vitro. J Virol 2014; 89:165-80. [PMID: 25320291 DOI: 10.1128/jvi.01677-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The precise role(s) and topological organization of different factors in the hepatitis C virus (HCV) RNA replication complex are not well understood. In order to elucidate the role of viral and host proteins in HCV replication, we have developed a novel in vitro replication system that utilizes a rolling-circle RNA template. Under close-to-physiological salt conditions, HCV NS5BΔ21, an RNA-dependent RNA polymerase, has poor affinity for the RNA template. Human replication protein A (RPA) and HCV NS5A recruit NS5BΔ21 to the template. Subsequently, NS3 is recruited to the replication complex by NS5BΔ21, resulting in RNA synthesis stimulation by helicase. Both RPA and NS5A(S25-C447), but not NS5A(S25-K215), enabled the NS5BΔ21-NS3 helicase complex to be stably associated with the template and synthesize RNA product in a highly processive manner in vitro. This new in vitro HCV replication system is a useful tool that may facilitate the study of other replication factors and aid in the discovery of novel inhibitors of HCV replication. IMPORTANCE The molecular mechanism of hepatitis C virus (HCV) replication is not fully understood, but viral and host proteins collaborate in this process. Using a rolling-circle RNA template, we have reconstituted an in vitro HCV replication system that allows us to interrogate the role of viral and host proteins in HCV replication and delineate the molecular interactions. We showed that HCV NS5A(S25-C447) and cellular replication protein A (RPA) functionally cooperate as a processivity factor to stimulate HCV replication by HCV NS5BΔ21 polymerase and NS3 helicase. This system paves the way to test other proteins and may be used as an assay for discovery of HCV inhibitors.
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Ehrenberg AE, Schmuck B, Anwar MI, Gustafsson SS, Stenberg G, Danielson UH. Accounting for strain variations and resistance mutations in the characterization of hepatitis C NS3 protease inhibitors. J Enzyme Inhib Med Chem 2014; 29:868-76. [PMID: 24517372 DOI: 10.3109/14756366.2013.864651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
CONTEXT Natural strain variation and rapid resistance development makes development of broad spectrum hepatitis C virus (HCV) drugs very challenging and evaluation of inhibitor selectivity and resistance must account for differences in the catalytic properties of enzyme variants. OBJECTIVE To understand how to study selectivity and relationships between efficacy and genotype or resistant mutants for NS3 protease inhibitors. MATERIALS AND METHODS The catalytic properties of NS3 protease from genotypes 1a, 1b and 3a, and their sensitivities to four structurally and mechanistically different NS3 protease inhibitors have been analysed under different experimental conditions. RESULTS The optimisation of buffer conditions for each protease variant enabled the comparison of their catalytic properties and sensitivities to the inhibitors. All inhibitors were most effective against genotype 1a protease, with VX-950 having the broadest selectivity. DISCUSSION AND CONCLUSION A new strategy for evaluation of inhibitors relevant for the discovery of broad spectrum HCV drugs was established.
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20
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LaPlante SR, Padyana AK, Abeywardane A, Bonneau P, Cartier M, Coulombe R, Jakalian A, Wildeson-Jones J, Li X, Liang S, McKercher G, White P, Zhang Q, Taylor SJ. Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus. J Med Chem 2014; 57:2074-90. [DOI: 10.1021/jm401432c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Steven R. LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | - Pierre Bonneau
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Mireille Cartier
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - René Coulombe
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Araz Jakalian
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | | | - Ginette McKercher
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Peter White
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
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21
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Ward DN, Talley DC, Tavag M, Menji S, Schaughency P, Baier A, Smith PJ. UK-1 and structural analogs are potent inhibitors of hepatitis C virus replication. Bioorg Med Chem Lett 2013; 24:609-12. [PMID: 24360997 DOI: 10.1016/j.bmcl.2013.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/25/2013] [Accepted: 12/02/2013] [Indexed: 12/12/2022]
Abstract
The bacterial natural product UK-1 and several structural analogs inhibit replication of the hepatitis C virus in the replicon assay, with IC50 values as low as 0.50 μM. The NS3 helicase has been identified as a possible target of inhibition for several of these compounds, while the remaining inhibitors act via an undetermined mechanism. Gel shift assays suggest that helicase inhibition is a direct result of inhibitor-enzyme binding as opposed to direct RNA binding, and the ATPase activity of NS3 is not affected. The syntheses and biological results are presented herein.
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Affiliation(s)
- Dawn N Ward
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Daniel C Talley
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Mrinalini Tavag
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Samrawit Menji
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Paul Schaughency
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Andrea Baier
- Department of Molecular Biology, John Paul II Catholic University of Lublin, Poland
| | - Paul J Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States.
