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de Divitiis M, Ami D, Pessina A, Palmioli A, Sciandrone B, Airoldi C, Regonesi ME, Brambilla L, Lotti M, Natalello A, Brocca S, Mangiagalli M. Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:30. [PMID: 36823649 PMCID: PMC9948444 DOI: 10.1186/s13068-023-02281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose. RESULTS The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness. CONCLUSIONS CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
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Affiliation(s)
- Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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2
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Plasmids for Controlled and Tunable High-Level Expression in E. coli. Appl Environ Microbiol 2022; 88:e0093922. [PMID: 36342148 PMCID: PMC9680613 DOI: 10.1128/aem.00939-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic systems for protein overexpression are required tools in microbiological and biochemical research. Ideally, these systems include standardized genetic parts with predictable behavior, enabling the construction of stable expression systems in the host organism.
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3
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Royes J, Talbot P, Le Bon C, Moncoq K, Uzan M, Zito F, Miroux B. Membrane Protein Production in Escherichia coli: Protocols and Rules. Methods Mol Biol 2022; 2507:19-39. [PMID: 35773575 DOI: 10.1007/978-1-0716-2368-8_2] [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: 06/15/2023]
Abstract
Despite recent progresses in the use of eukaryotic expression system, production of membrane proteins for structural studies still relies on microbial expression systems. In this review, we provide protocols to achieve high level expression of membrane proteins in Escherichia coli, especially using the T7 RNA polymerase based expression system. From the design of the construct, the choice of the appropriate vector-host combination, the assessment of the bacterial fitness, to the selection of bacterial mutant adapted to the production of the target membrane protein, the chapter covers all necessary methods for a rapid optimization of a specific target membrane protein. In addition, we provide a protocol for membrane protein solubilization based on our recent analysis of the Protein Data Bank.
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Affiliation(s)
- Jordi Royes
- Laboratoire de Colloïdes et Matériaux Divisés École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris 10, Paris, France
| | - Pauline Talbot
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Christel Le Bon
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Karine Moncoq
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Marc Uzan
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Francesca Zito
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Bruno Miroux
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France.
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4
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Karyolaimos A, Ampah-Korsah H, Zhang Z, de Gier JW. Shaping Escherichia coli for recombinant membrane protein production. FEMS Microbiol Lett 2018; 365:5040224. [DOI: 10.1093/femsle/fny152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022] Open
Affiliation(s)
- Alexandros Karyolaimos
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Henry Ampah-Korsah
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Zhe Zhang
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
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5
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Dilworth MV, Piel MS, Bettaney KE, Ma P, Luo J, Sharples D, Poyner DR, Gross SR, Moncoq K, Henderson PJF, Miroux B, Bill RM. Microbial expression systems for membrane proteins. Methods 2018; 147:3-39. [PMID: 29656078 DOI: 10.1016/j.ymeth.2018.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/08/2018] [Accepted: 04/10/2018] [Indexed: 12/19/2022] Open
Abstract
Despite many high-profile successes, recombinant membrane protein production remains a technical challenge; it is still the case that many fewer membrane protein structures have been published than those of soluble proteins. However, progress is being made because empirical methods have been developed to produce the required quantity and quality of these challenging targets. This review focuses on the microbial expression systems that are a key source of recombinant prokaryotic and eukaryotic membrane proteins for structural studies. We provide an overview of the host strains, tags and promoters that, in our experience, are most likely to yield protein suitable for structural and functional characterization. We also catalogue the detergents used for solubilization and crystallization studies of these proteins. Here, we emphasize a combination of practical methods, not necessarily high-throughput, which can be implemented in any laboratory equipped for recombinant DNA technology and microbial cell culture.
