1
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de Souza Neto LR, Montoya BO, Brandão-Neto J, Verma A, Bowyer S, Moreira-Filho JT, Dantas RF, Neves BJ, Andrade CH, von Delft F, Owens RJ, Furnham N, Silva-Jr FP. Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Sci Rep 2024; 14:1582. [PMID: 38238498 PMCID: PMC10796382 DOI: 10.1038/s41598-024-52018-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. Praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, but despite that it is ineffective against juvenile worms and size and taste issues with its pharmaceutical forms impose challenges for treating school-aged children. It is also important to note that PZQ resistant strains can be generated in laboratory conditions and observed in the field, hence its extensive use in mass drug administration programs raises concerns about resistance, highlighting the need to search for new schistosomicidal drugs. Schistosomes survival relies on the redox enzyme thioredoxin glutathione reductase (TGR), a validated target for the development of new anti-schistosomal drugs. Here we report a high-throughput fragment screening campaign of 768 compounds against S. mansoni TGR (SmTGR) using X-ray crystallography. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the "doorstop pocket" near the NADPH binding site. We have compared results from hotspots and pocket druggability analysis of SmTGR with the experimental binding sites found in this work, with our results indicating only limited coincidence between experimental and computational results. Finally, we discuss that binding sites at the doorstop/NADPH binding site and in the SmTGR dimer interface, should be prioritized for developing SmTGR inhibitors as new antischistosomal drugs.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bogar Omar Montoya
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
| | - Anil Verma
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sebastian Bowyer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rafael Ferreira Dantas
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
- CRAFT - Center for Research and Advancement of Fragments and Molecular Targets, University of São Paulo, São Paulo, Brazil
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Structural Biology, Rosalind Franklin Institute, Harwell, UK.
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Floriano Paes Silva-Jr
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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2
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Loup-Forest J, Matuchet M, Schnitzler C, Pichard S, Poterszman A. A Time and Cost-Effective Pipeline for Expression Screening and Protein Production in Insect Cells Based on the HR-Bac Toolbox to Generate Recombinant Baculoviruses. Methods Mol Biol 2024; 2829:21-48. [PMID: 38951325 DOI: 10.1007/978-1-0716-3961-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The baculovirus expression vector system (BEVS) is recognized as a powerful platform for producing challenging proteins and multiprotein complexes both in academia and industry. Since a baculovirus was first used to produce heterologous human IFN-β protein in insect cells, the BEVS has continuously been developed and its applications expanded. We have recently established a multigene expression toolbox (HR-bac) composed of a set of engineered bacmids expressing a fluorescent marker to monitor virus propagation and a library of transfer vectors. Unlike platforms that rely on Tn7-medidated transposition for the construction of baculoviruses, HR-bac relies on homologous recombination, which allows to evaluate expression constructs in 2 weeks and is thus perfectly adapted to parallel expression screening. In this chapter, we detail our standard operating procedures for the preparation of the reagents, the construction and evaluation of baculoviruses, and the optimization of protein production for both intracellularly expressed and secreted proteins.
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Affiliation(s)
- Jules Loup-Forest
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Manon Matuchet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Charlotte Schnitzler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France.
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3
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Liu X, Gennerich A. Insect Cell-Based Expression of Cytoskeletal Motor Proteins for Single-Molecule Studies. Methods Mol Biol 2024; 2694:69-90. [PMID: 37824000 PMCID: PMC10880877 DOI: 10.1007/978-1-0716-3377-9_4] [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] [Indexed: 10/13/2023]
Abstract
Cytoskeletal motor proteins are essential molecular machines that hydrolyze ATP to generate force and motion along cytoskeletal filaments. Members of the dynein and kinesin superfamilies play critical roles in transporting biological payloads (such as proteins, organelles, and vesicles) along microtubule pathways, cause the beating of flagella and cilia, and act within the mitotic and meiotic spindles to segregate replicated chromosomes to progeny cells. Understanding the underlying mechanisms and behaviors of motor proteins is critical to provide better strategies for the treatment of motor protein-related diseases. Here, we provide detailed protocols for the recombinant expression of the Kinesin-1 motor KIF5C using a baculovirus/insect cell system and provide updated protocols for performing single-molecule studies using total internal reflection fluorescence microscopy and optical tweezers to study the motility and force generation of the purified motor.
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Affiliation(s)
- Xinglei Liu
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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4
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Viola CM, Frittmann O, Jenkins HT, Shafi T, De Meyts P, Brzozowski AM. Structural conservation of insulin/IGF signalling axis at the insulin receptors level in Drosophila and humans. Nat Commun 2023; 14:6271. [PMID: 37805602 PMCID: PMC10560217 DOI: 10.1038/s41467-023-41862-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023] Open
Abstract
The insulin-related hormones regulate key life processes in Metazoa, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin signalling axis (IIS). In humans the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. In Drosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR). This report describes the cryoEM structure of the dmIR ectodomain:DILP5 complex, revealing high structural homology between dmIR and hIR. The excess of DILP5 yields dmIR complex in an asymmetric 'T' conformation, similar to that observed in some complexes of human IRs. However, dmIR binds three DILP5 molecules in a distinct arrangement, showing also dmIR-specific features. This work adds structural support to evolutionary conservation of the IIS axis at the IR level, and also underpins a better understanding of an important model organism.
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Affiliation(s)
- Cristina M Viola
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Orsolya Frittmann
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Department of Haematology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Talha Shafi
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Pierre De Meyts
- Department of Cell Signalling, de Duve Institute, B-1200, Brussels, Belgium
- Department of Cell Therapy Research, Novo Nordisk A/S, DK-2670, Maaloev, Denmark
| | - Andrzej M Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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5
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Le‐Trilling VTK, Banchenko S, Paydar D, Leipe PM, Binting L, Lauer S, Graziadei A, Klingen R, Gotthold C, Bürger J, Bracht T, Sitek B, Jan Lebbink R, Malyshkina A, Mielke T, Rappsilber J, Spahn CMT, Voigt S, Trilling M, Schwefel D. Structural mechanism of CRL4-instructed STAT2 degradation via a novel cytomegaloviral DCAF receptor. EMBO J 2023; 42:e112351. [PMID: 36762436 PMCID: PMC9975947 DOI: 10.15252/embj.2022112351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023] Open
Abstract
Human cytomegalovirus (CMV) is a ubiquitously distributed pathogen whose rodent counterparts such as mouse and rat CMV serve as common infection models. Here, we conducted global proteome profiling of rat CMV-infected cells and uncovered a pronounced loss of the transcription factor STAT2, which is crucial for antiviral interferon signalling. Via deletion mutagenesis, we found that the viral protein E27 is required for CMV-induced STAT2 depletion. Cellular and in vitro analyses showed that E27 exploits host-cell Cullin4-RING ubiquitin ligase (CRL4) complexes to induce poly-ubiquitylation and proteasomal degradation of STAT2. Cryo-electron microscopy revealed how E27 mimics molecular surface properties of cellular CRL4 substrate receptors called DCAFs (DDB1- and Cullin4-associated factors), thereby displacing them from the catalytic core of CRL4. Moreover, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, which partially overlaps with the IRF9 binding site. Structure-based mutations in M27, the murine CMV homologue of E27, impair the interferon-suppressing capacity and virus replication in mouse models, supporting the conserved importance of DCAF mimicry for CMV immune evasion.
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Affiliation(s)
| | - Sofia Banchenko
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Darius Paydar
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
- Zentrum für KinderpsychiatrieUniversitätsklinik ZürichZürichSwitzerland
| | - Pia Madeleine Leipe
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Lukas Binting
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Simon Lauer
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
| | - Robin Klingen
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Christine Gotthold
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Jörg Bürger
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Microscopy and Cryo‐Electron Microscopy Service GroupMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | - Thilo Bracht
- Medizinisches Proteom‐CenterRuhr‐University BochumBochumGermany
- Department of Anesthesia, Intensive Care Medicine and Pain TherapyUniversity Hospital Knappschaftskrankenhaus BochumBochumGermany
| | - Barbara Sitek
- Medizinisches Proteom‐CenterRuhr‐University BochumBochumGermany
- Department of Anesthesia, Intensive Care Medicine and Pain TherapyUniversity Hospital Knappschaftskrankenhaus BochumBochumGermany
| | - Robert Jan Lebbink
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Anna Malyshkina
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Thorsten Mielke
- Microscopy and Cryo‐Electron Microscopy Service GroupMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Christian MT Spahn
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Sebastian Voigt
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - Mirko Trilling
- Institute for VirologyUniversity Hospital Essen, University of Duisburg‐EssenEssenGermany
| | - David Schwefel
- Institute of Medical Physics and BiophysicsCharité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
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6
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Zhang X, He A, Zong Y, Tian H, Zhang Z, Zhao K, Xu X, Chen H. Improvement of protein production in baculovirus expression vector system by removing a total of 10 kb of nonessential fragments from Autographa californica multiple nucleopolyhedrovirus genome. Front Microbiol 2023; 14:1171500. [PMID: 37125202 PMCID: PMC10133524 DOI: 10.3389/fmicb.2023.1171500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Baculovirus expression vector system (BEVS) is a powerful and versatile platform for recombinant protein production in insect cells. As the most frequently used baculovirus, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) encodes 155 open reading frames (ORFs), including a considerable number of non-essential genes for the virus replication in cell culture. Studies have shown that protein production in BEVS can be improved by removing some viral dispensable genes, and these AcMNPV vectors also offer the possibility of accommodating larger exogenous gene fragments. In this study, we, respectively, deleted 14 DNA fragments from AcMNPV genome, each of them containing at least two contiguous genes that were known nonessential for viral replication in cell culture or functionally unknown. The effects of these fragment-deletions on virus replication and exogenous protein production were examined. The results showed that 11 of the 14 fragments, containing 43 genes, were dispensable for the virus replication in cultured cells. By detecting the expression of intracellularly expressed and secreted reporter proteins, we demonstrated that nine of the fragment-deletions benefited protein production in Sf9 cells and/or in High Five cells. After combining the deletion of some dispensable fragments, we obtained two AcMNPV vectors shortened by more than 10 kb but displayed an improved capacity for recombinant protein production. The deletion strategies used in this study has the potential to further improve the BEVS.