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22
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Adapted J6/JFH1-based Hepatitis C virus recombinants with genotype-specific NS4A show similar efficacies against lead protease inhibitors, alpha interferon, and a putative NS4A inhibitor. Antimicrob Agents Chemother 2013; 57:6034-49. [PMID: 24060868 DOI: 10.1128/aac.01176-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
To facilitate studies of hepatitis C virus (HCV) NS4A, we aimed at developing J6/JFH1-based recombinants with genotype 1- to 7-specific NS4A proteins. We developed efficient culture systems expressing NS4A proteins of genotypes (isolates) 1a (H77 and TN), 1b (J4), 2a (J6), 4a (ED43), 5a (SA13), 6a (HK6a), and 7a (QC69), with peak infectivity titers of ∼3.5 to 4.5 log10 focus-forming units per ml. Except for genotype 2a (J6), growth depended on adaptive mutations identified in long-term culture. Genotype 1a, 1b, and 4a recombinants were adapted by amino acid substitutions F772S (p7) and V1663A (NS4A), while 5a, 6a, and 7a recombinants required additional substitutions in the NS3 protease and/or NS4A. We demonstrated applicability of the developed recombinants for study of antivirals. Genotype 1 to 7 NS4A recombinants showed similar responses to the protease inhibitors telaprevir (VX-950), boceprevir (Sch503034), simeprevir (TMC435350), danoprevir (ITMN-191), and vaniprevir (MK-7009), to alpha interferon 2b, and to the putative NS4A inhibitor ACH-806. The efficacy of ACH-806 was lower than that of protease inhibitors and was not influenced by changes at amino acids 1042 and 1065 (in the NS3 protease), which have been suggested to mediate resistance to ACH-806 in replicons. Genotype 1a, 1b, and 2a recombinants showed viral spread under long-term treatment with ACH-806, without acquisition of resistance mutations in the NS3-NS4A region. Relatively high concentrations of ACH-806 inhibited viral assembly, but not replication, in a single-cycle production assay. The developed HCV culture systems will facilitate studies benefitting from expression of genotype-specific NS4A in a constant backbone in the context of the complete viral replication cycle, including functional studies and evaluations of the efficacy of antivirals.
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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.
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Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06536, USA
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Abstract
Hepatitis C Virus (HCV) particles exhibit several unusual properties that are not found in other enveloped RNA viruses, most notably their low buoyant density and interaction with serum lipoproteins. With the advent of systems to grow HCV in cell culture, the molecular basis of HCV particle assembly and release can now be addressed. The process of virus assembly involves protein-protein interactions between viral structural and nonstructural proteins and the coordinated action of host factors. This chapter reviews our current understanding of these interactions and factors.
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Affiliation(s)
- Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
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Moradpour D, Penin F. Hepatitis C virus proteins: from structure to function. Curr Top Microbiol Immunol 2013; 369:113-42. [PMID: 23463199 DOI: 10.1007/978-3-642-27340-7_5] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Great progress has been made over the past years in elucidating the structure and function of the hepatitis C virus (HCV) proteins, most of which are now actively being pursued as antiviral targets. The structural proteins, which form the viral particle, include the core protein and the envelope glycoproteins E1 and E2. The nonstructural proteins include the p7 viroporin, the NS2 protease, the NS3-4A complex harboring protease and NTPase/RNA helicase activities, the NS4B and NS5A proteins, and the NS5B RNA-dependent RNA polymerase. NS4B is a master organizer of replication complex formation while NS5A is a zinc-containing phosphoprotein involved in the regulation of HCV RNA replication versus particle production. Core to NS2 make up the assembly module while NS3 to NS5B represent the replication module (replicase). However, HCV proteins exert multiple functions during the viral life cycle, and these may be governed by different structural conformations and/or interactions with viral and/or cellular partners. Remarkably, each viral protein is anchored to intracellular membranes via specific determinants that are essential to protein function in the cell. This review summarizes current knowledge of the structure and function of the HCV proteins and highlights recent advances in the field.
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Affiliation(s)
- Darius Moradpour
- Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.
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Schomburg D, Schomburg I. DNA helicase 3.6.4.12. CLASS 3.4–6 HYDROLASES, LYASES, ISOMERASES, LIGASES 2013. [PMCID: PMC7123227 DOI: 10.1007/978-3-642-36260-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