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Affiliation(s)
- Marvin V Dilworth
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mathilde S Piel
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Kim E Bettaney
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Pikyee Ma
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ji Luo
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - David Sharples
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - David R Poyner
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephane R Gross
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Peter J F Henderson
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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6
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Satheeshkumar PK, Anu PV, Junaida MI, Madanan MG, Jebasingh T, Nair AJ, Nair GA, Nair GPM, Sudhakaran PR. Expression of Leptospira membrane proteins Signal Peptidase (SP) and Leptospira Endostatin like A (Len A) in BL-21(DE3) is toxic to the host cells. J Genet Eng Biotechnol 2018; 16:393-398. [PMID: 30733752 PMCID: PMC6353657 DOI: 10.1016/j.jgeb.2018.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023]
Abstract
Heterologous expression of Integral Membrane Proteins (IMPs) is reported to be toxic to the host system in many studies. Even though there are reports on various concerns like transformation efficiency, growth properties, protein toxicity, inefficient expression and protein degradation in IMP overexpression, no studies so far addressed these issues in a comprehensive way. In the present study, two transmembrane proteins of the pathogen Leptospira interrogans, namely Signal peptidase (SP), and Leptospira Endostatin like A (Len-A) were taken along with a cytosolic protein Hydrolase (HYD) to assess the differences in transformation efficiency, protein toxicity, and protein stability when over expressed in Escherichia coli (E. coli). Bioinformatics analysis to predict the transmembrane localization indicated that both SP and Len are targeted to the membrane. The three proteins were expressed in full length in the E. coli expression strain, BL 21 (DE3). Significant changes were observed for the strains transformed with IMP genes under the parameters analysed such as, the transformation efficiency, survival of colonies on IPTG-plate, culture growth kinetics and protein expression compared to the strain harbouring the cytosolic protein gene.
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Affiliation(s)
- Padikara K Satheeshkumar
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Prasannan V Anu
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Mohmed I Junaida
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | | | | | - Ananthakrishnan J Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Gangaprasad A Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Govinda Pillai M Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Perumana R Sudhakaran
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
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7
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Abstract
Functional and structural studies on membrane proteins are limited by the difficulty to produce them in large amount and in a functional state. In this review, we provide protocols to achieve high-level expression of membrane proteins in Escherichia coli. The T7 RNA polymerase-based expression system is presented in detail and protocols to assess and improve its efficiency are discussed. Protocols to isolate either membrane or inclusion bodies and to perform an initial qualitative test to assess the solubility of the recombinant protein are also included.
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8
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Baumgarten T, Schlegel S, Wagner S, Löw M, Eriksson J, Bonde I, Herrgård MJ, Heipieper HJ, Nørholm MHH, Slotboom DJ, de Gier JW. Isolation and characterization of the E. coli membrane protein production strain Mutant56(DE3). Sci Rep 2017; 7:45089. [PMID: 28338018 PMCID: PMC5364489 DOI: 10.1038/srep45089] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/20/2017] [Indexed: 11/09/2022] Open
Abstract
Membrane protein production is usually toxic to E. coli. However, using genetic screens strains can be isolated in which the toxicity of membrane protein production is reduced, thereby improving production yields. Best known examples are the C41(DE3) and C43(DE3) strains, which are both derived from the T7 RNA polymerase (P)-based BL21(DE3) protein production strain. In C41(DE3) and C43(DE3) mutations lowering t7rnap expression levels result in strongly reduced T7 RNAP accumulation levels. As a consequence membrane protein production stress is alleviated in the C41(DE3) and C43(DE3) strains, thereby increasing membrane protein yields. Here, we isolated Mutant56(DE3) from BL21(DE3) using a genetic screen designed to isolate BL21(DE3)-derived strains with mutations alleviating membrane protein production stress other than the ones in C41(DE3) and C43(DE3). The defining mutation of Mutant56(DE3) changes one amino acid in its T7 RNAP, which weakens the binding of the T7 RNAP to the T7 promoter governing target gene expression rather than lowering T7 RNAP levels. For most membrane proteins tested yields in Mutant56(DE3) were considerably higher than in C41(DE3) and C43(DE3). Thus, the isolation of Mutant56(DE3) shows that the evolution of BL21(DE3) can be promoted towards further enhanced membrane protein production.
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Affiliation(s)
- Thomas Baumgarten
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Susan Schlegel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Samuel Wagner
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Mirjam Löw
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Jonas Eriksson
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Ida Bonde
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Markus J Herrgård
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Hermann J Heipieper
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Biotechnology, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Morten H H Nørholm
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Dirk Jan Slotboom
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, AG, 9747, The Netherlands
| | - Jan-Willem de Gier
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
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9
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Schlegel S, Genevaux P, de Gier JW. Isolating Escherichia coli strains for recombinant protein production. Cell Mol Life Sci 2016; 74:891-908. [PMID: 27730255 PMCID: PMC5306230 DOI: 10.1007/s00018-016-2371-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.