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7
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Huang J, Liu H, Xu X. Homologous recombination risk in baculovirus expression vector system. Virus Res 2022; 321:198924. [PMID: 36089109 DOI: 10.1016/j.virusres.2022.198924] [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: 07/28/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022]
Abstract
The baculovirus expression vector system (BEVS) is widely used for producing recombinant proteins. To achieve high expression level of recombinant proteins, baculoviral elements, such as enhancers, promoters, signal peptide coding sequences and 3'-UTR, have been extensively employed. There is a recombination risk derived from homologous sequences between viral genome and functional baculovirus-derived elements associated with foreign genes. Although homologous recombination have distinct biological functions, these potential adverse recombination may trigger a DNA fragment being inverted or looped out, resulting in the production of defective viruses and eventual yields declines of recombinant proteins. However, the risk of such homologous recombination has not been systematically assessed. Here, we measured the recombination rate using a promoter-less fluorescent reporter integrated with various lengths homologous of p10 coding region. Homologous fragments longer than 60 bp possess sufficient recombination probability and exerts effect on purity and integrity of virus. Shortening the length of homologous fragments and separating homologous fragments by point mutations can effectively reduce unfavorable recombination. These findings reveal a homologous recombination risk resulted from genome-homologous baculoviral elements and propose reliable strategies reducing recombination rate to facilitate viral stability and integrity in baculovirus expression vector system.
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Affiliation(s)
- Jianan Huang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Huanlei Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xiaodong Xu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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8
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Sullivan E, Sung PY, Wu W, Berry N, Kempster S, Ferguson D, Almond N, Jones IM, Roy P. SARS-CoV-2 Virus-like Particles Produced by a Single Recombinant Baculovirus Generate Anti-S Antibody and Protect against Variant Challenge. Viruses 2022; 14:914. [PMID: 35632656 PMCID: PMC9143203 DOI: 10.3390/v14050914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has highlighted the need for the rapid generation of efficient vaccines for emerging disease. Virus-like particles, VLPs, are an established vaccine technology that produces virus-like mimics, based on expression of the structural proteins of a target virus. SARS-CoV-2 is a coronavirus where the basis of VLP formation has been shown to be the co-expression of the spike, membrane and envelope structural proteins. Here we describe the generation of SARS-CoV-2 VLPs by the co-expression of the salient structural proteins in insect cells using the established baculovirus expression system. VLPs were heterologous ~100 nm diameter enveloped particles with a distinct fringe that reacted strongly with SARS-CoV-2 convalescent sera. In a Syrian hamster challenge model, non-adjuvanted VLPs induced neutralizing antibodies to the VLP-associated Wuhan S protein and reduced virus shedding and protected against disease associated weight loss following a virulent challenge with SARS-CoV-2 (B.1.1.7 variant). Immunized animals showed reduced lung pathology and lower challenge virus replication than the non-immunized controls. Our data suggest SARS-CoV-2 VLPs offer an efficient vaccine that mitigates against virus load and prevents severe disease.
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Affiliation(s)
- Edward Sullivan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Po-Yu Sung
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Weining Wu
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Neil Berry
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Sarah Kempster
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Deborah Ferguson
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading RG6 6AH, UK;
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
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9
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Pichard S, Troffer-Charlier N, Kolb-Cheynel I, Poussin-Courmontagne P, Abdulrahman W, Birck C, Cura V, Poterszman A. Insect Cells-Baculovirus System for the Production of Difficult to Express Proteins: From Expression Screening for Soluble Constructs to Protein Quality Control. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2406:281-317. [PMID: 35089564 DOI: 10.1007/978-1-0716-1859-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid preparation of proteins for functional and structural analysis is a major challenge both in academia and industry. The number potential targets continuously increases and many are difficult to express proteins which, when produced in bacteria, result in insoluble and/or misfolded recombinant proteins, protein aggregates, or unusable low protein yield. We focus here on the baculovirus expression vector system which is now commonly used for heterologous production of human targets. This chapter describes simple and cost-effective protocols that enable iterative cycles of construct design, expression screening and optimization of protein production. We detail time- and cost-effective methods for generation of baculoviruses by homologous recombination and titer evaluation. Handling of insect cell cultures and preparation of bacmid for cotransfection are also presented.
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Affiliation(s)
- Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Nathalie Troffer-Charlier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | | | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France.
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10
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Kolesnikova O, Zachayus A, Pichard S, Osz J, Rochel N, Rossolillo P, Kolb-Cheynel I, Troffer-Charlier N, Compe E, Bensaude O, Berger I, Poterszman A. HR-Bac, a toolbox based on homologous recombination for expression, screening and production of multiprotein complexes using the baculovirus expression system. Sci Rep 2022; 12:2030. [PMID: 35132103 PMCID: PMC8821708 DOI: 10.1038/s41598-021-04715-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 11/25/2021] [Indexed: 11/09/2022] Open
Abstract
The Baculovirus/insect cell expression system is a powerful technology for reconstitution of eukaryotic macromolecular assemblies. Most multigene expression platforms rely on Tn7-mediated transposition for transferring the expression cassette into the baculoviral genome. This allows a rigorous characterization of recombinant bacmids but involves multiple steps, a limitation when many constructs are to be tested. For parallel expression screening and potential high throughput applications, we have established an open source multigene-expression toolbox exploiting homologous recombination, thus reducing the recombinant baculovirus generation to a single-step procedure and shortening the time from cloning to protein production to 2 weeks. The HR-bac toolbox is composed of a set of engineered bacmids expressing a fluorescent marker to monitor virus propagation and a library of transfer vectors. They contain single or dual expression cassettes bearing different affinity tags and their design facilitates the mix and match utilization of expression units from Multibac constructs. The overall cost of virus generation with HR-bac toolbox is relatively low as the preparation of linearized baculoviral DNA only requires standard reagents. Various multiprotein assemblies (nuclear hormone receptor heterodimers, the P-TEFb or the ternary CAK kinase complex associated with the XPD TFIIH subunit) are used as model systems to validate the toolbox presented.
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Affiliation(s)
- Olga Kolesnikova
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,EMBL, Heidelberg, Germany
| | - Amélie Zachayus
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Simon Pichard
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Paola Rossolillo
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nathalie Troffer-Charlier
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Emmanuel Compe
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, University of Bristol, Bristol, BS8 1TS, UK.,Bristol Synthetic Biology Centre BrisSynBio, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol, BS8 1TD, UK
| | - Arnaud Poterszman
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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11
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Structures of active melanocortin-4 receptor-Gs-protein complexes with NDP-α-MSH and setmelanotide. Cell Res 2021; 31:1176-1189. [PMID: 34561620 PMCID: PMC8563958 DOI: 10.1038/s41422-021-00569-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
The melanocortin-4 receptor (MC4R), a hypothalamic master regulator of energy homeostasis and appetite, is a class A G-protein-coupled receptor and a prime target for the pharmacological treatment of obesity. Here, we present cryo-electron microscopy structures of MC4R–Gs-protein complexes with two drugs recently approved by the FDA, the peptide agonists NDP-α-MSH and setmelanotide, with 2.9 Å and 2.6 Å resolution. Together with signaling data from structure-derived MC4R mutants, the complex structures reveal the agonist-induced origin of transmembrane helix (TM) 6-regulated receptor activation. The ligand-binding modes of NDP-α-MSH, a high-affinity linear variant of the endogenous agonist α-MSH, and setmelanotide, a cyclic anti-obesity drug with biased signaling toward Gq/11, underline the key role of TM3 in ligand-specific interactions and of calcium ion as a ligand-adaptable cofactor. The agonist-specific TM3 interplay subsequently impacts receptor–Gs-protein interfaces at intracellular loop 2, which also regulates the G-protein coupling profile of this promiscuous receptor. Finally, our structures reveal mechanistic details of MC4R activation/inhibition, and provide important insights into the regulation of the receptor signaling profile which will facilitate the development of tailored anti-obesity drugs.