EC number 3.6.4.12 Systematic name ATP phosphohydrolase (DNA helix unwinding) Recommended name DNA helicase Synonyms 3’ to 5’ DNA helicase <28> [35] 3’-5’ DNA helicase <11> [55] 3’-5’ PfDH <11> [55] 5’ to 3’ DNA helicase <26,27> [19,42] AvDH1 <47> [37] BACH1 helicase <19> [34] BLM <3> [28] BLM protein <3> [28] BRCA1-associated C-terminal helicase <19> [34] BcMCM <8> [52] CeWRN-1 <43> [9] DDX25 <3,48> [36] DNA helicase 120 <7> [15] DNA helicase A <4> [8] DNA helicase E <5> [44] DNA helicase II <9> [7] DNA helicase III <4> [27] DNA helicase RECQL5β <44> [17] DNA helicase VI <3> [45] Dbp9p <46> (<46> a member of the DEAD box protein family [24]) [24] DmRECQ5 <1> [50] DnaB helicase <29> [23] E1 helicase <17> [58] GRTH/DDX25 <3,48> [36] HCoV SF1 helicase <23> [3] HCoV helicase <23> [3] HDH IV <3> [45] Hel E <5> [44] Hmi1p <40> [60] MCM helicase <6,5,38> [43,54] MCM protein <6,35> [43] MER3 helicase <22> [30] MER3 protein <22> [30] MPH1 <28> [35] NS3 <12,50> (<12,50> ambiguous [38,65,66]) [38,65,66] NS3 NTPase/helicase <14> (<14> ambiguous [67]) [67] NS3 protein <12> (<12> ambiguous [63]) [63] NTPase/helicase <12,16> (<12> ambiguous [61]) [61,64] PDH120 <7> [15] PIF1 <33> [51] PIF1 helicase <33> [51,53] PcrA <37> [20] PcrA helicase <37,41,49> [20,21,39] PcrASpn <41> [21] PfDH A <11> [55] Pfh1p <27> [42] RECQ5 <1> [49,50] RECQ5 helicase <1> (<1> small isoform [49]) [49] RECQL5b <44> [17] REcQ <31> [13] RSF1010 RepA <30> [5] RecG <45> [6] RecQ helicase <32> [56] RecQsim <32> [56] Rep52 <24> [40] Rrm3p <26> [19] Sgs1 <36> [29] Sgs1 DNA helicase <36> [29] TWINKLE <21> [33] Tth UvrD <20> [16] UvrD <20,42> [16,22] UvrD helicase <39> [18] WRN <18> [31] WRN RecQ helicase <18> [12] WRN helicase <18> [12] WRN protein <18> [12] WRN-1 RecQ helicase <43> [9] Werner Syndrome helicase <18> [31] Werner syndrome RecQ helicase <18> [12] dheI I <1> [46] dnaB <29> [23] hPif1 <33> [53] helicase DnaB <2> [10] helicase II <25> [25] helicase PcrA <49> [39] helicase UvrD <20> [16] helicase domain of bacteriophage T7 gene 4 protein <10> [47] non structural protein 3 <12> (<12> ambiguous [61,62]) [61,62] nonstructural protein 3 <12,14,50,51> (<12,14,50> ambiguous [38,63,65,66,67]; <51> ambigous [4]) [4,38,63,65,66,67] protein NS3 <12> (<12> ambiguous [62]) [62] scHelI <4> [26] urvD <25> [25]
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Schomburg D, Schomburg I. RNA helicase 3.6.4.13. CLASS 3.4–6 HYDROLASES, LYASES, ISOMERASES, LIGASES 2013. [PMCID: PMC7123474 DOI: 10.1007/978-3-642-36260-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
EC number 3.6.4.13 Systematic name ATP phosphohydrolase (RNA helix unwinding) Recommended name RNA helicase Synonyms 1a NTPase/helicase <16> [5] ATP/dATP-dependent RNA helicase <1,42> [32] ATPase <10,12> [1,36] ATPase/RNA helicase <1,42> [32] ATPase/helicase <10> [36,41] BMV 1a protein <16> [5] BmL3-helicase <1,42> [32] Brr2p <6> [50] DBP2 <24> [30] DDX17 <33> [12] DDX19 <43> [56] DDX25 <23,34,35> [12,21] DDX3 <25> [8] DDX3X <25> (<25> the gene is localized to the X chromosome [12]) [12] DDX3Y <29> (<29> the gene is localized to the Y chromosome [12]) [12] DDX4 <30> [12] DDX5 <32> [12] DEAD box RNA helicase <1,2,3> [32,45,52] DEAD box helicase <2> [45] DEAD-box RNA helicase <4,5,7,38,47,48> [9,14,16,25,53,55] DEAD-box protein DED1 <38> [11] DEAD-box rRNA helicase <5> [26] DEAH-box RNA helicase <24> [30] DEAH-box protein 2 <24> [30] DED1 <38> [11,14] DENV NS3H <10> [41] DEXD/H-box RNA helicase <43> [56] DEx(H/D)RNA helicase <12> [23] DHX9 <44> [58] DbpA <5> [10,25,26] Dhx9/RNA helicase A <13> [61] EhDEAD1 <7> [16] EhDEAD1 RNA helicase <7> [16] FRH <9> [54] FRQ-interacting RNA helicase <9> [54] GRTH <3> [57] GRTH/DDX25 <3,35> [21,51] HCV NS3 helicase <12> [48] KOKV helicase <27> [7] Mtr4p <31> [22] NPH-II <8> [18,28] NS3 <10,12,17,20,39,41> (<12,39> ambiguous [27,42,44]) [1,2,4,27,35,36,39, 42,44,46] NS3 ATPase/helicase <10> [41] NS3 NTPase/helicase <17> (<17> ambiguous [46]) [46] NS3 helicase <10,12,17> [15,44,46] NS3 protein <10,12,17,18> (<12> ambiguous [39]) [15,39,40,41,62] NTPase/helicase <12> (<12> ambiguous [37]) [37,39] RHA <6> [31,49] RNA helicase <2> [45] RNA helicase A <6,44> [31,49,58] RNA helicase CrhR <14> [59] RNA helicase DDX3 <25> [8] RNA helicase Ddx39 <47> [53] RNA helicase Hera <4> [9] RNA-dependent ATPase <37> [34] RNA-dependent NTPase/helicase <12> [1] RTPase <10> [36] RhlB <5> [43] SpolvlgA <48> [55] Supv3L1 <46> [64] TGBp1 NTPase/helicase domain <22,28> [24] Tk-DeaD <15> [47] VRH1 <26> [33] YxiN <2> [45] eIF4A <36> [20] eIF4A helicase <36> [20] eIF4AIII <37> [34] eukaryotic initiation factor eIF 4A <36> [20] gonadotropin-regulated testicular RNA helicase <3> [51,57] helicase <10> [41] helicase B <5> [43] helicase/nucleoside triphosphatase <10> [4] non structural protein 3 <12> (<12> ambiguous [37,38]) [37,38] non-structural 3 <10> [36] non-structural protein 3 <17> [46] non-structural protein 3 protein <18> [40] nonstructural protein 3 <12,17,20,39,40,41> (<12,17,39,40> ambiguous [6,27, 39,42,44,46]) [1,2,6,27,35,39,42,44,46] nucleoside 5’-triphosphatase <10> [4] nucleoside triphosphatase/RNA helicase and 5’-RNA triphosphatase <20> [2] nucleoside triphosphatase/helicase <16> [5] p54 RNA helicase <45> [60] p68 RNA helicase <3,6> [52,63] protein NS3 <12> (<12> ambiguous [38]) [38]
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Brar I, Baxa D, Markowitz N. HCV enters the twenty-first century. Curr Infect Dis Rep 2012; 15:52-60. [PMID: 23263749 DOI: 10.1007/s11908-012-0313-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Almost one-third of Americans infected with human immunodeficiency virus (HIV) and 7 million worldwide are coinfected with hepatitis C virus (HCV). The principal route of HCV spread in the US is injection drug use but there are recent reports of outbreaks of acute HCV infection among HIV-infected men who have sex with men. With increased survival as a result of highly active antiretroviral therapy, HCV-associated liver disease has become a leading cause of death in HIV-infected individuals. Currently, telaprevir and boceprevir, both NS3/NS4A inhibitors that significantly improve sustained response when added to pegylated interferon and ribavirin, are approved only for HCV monoinfection. The optimal combination of agents, therapy durations and the timing of treatment remain major challenges in coinfected patients.
