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Maharjan A, Park JH. Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products. Biotechnol Appl Biochem 2023; 70:2136-2149. [PMID: 37735977 DOI: 10.1002/bab.2514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.
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Affiliation(s)
- Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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Machine learning modeling for solubility prediction of recombinant antibody fragment in four different E. coli strains. Sci Rep 2022; 12:5463. [PMID: 35361835 PMCID: PMC8971470 DOI: 10.1038/s41598-022-09500-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
The solubility of proteins is usually a necessity for their functioning. Recently an emergence of machine learning approaches as trained alternatives to statistical models has been evidenced for empirical modeling and optimization. Here, soluble production of anti-EpCAM extracellular domain (EpEx) single chain variable fragment (scFv) antibody was modeled and optimized as a function of four literature based numerical factors (post-induction temperature, post-induction time, cell density of induction time, and inducer concentration) and one categorical variable using artificial neural network (ANN) and response surface methodology (RSM). Models were established by the CCD experimental data derived from 232 separate experiments. The concentration of soluble scFv reached 112.4 mg/L at the optimum condition and strain (induction at cell density 0.6 with 0.4 mM IPTG for 24 h at 23 °C in Origami). The predicted value obtained by ANN for the response (106.1 mg/L) was closer to the experimental result than that obtained by RSM (97.9 mg/L), which again confirmed a higher accuracy of ANN model. To the author's knowledge this is the first report on comparison of ANN and RSM in statistical optimization of fermentation conditions of E.coli for the soluble production of recombinant scFv.
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Mochnáčová E, Petroušková P, Danišová O, Hudecová P, Bhide K, Kulkarni A, Bhide M. Simple and rapid pipeline for the production of cyclic and linear small-sized peptides in E. coli. Protein Expr Purif 2021; 191:106026. [PMID: 34838724 DOI: 10.1016/j.pep.2021.106026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
Small and medium-sized peptides are gaining popularity in biomedical applications, including therapeutic target development. As an alternative to chemical synthesis, we describe a complete pipeline for the production of linear as well as structurally constrained cyclic peptides in an E. coli expression system in this study. A plasmid vector containing a novel N terminal HOE tag (28 amino acids in length) that fuses with the peptide was created. The HOE tag contains sites for both chemical (CNBr) and enzymatic (enterokinase) cleavage, making it easy to isolate the peptide after production. A total of 21 peptides (17 cyclic and 4 linear) were synthesized, and the HOE tag was successfully removed using either CNBr (9 peptides) or enterokinase (12 peptides). The presence of a disulfide bond was confirmed in six representative cyclic peptides. In this study we have provided detailed instructions on primers design strategy, overexpression and purification of HOE tagged peptides, chemical and enzymatic cleavage, and confirmation of the cyclic form of peptides. We are confident that this pipeline will assist researchers in producing multiple recombinant peptides in a cost-effective and time-efficient manner.
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Affiliation(s)
- Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Patrícia Petroušková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Oľga Danišová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Patrícia Hudecová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia; Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia; Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia.
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Mofid MR, Babaeipour V, Jafari S, Haddad L, Moghim S, Ghanavi J. Efficient process development for high-level production, purification, formulation, and characterization of recombinant mecasermin in Escherichia coli. Biotechnol Appl Biochem 2020; 68:776-788. [PMID: 32692415 DOI: 10.1002/bab.1990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/18/2020] [Indexed: 11/08/2022]
Abstract
Overproduction of recombinant mecasermin was achieved by investigation of effect of three factors, temperature, inducer amount, and culture media, at three levels according to the Taguchi statistical design in Escherichia coli in a bench-scale bioreactor. In optimal conditions (induction temperature 28 °C, terrific broth with glucose (TB+G) medium, with 0.1 mM IPTG as inducer) 0.84 g/L mecasermin with expression levels of 38% of total protein and 4.13 g/L final dry cell biomass was produced, that is one of the highest values of recombinant protein has been reported in the batch system. The cell disruption was done by lysozyme pretreatment with sonication to the efficient purification of mecasermin. The isolated and washed inclusion bodies were solubilized in Gdn-HCl at pH 5.4 and folded with glutathione and purified with gel filtration. The purified rhIGF-1 (mecasermin) was formulated with arginine. Mecasermin protein remained t stable at 4 °C for up to 2 years. The quantitative and qualitative control indicated that mecasermin is expressed correctly (without the initial methionine by mass spectrometry), pure (without endotoxin and other protein impurities), correct folding (FTIR, RF-HPLC), monomer form (SEC-HPLC), and active (bioactivity test). Also, the purification results revealed that expression at low temperature results in the efficient purification of the overproduced mecasermin with high quantity and quality.