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12
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Orea-Ordóñez L, Masiá S, Bravo J. Peptides Targeting the Interaction Between Erb1 and Ytm1 Ribosome Assembly Factors. Front Mol Biosci 2021; 8:718941. [PMID: 34540895 PMCID: PMC8440923 DOI: 10.3389/fmolb.2021.718941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome biogenesis is an emerging therapeutic target. It has been proposed that cancer cells are addicted to ribosome production which is therefore considered a druggable pathway in cancer therapy. Cancer cells have been shown to be more sensitive to inhibition of the ribosome production than healthy cells. Initial attempts of inhibiting ribosome biogenesis have been focused on the inhibition of transcription by targeting RNA Pol I. Despite being a promising field of research, several limitations have been identified during the development of RNA Pol I inhibitors, like the lack of specificity or acquired resistance. Ribosome biogenesis is a multistep process and additional points of intervention, downstream the very initial stage, could be investigated. Eukaryotic ribosome maturation involves the participation of more than 200 essential assembly factors that will not be part of the final mature ribosome and frequently require protein-protein interactions to exert their biological action. Using mutagenesis, we have previously shown that alteration of the complex interface between assembly factors impairs proper ribosome maturation in yeast. As a first step toward the developing of ribosome biogenesis inhibitory tools, we have used our previously solved crystal structure of the Chaetomium thermophilum complex between the assembly factors Erb1 and Ytm1 to perform a structure-guided selection of interference peptides. The peptides have been assayed in vitro for their ability to bind their cellular partner using biophysical techniques.
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Affiliation(s)
| | | | - Jerónimo Bravo
- Department Genomics and Proteomics, Instituto de Biomedicina de Valencia, Spanish National Research Council (CSIC), Valencia, Spain
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13
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Banchenko S, Krupp F, Gotthold C, Bürger J, Graziadei A, O’Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D. Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses. PLoS Pathog 2021; 17:e1009775. [PMID: 34339457 PMCID: PMC8360603 DOI: 10.1371/journal.ppat.1009775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/12/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
Viruses have evolved means to manipulate the host's ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1 specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infecting Cercopithecus cephus (SIVmus). X-ray crystallography reveals commonalities between SIVmus Vpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmus Vpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1 assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.
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Affiliation(s)
- Sofia Banchenko
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Ferdinand Krupp
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Christine Gotthold
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Francis J. O’Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Olga Ruda
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Christian M. T. Spahn
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David Schwefel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
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14
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Jégouic SM, Jones IM, Edwards AD. Affordable mobile microfluidic diagnostics: minimum requirements for smartphones and digital imaging for colorimetric and fluorometric anti-dengue and anti-SARS-CoV-2 antibody detection. Wellcome Open Res 2021; 6:57. [PMID: 36312459 PMCID: PMC9614285 DOI: 10.12688/wellcomeopenres.16628.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Background: Miniaturised bioassays permit diagnostic testing near the patient, and the results can be recorded digitally using inexpensive cameras including smartphone and mobile phone cameras. Although digital cameras are now inexpensive and portable, the minimum performance required for microfluidic diagnostic bioassays has not been defined. We present a systematic comparison of a wide range of different digital cameras for capturing and measuring results of microfluidic bioassays and describe a framework to specify performance requirements to quantify immunoassays. Methods: A set of 200 µm diameter microchannels was filled with a range of concentrations of dyes used in colorimetric and fluorometric enzyme immunoassays. These were imaged in parallel using cameras of varying cost and performance ranging from <£30 to >£500. Results: Higher resolution imaging allowed larger numbers of microdevices to be resolved and analysed in a single image. In contrast, low quality cameras were still able to quantify results but for fewer samples. In some cases, an additional macro lens was added to focus closely. If image resolution was sufficient to identify individual microfluidic channels as separate lines, all cameras were able to quantify a similar range of concentrations of both colorimetric and fluorometric dyes. However, the mid-range cameras performed better, with the lowest cost cameras only allowing one or two samples to be quantified per image. Consistent with these findings, we demonstrate that quantitation (to determine endpoint titre) of antibodies against dengue and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses is possible using a wide range of digital imaging devices including the mid-range smartphone iPhone 6S and a budget Android smartphone costing <£50. Conclusions: In conclusion, while more expensive and higher quality cameras allow larger numbers of devices to be simultaneously imaged, even the lowest resolution and cheapest cameras were sufficient to record and quantify immunoassay results.
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Affiliation(s)
- Sophie M. Jégouic
- Reading School of Pharmacy, University of Reading, Reading, RG6 1EE, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, UK
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15
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Membrane Protein Production and Purification from Escherichia coli and Sf9 Insect Cells. Methods Mol Biol 2021. [PMID: 33582985 DOI: 10.1007/978-1-0716-0724-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
A major obstacle to studying membrane proteins by biophysical techniques is the difficulty in producing sufficient amounts of materials for functional and structural studies. To overexpress the target membrane protein heterologously, especially an eukaryotic protein, a key step is to find the optimal host expression system and perform subsequent expression optimization. In this chapter, we describe protocols for screening membrane protein production using bacterial and insect cells, solubilization screening, large-scale production, and commonly used affinity chromatography purification methods. We discuss general optimization conditions, such as promoters and tags, and describe current techniques that can be used in any laboratory without specialized expensive equipment. Especially for insect cells, GFP fusions are particularly useful for localization and in-gel fluorescence detection of the proteins on SDS-PAGE. We give detailed protocols that can be used to screen the best expression and purification conditions for membrane protein study.
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16
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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17
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Structural insights into Fe–S protein biogenesis by the CIA targeting complex. Nat Struct Mol Biol 2020; 27:735-742. [DOI: 10.1038/s41594-020-0454-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
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18
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Neuhold J, Radakovics K, Lehner A, Weissmann F, Garcia MQ, Romero MC, Berrow NS, Stolt-Bergner P. GoldenBac: a simple, highly efficient, and widely applicable system for construction of multi-gene expression vectors for use with the baculovirus expression vector system. BMC Biotechnol 2020; 20:26. [PMID: 32398045 PMCID: PMC7216392 DOI: 10.1186/s12896-020-00616-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/27/2020] [Indexed: 11/29/2022] Open
Abstract
Background Recombinant protein production and purification of large protein complexes in eukaryotes requires efficient methods to generate multi-gene expression constructs, where each individual gene is under the control of its own promoter and terminator. Current methods are based either on serial rounds of combination of several vectors containing loxP sites via the Cre-lox technology, or on multiple rounds of gene combination via PCR or other methods. These methods are multi-step, have lower efficiencies than single gene cloning, and may require laborious processes to verify that all genes of interest are present in the final product. Here, we describe a rapid and simple Golden Gate-based system for the generation of multi-gene expression constructs compatible with baculovirus expression vector systems (BEVS) using either Tn7 transposition or KO1629-based homologous recombination, which we refer to as “GoldenBac”. Results This method is based on the construction of a series of vectors containing a promoter-gene of interest-terminator cassette flanked by cleavage sites of the BsaI type IIS restriction enzyme. This series of vectors can be cut by BsaI to excise cassettes with unique overhangs. In the same reaction, the cassettes are then ligated in the correct sequence in a final destination vector to generate multi-gene expression constructs containing 2–15 genes. Individual expression constructs can therefore be combined into a single vector in a single reaction, with over 90% efficiency when combining up to 14 expression cassettes. We demonstrate successful construction and expression of three different co-expression systems, the proteosomal lid complex, the anaphase promoting complex/cyclosome (APC/C), and a series of constructs used to test the effect of chaperone co-expression on the solubility of the HOIP protein. Conclusions This robust, single-step cloning system provides an easy-to-use method for generation of multi-gene expression constructs for both transposition and homologous recombination-based baculovirus systems, making this technology available across all laboratories using baculovirus expression systems. This highly efficient and simple method allows for rapid incorporation of multi-gene expression cloning into the standardized service portfolio of protein production facilities and can also easily be adopted by any laboratory for routine generation of multi-gene baculovirus constructs.
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Affiliation(s)
- Jana Neuhold
- Protein Technologies Facility, Vienna BioCenter Core Facilities, Dr. Bohr-gasse 3, 1030, Vienna, Austria
| | - Katharina Radakovics
- Protein Technologies Facility, Vienna BioCenter Core Facilities, Dr. Bohr-gasse 3, 1030, Vienna, Austria
| | - Anita Lehner
- Protein Technologies Facility, Vienna BioCenter Core Facilities, Dr. Bohr-gasse 3, 1030, Vienna, Austria
| | - Florian Weissmann
- Research Institute of Molecular Pathology, Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Maria Queralt Garcia
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mari Carmen Romero
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Nicholas S Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Peggy Stolt-Bergner
- Protein Technologies Facility, Vienna BioCenter Core Facilities, Dr. Bohr-gasse 3, 1030, Vienna, Austria.