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Affiliation(s)
- Indira Brar
- Henry Ford Hospital, Division of Infectious Diseases, 2799 West Grand Boulevard, Detroit, Michigan, 48202, USA
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Raney VM, Reynolds KA, Harrison MK, Harrison DK, Cameron CE, Raney KD. Binding by the hepatitis C virus NS3 helicase partially melts duplex DNA. Biochemistry 2012; 51:7596-607. [PMID: 22916835 DOI: 10.1021/bi300654v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of NS3 helicase to DNA was investigated by footprinting with KMnO(4), which reacts preferentially with thymidine residues in single-stranded DNA (ssDNA) compared to those in double-stranded DNA (dsDNA). A distinct pattern of reactivity was observed on ssDNA, which repeated every 8 nucleotides (nt) and is consistent with the known binding site size of NS3. Binding to a DNA substrate containing a partial duplex was also investigated. The DNA contained a 15 nt overhang made entirely of thymidine residues adjacent to a 22 bp duplex that contained thymidine at every other position. Surprisingly, the KMnO(4) reactivity pattern extended from the ssDNA into the dsDNA region of the substrate. Lengthening the partial duplex to 30 bp revealed a similar pattern extending from the ssDNA into the dsDNA, indicating that NS3 binds within the duplex region. Increasing the length of the ssDNA portion of the partial duplex by 4 nt resulted in a shift in the footprinting pattern for the ssDNA by 4 nt, which is consistent with binding to the 3'-end of the ssDNA. However, the footprinting pattern in the dsDNA region was shifted by only 1-2 bp, indicating that binding to the ssDNA-dsDNA region was preferred. Footprinting performed as a function of time indicated that NS3 binds to the ssDNA rapidly, followed by slower binding to the duplex. Hence, multiple molecules of NS3 can bind along a ssDNA-dsDNA partial duplex by interacting with the ssDNA as well as the duplex DNA.
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Affiliation(s)
- Veronica M Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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30
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Ndjomou J, Kolli R, Mukherjee S, Shadrick WR, Hanson AM, Sweeney NL, Bartczak D, Li K, Frankowski KJ, Schoenen FJ, Frick DN. Fluorescent primuline derivatives inhibit hepatitis C virus NS3-catalyzed RNA unwinding, peptide hydrolysis and viral replicase formation. Antiviral Res 2012; 96:245-55. [PMID: 22940425 DOI: 10.1016/j.antiviral.2012.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/19/2012] [Accepted: 08/17/2012] [Indexed: 01/22/2023]
Abstract
The hepatitis C virus (HCV) multifunctional nonstructural protein 3 (NS3) is a protease that cleaves viral and host proteins and a helicase that separates DNA and RNA structures in reactions fueled by ATP hydrolysis. Li et al. (2012) recently synthesized a series of new NS3 helicase inhibitors from the benzothiazole dimer component of the fluorescent yellow dye primuline. This study further characterizes a subset of these primuline derivatives with respect to their specificity, mechanism of action, and effect on cells harboring HCV subgenomic replicons. All compounds inhibited DNA and RNA unwinding catalyzed by NS3 from different HCV genotypes, but only some inhibited the NS3 protease function, and few had any effect on HCV NS3 catalyzed ATP hydrolysis. A different subset contained potent inhibitors of RNA stimulated ATP hydrolysis catalyzed by the related NS3 protein from Dengue virus. In assays monitoring intrinsic protein fluorescence in the absence of nucleic acids, the compounds cooperatively bound NS3 with K(d)s that reflect their potency in assays. The fluorescent properties of the primuline derivatives both in vitro and in cells are also described. The primuline derivative that was the most active against subgenomic replicons in cells caused a 14-fold drop in HCV RNA levels (IC(50)=5±2μM). In cells, the most effective primuline derivative did not inhibit the cellular activity of NS3 protease but disrupted HCV replicase structures.
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Affiliation(s)
- Jean Ndjomou
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St., Milwaukee, WI 53211, United States
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31
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Ando T, Imamura H, Suzuki R, Aizaki H, Watanabe T, Wakita T, Suzuki T. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA. PLoS Pathog 2012; 8:e1002561. [PMID: 22396648 PMCID: PMC3291659 DOI: 10.1371/journal.ppat.1002561] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/18/2012] [Indexed: 12/22/2022] Open
Abstract
Adenosine 5′-triphosphate (ATP) is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV), a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET)-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome. ATP is the major energy currency of living cells. Replication of the virus genome is a physiological mechanism that is known to require energy for operations such as the synthesis of DNA or RNA and their unwinding. However, it has been difficult to comprehend how the ATP level is regulated inside single living cells where the virus replicates, since average ATP values in cell extracts have only been estimated using existing methods for ATP measurement. ATeam, which was established in 2009, is a genetically-encoded Förster resonance energy transfer (FRET)-based indicator for ATP that is composed of a small bacterial protein that specifically binds ATP sandwiched between two fluorescent proteins. In this study, by applying ATeam to the subgenomic replicon system, we have developed a method to monitor ATP at putative subcellular sites of RNA replication of the hepatitis C virus (HCV), a major human pathogen associated with liver disease, in living cells. We show here, for the first time, changes in ATP concentrations at distinct sites within cells undergoing HCV RNA replication. ATeam might open the door to understanding how regulation of ATP can affect the lifecycles of pathogens.
