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Gialama D, Delivoria DC, Michou M, Giannakopoulou A, Skretas G. Functional Requirements for DjlA- and RraA-Mediated Enhancement of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. J Mol Biol 2017; 429:1800-1816. [PMID: 28501587 DOI: 10.1016/j.jmb.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022]
Abstract
In previous work, we have generated the engineered Escherichia coli strains SuptoxD and SuptoxR, which upon co-expression of the effector genes djlA or rraA, respectively, are capable of suppressing the cytotoxicity caused by membrane protein (MP) overexpression and of producing dramatically enhanced yields for a variety of recombinant MPs of both prokaryotic and eukaryotic origin. Here, we investigated the functional requirements for DnaJ-like protein A (DjlA)- and regulator of ribonuclease activity A (RraA)-mediated enhancement of recombinant MP production in these strains and show that: (i) DjlA and RraA act independently, that is, the beneficial effects of each protein on recombinant MP production occur through a mechanism that does not involve the other, and in a non-additive manner; (ii) full-length and membrane-bound DjlA is required for exerting its beneficial effects on recombinant MP production in E. coli SuptoxD; (iii) the MP production-promoting properties of DjlA in SuptoxD involve the action of the molecular chaperone DnaK but do not rely on the activation of the regulation of capsular synthesis response, a well-established consequence of djlA overexpression; (iv) the observed RraA-mediated effects in E. coli SuptoxR involve the ribonucleolytic activity of RNase E, but not that of its paralogous ribonuclease RNase G; and (v) DjlA and RraA are unique among similar E. coli proteins in their ability to promote bacterial recombinant MP production. These observations provide important clues about the molecular requirements for suppressed toxicity and enhanced MP accumulation in SuptoxD/SuptoxR and will guide future studies aiming to decipher the exact mechanism of DjlA- and RraA-mediated enhancement of recombinant MP production in these strains.
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Affiliation(s)
- Dimitra Gialama
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, 41500, Greece
| | - Artemis Giannakopoulou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece.
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52
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Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins. Proc Natl Acad Sci U S A 2017; 114:E2624-E2633. [PMID: 28283661 DOI: 10.1073/pnas.1700269114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Integral membrane proteins (MPs) are key engineering targets due to their critical roles in regulating cell function. In engineering MPs, it can be extremely challenging to retain membrane localization capability while changing other desired properties. We have used structure-guided SCHEMA recombination to create a large set of functionally diverse chimeras from three sequence-diverse channelrhodopsins (ChRs). We chose 218 ChR chimeras from two SCHEMA libraries and assayed them for expression and plasma membrane localization in human embryonic kidney cells. The majority of the chimeras express, with 89% of the tested chimeras outperforming the lowest-expressing parent; 12% of the tested chimeras express at even higher levels than any of the parents. A significant fraction (23%) also localize to the membrane better than the lowest-performing parent ChR. Most (93%) of these well-localizing chimeras are also functional light-gated channels. Many chimeras have stronger light-activated inward currents than the three parents, and some have unique off-kinetics and spectral properties relative to the parents. An effective method for generating protein sequence and functional diversity, SCHEMA recombination can be used to gain insights into sequence-function relationships in MPs.
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53
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Ho TT, Nguyen JT, Liu J, Stanczak P, Thompson AA, Yan YG, Chen J, Allerston CK, Dillard CL, Xu H, Shoger NJ, Cameron JS, Massari ME, Aertgeerts K. Method for rapid optimization of recombinant GPCR protein expression and stability using virus-like particles. Protein Expr Purif 2017; 133:41-49. [PMID: 28263854 DOI: 10.1016/j.pep.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/24/2017] [Accepted: 03/01/2017] [Indexed: 10/20/2022]
Abstract
Recent innovative approaches to stabilize and crystallize GPCRs have resulted in an unprecedented breakthrough in GPCR crystal structures as well as application of the purified receptor protein in biophysical and biochemical ligand binding assays. However, the protein optimization process to enable these technologies is lengthy and requires iterative overexpression, solubilization, purification and functional analysis of tens to hundreds of protein variants. Here, we report a new and versatile method to screen in parallel hundreds of GPCR variants in HEK293 produced virus-like particles (VLPs) for protein yield, stability, functionality and ligand binding. This approach reduces the time and resources during GPCR construct optimization by eliminating lengthy protein solubilization and purification steps and by its adaptability to many binding assay formats (label or label-free detection). We exemplified the robustness of our VLP method by screening 210 GALR3-VLP variants in a radiometric agonist-based binding assay and a subset of 88 variants in a label-free antagonist-based assay. The resulting GALR3 agonist or antagonist stabilizing variants were then further used for recombinant protein expression in transfected insect cells. The final purified protein variants were successfully immobilized on a biosensor chip and used in a surface plasmon resonance binding assay.