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19
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Hustedt N, Saito Y, Zimmermann M, Álvarez-Quilón A, Setiaputra D, Adam S, McEwan A, Yuan JY, Olivieri M, Zhao Y, Kanemaki MT, Jurisicova A, Durocher D. Control of homologous recombination by the HROB-MCM8-MCM9 pathway. Genes Dev 2019; 33:1397-1415. [PMID: 31467087 PMCID: PMC6771392 DOI: 10.1101/gad.329508.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022]
Abstract
In this study, Hustedt et al. use CRISPR-based genetic screens to build a clear picture of the postsynaptic steps of homologous recombination in mammalian cells. They report the identification of C17orf53/HROB, a factor required for cell survival after exposure to a variety of replication stress-inducing genotoxins and for the resolution but not formation of Rad51 foci. DNA repair by homologous recombination (HR) is essential for genomic integrity, tumor suppression, and the formation of gametes. HR uses DNA synthesis to repair lesions such as DNA double-strand breaks and stalled DNA replication forks, but despite having a good understanding of the steps leading to homology search and strand invasion, we know much less of the mechanisms that establish recombination-associated DNA polymerization. Here, we report that C17orf53/HROB is an OB-fold-containing factor involved in HR that acts by recruiting the MCM8–MCM9 helicase to sites of DNA damage to promote DNA synthesis. Mice with targeted mutations in Hrob are infertile due to depletion of germ cells and display phenotypes consistent with a prophase I meiotic arrest. The HROB–MCM8–MCM9 pathway acts redundantly with the HELQ helicase, and cells lacking both HROB and HELQ have severely impaired HR, suggesting that they underpin two major routes for the completion of HR downstream from RAD51. The function of HROB in HR is reminiscent of that of gp59, which acts as the replicative helicase loader during bacteriophage T4 recombination-dependent DNA replication. We therefore propose that the loading of MCM8–MCM9 by HROB may similarly be a key step in the establishment of mammalian recombination-associated DNA synthesis.
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Affiliation(s)
- Nicole Hustedt
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Michal Zimmermann
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | | | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrea McEwan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jing Yi Yuan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Michele Olivieri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Andrea Jurisicova
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario M5G 0D8, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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20
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Bertinelli M, Paesen GC, Grimes JM, Renner M. High-resolution crystal structure of arthropod Eiger TNF suggests a mode of receptor engagement and altered surface charge within endosomes. Commun Biol 2019; 2:293. [PMID: 31396573 PMCID: PMC6684607 DOI: 10.1038/s42003-019-0541-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
The tumour necrosis factor alpha (TNFα) superfamily of proteins are critical in numerous biological processes, such as in development and immunity. Eiger is the sole TNFα member described in arthropods such as in the important model organism Drosophila. To date there are no structural data on any Eiger protein. Here we present the structure of the TNF domain of Eiger from the fall armyworm Spodoptera frugiperda (SfEiger) to 1.7 Å from a serendipitously obtained crystal without prior knowledge of the protein sequence. Our structure confirms that canonical trimerization is conserved from ancestral TNFs and points towards a mode of receptor engagement. Furthermore, we observe numerous surface histidines on SfEiger, potentially acting as pH switches following internalization into endosomes. Our data contributes to the genome annotation of S. frugiperda, a voracious agricultural pest, and can serve as a basis for future structure-function investigations of the TNF system in related arthropods such as Drosophila.
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Affiliation(s)
- Mattia Bertinelli
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE UK
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, 10 Roosevelt Drive, Oxford, OX3 7BN UK
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21
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Magini P, Marco-Marin C, Escamilla-Honrubia JM, Martinelli D, Dionisi-Vici C, Faravelli F, Forzano F, Seri M, Rubio V, Panza E. P5CS expression study in a new family with ALDH18A1-associated hereditary spastic paraplegia SPG9. Ann Clin Transl Neurol 2019; 6:1533-1540. [PMID: 31402623 PMCID: PMC6689680 DOI: 10.1002/acn3.50821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/14/2019] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
In 2015–2016, we and others reported ALDH18A1 mutations causing dominant (SPG9A) or recessive (SPG9B) spastic paraplegia. In vitro production of the ALDH18A1 product, Δ1‐pyrroline‐5‐carboxylate synthetase (P5CS), appeared necessary for cracking SPG9 disease‐causing mechanisms. We now describe a baculovirus–insect cell system that yields mgs of pure human P5CS and that has proven highly valuable with two novel P5CS mutations reported here in new SPG9B patients. We conclude that both mutations are disease‐causing, that SPG9B associates with partial P5CS deficiency and that it is clinically more severe than SPG9A, as reflected in onset age, disability, cognitive status, growth, and dysmorphic traits.
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Affiliation(s)
- Pamela Magini
- Medical Genetics Unit, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Clara Marco-Marin
- Instituto de Biomedicina de Valencia of the CSIC, Valencia, Spain.,Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Juan M Escamilla-Honrubia
- Instituto de Biomedicina de Valencia of the CSIC, Valencia, Spain.,Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Research Hospital, Rome, Italy
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Research Hospital, Rome, Italy
| | - Francesca Faravelli
- Clinical Genetics, NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Francesca Forzano
- Clinical Genetics Department, SE Thames Regional Genetics Service, Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Marco Seri
- Medical Genetics Unit, S. Orsola-Malpighi Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSIC, Valencia, Spain.,Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Emanuele Panza
- Medical Genetics Unit, S. Orsola-Malpighi Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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22
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Lemaitre RP, Bogdanova A, Borgonovo B, Woodruff JB, Drechsel DN. FlexiBAC: a versatile, open-source baculovirus vector system for protein expression, secretion, and proteolytic processing. BMC Biotechnol 2019; 19:20. [PMID: 30925874 PMCID: PMC6441187 DOI: 10.1186/s12896-019-0512-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/18/2019] [Indexed: 12/21/2022] Open
Abstract
Background Baculovirus-mediated expression in insect cells is a powerful approach for protein production. However, many existing methods are time-consuming, offer limited options for protein tagging, and are unsuitable for secreted proteins requiring proteolytic maturation, such as TGF-β family growth factors. Results To overcome the limitations of traditional baculovirus expression systems, we engineered “FlexiBAC”. This system allows recombinant baculovirus formation inside insect cells and reduces the time between initial cloning and protein production to 13 days. FlexiBAC includes 143 shuttle vectors that append combinations of purification tags, fluorescent markers, proteolytic cleavage sites, trafficking signals, and chemical conjugation tags to the termini of the target protein. This system also overexpresses recombinant furin convertase to allow efficient proteolytic processing of secreted proteins. We demonstrate that FlexiBAC can be used to produce high levels of mature, active forms of TGF-β family growth factors, such as Activin A, as well as other proteins that are typically difficult to reconstitute, such as proteins rich in coiled-coil, low complexity, and disordered domains. Conclusions FlexiBAC is a protein expression system for production of both cytosolic proteins and secreted proteins that require proteolytic maturation. The design of FlexiBAC and its expansive complementary shuttle vector system reduces cloning steps and simplifies baculovirus production. Electronic supplementary material The online version of this article (10.1186/s12896-019-0512-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Régis P Lemaitre
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Barbara Borgonovo
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Jeffrey B Woodruff
- Department of Cell Biology, Dept. of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - David N Drechsel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany. .,Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
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23
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Nan H, Chen H, Tuite MF, Xu X. A viral expression factor behaves as a prion. Nat Commun 2019; 10:359. [PMID: 30664652 PMCID: PMC6341119 DOI: 10.1038/s41467-018-08180-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Prions are proteins that can fold into multiple conformations some of which are self-propagating. Such prion-forming proteins have been found in animal, plant, fungal and bacterial species, but have not yet been identified in viruses. Here we report that LEF-10, a baculovirus-encoded protein, behaves as a prion. Full-length LEF-10 or its candidate prion-forming domain (cPrD) can functionally replace the PrD of Sup35, a widely studied prion-forming protein from yeast, displaying a [PSI+]-like phenotype. Furthermore, we observe that high multiplicity of infection can induce the conversion of LEF-10 into an aggregated state in virus-infected cells, resulting in the inhibition of viral late gene expression. Our findings extend the knowledge of current prion proteins from cellular organisms to non-cellular life forms and provide evidence to support the hypothesis that prion-forming proteins are a widespread phenomenon in nature.
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Affiliation(s)
- Hao Nan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Hongying Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Mick F Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China.
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24
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Nettleship JE, Rada H, Owens RJ. Overview of a High-Throughput Pipeline for Streamlining the Production of Recombinant Proteins. Methods Mol Biol 2019; 2025:33-49. [PMID: 31267447 DOI: 10.1007/978-1-4939-9624-7_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Production of high quality protein is an essential step for both structural and functional studies. Throughput has increased in the past decade by the use of streamlined workflows with standard operating procedures and automation. In this chapter, we describe the Oxford Protein Production Facility (OPPF) pipeline for protein production, from conception, through vector construction, to expression and purification. Results from projects run in the OPPF demonstrate the value of using parallel expression screening of intracellular proteins in both E. coli and insect cells. Transient expression in Human Embryonic Kidney (HEK) cells is used exclusively for production of secreted glycoproteins. Protein purification and quality assessment are independent of the expression system and enable sample preparation to be simplified and streamlined.