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Affiliation(s)
- Tomomi Ando
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiromi Imamura
- The Hakubi Center and Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshiki Watanabe
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Suzuki
- Hamamatsu University School of Medicine, Department of Infectious Diseases, Hamamatsu, Japan
- * E-mail:
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George SL, Varmaz D, Tavis JE, Chowdhury A. The GB virus C (GBV-C) NS3 serine protease inhibits HIV-1 replication in a CD4+ T lymphocyte cell line without decreasing HIV receptor expression. PLoS One 2012; 7:e30653. [PMID: 22292009 PMCID: PMC3264616 DOI: 10.1371/journal.pone.0030653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 12/26/2011] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Persistent infection with GBV-C (GB Virus C), a non-pathogenic virus related to hepatitis C virus (HCV), prolongs survival in HIV infection. Two GBV-C proteins, NS5A and E2, have been shown previously to inhibit HIV replication in vitro. We investigated whether the GBV-C NS3 serine protease affects HIV replication. RESULTS GBV-C NS3 protease expressed in a human CD4+ T lymphocyte cell line significantly inhibited HIV replication. Addition of NS4A or NS4A/4B coding sequence to GBV-C NS3 increased the effect on HIV replication. Inhibition of HIV replication was dose-dependent and was not mediated by increased cell toxicity. Mutation of the NS3 catalytic serine to alanine resulted in loss of both HIV inhibition and protease activity. GBV-C NS3 expression did not measurably decrease CD4 or CXCR4 expression. CONCLUSION GBV-C NS3 serine protease significantly inhibited HIV replication without decreasing HIV receptor expression. The requirement for an intact catalytic serine at the active site indicates that inhibition was mediated by proteolytic cleavage of an unidentified target(s).
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Affiliation(s)
- Sarah L George
- Division of Infectious Diseases, Department of Internal Medicine, St. Louis University, St. Louis, Missouri, United States of America.
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33
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Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS. Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. J Med Chem 2012; 55:2481-531. [PMID: 22185586 DOI: 10.1021/jm201384j] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael J Sofia
- Pharmasset, Inc., 303A College Road East, Princeton, New Jersey 08540, United States.
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34
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Hanson AM, Hernandez JJ, Shadrick WR, Frick DN. Identification and analysis of inhibitors targeting the hepatitis C virus NS3 helicase. Methods Enzymol 2012; 511:463-83. [PMID: 22713333 DOI: 10.1016/b978-0-12-396546-2.00021-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This chapter describes two types of FRET-based fluorescence assays that can be used to identify and analyze compounds that inhibit the helicase encoded by the hepatitis C virus (HCV). Both assays use a fluorescently labeled DNA or RNA oligonucleotide to monitor helicase-catalyzed strand separation, and they differ from other real-time helicase assays in that they do not require the presence of other nucleic acids to trap the reaction products. The first assay is a molecular beacon-based helicase assay (MBHA) that monitors helicase-catalyzed displacement of a hairpin-forming oligonucleotide with a fluorescent moiety on one end and a quencher on the other. DNA-based MBHAs have been used extensively for high-throughput screening (HTS), but RNA-based MBHAs are typically less useful because of poor signal to background ratios. In the second assay discussed, the fluorophore and quencher are split between two hairpin-forming oligonucleotides annealed in tandem to a third oligonucleotide. This split beacon helicase assay can be used for HTS with either DNA or RNA oligonucleotides. These assays should be useful to the many labs searching for HCV helicase inhibitors in order to develop new HCV therapies that are still desperately needed.
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Affiliation(s)
- Alicia M Hanson
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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Gottwein JM, Scheel TKH, Jensen TB, Ghanem L, Bukh J. Differential efficacy of protease inhibitors against HCV genotypes 2a, 3a, 5a, and 6a NS3/4A protease recombinant viruses. Gastroenterology 2011; 141:1067-79. [PMID: 21699793 DOI: 10.1053/j.gastro.2011.06.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/06/2011] [Accepted: 06/03/2011] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS The hepatitis C virus (HCV) genotype influences efficacy of interferon (IFN)-based therapy. HCV protease inhibitors are being licensed for treatment of genotype 1 infection. Because there are limited or no data on efficacy against HCV genotypes 2-7, we aimed at developing recombinant infectious cell culture systems expressing genotype-specific nonstructural (NS) protein 3 protease (NS3P). METHODS Viability of J6/JFH1-based recombinants with genotypes 1-7 NS3P/NS4A was evaluated in Huh7.5 human hepatoma cells. Adaptive mutations were identified in reverse genetic studies. Efficacy of lead compound linear protease inhibitors VX-950 (telaprevir) and SCH503034 (boceprevir) and macrocyclic inhibitors TMC435350, ITMN-191 (danoprevir), and MK-7009 (vaniprevir) was determined in high-throughput infection assays. RESULTS For genotype(isolate) 2a(J6), 3a(S52), 5a(SA13), and 6a(HK6a), we developed culture systems producing supernatant infectivity titers of 3.5-4.0 log₁₀ focus forming units/mL. Against 2a(J6), 5a(SA13), and 6a(HK6a), all inhibitors showed similar efficacy; macrocyclic inhibitors had ~10-fold greater potency than linear inhibitors. However, compared with 2a recombinant J6/JFH1, efficacy against 3a(S52) was 16- to 70-fold lower for macrocyclic inhibitors and 2- to 7-fold lower for linear inhibitors. Testing of additional genotype 2a and 3a isolates showed that these differences were genotype specific. The resistance of 3a isolates was similar to J6/JFH1 with engineered resistance mutations originally observed for genotype 1 patients. In contrast, we found similar efficacy of NS5A inhibitor BMS-790052 and interferon-alfa2. CONCLUSIONS Novel HCV culture systems with genotype specific NS3P/NS4A revealed similar efficacy of protease inhibitors against genotypes 2a, 5a, and 6a and comparatively low but varying efficacy against genotype 3a isolates. These systems will facilitate genotype-specific studies of HCV protease inhibitors and of viral resistance.
