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Hashemzadeh MS, Mohammadi M, Ghaleh HEG, Sharti M, Choopani A, Panda AK. Expression, Solubilization, Refolding and Final Purification of Recombinant Proteins as Expressed in the form of "Classical Inclusion Bodies" in E. coli. Protein Pept Lett 2021; 28:122-130. [PMID: 32729411 DOI: 10.2174/0929866527999200729182831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/22/2022]
Abstract
Escherichia coli has been most widely used for production of the recombinant proteins. Over-expression of the recombinant proteins is the mainspring of the inclusion bodies formation. The refolding of these proteins into bioactive forms is cumbersome and partly time-consuming. In the present study, we reviewed and discussed most issues regarding the recovery of "classical inclusion bodies" by focusing on our previous experiences. Performing proper methods of expression, solubilization, refolding and final purification of these proteins, would make it possible to recover higher amounts of proteins into the native form with appropriate conformation. Generally, providing mild conditions and proper refolding buffers, would lead to recover more than 40% of inclusion bodies into bioactive and native conformation.
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Affiliation(s)
| | - Mozafar Mohammadi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Mojtaba Sharti
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Choopani
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amulya Kumar Panda
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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Carballo-Amador MA, McKenzie EA, Dickson AJ, Warwicker J. Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation. BMC Biotechnol 2019; 19:26. [PMID: 31072369 PMCID: PMC6507049 DOI: 10.1186/s12896-019-0520-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein solubility characteristics are important determinants of success for recombinant proteins in relation to expression, purification, storage and administration. Escherichia coli offers a cost-efficient expression system. An important limitation, whether for biophysical studies or industrial-scale production, is the formation of insoluble protein aggregates in the cytoplasm. Several strategies have been implemented to improve soluble expression, ranging from modification of culture conditions to inclusion of solubility-enhancing tags. RESULTS Surface patch analysis has been applied to predict amino acid changes that can alter the solubility of expressed recombinant human erythropoietin (rHuEPO) in E. coli, a factor that has importance for both yield and subsequent downstream processing of recombinant proteins. A set of rHuEPO proteins (rHuEPO E13K, F48D, R150D, and F48D/R150D) was designed (from the framework of wild-type protein, rHuEPO WT, via amino acid mutations) that varied in terms of positively-charged patches. A variant predicted to promote aggregation (rHuEPO E13K) decreased solubility significantly compared to rHuEPO WT. In contrast, variants predicted to diminish aggregation (rHuEPO F48D, R150D, and F48D/R150D) increased solubility up to 60% in relation to rHuEPO WT. CONCLUSIONS These findings are discussed in the wider context of biophysical calculations applied to the family of EPO orthologues, yielding a diverse range of calculated values. It is suggested that combining such calculations with naturally-occurring sequence variation, and 3D model generation, could lead to a valuable tool for protein solubility design.
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Affiliation(s)
- M. Alejandro Carballo-Amador
- Facultad de Ciencias, Universidad Autónoma de Baja California, Km. 103 Carretera Tijuana–Ensenada, Pedregal Playitas, 22860 Ensenada, Baja California Mexico
| | - Edward A. McKenzie
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Alan J. Dickson
- Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Jim Warwicker
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
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Jiang W, Yang R, Lin P, Hong W, Fang B. Bioinspired genetic engineering of supramolecular assembled formate dehydrogenase with enhanced biocatalysis activities. J Biotechnol 2019; 292:50-56. [PMID: 30690097 DOI: 10.1016/j.jbiotec.2018.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/22/2018] [Accepted: 12/09/2018] [Indexed: 11/25/2022]
Abstract
A bioinspired strategy for the synthesis of supramolecular and biocatalytical materials was developed base on protein-protein supramolecular interaction and genetic engineering. Formate dehydrogenase (FDH) and its functional fragments were separately fused to form a multi-function domain. The fusion proteins and functional fragments self-assembled into the expanded and controllable supramolecular interaction networks. Morphology characterization by scanning-electron microscopy showed that the assembled functional fragments and fusion proteins formed multi-dimensional (3D) and two-dimensional (2D) layer-like structures. Moreover, the oligomeric biocatalysts exhibited higher structural stability and NAD(H) recycling efficiency than the unassembled structures when they were applied to a co-enzyme regeneration system. These results suggest that the bioinspired strategy provides a promising approach for the fabrication of supramolecular FDH materials via genetic engineering and self-assembly. The significant improvement on the biocatalytical activity reveals the essential role of supramolecular interface design in their biocatalysis applications.