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Affiliation(s)
- Joanne E Nettleship
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
| | - Heather Rada
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
| | - Raymond J Owens
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK.
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.
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25
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Roed NK, Viola CM, Kristensen O, Schluckebier G, Norrman M, Sajid W, Wade JD, Andersen AS, Kristensen C, Ganderton TR, Turkenburg JP, De Meyts P, Brzozowski AM. Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones. Nat Commun 2018; 9:3860. [PMID: 30242155 PMCID: PMC6155051 DOI: 10.1038/s41467-018-06192-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The insulin/insulin-like growth factor signalling axis is an evolutionary ancient and highly conserved hormonal system involved in the regulation of metabolism, growth and lifespan in animals. Human insulin is stored in the pancreas, while insulin-like growth factor-1 (IGF-1) is maintained in blood in complexes with IGF-binding proteins (IGFBP1-6). Insect insulin-like polypeptide binding proteins (IBPs) have been considered as IGFBP-like structural and functional homologues. Here, we report structures of the Drosophila IBP Imp-L2 in its free form and bound to Drosophila insulin-like peptide 5 and human IGF-1. Imp-L2 contains two immunoglobulin-like fold domains and its architecture is unrelated to human IGFBPs, suggesting a distinct strategy for bioavailability regulation of insulin-like hormones. Similar hormone binding modes may exist in other insect vectors, as the IBP sequences are highly conserved. Therefore, these findings may open research routes towards a rational interference of transmission of diseases such as malaria, dengue and yellow fevers.
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Affiliation(s)
| | - Cristina M Viola
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Ole Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - Gerd Schluckebier
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Mathias Norrman
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Waseem Sajid
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - John D Wade
- Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Claus Kristensen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2100, Copenhagen N, Denmark
| | - Timothy R Ganderton
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Johan P Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Pierre De Meyts
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
- Department of Cell Signalling, de Duve Institute, B-1200, Brussels, Belgium
| | - Andrzej M Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK.
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26
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McKenzie EA, Abbott WM. Expression of recombinant proteins in insect and mammalian cells. Methods 2018; 147:40-49. [PMID: 29778647 DOI: 10.1016/j.ymeth.2018.05.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
Purified recombinant proteins are key reagents in academic and industrial research. The ability to make these proteins quickly often relies on the availability of higher eukaryotic cell hosts such as insect and mammalian cells where there is a very wide range of post-translational modifications, protein folding and trafficking pathways. This enables the generation of many proteins that cannot be made in microbial hosts. In this article we outline some of the most commonly used methods to express recombinant proteins in insect and mammalian cells.
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Affiliation(s)
- Edward A McKenzie
- Protein Expression Facility, Manchester Institute of Biotechnology, Faculty of Life Sciences, 131 Princess Street, Manchester M1 7DN, UK
| | - W Mark Abbott
- Peak Proteins Ltd, Alderley Park, Cheshire SK10 4TG, UK.
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27
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Development of a baculovirus vector carrying a small hairpin RNA for suppression of sf-caspase-1 expression and improvement of recombinant protein production. BMC Biotechnol 2018; 18:24. [PMID: 29720159 PMCID: PMC5930690 DOI: 10.1186/s12896-018-0434-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Background The Baculovirus expression vector system (BEVS) is a transient expression platform for recombinant protein production in insect cells. Baculovirus infection of insect cells will shutoff host translation and induce apoptosis and lead to the termination of protein expression. Previous reports have demonstrated the enhancement of protein yield in BEVS using stable insect cell lines expressing interference RNA to suppress the expression of caspase-1. Results In this study, short-hairpin RNA (shRNA) expression cassettes targeting Spodoptera frugiperda caspase-1 (Sf-caspase-1) were constructed and inserted into an Autographa californica multiple nucleopolyhedrovirus (AcMNPV) vector. Using the recombinant baculovirus vectors, we detected the suppression of Sf-caspase-1 expression and cell apoptosis. Green fluorescent protein (GFP), Discosoma sp. Red (DsRed) and firefly luciferase were then expressed as reporter proteins. The results showed that suppression of apoptosis enhanced the accumulation of exogenous proteins at 2 and 3 days post infection. After 4 days post infection, the activity of the reporter proteins remained higher in BEVS using the baculovirus carrying shRNA in comparison with the control without shRNA, but the accumulated protein levels showed no obvious difference between them, suggesting that apoptosis suppression resulted in improved protein folding rather than translation efficiency at the very late stage of baculovirus infection. Conclusions The baculovirus vector developed in this study would be a useful tool for the production of active proteins suitable for structural and functional studies or pharmaceutical applications in Sf9 cells, and it also has the potential to be adapted for the improvement of protein expression in different insect cell lines that can be infected by AcMNPV.
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28
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Fiege B, Leuthold M, Parra F, Dalton KP, Meloncelli PJ, Lowary TL, Peters T. Epitope mapping of histo blood group antigens bound to norovirus VLPs using STD NMR experiments reveals fine details of molecular recognition. Glycoconj J 2017; 34:679-689. [PMID: 28823097 DOI: 10.1007/s10719-017-9792-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
Attachment of human noroviruses to histo blood group antigens (HBGAs) is thought to be critical for the infection process. Therefore, we have determined binding epitopes of synthetic type 1 to 6 blood group A- and B-tetrasaccharides binding to GII.4 human Norovirus virus like particles (VLPs) using STD NMR experiments. So far, little information is available from crystal structure analysis studies on the interactions of the reducing-end sugars with the protruding domain (P-domain) of the viral coat protein VP1. Here, we show that the reducing-end sugars make notable contacts with the protein surface. The type of glycosidic linkage, and the identity of the sugar at the reducing end modulate HBGA recognition. Most strikingly, type 2 structures yield only very poor saturation transfer indicating impeded binding. This observation is in accordance with previous mass spectrometry based affinity measurements, and can be understood based on recent crystal structure data of a complex of highly homologous GII.4 P-dimers with H-type 2 trisaccharide where the N-acetyl group of the reducing N-acetyl glucosamine residue points towards a loop comprising amino acids Q390 to H395. We suggest that in our case, binding of type 2 A- and B-tetrasaccharides leads to steric conflicts with this loop. In order to identify factors determining L-Fuc recognition, we also synthesized GII.4 VLPs with point mutations D391A and H395A. Prior studies had suggested that these residues, located in a second shell around the L-Fuc binding site, assist L-Fuc binding. STD NMR experiments with L-Fuc and B-trisaccharide in the presence of wild type and mutant VLPs yield virtually identical binding epitopes suggesting that these two mutations do not significantly alter HBGA recognition. Our study emphasizes that recognition of α-(1→2)-linked L-Fuc residues is a conserved feature of GII.4 noroviruses. However, structural variation of the HBGA core structures clearly modulates molecular recognition depending on the genotype.
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Affiliation(s)
- Brigitte Fiege
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Mila Leuthold
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
- Molecular Virology, Heidelberg University Hospital, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Kevin P Dalton
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Peter J Meloncelli
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, The University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G G2, Canada
| | - Todd L Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, The University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G G2, Canada
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany.
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29
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Bláha J, Kalousková B, Skořepa O, Pažický S, Novák P, Vaněk O. High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI - cells. Protein Expr Purif 2017; 140:36-43. [PMID: 28757467 DOI: 10.1016/j.pep.2017.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 02/09/2023]
Abstract
Human natural killer receptor protein 1 (NKR-P1, CD161, gene klrb1) is a C-type lectin-like receptor of natural killer (NK) cells responsible for recognition of its cognate protein ligand lectin-like transcript 1 (LLT1). NKR-P1 is the single human orthologue of the prototypical rodent NKR-P1 receptors. Naturally, human NKR-P1 is expressed on the surface of NK cells, where it serves as inhibitory receptor; and on T and NKT cells functioning as co-stimulatory receptor promoting secretion of IFNγ. Most notably, it is expressed on Th17 and Tc17 lymphocytes where presumably promotes targeting into LLT1 expressing immunologically privileged niches. We tested effect of different protein tags (SUMO, TRX, GST, MsyB) on expression of soluble NKR-P1 in E. coli. Then we optimized the expression construct of soluble NKR-P1 by preparing a library of expression constructs in pOPING vector containing the extracellular lectin-like domain with different length of the putative N-terminal stalk region and tested its expression in Sf9 and HEK293 cells. Finally, a high-level expression of soluble NKR-P1 was achieved by stable expression in suspension-adapted HEK293S GnTI- cells utilizing pOPINGTTneo expression vector. Purified soluble NKR-P1 is homogeneous, deglycosylatable, crystallizable and monomeric in solution, as shown by size-exclusion chromatography, multi-angle light scattering and analytical ultracentrifugation.
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Affiliation(s)
- Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Samuel Pažický
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Petr Novák
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic; Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic.