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Affiliation(s)
- Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre and Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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36
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Bouchard MJ, Navas-Martin S. Hepatitis B and C virus hepatocarcinogenesis: lessons learned and future challenges. Cancer Lett 2011; 305:123-43. [PMID: 21168955 PMCID: PMC3071446 DOI: 10.1016/j.canlet.2010.11.014] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 11/15/2010] [Accepted: 11/25/2010] [Indexed: 12/15/2022]
Abstract
Worldwide, hepatocellular carcinoma (HCC) is one of the most common cancers. It is thought that 80% of hepatocellular carcinomas are linked to chronic infections with the hepatitis B (HBV) or hepatitis C (HCV) viruses. Chronic HBV and HCV infections can alter hepatocyte physiology in similar ways and may utilize similar mechanisms to influence the development of HCC. There has been significant progress towards understanding the molecular biology of HBV and HCV and identifying the cellular signal transduction pathways that are altered by HBV and HCV infections. Although the precise molecular mechanisms that link HBV and HCV infections to the development of HCC are not entirely understood, there is considerable evidence that both inflammatory responses to infections with these viruses, and associated destruction and regeneration of hepatocytes, as well as activities of HBV- or HCV-encoded proteins, contribute to hepatocyte transformation. In this review, we summarize progress in defining mechanisms that may link HBV and HCV infections to the development of HCC, discuss the challenges of directly defining the processes that underlie HBV- and HCV-associated HCC, and describe areas that remain to be explored.
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Affiliation(s)
- Michael J Bouchard
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102, USA.
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Morikawa K, Lange CM, Gouttenoire J, Meylan E, Brass V, Penin F, Moradpour D. Nonstructural protein 3-4A: the Swiss army knife of hepatitis C virus. J Viral Hepat 2011; 18:305-15. [PMID: 21470343 DOI: 10.1111/j.1365-2893.2011.01451.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) nonstructural protein 3-4A (NS3-4A) is a complex composed of NS3 and its cofactor NS4A. It harbours serine protease as well as NTPase/RNA helicase activities and is essential for viral polyprotein processing, RNA replication and virion formation. Specific inhibitors of the NS3-4A protease significantly improve sustained virological response rates in patients with chronic hepatitis C when combined with pegylated interferon-α and ribavirin. The NS3-4A protease can also target selected cellular proteins, thereby blocking innate immune pathways and modulating growth factor signalling. Hence, NS3-4A is not only an essential component of the viral replication complex and prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV. This review provides a concise update on the biochemical and structural aspects of NS3-4A, its role in the pathogenesis of chronic hepatitis C and the clinical development of NS3-4A protease inhibitors.
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Affiliation(s)
- K Morikawa
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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Appleby TC, Anderson R, Fedorova O, Pyle AM, Wang R, Liu X, Brendza KM, Somoza JR. Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV. J Mol Biol 2010; 405:1139-53. [PMID: 21145896 DOI: 10.1016/j.jmb.2010.11.034] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 11/08/2010] [Accepted: 11/16/2010] [Indexed: 02/07/2023]
Abstract
The structural mechanism by which nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) translocates along RNA is currently unknown. HCV NS3 is an ATP-dependent motor protein essential for viral replication and a member of the superfamily 2 helicases. Crystallographic analysis using a labeled RNA oligonucleotide allowed us to unambiguously track the positional changes of RNA bound to full-length HCV NS3 during two discrete steps of the ATP hydrolytic cycle. The crystal structures of HCV NS3, NS3 bound to bromine-labeled RNA, and a tertiary complex of NS3 bound to labeled RNA and a non-hydrolyzable ATP analog provide a direct view of how large domain movements resulting from ATP binding and hydrolysis allow the enzyme to translocate along the phosphodiester backbone. While directional translocation of HCV NS3 by a single base pair per ATP hydrolyzed is observed, the 3' end of the RNA does not shift register with respect to a conserved tryptophan residue, supporting a "spring-loading" mechanism that leads to larger steps by the enzyme as it moves along a nucleic acid substrate.
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Affiliation(s)
- Todd C Appleby
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
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Hepatitis C virus NS2 coordinates virus particle assembly through physical interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes. J Virol 2010; 85:1706-17. [PMID: 21147927 DOI: 10.1128/jvi.02268-10] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The hepatitis C virus (HCV) NS2 protein is essential for particle assembly, but its function in this process is unknown. We previously identified critical genetic interactions between NS2 and the viral E1-E2 glycoprotein and NS3-NS4A enzyme complexes. Based on these data, we hypothesized that interactions between these viral proteins are essential for HCV particle assembly. To identify interaction partners of NS2, we developed methods to site-specifically biotinylate NS2 in vivo and affinity capture NS2-containing protein complexes from virus-producing cells with streptavidin magnetic beads. By using these methods, we confirmed that NS2 physically interacts with E1, E2, and NS3 but did not stably interact with viral core or NS5A proteins. We further characterized these protein complexes by blue native polyacrylamide gel electrophoresis and identified ≈ 520-kDa and ≈ 680-kDa complexes containing E2, NS2, and NS3. The formation of NS2 protein complexes was dependent on coexpression of the viral p7 protein and enhanced by cotranslation of viral proteins as a polyprotein. Further characterization indicated that the glycoprotein complex interacts with NS2 via E2, and the pattern of N-linked glycosylation on E1 and E2 suggested that these interactions occur in the early secretory pathway. Importantly, several mutations that inhibited virus assembly were shown to inhibit NS2 protein complex formation, and NS2 was essential for mediating the interaction between E2 and NS3. These studies demonstrate that NS2 plays a central organizing role in HCV particle assembly by bringing together viral structural and nonstructural proteins.
