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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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2
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Venkatesan M, Semper C, Skrivergaard S, Di Leo R, Mesa N, Rasmussen MK, Young JF, Therkildsen M, Stogios PJ, Savchenko A. Recombinant production of growth factors for application in cell culture. iScience 2022; 25:105054. [PMID: 36157583 PMCID: PMC9489951 DOI: 10.1016/j.isci.2022.105054] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/07/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022] Open
Abstract
Culturing eukaryotic cells has widespread applications in research and industry, including the emerging field of cell-cultured meat production colloquially referred to as “cellular agriculture”. These applications are often restricted by the high cost of growth medium necessary for cell growth. Mitogenic protein growth factors (GFs) are essential components of growth medium and account for upwards of 90% of the total costs. Here, we present a set of expression constructs and a simplified protocol for recombinant production of functionally active GFs, including FGF2, IGF1, PDGF-BB, and TGF-β1 in Escherichia coli. Using this E. coli expression system, we produced soluble GF orthologs from species including bovine, chicken, and salmon. Bioactivity analysis revealed orthologs with improved performance compared to commercially available alternatives. We estimated that the production cost of GFs using our methodology will significantly reduce the cost of cell culture medium, facilitating low-cost protocols tailored for cultured meat production and tissue engineering. Developed methodology for low-cost production of soluble, bioactive GFs Purified GFs were active on NIH-3T3 and bovine satellite cells Some GF orthologs outperformed commercially sourced GFs Production of GFs using these methods can foster significant cost savings
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | | | | | | | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
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Maksum IP, Yosua Y, Nabiel A, Pratiwi RD, Sriwidodo S, Soedjanaatmadja UM. Refolding of bioactive human epidermal growth factor from E. coli BL21(DE3) inclusion bodies & evaluations on its in vitro & in vivo bioactivity. Heliyon 2022; 8:e09306. [PMID: 35497033 PMCID: PMC9039848 DOI: 10.1016/j.heliyon.2022.e09306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/10/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Human epidermal growth factor (hEGF) is a mitogenic protein widely used in pharmaceutical and cosmetic industries, thus recombinant DNA technology has been applied to meet the high demand for hEGF. The overexpression of recombinant protein in E. coli often leads to the formation of inclusion bodies (IBs). Mild solubilisation preserves the native secondary protein structure in IBs, thereby the high recovery of active protein from IBs. The redox system also plays a pivotal role in the formation of disulphide bonds during refolding of disulphide bond-containing protein. This study aimed to recover hEGF from bacterial IBs through freeze-thawing solubilisation and glutathione-based oxidative refolding. CBD-Ssp DnaB-hEGF fusion protein was expressed as IBs in E. coli, washed with Triton X-100 and urea to remove most protein contaminants, then the solubilised fusion protein was obtained by freeze-thawing with the addition of 2 M urea. The solubilised protein was subsequently refolded by intein cleavage via a glutathione-based redox system. The refolded hEGF demonstrated heat-resistant properties, interacted with specific antibodies on ELISA, stimulated keratinocyte proliferation and possessed significant in vivo wound healing properties on the 8th day, confirming that hEGF was correctly folded. In summary, the protocol described is suitable for the recovery of refolded hEGF from bacterial IBs by mild solubilisation and oxidative refolding.
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Affiliation(s)
- Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
- Corresponding author.