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30
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Legastelois I, Buffin S, Peubez I, Mignon C, Sodoyer R, Werle B. Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules. Hum Vaccin Immunother 2016; 13:947-961. [PMID: 27905833 DOI: 10.1080/21645515.2016.1260795] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids.
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Affiliation(s)
| | - Sophie Buffin
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | - Isabelle Peubez
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | | | - Régis Sodoyer
- b Technology Research Institute Bioaster , Lyon , France
| | - Bettina Werle
- b Technology Research Institute Bioaster , Lyon , France
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31
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Martino L, Holland L, Christodoulou E, Kunzelmann S, Esposito D, Rittinger K. The Biophysical Characterisation and SAXS Analysis of Human NLRP1 Uncover a New Level of Complexity of NLR Proteins. PLoS One 2016; 11:e0164662. [PMID: 27727326 PMCID: PMC5058472 DOI: 10.1371/journal.pone.0164662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/28/2016] [Indexed: 12/02/2022] Open
Abstract
NOD-like receptors represent an important class of germline-encoded pattern recognition receptors that play key roles in the regulation of inflammatory signalling pathways. They function as danger sensors and initiate inflammatory responses and the production of cytokines. Since NLR malfunction results in chronic inflammation and auto-immune diseases, there is a great interest in understanding how they work on a molecular level. To date, a lot of insight into the biological functions of NLRs is available but biophysical and structural studies have been hampered by the difficulty to produce soluble and stable recombinant NLR proteins. NLRP1 is an inflammasome forming NLR that is believed to be activated by binding to MDP and induces activation of caspase 1. Here, we report the identification of a soluble fragment of NLRP1 that contains the NACHT oligomerization domain and the putative MDP-sensing LRR domain. We describe the biophysical and biochemical characterization of this construct and a SEC-SAXS analysis that allowed the calculation of a low resolution molecular envelope. Our data indicate that the protein is constitutively bound to ATP with a negligible ability to hydrolyse the triphosphate nucleotide and that it adopts a monomeric extended conformation that is reminiscent of the structure adopted by NLRC4 in the inflammasome complex. Furthermore, we show that the presence of MDP is not sufficient to promote self-oligomerization of the NACHT-LRR fragment suggesting that MDP may either bind to regions outside the NACHT-LRR module or that it may not be the natural ligand of NLRP1. Taken together, our data suggest that the NLRP1 mechanism of action differs from that recently reported for other NLRs.
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Affiliation(s)
- Luigi Martino
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Louise Holland
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Diego Esposito
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
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Abstract
Since its inception more than 30 years ago, the baculovirus expression vector system (BEVS) has been used prolifically to produce heterologous proteins for research and development. In the cell, a cornerstone of biological activity are multiprotein complexes, catalyzing essential functions. BEVS has been uniquely successful to unlock such complex assemblies for high-resolution structural and functional analysis. Synthetic biology approaches have been implemented to optimize multigene assembly methods, accelerating upstream processes. Specialized baculoviral genomes are being created with functions tailored to enhance production of particular target protein classes. Here we comment on current and emerging developments in the field and their potential to accelerate protein complex research.
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Affiliation(s)
- Imre Berger
- a The European Molecular Biology Laboratory (EMBL); Grenoble Outstation and Unit of Virus Host-Cell Interactions (UVHCI); Université Grenoble Alpes-EMBL-CNRS ; UMR 5233; Grenoble , France.,b The School of Biochemistry; University of Bristol ; Clifton , United Kingdom
| | - Arnaud Poterszman
- c Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); Center for Integrative Biology (CBI) ; Department of Integrated Structural Biology ; Illkirch ; France.,d Center National de la Recherche Scientifique (CNRS) UMR 7104 ; Illkirch , France.,e Institut National de la Santé et de la Recherche Médicale (INSERM) U964 ; Illkirch , France.,f Université de Strasbourg ; Strasbourg , France
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Mallagaray A, Rademacher C, Parra F, Hansman G, Peters T. Saturation transfer difference nuclear magnetic resonance titrations reveal complex multistep-binding of l-fucose to norovirus particles. Glycobiology 2016; 27:80-86. [PMID: 27496762 DOI: 10.1093/glycob/cww070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/24/2016] [Accepted: 06/25/2016] [Indexed: 01/20/2023] Open
Abstract
Recently, combined nuclear magnetic resonance (NMR), native mass spectrometry (MS) and X-ray crystallographic studies have demonstrated that binding of histo-blood group antigens (HBGAs) to norovirus capsid protein (P-dimers) is a cooperative process involving four binding pockets. Here, we show that binding to norovirus virus-like particles (VLPs) is even more complex. We performed saturation transfer difference (STD) NMR titration experiments with two representative genotypes of norovirus VLPs using l-fucose as a minimal HBGA. Compared to titrations with P-dimers, the corresponding binding isotherms reflect at least six distinct binding events.
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Affiliation(s)
- Alvaro Mallagaray
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Francisco Parra
- Universidad de Oviedo, Instituto Universitario de Biotecnología de Asturias, 33006 Oviedo Spain
| | - Grant Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, 69120 Heidelberg, Germany.,Department of Infectious Diseases and Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
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Xu X, Zhou X, Nan H, Zhao Y, Bai Y, Ou Y, Chen H. Aggregation of AcMNPV LEF-10 and Its Impact on Viral Late Gene Expression. PLoS One 2016; 11:e0154835. [PMID: 27152613 PMCID: PMC4859499 DOI: 10.1371/journal.pone.0154835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/20/2016] [Indexed: 12/24/2022] Open
Abstract
The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) late expression factor gene lef-10 has been identified to be required for viral late gene expression by transient expression assay. Our previous work has shown that the gene product LEF-10 can form very stable high-molecular-weight complexes, but the structure and function of the protein remain unknown. In this study, we demonstrated that LEF-10 was essential for the replication of AcMNPV, and its truncated fragment containing amino acid residues 1 to 48 were sufficient to support the virus survival. Our data also suggested that the LEF-10 could spontaneously aggregate to form punctate spots in virus infected Sf9 cells at low frequency, and the aggregation of the protein could be induced by LEF-10 over-expression. When the protein aggregated to form punctate spots, soluble LEF-10 proteins were depleted and this could result in the down-regulation of viral late gene expression.
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Affiliation(s)
- Xiaodong Xu
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
- * E-mail: (XX); (HC)
| | - Xinyu Zhou
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Hao Nan
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yu Zhao
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yu Bai
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yanmei Ou
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Hongying Chen
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
- * E-mail: (XX); (HC)
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Patel A, Mohl BP, Roy P. Entry of Bluetongue Virus Capsid Requires the Late Endosome-specific Lipid Lysobisphosphatidic Acid. J Biol Chem 2016; 291:12408-19. [PMID: 27036941 PMCID: PMC4933286 DOI: 10.1074/jbc.m115.700856] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/03/2022] Open
Abstract
The entry of viruses into host cells is one of the key processes of infection. The mechanisms of cellular entry for enveloped virus have been well studied. The fusion proteins as well as the facilitating cellular lipid factors involved in the viral fusion entry process have been well characterized. The process of non-enveloped virus cell entry, in comparison, remains poorly defined, particularly for large complex capsid viruses of the family Reoviridae, which comprises a range of mammalian pathogens. These viruses enter cells without the aid of a limiting membrane and thus cannot fuse with host cell membranes to enter cells. Instead, these viruses are believed to penetrate membranes of the host cell during endocytosis. However, the molecular mechanism of this process is largely undefined. Here we show, utilizing an in vitro liposome penetration assay and cell biology, that bluetongue virus (BTV), an archetypal member of the Reoviridae, utilizes the late endosome-specific lipid lysobisphosphatidic acid for productive membrane penetration and viral entry. Further, we provide preliminary evidence that lipid lysobisphosphatidic acid facilitates pore expansion during membrane penetration, suggesting a mechanism for lipid factor requirement of BTV. This finding indicates that despite the lack of a membrane envelope, the entry process of BTV is similar in specific lipid requirements to enveloped viruses that enter cells through the late endosome. These results are the first, to our knowledge, to demonstrate that a large non-enveloped virus of the Reoviridae has specific lipid requirements for membrane penetration and host cell entry.
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Affiliation(s)
- Avnish Patel
- From the Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Bjorn-Patrick Mohl
- From the Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Polly Roy
- From the Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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36
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Liu X, Wei Y, Li Y, Li H, Yang X, Yi Y, Zhang Z. A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus. PLoS One 2016; 11:e0152140. [PMID: 27008267 PMCID: PMC4805210 DOI: 10.1371/journal.pone.0152140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/09/2016] [Indexed: 12/23/2022] Open
Abstract
The silkworm baculovirus expression system is widely used to produce recombinant proteins. Several strategies for constructing recombinant viruses that contain foreign genes have been reported. Here, we developed a novel defective-rescue BmNPV Bacmid (reBmBac) expression system. A CopyControl origin of replication was introduced into the viral genome to facilitate its genetic manipulation in Escherichia coli and to ensure the preparation of large amounts of high quality reBmBac DNA as well as high quality recombinant baculoviruses. The ORF1629, cathepsin and chitinase genes were partially deleted or rendered defective to improve the efficiency of recombinant baculovirus generation and the expression of foreign genes. The system was validated by the successful expression of luciferase reporter gene and porcine interferon γ. This system can be used to produce batches of recombinant baculoviruses and target proteins rapidly and efficiently in silkworms.