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Affiliation(s)
- Mohammad Reza Mofid
- Department of Clinical Biochemistry, School of Pharmacy and Bioinformatics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Valiollah Babaeipour
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
| | - Sevda Jafari
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Leila Haddad
- Department of Clinical Biochemistry, School of Pharmacy and Bioinformatics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jalaledin Ghanavi
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Efficient Soluble Expression and Purification of Recombinant Human Acidic Fibroblast Growth Factor from Escherichia coli via Fusion with a Novel Collagen-like Protein Scl2. Appl Biochem Biotechnol 2020; 191:1562-1579. [PMID: 32166590 DOI: 10.1007/s12010-020-03269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
Abstract
Human acidic fibroblast growth factor (haFGF) is a multifunctional protein involved in regulating a wide range of cellular processes. As a potent therapeutic agent, it is highly desirable to produce recombinant haFGF (r-haFGF) at low cost. However, the complex structure and formation of aggregation confines its high-level soluble expression and functional form. Herein, to produce r-haFGF efficiently in E. coli, we devised a novel soluble expression and cost-effective purification approach based on fusion with Scl2-M (a novel modified collagen-like protein) for the first time. By using this strategy, more than 95% of the Scl2-M-haFGF fusion protein was highly expressed in soluble form and the expression level of targeted fusion protein in shake flasks and 5-L fermenter was 0.42 g/L and 2.28 g/L, respectively. Subsequently, the recombinant Scl2-M-haFGF was readily purified through a facile process of acid precipitation and subjected to enterokinase (EK) cleavage. After Scl2-M cleavage, tag-free r-haFGF was further purified using ion-exchange chromatography. The recovery rate of the whole purification process attained 34.2%. Furthermore, the resulting high-purity (96.0%) r-haFGF was prepared by freeze-drying as a final product, and its bioactivity was confirmed to potentiate the proliferation of L929 and BALB-3T3 fibroblasts. Overall, our developed method has the potential for the massive production of the r-haFGF in the future.
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Assessing the bioactivity of the codon optimized sfGFP-IGF1 fusion protein via interaction with IGFBP3 and induction of cell proliferation. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Emamipour N, Vossoughi M, Mahboudi F, Golkar M, Fard-Esfahani P. Soluble expression of IGF1 fused to DsbA in SHuffle™ T7 strain: optimization of expression and purification by Box-Behnken design. Appl Microbiol Biotechnol 2019; 103:3393-3406. [PMID: 30868206 DOI: 10.1007/s00253-019-09719-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
Production of insulin-like growth factor 1 (IGF1) in Escherichia coli mostly results in the formation of inclusion bodies. In the present study, IGF1 was fused to disulfide bond oxidoreductase A (DsbA) and expressed in SHuffle™ T7 strain, in order to obtain correctly folded protein. Soluble expression and IMAC purification of DsbA-IGF1 were optimized by applying the Box-Behnken design of response surface methodology. The optimization greatly increased concentration of soluble protein from 317 to 2600 mg/L, and IMAC yield from 400 to 1900 mg/L. Results of ANOVA showed induction OD600 and temperature had significant effects on the soluble protein expression while isopropyl-β-d thiogalactoside, in the concentrations tested, displayed no significant effect. Moreover, the three parameters of the binding buffer including, pH, concentration of NaCl, and imidazole displayed significant effects on the IMAC yield. Then, purified DsbA-IGF1 was cleaved by human rhinovirus 3C protease, and authentic IGF1 was obtained in flow through of a subtractive IMAC. Final polishing of the protein by reversed-phase HPLC yielded IGF1 with purity of 96%. The quality attributes of purified IGF1 such as purity, identity, molecular size, molecular weight, secondary structure, and biological activity were assessed and showed to be comparable to the standard IGF1. The final yield of purified IGF1 was estimated to be 120 ± 18 mg from 1 L of the culture. Our results demonstrated a simple and easily scalable strategy for production of large amounts of bioactive IGF1 by rational designing soluble protein expression, and further optimization of expression and purification methods.
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Affiliation(s)
- Nabbi Emamipour
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Manouchehr Vossoughi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Fereidoun Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran
| | - Majid Golkar
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
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Wang J, Yu H, Tian S, Yang H, Wang J, Zhu W. Recombinant expression insulin-like growth factor 1 in Bacillus subtilis using a low-cost heat-purification technology. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Efficient Production of Hydroxylated Human-Like Collagen Via the Co-Expression of Three Key Genes in Escherichia coli Origami (DE3). Appl Biochem Biotechnol 2015; 178:1458-70. [DOI: 10.1007/s12010-015-1959-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022]
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Periplasmic expression optimization of VEGFR2 D3 adopting response surface methodology: Antiangiogenic activity study. Protein Expr Purif 2013; 90:55-66. [DOI: 10.1016/j.pep.2013.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 11/22/2022]
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Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering. J Ind Microbiol Biotechnol 2011; 38:1891-910. [PMID: 21901404 DOI: 10.1007/s10295-011-1034-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/20/2011] [Indexed: 10/17/2022]
Abstract
Different hosts have been used for recombinant protein production, ranging from simple bacteria, such as Escherichia coli and Bacillus subtilis, to more advanced eukaryotes as Saccharomyces cerevisiae and Pichia pastoris, to very complex insect and animal cells. All have their advantages and drawbacks and not one seems to be the perfect host for all purposes. In this review we compare the characteristics of all hosts used in commercial applications of recombinant protein production, both in the area of biopharmaceuticals and industrial enzymes. Although the bacterium E. coli remains a very often used organism, several drawbacks limit its possibility to be the first-choice host. Furthermore, we show what E. coli strains are typically used in high cell density cultivations and compare their genetic and physiological differences. In addition, we summarize the research efforts that have been done to improve yields of heterologous protein in E. coli, to reduce acetate formation, to secrete the recombinant protein into the periplasm or extracellular milieu, and to perform post-translational modifications. We conclude that great progress has been made in the incorporation of eukaryotic features into E. coli, which might allow the bacterium to regain its first-choice status, on the condition that these research efforts continue to gain momentum.
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