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Affiliation(s)
- Thao T Ho
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jasmine T Nguyen
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Juping Liu
- Department of Preclinical Development, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Pawel Stanczak
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Aaron A Thompson
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Yingzhuo G Yan
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jasmine Chen
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Charles K Allerston
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Charles L Dillard
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Hao Xu
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Nicholas J Shoger
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jill S Cameron
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Mark E Massari
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Kathleen Aertgeerts
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
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54
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Gialama D, Kostelidou K, Michou M, Delivoria DC, Kolisis FN, Skretas G. Development of Escherichia coli Strains That Withstand Membrane Protein-Induced Toxicity and Achieve High-Level Recombinant Membrane Protein Production. ACS Synth Biol 2017; 6:284-300. [PMID: 27797488 DOI: 10.1021/acssynbio.6b00174] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins perform critical cellular functions in all living organisms and constitute major targets for drug discovery. Escherichia coli has been the most popular overexpression host for membrane protein biochemical/structural studies. Bacterial production of recombinant membrane proteins, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low final biomass and minute volumetric yields. In this work, we aimed to rewire the E. coli protein-producing machinery to withstand the toxicity caused by membrane protein overexpression in order to generate engineered bacterial strains with the ability to achieve high-level membrane protein production. To achieve this, we searched for bacterial genes whose coexpression can suppress membrane protein-induced toxicity and identified two highly potent effectors: the membrane-bound DnaK cochaperone DjlA, and the inhibitor of the mRNA-degrading activity of the E. coli RNase E, RraA. E. coli strains coexpressing either djlA or rraA, termed SuptoxD and SuptoxR, respectively, accumulated markedly higher levels of final biomass and produced dramatically enhanced yields for a variety of prokaryotic and eukaryotic recombinant membrane proteins. In all tested cases, either SuptoxD, or SuptoxR, or both, outperformed the capabilities of commercial strains frequently utilized for recombinant membrane protein production purposes.
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Affiliation(s)
- Dimitra Gialama
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Kalliopi Kostelidou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Fragiskos N. Kolisis
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
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55
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Alves NS, Astrinidis SA, Eisenhardt N, Sieverding C, Redolfi J, Lorenz M, Weberruss M, Moreno-Andrés D, Antonin W. MISTIC-fusion proteins as antigens for high quality membrane protein antibodies. Sci Rep 2017; 7:41519. [PMID: 28148968 PMCID: PMC5288655 DOI: 10.1038/srep41519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/21/2016] [Indexed: 02/08/2023] Open
Abstract
Lack of high-quality antibodies against transmembrane proteins is a widely recognized hindrance in biomedical and cell biological research. Here we present a robust pipeline for the generation of polyclonal antibodies employing full-length membrane proteins as immunogens to overcome this "antibody bottleneck". We express transmembrane proteins fused to a MISTIC fragment that enhances expression of eukaryotic membrane proteins in E. coli. Purified membrane proteins are used as immunogen for rabbit injection employing standard immunizing protocols. The raised antibodies against membrane proteins of the endoplasmic reticulum and the nuclear envelope, which we use as test cases, function in a wide range of applications and are superior to ones produced against soluble domains as immunogens.
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Affiliation(s)
- Natalia Silva Alves
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Susanne Adina Astrinidis
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Nathalie Eisenhardt
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Cornelia Sieverding
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Josef Redolfi
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Michael Lorenz
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Marion Weberruss
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Daniel Moreno-Andrés
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany
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56
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Belloir C, Miller-Leseigneur ML, Neiers F, Briand L, Le Bon AM. Biophysical and functional characterization of the human olfactory receptor OR1A1 expressed in a mammalian inducible cell line. Protein Expr Purif 2017; 129:31-43. [DOI: 10.1016/j.pep.2016.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 10/21/2022]
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57
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Abstract
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection. Additionally, we describe the protein quality-control assays that are often instrumental as a guideline for a shorter path toward the structure.
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Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Enrique E Abola
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.