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Affiliation(s)
- Xingjian Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonglong Wei
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haoyang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhu Yi
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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37
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Alshaikhahmed K, Roy P. Generation of virus-like particles for emerging epizootic haemorrhagic disease virus: Towards the development of safe vaccine candidates. Vaccine 2016; 34:1103-8. [PMID: 26805595 DOI: 10.1016/j.vaccine.2015.12.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/17/2015] [Accepted: 12/19/2015] [Indexed: 11/25/2022]
Abstract
Epizootic haemorrhagic disease virus (EHDV) is an insect-transmitted pathogen which causes high mortality in deer populations and may also cause high morbidity in cattle. EHDV belongs to the Orbivirus genus and is closely related to the prototype Bluetongue virus (BTV). To date seven distinct serotypes have been recognized. However, a live-attenuated vaccine is commercially available against only one serotype namely EHDV-2, which has been responsible for multiple outbreaks in North America, Canada, Asia and Australia. Here we expressed four major capsid proteins (VP2, VP3, VP5 and VP7) of EHDV-1 using baculovirus multiple gene expression systems and demonstrated that three-layered VLPs were assembled mimicking the authentic EHDV particles but lacking the viral genomic RNA segments and the transcriptase complex (TC). Antibodies generated with VLPs not only neutralized EHDV-1 infection in cell culture but also showed cross neutralizing reactivity against two other serotypes, EHDV-2 and EHDV-6. For proof of concept, we demonstrated that EHDV-2 VLPs could be generated rapidly by expressing the EHDV-2 variable outer capsid proteins (VP2, VP5) together with EHDV-1 VP3 and VP7, the two inner capsid proteins, which are highly conserved among the 7 serotypes. Data presented in this study validate the VLPs as a potential vaccine and demonstrate that a vaccine could be developed rapidly in the event of an outbreak of a new serotype.
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Affiliation(s)
- Kinda Alshaikhahmed
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Polly Roy
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom.
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38
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Abstract
Although there are several different methods available of making recombinant baculovirus expression vectors (reviewed in Chapter 3 ), all require a stage in which insect cells are transfected with either the virus genome alone (Bac-to-Bac(®) or BaculoDirect™, Invitrogen) or virus genome and transfer vector. In the latter case, this allows the natural process of homologous recombination to transfer the foreign gene, under control of the polyhedrin or other baculovirus gene promoter, from the transfer vector to the virus genome to create the recombinant virus. Previously, many methods required a plaque-assay to separate parental and recombinant virus prior to amplification and use of the recombinant virus. Fortunately, this step is no longer required for most systems currently available. This chapter provides an overview of the historical development of increasingly more efficient systems for the isolation of recombinant baculoviruses (Chapter 3 provides a full account of the different systems and transfer vectors available). The practical details cover: transfection of insect cells with either virus DNA or virus DNA and plasmid transfer vector; a reliable plaque-assay method that can be used to separate recombinant virus from parental (nonrecombinant) virus where this is necessary; methods for the small-scale amplification of recombinant virus; and subsequent titration by plaque-assay or real-time polymerase chain reaction (PCR). Methods unique to the Bac-to-Bac(®) system are also covered and include the transformation of bacterial cells and isolation of bacmid DNA ready for transfection of insect cells.
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Affiliation(s)
- Linda A King
- School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, UK
| | - Richard Hitchman
- School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, UK
| | - Robert D Possee
- NERC CEH (Oxford), Mansfield Road, Oxford, OX1, UK.
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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39
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Abstract
The production of a recombinant baculovirus expression vector normally involves mixing infectious virus DNA with a plasmid-based transfer vector and then co-transfecting insect cells to initiate virus infection. The aim of this chapter is to provide an update on the range of baculovirus transfer vectors currently available. Some of the original transfer vectors developed are now difficult to obtain but generally have been replaced by superior reagents. We focus on those that are available commercially and should be easy to locate. These vectors permit the insertion of single or multiple genes for expression, or the production of proteins with specific peptide tags that aid subsequent protein purification. Others have signal peptide coding regions permitting protein secretion or plasma membrane localization. A table listing the transfer vectors also includes information on the parental virus that should be used with each one. Methods are described for the direct insertion of a recombinant gene into the virus genome without the requirement for a transfer vector. The information provided should enable new users of the system to choose those reagents most suitable for their purposes.
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Affiliation(s)
- Robert D Possee
- NERC CEH (Oxford), Mansfield Road, Oxford, OX1, UK. .,Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
| | - Linda A King
- School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, UK
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40
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Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System. PLoS One 2015; 10:e0145887. [PMID: 26697848 PMCID: PMC4689351 DOI: 10.1371/journal.pone.0145887] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022] Open
Abstract
By introducing synonymous mutations into the coding sequences of GP64sp and FibHsp signal peptides, the influences of mRNA secondary structure and codon usage of signal sequences on protein expression and secretion were investigated using baculovirus/insect cell expression system. The results showed that mRNA structural stability of the signal sequences was not correlated with the protein production and secretion levels, and FibHsp was more tolerable to codon changes than GP64sp. Codon bias analyses revealed that codons for GP64sp were well de-optimized and contained more non-optimal codons than FibHsp. Synonymous mutations in GP64sp sufficiently increased its average codon usage frequency and resulted in dramatic reduction of the activity and secretion of luciferase. Protein degradation inhibition assay with MG-132 showed that higher codon usage frequency in the signal sequence increased the production as well as the degradation of luciferase protein, indicating that the synonymous codon substitutions in the signal sequence caused misfolding of luciferase instead of slowing down the protein production. Meanwhile, we found that introduction of more non-optimal codons into FibHsp could increase the production and secretion levels of luciferase, which suggested a new strategy to improve the production of secretory proteins in insect cells.
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41
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Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A. DNA Gyrase Is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem 2015; 291:3136-44. [PMID: 26663076 PMCID: PMC4751362 DOI: 10.1074/jbc.m115.689554] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
The Arabidopsis thaliana genome contains four genes that were originally annotated as potentially encoding DNA gyrase: ATGYRA, ATGYRB1, ATGYRB2, and ATGYRB3. Although we subsequently showed that ATGYRB3 does not encode a gyrase subunit, the other three genes potentially encode subunits of a plant gyrase. We also showed evidence for the existence of supercoiling activity in A. thaliana and that the plant is sensitive to quinolone and aminocoumarin antibiotics, compounds that target DNA gyrase in bacteria. However, it was not possible at that time to show whether the A. thaliana genes encoded an active gyrase enzyme, nor whether that enzyme is indeed the target for the quinolone and aminocoumarin antibiotics. Here we show that an A. thaliana mutant resistant to the quinolone drug ciprofloxacin has a point mutation in ATGYRA. Moreover we show that, as in bacteria, the quinolone-sensitive (wild-type) allele is dominant to the resistant gene. Further we have heterologously expressed ATGYRA and ATGYRB2 in a baculovirus expression system and shown supercoiling activity of the partially purified enzyme. Expression/purification of the quinolone-resistant A. thaliana gyrase yields active enzyme that is resistant to ciprofloxacin. Taken together these experiments now show unequivocally that A. thaliana encodes an organelle-targeted DNA gyrase that is the target of the quinolone drug ciprofloxacin; this has important consequences for plant physiology and the development of herbicides.
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Affiliation(s)
- Katherine M Evans-Roberts
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Lesley A Mitchenall
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Melisa K Wall
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Julie Leroux
- the School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia, and the Australian Research Council Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S Mylne
- the School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia, and the Australian Research Council Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Anthony Maxwell
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom,
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Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI. Polyhedra structures and the evolution of the insect viruses. J Struct Biol 2015; 192:88-99. [PMID: 26291392 PMCID: PMC4597613 DOI: 10.1016/j.jsb.2015.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 01/07/2023]
Abstract
Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each). Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%. These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability. The conservation of crystal contacts is maintained across most of the molecular surface, except for a dispensable virus recognition domain. By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes. Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.
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Affiliation(s)
- Xiaoyun Ji
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Danny Axford
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Robin Owen
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Gwyndaf Evans
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom,Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom,Corresponding author at: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.Division of Structural BiologyThe Wellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOxfordshireOX3 7BNUnited Kingdom
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43
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Panza E, Escamilla-Honrubia JM, Marco-Marín C, Gougeard N, De Michele G, Morra VB, Liguori R, Salviati L, Donati MA, Cusano R, Pippucci T, Ravazzolo R, Németh AH, Smithson S, Davies S, Hurst JA, Bordo D, Rubio V, Seri M. ALDH18A1gene mutations cause dominant spastic paraplegia SPG9: loss of function effect and plausibility of a dominant negative mechanism. Brain 2015; 139:e3. [DOI: 10.1093/brain/awv247] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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44
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A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering. Sci Rep 2015; 5:10451. [PMID: 26022615 PMCID: PMC4448500 DOI: 10.1038/srep10451] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/14/2015] [Indexed: 12/02/2022] Open
Abstract
At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.