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Affiliation(s)
- Susan Schlegel
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16C, 106 91, Stockholm, Sweden.
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10
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Schmideder A, Cremer JH, Weuster-Botz D. Parallel steady state studies on a milliliter scale accelerate fed-batch bioprocess design for recombinant protein production with Escherichia coli. Biotechnol Prog 2016; 32:1426-1435. [PMID: 27604066 DOI: 10.1002/btpr.2360] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/11/2016] [Indexed: 12/12/2022]
Abstract
In general, fed-batch processes are applied for recombinant protein production with Escherichia coli (E. coli). However, state of the art methods for identifying suitable reaction conditions suffer from severe drawbacks, i.e. direct transfer of process information from parallel batch studies is often defective and sequential fed-batch studies are time-consuming and cost-intensive. In this study, continuously operated stirred-tank reactors on a milliliter scale were applied to identify suitable reaction conditions for fed-batch processes. Isopropyl β-d-1-thiogalactopyranoside (IPTG) induction strategies were varied in parallel-operated stirred-tank bioreactors to study the effects on the continuous production of the recombinant protein photoactivatable mCherry (PAmCherry) with E. coli. Best-performing induction strategies were transferred from the continuous processes on a milliliter scale to liter scale fed-batch processes. Inducing recombinant protein expression by dynamically increasing the IPTG concentration to 100 µM led to an increase in the product concentration of 21% (8.4 g L-1 ) compared to an implemented high-performance production process with the most frequently applied induction strategy by a single addition of 1000 µM IPGT. Thus, identifying feasible reaction conditions for fed-batch processes in parallel continuous studies on a milliliter scale was shown to be a powerful, novel method to accelerate bioprocess design in a cost-reducing manner. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1426-1435, 2016.
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Affiliation(s)
- Andreas Schmideder
- Inst. of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Johannes H Cremer
- Inst. of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Dirk Weuster-Botz
- Inst. of Biochemical Engineering, Technical University of Munich, Garching, Germany
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11
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The promises and challenges of fusion constructs in protein biochemistry and enzymology. Appl Microbiol Biotechnol 2016; 100:8273-81. [PMID: 27541749 DOI: 10.1007/s00253-016-7795-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023]
Abstract
Fusion constructs are used to improve the properties of or impart novel functionality to proteins for biotechnological applications. The biochemical characteristics of enzymes or functional proteins optimized by fusion include catalytic efficiency, stability, activity, expression, secretion, and solubility. In this review, we summarize the parameters of enzymes or functional proteins that can be modified by fusion constructs. For each parameter, fusion strategies and molecular partners are examined using examples from recent studies. Future prospects in this field are also discussed. This review is expected to increase interest in and advance fusion strategies for optimization of enzymes and other functional proteins.
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12
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Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction. Sci Rep 2015; 5:16076. [PMID: 26531007 PMCID: PMC4632034 DOI: 10.1038/srep16076] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 10/08/2015] [Indexed: 11/08/2022] Open
Abstract
Achieving sufficient yields of proteins in their functional form represents the first bottleneck in contemporary bioscience and biotechnology. To accomplish successful overexpression of membrane proteins in a workhorse organism such as E. coli, defined and rational optimization strategies based on an understanding of the genetic background of the toxicity-escape mechanism are desirable. To this end, we sequenced the genomes of E. coli C41(DE3) and its derivative C43(DE3), which were developed for membrane protein production. Comparative analysis of their genomes with those of their ancestral strain E. coli BL21(DE3) revealed various genetic changes in both strains. A series of E. coli variants that are able to tolerate transformation with or overexpression of membrane proteins were generated by in vitro evolution. Targeted sequencing of the evolved strains revealed the mutational hotspots among the acquired genetic changes. By these combinatorial approaches, we found non-synonymous changes in the lac repressor gene of the lac operon as well as nucleotide substitutions in the lacUV5 promoter of the DE3 region, by which the toxic effect to the host caused by overexpression of membrane proteins could be relieved. A mutation in lacI was demonstrated to be crucial for conferring tolerance to membrane protein overexpression.