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58
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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59
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Zhou RB, Lu HM, Liu J, Shi JY, Zhu J, Lu QQ, Yin DC. A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive. PLoS One 2016; 11:e0161254. [PMID: 27517583 PMCID: PMC4982684 DOI: 10.1371/journal.pone.0161254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms.
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Affiliation(s)
- Ren-Bin Zhou
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Hui-Meng Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Jie Liu
- School of Computer Science and Technology, Xidian University, Xi’an, PR China
| | - Jian-Yu Shi
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Jing Zhu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Qin-Qin Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
- * E-mail:
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60
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Boggavarapu R, Hirschi S, Harder D, Meury M, Ucurum Z, Bergeron MJ, Fotiadis D. Purification of Human and Mammalian Membrane Proteins Expressed in Xenopus laevis Frog Oocytes for Structural Studies. Methods Mol Biol 2016; 1432:223-42. [PMID: 27485339 DOI: 10.1007/978-1-4939-3637-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This protocol describes the isolation of recombinant human and mammalian membrane proteins expressed in Xenopus laevis frog oocytes for structural studies. The cDNA-derived cRNA of the desired genes is injected into several hundreds of oocytes, which are incubated for several days to allow protein expression. Recombinant proteins are then purified via affinity chromatography. The novelty of this method comes from the design of a plasmid that produces multi-tagged proteins and, most importantly, the development of a protocol for efficiently discarding lipids, phospholipids, and lipoproteins from the oocyte egg yolk, which represent the major contaminants in protein purifications. Thus, the high protein purity and good yield obtained from this method allows protein structure determination by transmission electron microscopy of single detergent-solubilized protein particles and of 2D crystals of membrane protein embedded in lipid bilayers. Additionally, a radiotracer assay for functional analysis of the expressed target proteins in oocytes is described. Overall, this method is a valuable option for structural studies of mammalian and particularly human proteins, for which other expression systems often fail.
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Affiliation(s)
- Rajendra Boggavarapu
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Marcel Meury
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Marc J Bergeron
- Division of Cellular and Molecular Neuroscience, Institut Universitaire en Santé Mentale de Québec, Québec, QC, Canada, G1J 2G3
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
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61
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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62
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Ooi A, Wong A, Esau L, Lemtiri-Chlieh F, Gehring C. A Guide to Transient Expression of Membrane Proteins in HEK-293 Cells for Functional Characterization. Front Physiol 2016; 7:300. [PMID: 27486406 PMCID: PMC4949579 DOI: 10.3389/fphys.2016.00300] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023] Open
Abstract
The human embryonic kidney 293 (HEK-293) cells are commonly used as host for the heterologous expression of membrane proteins not least because they have a high transfection efficiency and faithfully translate and process proteins. In addition, their cell size, morphology and division rate, and low expression of native channels are traits that are particularly attractive for current-voltage measurements. Nevertheless, the heterologous expression of complex membrane proteins such as receptors and ion channels for biological characterization and in particular for single-cell applications such as electrophysiology remains a challenge. Expression of functional proteins depends largely on careful step-by-step optimization that includes the design of expression vectors with suitable identification tags, as well as the selection of transfection methods and detection parameters appropriate for the application. Here, we use the heterologous expression of a plant potassium channel, the Arabidopsis thaliana guard cell outward-rectifying K(+) channel, AtGORK (At5G37500) in HEK-293 cells as an example, to evaluate commonly used transfection reagents and fluorescent detection methods, and provide a detailed methodology for optimized transient transfection and expression of membrane proteins for in vivo studies in general and for single-cell applications in particular. This optimized protocol will facilitate the physiological and cellular characterization of complex membrane proteins.