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45
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Structural and Kinetic Characterization of Thymidine Kinase from Leishmania major. PLoS Negl Trop Dis 2015; 9:e0003781. [PMID: 25978379 PMCID: PMC4433323 DOI: 10.1371/journal.pntd.0003781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/23/2015] [Indexed: 01/17/2023] Open
Abstract
Leishmania spp. is a protozoan parasite and the causative agent of leishmaniasis. Thymidine kinase (TK) catalyses the transfer of the γ-phosphate of ATP to 2’-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). L. major Type II TK (LmTK) has been previously shown to be important for infectivity of the parasite and therefore has potential as a drug target for anti-leishmanial therapy. In this study, we determined the enzymatic properties and the 3D structures of holo forms of the enzyme. LmTK efficiently phosphorylates dThd and dUrd and has high structural homology to TKs from other species. However, it significantly differs in its kinetic properties from Trypanosoma brucei TK since purines are not substrates of the enzyme and dNTPs such as dUTP inhibit LmTK. The enzyme had Km and kcat values for dThd of 1.1 μM and 2.62 s-1 and exhibits cooperative binding for ATP. Additionally, we show that the anti-retroviral prodrug zidovudine (3-azido-3-deoxythymidine, AZT) and 5’-modified dUrd can be readily phosphorylated by LmTK. The production of recombinant enzyme at a level suitable for structural studies was achieved by the construction of C-terminal truncated versions of the enzyme and the use of a baculoviral expression system. The structures of the catalytic core of LmTK in complex with dThd, the negative feedback regulator dTTP and the bi-substrate analogue AP5dT, were determined to 2.74, 3.00 and 2.40 Å, respectively, and provide the structural basis for exclusion of purines and dNTP inhibition. The results will aid the process of rational drug design with LmTK as a potential target for anti-leishmanial drugs. The DNA within the genome of an organism encodes all the information, firstly for reproduction and secondly for translation into proteins—the workhorses of a biological cell. Proteins carry out a host of essential biological activities within the cell. A full understanding of a protein now requires determination of a wide range of its properties in solution in the cell and in vitro in solution, but in addition, its 3D structure usually determined by X-ray crystallography. Leishmania species are a family of protozoan parasites of humans and the causative agent of leishmaniasis, a major health concern in the developing world. Selective inhibition of key enzymes in these parasites is a key route for combating these diseases. We have focused our work on thymidine kinase, an important enzyme from Leishmania major, and a potential target for the development of new drugs. We have carried out kinetic studies of the enzyme’s activity in solution and determined its 3D crystal structure, enabling rational drug design.
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Ginn HM, Messerschmidt M, Ji X, Zhang H, Axford D, Gildea RJ, Winter G, Brewster AS, Hattne J, Wagner A, Grimes JM, Evans G, Sauter NK, Sutton G, Stuart DI. Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data. Nat Commun 2015; 6:6435. [PMID: 25751308 PMCID: PMC4403592 DOI: 10.1038/ncomms7435] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/28/2015] [Indexed: 11/09/2022] Open
Abstract
The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis. Serial femtosecond crystallography and the use of X-ray free-electron lasers (XFEL) promise to revolutionize structural biology. Here, the authors describe refinements that reduce the redundancy required to obtain quality XFEL data and report a 1.75-Å structure—not obtainable by synchrotron radiation—using less than 6,000 crystals.
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Affiliation(s)
- Helen M Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Xiaoyun Ji
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Hanwen Zhang
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Danny Axford
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Richard J Gildea
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Graeme Winter
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Armin Wagner
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Jonathan M Grimes
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Gwyndaf Evans
- Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - David I Stuart
- 1] Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK [2] Diamond House, Diamond Light Source, Harwell Science &Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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Stewart ME, Roy P. Structure-based identification of functional residues in the nucleoside-2'-O-methylase domain of Bluetongue virus VP4 capping enzyme. FEBS Open Bio 2015; 5:138-46. [PMID: 25834778 PMCID: PMC4359970 DOI: 10.1016/j.fob.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/29/2015] [Accepted: 02/18/2015] [Indexed: 11/26/2022] Open
Abstract
Bluetongue virus (BTV) encodes a single capping protein, VP4, which catalyzes all reactions required to generate cap1 structures on nascent viral transcripts. Further, structural analysis by X-ray crystallography indicated each catalytic reaction is arranged as a discrete domain, including a nucleoside-2'-O-methyltransferase (2'-O MTase). In this study, we have exploited the structural information to identify the residues that are important for the catalytic activity of 2'-O MTase of VP4 and their influence on BTV replication. The effect of these mutations on GMP binding, guanylyltransferase (GTase) and methylase activities were analysed by a series of in vitro biochemical assays using recombinant mutant proteins; subsequently their effects on virus replication were assessed by introducing the same mutations in replicating viral genome using a reverse genetics system. Our data showed that single substitution mutations in the catalytic tetrad K-D-K-E were sufficient to abolish 2'-O MTase activity in vitro and to completely abrogate BTV replication in cells; although these mutants retained the upstream GMP binding, GTase and guanine-N7-methyltransferase activities. Mutations of the surrounding substrate-binding pocket (predicted to recruit cap0) had variable effects on in vitro VP4 capping activity. Only triple but not single substitution mutations of these residues in genome resulted in reduced virus replication kinetics. This is the first report investigating the importance of 2'-O MTase function for any member of the Reoviridae and highlights the significance of K-D-K-E tetrad and surrounding residues for the efficiency of 2'-O MTase activity and in turn, for virus fitness.
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Key Words
- 2′-O MT, nucleoside-2′-O-methyltransferase domain
- 2′-O MTase, nucleoside-2′-O-methyltransferase
- 2′-O-methyltransferase
- AdoMet, S-adenosyl methionine
- BSR4, BHK-21 sub-clone expressing VP4
- BTV
- BTV, Bluetongue virus
- Capping enzyme
- GTase, guanylyltransferase
- JEV, Japanese encephalitis virus
- Mutagenesis
- N7MTase, guanine-N7-methyltransferase
- PC, polymerase complex
- VSV, vesicular stomatitis virus
- WNV, West Nile virus
- m7, methyl group associated with m7G
- m7G, 7-methylguanosine
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Affiliation(s)
| | - Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Osz-Papai J, Radu L, Abdulrahman W, Kolb-Cheynel I, Troffer-Charlier N, Birck C, Poterszman A. Insect cells-baculovirus system for the production of difficult to express proteins. Methods Mol Biol 2015; 1258:181-205. [PMID: 25447865 DOI: 10.1007/978-1-4939-2205-5_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production of sufficient quantities of homogenous protein not only is an essential prelude for structural investigations but also represents a rate-limiting step for many human functional studies. Although technologies for expression of recombinant proteins and complexes have been improved tremendously, in many cases, protein production remains a challenge and can be associated with considerable investment. This chapter describes simple and efficient protocols for expression screening and optimization of protein production in insect cells using the baculovirus expression system. We describe the procedure, starting from the cloning of a gene of interest into an expression transfer baculovirus vector, followed by generation of the recombinant virus by homologous recombination, evaluation of protein expression, and scale-up. Handling of insect cell cultures and preparation of bacmid for co-transfection are also detailed.
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Affiliation(s)
- Judit Osz-Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, BP 163, Illkirch, Cedex 67404, France
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Hu NJ, Rada H, Rahman N, Nettleship JE, Bird L, Iwata S, Drew D, Cameron AD, Owens RJ. GFP-based expression screening of membrane proteins in insect cells using the baculovirus system. Methods Mol Biol 2015; 1261:197-209. [PMID: 25502201 DOI: 10.1007/978-1-4939-2230-7_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A key step in the production of recombinant membrane proteins for structural studies is the optimization of protein yield and quality. One commonly used approach is to fuse the protein to green fluorescent protein (GFP), enabling expression to be tracked without the need to purify the protein. Combining fusion to green fluorescent protein with the baculovirus expression system provides a useful platform for both screening and production of eukaryotic membrane proteins. In this chapter we describe our protocol for the expression screening of membrane proteins in insect cells using fusion to GFP as a reporter. We use both SDS-PAGE with in-gel fluorescence imaging and fluorescence-detection size-exclusion chromatography (FSEC) to screen for expression.
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Affiliation(s)
- Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, Taichung, 40227, Taiwan,
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Abdulrahman W, Radu L, Garzoni F, Kolesnikova O, Gupta K, Osz-Papai J, Berger I, Poterszman A. The production of multiprotein complexes in insect cells using the baculovirus expression system. Methods Mol Biol 2015; 1261:91-114. [PMID: 25502195 DOI: 10.1007/978-1-4939-2230-7_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.
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Affiliation(s)
- Wassim Abdulrahman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, BP 163, 67404, Illkirch Cedex, France
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