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13
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Zhang Z, Kuipers G, Niemiec Ł, Baumgarten T, Slotboom DJ, de Gier JW, Hjelm A. High-level production of membrane proteins in E. coli BL21(DE3) by omitting the inducer IPTG. Microb Cell Fact 2015; 14:142. [PMID: 26377812 PMCID: PMC4574001 DOI: 10.1186/s12934-015-0328-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/28/2015] [Indexed: 11/17/2022] Open
Abstract
Background For membrane protein production, the Escherichia coli T7 RNA polymerase (T7 RNAP)-based protein production strain BL21(DE3) in combination with T7-promoter based expression vectors is widely used. Cells are routinely cultured in Lysogeny broth (LB medium) and expression of the chromosomally localized t7rnap gene is governed by the isopropyl-β-d-1-thiogalactopyranoside (IPTG) inducible lacUV5 promoter. The T7 RNAP drives the expression of the plasmid borne gene encoding the recombinant membrane protein. Production of membrane proteins in the cytoplasmic membrane rather than in inclusion bodies in a misfolded state is usually preferred, but often hampered due to saturation of the capacity of the Sec-translocon, resulting in low yields. Results Contrary to expectation we observed that omission of IPTG from BL21(DE3) cells cultured in LB medium can lead to significantly higher membrane protein production yields than when IPTG is added. In the complete absence of IPTG cultures stably produce membrane proteins in the cytoplasmic membrane, whereas upon the addition of IPTG membrane proteins aggregate in the cytoplasm and non-producing clones are selected for. Furthermore, in the absence of IPTG, membrane proteins are produced at a lower rate than in the presence of IPTG. These observations indicate that in the absence of IPTG the Sec-translocon capacity is not/hardly saturated, leading to enhanced membrane protein production yields in the cytoplasmic membrane. Importantly, for more than half of the targets tested the yields obtained using un-induced BL21(DE3) cells were higher than the yields obtained in the widely used membrane protein production strains C41(DE3) and C43(DE3). Since most secretory proteins reach the periplasm via the Sec-translocon, we also monitored the production of three secretory recombinant proteins in the periplasm of BL21(DE3) cells in the presence and absence of IPTG. For all three targets tested omitting IPTG led to the highest production levels in the periplasm. Conclusions Omission of IPTG from BL21(DE3) cells cultured in LB medium provides a very cost- and time effective alternative for the production of membrane and secretory proteins. Therefore, we recommend that this condition is incorporated in membrane- and secretory protein production screens. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0328-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhe Zhang
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91, Stockholm, Sweden.
| | | | - Łukasz Niemiec
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91, Stockholm, Sweden.
| | - Thomas Baumgarten
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91, Stockholm, Sweden.
| | - Dirk Jan Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91, Stockholm, Sweden.
| | - Anna Hjelm
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91, Stockholm, Sweden.
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14
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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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De-convoluting the Genetic Adaptations of E. coli C41(DE3) in Real Time Reveals How Alleviating Protein Production Stress Improves Yields. Cell Rep 2015; 10:1758-1766. [DOI: 10.1016/j.celrep.2015.02.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/08/2015] [Indexed: 11/20/2022] Open
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16
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Wyre C, Overton TW. Use of a stress-minimisation paradigm in high cell density fed-batch Escherichia coli fermentations to optimise recombinant protein production. J Ind Microbiol Biotechnol 2014; 41:1391-404. [PMID: 25056840 DOI: 10.1007/s10295-014-1489-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/08/2014] [Indexed: 11/25/2022]
Abstract
Production of recombinant proteins is an industrially important technique in the biopharmaceutical sector. Many recombinant proteins are problematic to generate in a soluble form in bacteria as they readily form insoluble inclusion bodies. Recombinant protein solubility can be enhanced by minimising stress imposed on bacteria through decreasing growth temperature and the rate of recombinant protein production. In this study, we determined whether these stress-minimisation techniques can be successfully applied to industrially relevant high cell density Escherichia coli fermentations generating a recombinant protein prone to forming inclusion bodies, CheY-GFP. Flow cytometry was used as a routine technique to rapidly determine bacterial productivity and physiology at the single cell level, enabling determination of culture heterogeneity. We show that stress minimisation can be applied to high cell density fermentations (up to a dry cell weight of >70 g L(-1)) using semi-defined media and glucose or glycerol as carbon sources, and using early or late induction of recombinant protein production, to produce high yields (up to 6 g L(-1)) of aggregation-prone recombinant protein in a soluble form. These results clearly demonstrate that stress minimisation is a viable option for the optimisation of high cell density industrial fermentations for the production of high yields of difficult-to-produce recombinant proteins, and present a workflow for the application of stress-minimisation techniques in a variety of fermentation protocols.