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Affiliation(s)
- Wei Jiang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, 361021, China; Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Ruonan Yang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Peng Lin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China; Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
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Physiologically distinct subpopulations formed in Escherichia coli cultures in response to heat shock. Microbiol Res 2018; 209:33-42. [DOI: 10.1016/j.micres.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 11/21/2022]
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Diener M, Kopka B, Pohl M, Jaeger KE, Krauss U. Fusion of a Coiled-Coil Domain Facilitates the High-Level Production of Catalytically Active Enzyme Inclusion Bodies. ChemCatChem 2015. [DOI: 10.1002/cctc.201501001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martin Diener
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich; 52426 Jülich Germany
| | - Benita Kopka
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich; 52426 Jülich Germany
| | - Martina Pohl
- Bioeconomy Science Center (BioSc); 52426 Jülich Germany
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH and Bioeconomy Science Center (BioSc), Wilhelm-Johnen-Strasse; 52425 Jülich Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich; 52426 Jülich Germany
- Bioeconomy Science Center (BioSc); 52426 Jülich Germany
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH and Bioeconomy Science Center (BioSc), Wilhelm-Johnen-Strasse; 52425 Jülich Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich; 52426 Jülich Germany
- Bioeconomy Science Center (BioSc); 52426 Jülich Germany
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High-yield expression in Escherichia coli, purification and application of budding yeast K2 killer protein. Mol Biotechnol 2015; 56:644-52. [PMID: 24532228 DOI: 10.1007/s12033-014-9740-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Saccharomyces cerevisiae K2 toxin is a highly active extracellular protein, important as a biocontrol agent for biotechnological applications in the wine industry. This protein is produced at negligible levels in yeast, making difficult to isolate it in amounts sufficient for investigation and generation of analysis tools. In this work, we demonstrate the use of a bacterial system for expression of the recombinant K2 protein, suitable for generation of antibodies specific for toxin of the yeast origin. Synthesis of the full-length S. cerevisiae K2 preprotoxin in Escherichia coli was found to be toxic to the host cell, resulting in diminished growth. Such effect was abolished by the introduction of the C-terminal truncation into K2 protein, directing it into non-toxic inclusion body fraction. The obtained protein is of limited solubility thus, facilitating the purification by simple and efficient chromatography-free procedure. The protein aggregates were successfully refolded into a soluble form yielding sufficient amounts of a tag-less truncated K2 protein suitable for polyclonal antibody production. Antibodies were raised in rabbit and found to be specific for detection of both antigen and native S. cerevisiae K2 toxin.
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Seras-Franzoso J, Peebo K, García-Fruitós E, Vázquez E, Rinas U, Villaverde A. Improving protein delivery of fibroblast growth factor-2 from bacterial inclusion bodies used as cell culture substrates. Acta Biomater 2014; 10:1354-9. [PMID: 24361427 DOI: 10.1016/j.actbio.2013.12.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/13/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
Abstract
Bacterial inclusion bodies (IBs) have recently been used to generate biocompatible cell culture interfaces, with diverse effects on cultured cells such as cell adhesion enhancement, stimulation of cell growth or induction of mesenchymal stem cell differentiation. Additionally, novel applications of IBs as sustained protein delivery systems with potential applications in regenerative medicine have been successfully explored. In this scenario, with IBs gaining significance in the biomedical field, the fine tuning of this functional biomaterial is crucial. In this work, the effect of temperature on fibroblast growth factor-2 (FGF-2) IB production and performance has been evaluated. FGF-2 was overexpressed in Escherichia coli at 25 and 37 °C, producing IBs with differences in size, particle structure and biological activity. Cell culture topographies made with FGF-2 IBs biofabricated at 25 °C showed higher levels of biological activity as well as a looser supramolecular structure, enabling a higher protein release from the particles. In addition, the controlled use of FGF-2 protein particles enabled the generation of functional topographies with multiple biological activities being effective on diverse cell types.
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Recombinant polypeptide production in E. coli: towards a rational approach to improve the yields of functional proteins. Microb Cell Fact 2013; 12:101. [PMID: 24176192 PMCID: PMC3832250 DOI: 10.1186/1475-2859-12-101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 10/30/2013] [Indexed: 11/16/2022] Open
Abstract
The development of complementary technologies enabled the successful production of recombinant polypeptides in bacteria and opened to biology researchers new avenues as obtaining suitable amounts of proteins necessary for their experimental work became easy, fast, and inexpensive. Nevertheless, the recombinant approach remained somehow unpredictable, since many constructs resisted to apparent production or accumulated as aggregates. Several factors and physical/chemical conditions that could improve the accumulation of native-like protein were identified. At the same time, it was acknowledged that the outcome of most of them was erratic and that almost any protein required its own specific optimized set of conditions to achieve its correct folding. The attempt to understand the critical points specific for recombinant protein production missed the goal of setting universally useful protocols, but contributed to the increase of the rate of success by proposing always new empiric combinations. Nevertheless, the results published in the recent literature allow for a better comprehension of some key mechanisms controlling protein production in E. coli and could enable the elaboration of rational methodologies for improving the quantitative and qualitative features of the produced polypeptides. This result will be achieved when the identification of the limiting step that impairs the accomplishment of the native folding for any single construct will become straightforward. This minireview will discuss how factors such as the expression rate, the folding machinery, and the secretion efficiency may impact the final protein yields.
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Characterization of CpdC, a large-ring lactone-hydrolyzing enzyme from Pseudomonas sp. strain HI-70, and its use as a fusion tag facilitating overproduction of proteins in Escherichia coli. Appl Environ Microbiol 2013; 79:7091-100. [PMID: 24038681 DOI: 10.1128/aem.02435-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are few entries of carbon-carbon bond hydrolases (EC 3.7.1.-) in the ExPASy database. In microbes, these enzymes play an essential role in the metabolism of alicyclic or aromatic compounds as part of the global carbon cycle. CpdC is a ω-pentadecalactone hydrolase derived from the degradation pathway of cyclopentadecanol or cyclopentadecanone by Pseudomonas sp. strain HI-70. CpdC was purified to homogeneity and characterized. It is active as a dimer of 56,000 Da with a subunit molecular mass of 33,349. Although CpdC has the highest activity and reaction rate (kcat) toward ω-pentadecalactone, its catalytic efficiency favors lauryl lactone as a substrate. The melting temperature (Tm) of CpdC was estimated to be 50.9 ± 0.1°C. The half-life of CpdC at 35°C is several days. By virtue of its high level of expression in Escherichia coli, the intact CpdC-encoding gene and progressive 3'-end deletions were employed in the construction of a series of fusion plasmid system. Although we found them in inclusion bodies, proof-of-concept of overproduction of three microbial cutinases of which the genes were otherwise expressed poorly or not at all in E. coli was demonstrated. On the other hand, two antigenic proteins, azurin and MPT63, were readily produced in soluble form.
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