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Affiliation(s)
- Amanda Ooi
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Aloysius Wong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia; Institute of Integrative Biology of the Cell, Centre National de la Recherche Scientifique, Le Commissariat à l'Energie Atomique et aux Energies Alternatives, Paris-Sud UniversityGif-Sur-Yvette, France
| | - Luke Esau
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Fouad Lemtiri-Chlieh
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Chris Gehring
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
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63
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Lyons JA, Shahsavar A, Paulsen PA, Pedersen BP, Nissen P. Expression strategies for structural studies of eukaryotic membrane proteins. Curr Opin Struct Biol 2016; 38:137-44. [DOI: 10.1016/j.sbi.2016.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
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64
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Recombinant protein production from stable mammalian cell lines and pools. Curr Opin Struct Biol 2016; 38:129-36. [DOI: 10.1016/j.sbi.2016.06.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 11/23/2022]
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65
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Fogeron ML, Jirasko V, Penzel S, Paul D, Montserret R, Danis C, Lacabanne D, Badillo A, Gouttenoire J, Moradpour D, Bartenschlager R, Penin F, Meier BH, Böckmann A. Cell-free expression, purification, and membrane reconstitution for NMR studies of the nonstructural protein 4B from hepatitis C virus. JOURNAL OF BIOMOLECULAR NMR 2016; 65:87-98. [PMID: 27233794 DOI: 10.1007/s10858-016-0040-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/21/2016] [Indexed: 06/05/2023]
Abstract
We describe the expression of the hepatitis C virus nonstructural protein 4B (NS4B), which is an integral membrane protein, in a wheat germ cell-free system, the subsequent purification and characterization of NS4B and its insertion into proteoliposomes in amounts sufficient for multidimensional solid-state NMR spectroscopy. First spectra of the isotopically [(2)H,(13)C,(15)N]-labeled protein are shown to yield narrow (13)C resonance lines and a proper, predominantly α-helical fold. Clean residue-selective leucine, isoleucine and threonine-labeling is demonstrated. These results evidence the suitability of the wheat germ-produced integral membrane protein NS4B for solid-state NMR. Still, the proton linewidth under fast magic angle spinning is broader than expected for a perfect sample and possible causes are discussed.
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Affiliation(s)
- Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Vlastimil Jirasko
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Susanne Penzel
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Clément Danis
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Denis Lacabanne
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
- Recombinant Protein Unit, RD-Biotech, 3 rue Henri Baigue, 25000, Besançon, France
| | - Jérôme Gouttenoire
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011, Lausanne, Switzerland
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011, Lausanne, Switzerland
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
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66
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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67
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Andréll J, Edwards PC, Zhang F, Daly M, Tate CG. Generation of Tetracycline-Inducible Mammalian Cell Lines by Flow Cytometry for Improved Overproduction of Membrane Proteins. Methods Mol Biol 2016; 1432:63-78. [PMID: 27485330 DOI: 10.1007/978-1-4939-3637-3_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Overexpression of mammalian membrane proteins in mammalian cells is an effective strategy to produce sufficient protein for biophysical analyses and structural studies, because the cells generally express proteins in a correctly folded state. However, obtaining high levels of expression suitable for protein purification on a milligram scale can be challenging. As membrane protein overexpression often has a negative impact on cell viability, it is usual to make stable cell lines where the protein of interest is expressed from an inducible promoter. Here we describe a methodology for optimizing the inducible production of any membrane protein fused to GFP through the isolation of clonal cell lines. Flow cytometry is used to sort uninduced cells and the most fluorescent 5 % of the cell population are used to make clonal cell lines.
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Affiliation(s)
- Juni Andréll
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patricia C Edwards
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Fan Zhang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Maria Daly
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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68
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Abstract
The large-scale production of recombinant G protein-coupled receptors (GPCRs) is one of the major bottlenecks that hamper functional and structural studies of this important class of integral membrane proteins. Heterologous overexpression of GPCRs often results in low yields of active protein, usually due to a combination of several factors, such as low expression levels, protein insolubility, host cell toxicity, and the need to use harsh and often denaturing detergents (e.g., SDS, LDAO, OG, and DDM, among others) to extract the recombinant receptor from the host cell membrane. Many of these problematic issues are inherently linked to cell-based expression systems and can therefore be circumvented by the use of cell-free systems. In this unit, we provide a range of protocols for the production of GPCRs in a cell-free expression system. Using this system, we typically obtain GPCR expression levels of ∼1 mg per ml of reaction mixture in the continuous-exchange configuration. Although the protocols in this unit have been optimized for the cell-free expression of GPCRs, they should provide a good starting point for the production of other classes of membrane proteins, such as ion channels, aquaporins, carrier proteins, membrane-bound enzymes, and even large molecular complexes.
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Affiliation(s)
- Kenneth Segers
- VIB Center for the Biology of Disease, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.,Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
| | - Stefan Masure
- Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
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69
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Hattab G, Warschawski DE, Moncoq K, Miroux B. Escherichia coli as host for membrane protein structure determination: a global analysis. Sci Rep 2015; 5:12097. [PMID: 26160693 PMCID: PMC4498379 DOI: 10.1038/srep12097] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/11/2015] [Indexed: 11/13/2022] Open
Abstract
The structural biology of membrane proteins (MP) is hampered by the difficulty in producing and purifying them. A comprehensive analysis of protein databases revealed that 213 unique membrane protein structures have been obtained after production of the target protein in E. coli. The primary expression system used was the one based on the T7 RNA polymerase, followed by the arabinose and T5 promoter based expression systems. The C41λ(DE3) and C43λ(DE3) bacterial mutant hosts have contributed to 28% of non E. coli membrane protein structures. A large scale analysis of expression protocols demonstrated a preference for a combination of bacterial host-vector together with a bimodal distribution of induction temperature and of inducer concentration. Altogether our analysis provides a set of rules for the optimal use of bacterial expression systems in membrane protein production.