| | - Yosua Yosua
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ahmad Nabiel
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Riyona Desvy Pratiwi
- Research Centre of Biotechnology, Indonesian Institute of Science, Bogor, Indonesia
| | - Sriwidodo Sriwidodo
- Department of Pharmaceutics & Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ukun M.S. Soedjanaatmadja
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
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Ferreira AS, Lopacinski A, Batista M, Hiraiwa PM, Guimarães BG, Zanchin NIT. A toolkit for recombinant production of seven human EGF family growth factors in active conformation. Sci Rep 2022; 12:5034. [PMID: 35322149 PMCID: PMC8943033 DOI: 10.1038/s41598-022-09060-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
Epidermal growth factors (EGF) play a wide range of roles in embryogenesis, skin development, immune response homeostasis. They are involved in several pathologies as well, including several cancer types, psoriasis, chronic pain and chronic kidney disease. All members share the structural EGF domain, which is responsible for receptor interaction, thereby initiating transduction of signals. EGF growth factors have intense use in fundamental research and high potential for biotechnological applications. However, due to their structural organization with three disulfide bonds, recombinant production of these factors in prokaryotic systems is not straightforward. A significant fraction usually forms inclusion bodies. For the fraction remaining soluble, misfolding and incomplete disulfide bond formation may affect the amount of active factor in solution, which can compromise experimental conclusions and biotechnological applications. In this work, we describe a reliable procedure to produce seven human growth factors of the EGF family in Escherichia coli. Biophysical and stability analyses using limited proteolysis, light scattering, circular dichroism and nanoDSF show that the recombinant factors present folded and stable conformation. Cell proliferation and scratch healing assays confirmed that the recombinant factors are highly active at concentrations as low as 5 ng/ml.
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Affiliation(s)
- Arthur Schveitzer Ferreira
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil.,Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil
| | - Amanda Lopacinski
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil.,Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil
| | - Michel Batista
- Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Priscila Mazzocchi Hiraiwa
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Beatriz Gomes Guimarães
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil
| | - Nilson Ivo Tonin Zanchin
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba, PR, Brazil. .,Cellular and Molecular Biology Graduate Program, Federal University of Paraná, Curitiba, PR, Brazil.
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An Intrinsically Disordered Peptide Tag that Confers an Unusual Solubility to Aggregation-Prone Proteins. Appl Environ Microbiol 2022; 88:e0009722. [PMID: 35285717 DOI: 10.1128/aem.00097-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is a high demand for the production of recombinant proteins in Escherichia coli for biotechnological applications, but their production is still limited by their insolubility. Fusion tags have been successfully used to enhance the solubility of aggregation-prone proteins; however, smaller and more powerful tags are desired for increasing the yield and quality of target proteins. Here, the NEXT tag, a 53-amino-acid-long solubility enhancer, is described. The NEXT tag showed outstanding ability to improve both in vivo and in vitro solubilities, with minimal effect on passenger proteins. The C-terminal region of the tag was mostly responsible for in vitro solubility, while the N-terminal region was essential for in vivo soluble expression. The NEXT tag appeared to be intrinsically disordered and seemed to exclude neighboring molecules and prevent protein aggregation by acting as an entropic bristle. This novel peptide tag should have general use as a fusion partner to increase the yield and quality of difficult-to-express proteins. IMPORTANCE Production of recombinant proteins in Escherichia coli still suffers from the insolubility problem. Conventional solubility enhancers with large sizes, represented by maltose-binding protein (MBP), have remained the first-choice tags; however, the success of the soluble expression of tagged proteins is largely unpredictable. In addition, the large tags can negatively affect the function of target proteins. In this work, the NEXT tag, an intrinsically disordered peptide, was introduced as a small but powerful alternative to MBP. The NEXT tag could significantly improve both the expression level and the solubility of target proteins, including a thermostable carbonic anhydrase and a polyethylene terephthalate (PET)-degrading enzyme that are remarkable enzymes for environmental bioremediation.