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Affiliation(s)
- Chris Wyre
- Bioengineering, School of Chemical Engineering, and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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17
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Overton TW. Recombinant protein production in bacterial hosts. Drug Discov Today 2014; 19:590-601. [DOI: 10.1016/j.drudis.2013.11.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/03/2013] [Accepted: 11/08/2013] [Indexed: 10/26/2022]
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18
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Liu L, Yang H, Shin HD, Chen RR, Li J, Du G, Chen J. How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioengineered 2013; 4:212-23. [PMID: 23686280 DOI: 10.4161/bioe.24761] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbial enzymes have been used in a large number of fields, such as chemical, agricultural and biopharmaceutical industries. The enzyme production rate and yield are the main factors to consider when choosing the appropriate expression system for the production of recombinant proteins. Recombinant enzymes have been expressed in bacteria (e.g., Escherichia coli, Bacillus and lactic acid bacteria), filamentous fungi (e.g., Aspergillus) and yeasts (e.g., Pichia pastoris). The favorable and very advantageous characteristics of these species have resulted in an increasing number of biotechnological applications. Bacterial hosts (e.g., E. coli) can be used to quickly and easily overexpress recombinant enzymes; however, bacterial systems cannot express very large proteins and proteins that require post-translational modifications. The main bacterial expression hosts, with the exception of lactic acid bacteria and filamentous fungi, can produce several toxins which are not compatible with the expression of recombinant enzymes in food and drugs. However, due to the multiplicity of the physiological impacts arising from high-level expression of genes encoding the enzymes and expression hosts, the goal of overproduction can hardly be achieved, and therefore, the yield of recombinant enzymes is limited. In this review, the recent strategies used for the high-level expression of microbial enzymes in the hosts mentioned above are summarized and the prospects are also discussed. We hope this review will contribute to the development of the enzyme-related research field.
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Affiliation(s)
- Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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19
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Weber E, Guth C, Weiss IM. GFP facilitates native purification of recombinant perlucin derivatives and delays the precipitation of calcium carbonate. PLoS One 2012; 7:e46653. [PMID: 23056388 PMCID: PMC3463529 DOI: 10.1371/journal.pone.0046653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/02/2022] Open
Abstract
Insolubility is one of the possible functions of proteins involved in biomineralization, which often limits their native purification. This becomes a major problem especially when recombinant expression systems are required to obtain larger amounts. For example, the mollusc shell provides a rich source of unconventional proteins, which can interfere in manifold ways with different mineral phases and interfaces. Therefore, the relevance of such proteins for biotechnological processes is still in its infancy. Here we report a simple and reproducible purification procedure for a GFP-tagged lectin involved in biomineralization, originally isolated from mother-of-pearl in abalone shells. An optimization of E. coli host cell culture conditions was the key to obtain reasonable yields and high degrees of purity by using simple one-step affinity chromatography. We identified a dual functional role for the GFP domain when it became part of a mineralizing system in vitro. First, the GFP domain improved the solubility of an otherwise insoluble protein, in this case recombinant perlucin derivatives. Second, GFP inhibited calcium carbonate precipitation in a concentration dependent manner. This was demonstrated here using a simple bulk assay over a time period of 400 seconds. At concentrations of 2 µg/ml and higher, the inhibitory effect was observed predominantly for HCO(3) (-) as the first ionic interaction partner, but not necessarily for Ca(2+). The interference of GFP-tagged perlucin derivatives with the precipitation of calcium carbonate generated different types of GFP-fluorescent composite calcite crystals. GFP-tagging offers therefore a genetically tunable tool to gently modify mechanical and optical properties of synthetic biocomposite minerals.
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Affiliation(s)
- Eva Weber
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Christina Guth
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Ingrid M. Weiss
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
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