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Affiliation(s)
- Georges Hattab
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Dror E Warschawski
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
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70
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Xiao S, Chen YC, Betenbaugh MJ, Martin SE, Shiloach J. MiRNA mimic screen for improved expression of functional neurotensin receptor from HEK293 cells. Biotechnol Bioeng 2015; 112:1632-43. [PMID: 25676429 DOI: 10.1002/bit.25567] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/23/2015] [Accepted: 02/05/2015] [Indexed: 01/17/2023]
Abstract
Obtaining adequate quantities of functional mammalian membrane proteins has been a bottleneck in their structural and functional studies because the expression of these proteins from mammalian cells is relatively low. To explore the possibility of enhancing expression of these proteins using miRNA, a stable T-REx-293 cell line expressing the neurotensin receptor type 1 (NTSR1), a hard-to-express G protein-coupled receptor (GPCR), was constructed. The cell line was then subjected to human miRNA mimic library screening. In parallel, an HEK293 cell line expressing luciferase was also screened with the same human miRNA mimic library. Five microRNA mimics: hsa-miR-22-5p, hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-429, and hsa-miR-2110were identified from both screens. They led to 48% increase in the expression of functional NTSR1 and to 239% increase of luciferase expression. These miRNAs were also effective in enhancing the expression of secretedglypican-3 hFc-fusion protein from HEK293 cells.The results indicate that these molecules may have a wide role in enhancing the production of proteins with biomedical interest.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.,Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Yu-Chi Chen
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850
| | - Michael J Betenbaugh
- Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E Martin
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.
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71
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Bill RM, von der Haar T. Hijacked then lost in translation: the plight of the recombinant host cell in membrane protein structural biology projects. Curr Opin Struct Biol 2015; 32:147-55. [PMID: 26037971 PMCID: PMC4521084 DOI: 10.1016/j.sbi.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/10/2015] [Accepted: 04/10/2015] [Indexed: 11/13/2022]
Abstract
Membrane protein structural biologists need high-quality protein for crystallisation. Recombinant proteins are central to the structural biology supply chain. Understanding quality control in protein production is an emerging trend. The roles of translation and protein folding in the host cell are examined.
Membrane protein structural biology is critically dependent upon the supply of high-quality protein. Over the last few years, the value of crystallising biochemically characterised, recombinant targets that incorporate stabilising mutations has been established. Nonetheless, obtaining sufficient yields of many recombinant membrane proteins is still a major challenge. Solutions are now emerging based on an improved understanding of recombinant host cells; as a ‘cell factory’ each cell is tasked with managing limited resources to simultaneously balance its own growth demands with those imposed by an expression plasmid. This review examines emerging insights into the role of translation and protein folding in defining high-yielding recombinant membrane protein production in a range of host cells.
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Affiliation(s)
- Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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72
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Molecular and biochemical characterization of recombinant guinea pig tumor necrosis factor-alpha. Mediators Inflamm 2015; 2015:619480. [PMID: 25999670 PMCID: PMC4427127 DOI: 10.1155/2015/619480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/20/2015] [Accepted: 03/30/2015] [Indexed: 12/15/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is a cytokine which plays opposing roles in the context of infectious disease pathogenesis. TNF-α is essential for the development of a protective immune response to some pathogens, for example, Mycobacterium tuberculosis, by synergizing with other cytokines. However, exorbitant or uncontrolled TNF-α activity may also drive pathology and disease symptoms in many infectious diseases. In order to elucidate the beneficial and detrimental roles of TNF-α in tuberculosis (TB) and other diseases for which the guinea pig is the small animal model of choice, recombinant guinea pig (rgp)TNF-α has been produced using prokaryotic expression systems. However, it is unknown whether posttranslational modifications which cannot be made in the prokaryotic expression systems may be important for rgpTNF-α structure and function. Therefore, we carried out a comparative study by expressing rgpTNF-α in prokaryotic and eukaryotic expression systems and analyzed the eukaryotic-expressed rgpTNF-α for the presence of posttranslational modifications by subjecting it to NanoLC-MS/MS. We conclude that the eukaryotic-expressed rgpTNF-α lacks posttranslational modifications, and we found no significant difference in terms of the biological activity between prokaryotic- and eukaryotic-expressed rgpTNF-α. Taken together, results from our study show that a prokaryotic expression system can be used for generating large amounts of rgpTNF-α without concern for the biological integrity.