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The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly. J Virol 2010; 85:1193-204. [PMID: 21047963 DOI: 10.1128/jvi.01889-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Hepatitis C virus NS3-4A is a membrane-bound enzyme complex that exhibits serine protease, RNA helicase, and RNA-stimulated ATPase activities. This enzyme complex is essential for viral genome replication and has been recently implicated in virus particle assembly. To help clarify the role of NS4A in these processes, we conducted alanine scanning mutagenesis on the C-terminal acidic domain of NS4A in the context of a chimeric genotype 2a reporter virus. Of 13 mutants tested, two (Y45A and F48A) had severe defects in replication, while seven (K41A, L44A, D49A, E50A, M51A, E52A, and E53A) efficiently replicated but had severe defects in virus particle assembly. Multiple strategies were used to identify second-site mutations that suppressed these NS4A defects. The replication defect of NS4A F48A was partially suppressed by mutation of NS4B I7F, indicating that a genetic interaction between NS4A and NS4B contributes to RNA replication. Furthermore, the virus assembly defect of NS4A K41A was suppressed by NS3 Q221L, a mutation previously implicated in overcoming other virus assembly defects. We therefore examined the known enzymatic activities of wild-type or mutant forms of NS3-4A but did not detect specific defects in the mutants. Taken together, our data reveal interactions between NS4A and NS4B that control genome replication and between NS3 and NS4A that control virus assembly.
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Shiryaev SA, Chernov AV, Shiryaeva TN, Aleshin AE, Strongin AY. The acidic sequence of the NS4A cofactor regulates ATP hydrolysis by the HCV NS3 helicase. Arch Virol 2010; 156:313-8. [PMID: 20978807 DOI: 10.1007/s00705-010-0838-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 10/09/2010] [Indexed: 12/14/2022]
Abstract
In flaviviruses and hepatitis C virus (HCV), the NS3 gene encodes the N-terminal protease (NS3pro) and the C-terminal helicase (NS3hel). In HCV, the downstream NS4A is required for the NS3pro activity and exhibits a conserved EFDEMEE motif. To identify the role of this motif, we compared the ATPase and helicase activities of NS3 alone with those of the NS3-NS4A constructs. Our results suggest that the EFDEMEE motif is essential for regulating the ATPase activity of NS3hel. It is likely that this motif interferes with the ATP-binding site of NS3hel. It is becoming clear that NS4A functions as a cofactor of both proteinase and helicase in HCV.
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Affiliation(s)
- Sergey A Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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Shiryaev SA, Strongin AY. Structural and functional parameters of the flaviviral protease: a promising antiviral drug target. Future Virol 2010; 5:593-606. [PMID: 21076642 DOI: 10.2217/fvl.10.39] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Flaviviruses have a single-strand, positive-polarity RNA genome that encodes a single polyprotein. The polyprotein is comprised of seven nonstructural (NS) and three structural proteins. The N- and C-terminal parts of NS3 represent the serine protease and the RNA helicase, respectively. The cleavage of the polyprotein by the protease is required to produce the individual viral proteins, which assemble a new viral progeny. Conversely, inactivation of the protease blocks viral infection. Both the protease and the helicase are conserved among flaviviruses. As a result, NS3 is a promising drug target in flaviviral infections. This article examines the West Nile virus NS3 with an emphasis on the structural and functional parameters of the protease, the helicase and their cofactors.
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Affiliation(s)
- Sergey A Shiryaev
- Inflammatory & Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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Raney KD, Sharma SD, Moustafa IM, Cameron CE. Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target. J Biol Chem 2010; 285:22725-31. [PMID: 20457607 PMCID: PMC2906261 DOI: 10.1074/jbc.r110.125294] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus non-structural protein 3 contains a serine protease and an RNA helicase. Protease cleaves the genome-encoded polyprotein and inactivates cellular proteins required for innate immunity. Protease has emerged as an important target for the development of antiviral therapeutics, but drug resistance has turned out to be an obstacle in the clinic. Helicase is required for both genome replication and virus assembly. Mechanistic and structural studies of helicase have hurled this enzyme into a prominent position in the field of helicase enzymology. Nevertheless, studies of helicase as an antiviral target remain in their infancy.
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Affiliation(s)
- Kevin D. Raney
- From the
Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Suresh D. Sharma
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ibrahim M. Moustafa
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E. Cameron
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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Rajagopal V, Gurjar M, Levin MK, Patel SS. The protease domain increases the translocation stepping efficiency of the hepatitis C virus NS3-4A helicase. J Biol Chem 2010; 285:17821-32. [PMID: 20363755 PMCID: PMC2878546 DOI: 10.1074/jbc.m110.114785] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/01/2010] [Indexed: 01/24/2023] Open
Abstract
Hepatitis C virus (HCV) NS3 protein has two enzymatic activities of helicase and protease that are essential for viral replication. The helicase separates the strands of DNA and RNA duplexes using the energy from ATP hydrolysis. To understand how ATP hydrolysis is coupled to helicase movement, we measured the single turnover helicase translocation-dissociation kinetics and the pre-steady-state P(i) release kinetics on single-stranded RNA and DNA substrates of different lengths. The parameters of stepping were determined from global fitting of the two types of kinetic measurements into a computational model that describes translocation as a sequence of coupled hydrolysis-stepping reactions. Our results show that the HCV helicase moves with a faster rate on single stranded RNA than on DNA. The HCV helicase steps on the RNA or DNA one nucleotide at a time, and due to imperfect coupling, not every ATP hydrolysis event produces a successful step. Comparison of the helicase domain (NS3h) with the protease-helicase (NS3-4A) shows that the most significant contribution of the protease domain is to improve the translocation stepping efficiency of the helicase. Whereas for NS3h, only 20% of the hydrolysis events result in translocation, the coupling for NS3-4A is near-perfect 93%. The presence of the protease domain also significantly reduces the stepping rate, but it doubles the processivity. These effects of the protease domain on the helicase can be explained by an improved allosteric cross-talk between the ATP- and nucleic acid-binding sites achieved by the overall stabilization of the helicase domain structure.