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Song SJ, Diao HP, Moon B, Yun A, Hwang I. The B1 Domain of Streptococcal Protein G Serves as a Multi-Functional Tag for Recombinant Protein Production in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:878677. [PMID: 35548280 PMCID: PMC9083265 DOI: 10.3389/fpls.2022.878677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 05/17/2023]
Abstract
Plants have long been considered a cost-effective platform for recombinant production. A recently recognized additional advantage includes the low risk of contamination of human pathogens, such as viruses and bacterial endotoxins. Indeed, a great advance has been made in developing plants as a "factory" to produce recombinant proteins to use for biopharmaceutical purposes. However, there is still a need to develop new tools for recombinant protein production in plants. In this study, we provide data showing that the B1 domain of Streptococcal protein G (GB1) can be a multi-functional domain of recombinant proteins in plants. N-terminal fusion of the GB1 domain increased the expression level of various target proteins ranging from 1.3- to 3.1-fold at the protein level depending on the target proteins. GB1 fusion led to the stabilization of the fusion proteins. Furthermore, the direct detection of GB1-fusion proteins by the secondary anti-IgG antibody eliminated the use of the primary antibody for western blot analysis. Based on these data, we propose that the small GB1 domain can be used as a versatile tag for recombinant protein production in plants.
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Santo AAE, Feliciano GT. Genetic Algorithms Applied to Thermodynamic Rational Design of Mimetic Antibodies Based on the GB1 Domain of Streptococcal Protein G: An Atomistic Simulation Study. J Phys Chem B 2021; 125:7985-7996. [PMID: 34264671 DOI: 10.1021/acs.jpcb.1c03324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of mimetic antibodies (MA) capable of combining the high affinity and selectivity of antibodies with the small size of the peptides has enormous potential for applications in current biotechnology. In this work, we demonstrate that in silico MA design is possible through genetic algorithms (GA) developed from shell scripts capable of combining software commonly used for atomistic simulation. Our results demonstrate that, using the GB1 domain of the streptococcal G protein as a model, it is possible to optimize the molecular recognition capacity of a large MA population in a few generations. In the first case, GA was able to generate 10 MA with binding free energy (BFE) less than the vascular endothelial cell growth factor conjugated with the fms-type tyrosine kinase receptor. In the second case, it generated 13 MA with BFE less than that of the hepatitis C-E2 viral envelope conjugate with the antibody. Through the GA developed in this work, we demonstrate the use of a new protocol, capable of guiding experimental methods for the design of bioactive peptides that can assist in the development of new therapeutic molecules.
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Affiliation(s)
- Anderson A E Santo
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
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Sriwidodo S, Maksum IP, Subroto T, Wathoni N, Subarnas A, Umar AK. Activity and Effectiveness of Recombinant hEGF Excreted by Escherichia coli BL21 on Wound Healing in Induced Diabetic Mice. J Exp Pharmacol 2020; 12:339-348. [PMID: 33061675 PMCID: PMC7532914 DOI: 10.2147/jep.s265727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/28/2020] [Indexed: 01/13/2023] Open
Abstract
Context Human epidermal growth factor (hEGF) has biological activities and can be used in medicines and cosmetics. A high level of effectiveness of hEGF can be obtained when three disulfide bonds fold perfectly. Extracellular secretion from E. coli BL21 using the PelB signal peptide is a new way to obtain hEGF with a structure that folds appropriately. Object This study aimed to determine the activity and effectiveness of recombinant hEGF excreted by E. coli BL21 on wound healing in induced diabetic mice. Methods Cell proliferation and migration tests were performed on NIH3T3 cells, followed by wound healing tests in induced diabetic mice, along with histological and endotoxin test at various hEGF concentrations (25, 50, and 75 µg/mL). Results Based on the results, hEGF at a level of 50 μg/mL showed optimal proliferation and migration activities. Wound healing in induced diabetic mice showed faster-wound closure within 12 days at hEGF 50 and 75 µg/mL with a percentage wound closure of 95% and 98.5%, respectively, which was significant versus control. In the histology test, the number of fibroblasts showed an increase and was significant at hEGF 75 µg/mL compared to the control group. The single test vial (STV) showed that hEGF solution was free of endotoxin. Conclusion Recombinant hEGF produced by extracellular secretion using E. coli BL21 has optimal diabetic wound healing activity through increased fibroblast proliferation.
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Affiliation(s)
- Sriwidodo Sriwidodo
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Nasrul Wathoni
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Anas Subarnas
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor 45363, Indonesia
| | - Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor 45363, Indonesia
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