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73
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Thomas JA, Tate CG. Quality control in eukaryotic membrane protein overproduction. J Mol Biol 2015; 426:4139-4154. [PMID: 25454020 PMCID: PMC4271737 DOI: 10.1016/j.jmb.2014.10.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/12/2014] [Accepted: 10/13/2014] [Indexed: 10/25/2022]
Abstract
The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a detailed analysis by radioligand binding and comparative Western blotting of G protein-coupled receptors and a transporter produced in insect cells showed that a considerable proportion of the expressed protein was misfolded and incapable of ligand binding. In contrast, production of the same membrane proteins in stable inducible mammalian cell lines suggested that the majority was folded correctly. It was noted that detergent solubilisation of the misfolded membrane proteins using either digitonin or dodecylmaltoside was considerablyless efficient than using sodium dodecyl sulfate or foscholine-12, whilst these detergents were equally efficient at solubilising correctly folded membrane proteins. This provides a simple and rapid test to suggest whether heterologously expressed mammalian membrane proteins are indeed correctly folded, without requiring radioligand binding assays. This will greatly facilitate the high-throughput production of fully functional membrane proteins for structural studies.
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Affiliation(s)
- Jennifer A Thomas
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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74
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Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
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Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
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75
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Caro LN, Li Z, Balo AR, Van Eps N, Rini JM, Ernst OP. Rapid and facile recombinant expression of bovine rhodopsin in HEK293S GnTI(-) cells using a PiggyBac inducible system. Methods Enzymol 2015; 556:307-30. [PMID: 25857788 DOI: 10.1016/bs.mie.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rhodopsin is a class A G protein-coupled receptor (GPCR) that provides important insights into the structure and function of the GPCR superfamily. Bovine rhodopsin is widely used as a model for GPCRs and was the first GPCR whose X-ray crystal structure was solved. One of the advantages of rhodopsin is that it is abundant in native tissue, and as a result, milligram quantities can be purified from the retinal rod cells of bovine eyes. Nonetheless, the study of GPCR conformation and dynamics, e.g., by electron paramagnetic resonance or (19)F nuclear magnetic resonance spectroscopy, typically requires mutagenesis to enable site-directed labeling of the protein. Mutations are also of great importance as they can stabilize the receptor and can be necessary to study different receptor conformations. Recombinant production of rhodopsins for biophysical studies has been achieved in different systems, including mammalian, insect, and yeast cells in culture, and from Drosophila melanogaster and Caenorhabditis elegans tissue. The piggyBac (PB) transposon system is used for gene delivery into a variety of cell types (e.g., HEK293 and CHO cells, fibroblasts, stem cells) and living organisms (e.g., honeybees, pigs, chicken, mice). Recently, the PB transposon has been described as an efficient tool for inducible protein expression in HEK293T and HEK293S N-acetylglucosaminyltransferase I-deficient (GnTI(-)) cells. This chapter describes a protocol for using the PB-based system for inducible expression of bovine rhodopsin in HEK293S GnTI(-) cells. Using this protocol, we expressed and purified 26 rhodopsin mutants to be used for site-directed spin labeling.
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Affiliation(s)
- Lydia N Caro
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Aidin R Balo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James M Rini
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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76
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Fernández-Núñez EG, de Rezende AG, Puglia ALP, Leme J, Boldorini VLL, Caricati CP, Tonso A. Transient expression of rabies virus G-glycoprotein using BHK-21 cells cultured in suspension. Biotechnol Lett 2015; 37:1153-63. [PMID: 25700821 DOI: 10.1007/s10529-015-1787-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To assess the expression of rabies virus G-glycoprotein (RVGP) expression using Semliki Forest virus as a vector in combination with BHK-21 cells cultured in suspension. RESULTS A multilevel factorial design was used to quantify effects of temperature (33-37 °C), fresh medium addition after the viral adsorption step (100-200 % with respect to the initial cell suspension volume before infection) and harvest time (8-40 h) on RVGP production. Experimental runs were performed in 24-well cell culture plates at a multiplicity of infection (MOI) of 16. An additional experiment in spinner-flask was performed at MOI of 9, using the optimal conditions determined in cell culture plates. Values for temperature, fresh medium addition and harvest time of 33 °C, 100 % and 16 h, respectively, ensured the optimal RVGP production in culture plates. The volumetric yield (239 ng ml(-1)) in these conditions was higher than that reported previously for adherent cell culture. In spinner-flasks, the volumetric yield was improved (559 ng ml(-1)). CONCLUSION These results establish the basis for designing bioprocess to produce RVGP.