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Affiliation(s)
- Vaishnavi Rajagopal
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
| | - Madhura Gurjar
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
| | - Mikhail K. Levin
- the
Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710
| | - Smita S. Patel
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
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Geitmann M, Dahl G, Danielson UH. Mechanistic and kinetic characterization of hepatitis C virus NS3 protein interactions with NS4A and protease inhibitors. J Mol Recognit 2010; 24:60-70. [DOI: 10.1002/jmr.1023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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Belon CA, High YD, Lin TI, Pauwels F, Frick DN. Mechanism and specificity of a symmetrical benzimidazolephenylcarboxamide helicase inhibitor. Biochemistry 2010; 49:1822-32. [PMID: 20108979 DOI: 10.1021/bi901974a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study examines the effects of 1-N,4-N-bis[4-(1H-benzimidazol-2-yl)phenyl]benzene-1,4-dicarboxamide ((BIP)(2)B) on the NS3 helicase encoded by the hepatitis C virus (HCV). Molecular beacon-based helicase assays were used to show that (BIP)(2)B inhibits the ability of HCV helicase to separate a variety of RNA and DNA duplexes with half-maximal inhibitory concentrations ranging from 0.7 to 5 microM, depending on the nature of the substrate. In single turnover assays, (BIP)(2)B only inhibited unwinding reactions when it was preincubated with the helicase-nucleic acid complex. (BIP)(2)B quenched NS3 intrinsic protein fluorescence with an apparent dissociation constant of 5 microM, and in the presence of (BIP)(2)B, HCV helicase did not appear to interact with a fluorescent DNA oligonucleotide. In assays monitoring HCV helicase-catalyzed ATP hydrolysis, (BIP)(2)B only inhibited helicase-catalyzed ATP hydrolysis in the presence of intermediate concentrations of RNA, suggesting RNA and (BIP)(2)B compete for the same binding site. HCV helicases isolated from various HCV genotypes were similarly sensitive to (BIP)(2)B, with half-maximal inhibitory concentrations ranging from 0.7 to 2.4 microM. (BIP)(2)B also inhibited ATP hydrolysis catalyzed by related helicases from Dengue virus, Japanese encephalitis virus, and humans. (BIP)(2)B appeared to bind the HCV and human proteins with similar affinity (K(i) = 7 and 8 microM, respectively), but it bound the flavivirus proteins up to 270 times more tightly. Results are discussed in light of a molecular model of a (BIP)(2)B-HCV helicase complex, which is unable to bind nucleic acid, thus preventing the enzyme from separating double-stranded nucleic acid.
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Affiliation(s)
- Craig A Belon
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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Joyce MA, Tyrrell DLJ. The cell biology of hepatitis C virus. Microbes Infect 2010; 12:263-71. [PMID: 20080204 DOI: 10.1016/j.micinf.2009.12.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 12/22/2009] [Indexed: 12/16/2022]
Abstract
Hepatitis C virus infects 3% of the world's population and has a variable disease course with potentially sever outcomes, liver failure and hepatocellular carcinoma. The influence of HCV the biology of infected hepatocytes is now just becoming known. This review will focus on effect of HCV on host cells.
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Affiliation(s)
- Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
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Hepatitis C virus NS2 protein contributes to virus particle assembly via opposing epistatic interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes. J Virol 2009; 83:8379-95. [PMID: 19515772 DOI: 10.1128/jvi.00891-09] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The hepatitis C virus NS2 protein has been recently implicated in virus particle assembly. To further understand the role of NS2 in this process, we conducted a reverse genetic analysis of NS2 in the context of a chimeric genotype 2a infectious cell culture system. Of 32 mutants tested, all were capable of RNA replication and 25 had moderate-to-severe defects in virus assembly. Through forward genetic selection for variants capable of virus spread, we identified second-site mutations in E1, E2, NS2, NS3, and NS4A that suppressed NS2 defects in assembly. Two suppressor mutations, E1 A78T and NS3 Q221L, were further characterized by additional genetic and biochemical experiments. Both mutations were shown to suppress other NS2 defects, often with mutual exclusivity. Thus, several NS2 mutants were enhanced by NS3 Q221L and inhibited by E1 A78T, while others were enhanced by E1 A78T and inhibited by NS3 Q221L. Furthermore, we show that the NS3 Q221L mutation lowers the affinity of native, full-length NS3-NS4A for functional RNA binding. These data reveal a complex network of interactions involving NS2 and other viral structural and nonstructural proteins during virus assembly.
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Shiryaev SA, Chernov AV, Aleshin AE, Shiryaeva TN, Strongin AY. NS4A regulates the ATPase activity of the NS3 helicase: a novel cofactor role of the non-structural protein NS4A from West Nile virus. J Gen Virol 2009; 90:2081-5. [PMID: 19474250 DOI: 10.1099/vir.0.012864-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using constructs that encode the individual West Nile virus (WNV) NS3helicase (NS3hel) and NS3hel linked to the hydrophilic, N-terminal 1-50 sequence of NS4A, we demonstrated that the presence of NS4A allows NS3hel to conserve energy in the course of oligonucleotide substrate unwinding. Using NS4A mutants, we also determined that the C-terminal acidic EELPD/E motif of NS4A, which appears to be functionally similar to the acidic EFDEMEE motif of hepatitis C virus (HCV) NS4A, is essential for regulating the ATPase activity of NS3hel. We concluded that, similar to HCV NS4A, NS4A of WNV acts as a cofactor for NS3hel and allows helicase to sustain the unwinding rate of the viral RNA under conditions of ATP deficiency.
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