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Affiliation(s)
- Eutimio Gustavo Fernández-Núñez
- Laboratório de Células Animais, Departamento de Engenharia Química, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, trav. 3, 380, São Paulo, SP, 05508-900, Brazil,
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77
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Expression of Membrane Proteins in the Eyes of Transgenic Drosophila melanogaster. Methods Enzymol 2015; 556:219-39. [DOI: 10.1016/bs.mie.2014.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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78
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Xiao S, Shiloach J, Grisshammer R. Construction of recombinant HEK293 cell lines for the expression of the neurotensin receptor NTSR1. Methods Mol Biol 2015; 1272:51-64. [PMID: 25563176 DOI: 10.1007/978-1-4939-2336-6_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
G protein-coupled receptors (GPCRs) are associated with a wide array of diseases and are targets of most of the medicines sold worldwide. Despite their clinical importance, only 25 unique GPCR structures have been determined as of April 2014. The first step for structural studies is to establish the expression of correctly folded, functional receptors in recombinant host cells at quantities to allow subsequent purification and crystallization trials. Here we describe the T-REx™-inducible expression system to construct and select a stable HEK293 cell line for high-level expression of functional neurotensin receptor type I (NTSR1). We also present the protocols used for the adaptation of the cells into suspension culture, as well as the optimization of the induction parameters for NTSR1 expression, which led to 1 mg of purified NTSR1 per liter suspension culture in bioreactors.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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79
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Seiradake E, Zhao Y, Lu W, Aricescu AR, Jones EY. Production of cell surface and secreted glycoproteins in mammalian cells. Methods Mol Biol 2015; 1261:115-27. [PMID: 25502196 DOI: 10.1007/978-1-4939-2230-7_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mammalian protein expression systems are becoming increasingly popular for the production of eukaryotic secreted and cell surface proteins. Here we describe methods to produce recombinant proteins in adherent or suspension human embryonic kidney cell cultures, using transient transfection or stable cell lines. The protocols are easy to scale up and cost-efficient, making them suitable for protein crystallization projects and other applications that require high protein yields.
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Affiliation(s)
- Elena Seiradake
- The Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
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80
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Chaubey N, Ghosh SS. Overexpression of Granulocyte Macrophage Colony Stimulating Factor in Breast Cancer Cells Leads Towards Drug Sensitization. Appl Biochem Biotechnol 2014; 175:1948-59. [DOI: 10.1007/s12010-014-1373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/10/2014] [Indexed: 12/18/2022]
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81
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Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat Protoc 2014; 9:2574-85. [PMID: 25299155 DOI: 10.1038/nprot.2014.173] [Citation(s) in RCA: 455] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.
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82
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Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology. J Membr Biol 2014; 247:815-26. [DOI: 10.1007/s00232-014-9663-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
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83
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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84
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Mary S, Damian M, Rahmeh R, Mouillac B, Marie J, Granier S, Banères JL. Amphipols in G protein-coupled receptor pharmacology: what are they good for? J Membr Biol 2014; 247:853-60. [PMID: 24801284 DOI: 10.1007/s00232-014-9665-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
Abstract
G protein-coupled receptors are at a central node of all cell communications. Investigating their molecular functioning is therefore crucial for both academic purposes and drug design. However, getting the receptors as isolated, stable and purified proteins for such studies still stumbles over their instability out of the membrane environment. Different membrane-mimicking environments have been developed so far to increase the stability of purified receptors. Among them are amphipols. These polymers not only preserve the native fold of receptors purified from membrane fractions but they also allow specific applications such as folding receptors purified from inclusion bodies back to their native state. Of importance, amphipol-trapped G protein-coupled receptors essentially maintain their pharmacological properties so that they are perfectly adapted to further investigate the molecular mechanisms underlying signaling processes. We review here how amphipols have been used to refold and stabilize detergent-solubilized purified receptors and what are the main subsequent molecular pharmacology analyses that were performed using this strategy.
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Affiliation(s)
- Sophie Mary
- Faculté de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Université Montpellier 1 et 2, BP 14491, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
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85
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Engineering cells to improve protein expression. Curr Opin Struct Biol 2014; 26:32-8. [PMID: 24704806 DOI: 10.1016/j.sbi.2014.03.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 12/22/2022]
Abstract
Cellular engineering of bacteria, fungi, insect cells and mammalian cells is a promising methodology to improve recombinant protein production for structural, biochemical, and commercial applications. Increased understanding of the host organism biology has suggested engineering strategies targeting bottlenecks in transcription, translation, protein processing and secretory pathways, as well as cell growth and survival. A combination of metabolic engineering and synthetic biology has been used to improve the properties of cells for protein production, which has resulted in enhanced yields of multiple protein classes.
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86
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Bacterial-based membrane protein production. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1739-49. [PMID: 24200679 DOI: 10.1016/j.bbamcr.2013.10.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/20/2013] [Accepted: 10/29/2013] [Indexed: 01/08/2023]
Abstract
Escherichia coli is by far the most widely used bacterial host for the production of membrane proteins. Usually, different strains, culture conditions and production regimes are screened for to design the optimal production process. However, these E. coli-based screening approaches often do not result in satisfactory membrane protein production yields. Recently, it has been shown that (i) E. coli strains with strongly improved membrane protein production characteristics can be engineered or selected for, (ii) many membrane proteins can be efficiently produced in E. coli-based cell-free systems, (iii) bacteria other than E. coli can be used for the efficient production of membrane proteins, and, (iv) membrane protein variants that retain functionality but are produced at higher yields than the wild-type protein can be engineered or selected for. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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87
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Hacker DL, Kiseljak D, Rajendra Y, Thurnheer S, Baldi L, Wurm FM. Polyethyleneimine-based transient gene expression processes for suspension-adapted HEK-293E and CHO-DG44 cells. Protein Expr Purif 2013; 92:67-76. [PMID: 24021764 PMCID: PMC7129890 DOI: 10.1016/j.pep.2013.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 12/30/2022]
Abstract
A brief overview of principles of TGE using mammalian cells. Description of TGE processes for HEK293 and CHO cells. Description of orbitally shaken bioreactors for suspension cell cultivation. Description of polyethylenime-based transfection processes.
Transient gene expression (TGE) from mammalian cells is an increasingly important tool for the rapid production of recombinant proteins for research applications in biochemistry, structural biology, and biomedicine. Here we review methods for the transfection of human embryo kidney (HEK-293) and Chinese hamster ovary (CHO) cells in suspension culture using the cationic polymer polyethylenimine (PEI) for gene delivery.
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Affiliation(s)
- David L Hacker
- Protein Expression Core Facility, EPFL, CH-1015 Lausanne, Switzerland; Laboratory of Cellular Biotechnology, EPFL, CH-1015 Lausanne, Switzerland.
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88
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Transient and stable expression of the neurotensin receptor NTS1: a comparison of the baculovirus-insect cell and the T-REx-293 expression systems. PLoS One 2013; 8:e63679. [PMID: 23696845 PMCID: PMC3656039 DOI: 10.1371/journal.pone.0063679] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 04/05/2013] [Indexed: 01/06/2023] Open
Abstract
Nowadays, baculovirus-infected insect cells and tetracycline-inducible mammalian cell lines (T-REx-293) are intensively used for G protein-coupled receptor (GPCR) production for crystallography purposes. Here we constructed a suspension T-REx-293 cell line to stably express an engineered neurotensin receptor 1 (NTS1) mutant and we quantitatively compared this cell line with the transient baculovirus-insect cell system throughout a milligram-scale NTS1 expression and purification process. The two systems were comparable with respect to functional NTS1 expression levels and receptor binding affinity for the agonist [3H] neurotensin. However, NTS1 surface display on T-REx-293 cells determined by radio-ligand binding assays was 2.8 fold higher than that on insect cells. This work demonstrates two approaches for preparing milligram quantities of purified NTS1 suitable for structural studies and provides useful input to users in choosing and optimizing an appropriate expression host for other GPCRs.
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89
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Aricescu AR, Owens RJ. Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology. Curr Opin Struct Biol 2013; 23:345-56. [PMID: 23623336 DOI: 10.1016/j.sbi.2013.04.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 01/26/2023]
Abstract
Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context.
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Affiliation(s)
- A Radu Aricescu
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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