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Haeger G, Wirges J, Tanzmann N, Oyen S, Jolmes T, Jaeger KE, Schörken U, Bongaerts J, Siegert P. Chaperone assisted recombinant expression of a mycobacterial aminoacylase in Vibrio natriegens and Escherichia coli capable of N-lauroyl-L-amino acid synthesis. Microb Cell Fact 2023; 22:77. [PMID: 37085846 PMCID: PMC10122368 DOI: 10.1186/s12934-023-02079-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Aminoacylases are highly promising enzymes for the green synthesis of acyl-amino acids, potentially replacing the environmentally harmful Schotten-Baumann reaction. Long-chain acyl-amino acids can serve as strong surfactants and emulsifiers, with application in cosmetic industries. Heterologous expression of these enzymes, however, is often hampered, limiting their use in industrial processes. RESULTS We identified a novel mycobacterial aminoacylase gene from Mycolicibacterium smegmatis MKD 8, cloned and expressed it in Escherichia coli and Vibrio natriegens using the T7 overexpression system. The recombinant enzyme was prone to aggregate as inclusion bodies, and while V. natriegens Vmax™ could produce soluble aminoacylase upon induction with isopropyl β-d-1-thiogalactopyranoside (IPTG), E. coli BL21 (DE3) needed autoinduction with lactose to produce soluble recombinant protein. We successfully conducted a chaperone co-expression study in both organisms to further enhance aminoacylase production and found that overexpression of chaperones GroEL/S enhanced aminoacylase activity in the cell-free extract 1.8-fold in V. natriegens and E. coli. Eventually, E. coli ArcticExpress™ (DE3), which co-expresses cold-adapted chaperonins Cpn60/10 from Oleispira antarctica, cultivated at 12 °C, rendered the most suitable expression system for this aminoacylase and exhibited twice the aminoacylase activity in the cell-free extract compared to E. coli BL21 (DE3) with GroEL/S co-expression at 20 °C. The purified aminoacylase was characterized based on hydrolytic activities, being most stable and active at pH 7.0, with a maximum activity at 70 °C, and stability at 40 °C and pH 7.0 for 5 days. The aminoacylase strongly prefers short-chain acyl-amino acids with smaller, hydrophobic amino acid residues. Several long-chain amino acids were fairly accepted in hydrolysis as well, especially N-lauroyl-L-methionine. To initially evaluate the relevance of this aminoacylase for the synthesis of N-acyl-amino acids, we demonstrated that lauroyl-methionine can be synthesized from lauric acid and methionine in an aqueous system. CONCLUSION Our results suggest that the recombinant enzyme is well suited for synthesis reactions and will thus be further investigated.
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Affiliation(s)
- Gerrit Haeger
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Jessika Wirges
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Nicole Tanzmann
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Sven Oyen
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | | | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | | | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany.
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Yang L, Zhou H, Chen G, Li H, Yang D, Pan L. Expression and Purification of Glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 and Study on Catalytic Characterization of Its Reverse Glycosyltransferase Reaction. Microorganisms 2023; 11:microorganisms11030762. [PMID: 36985335 PMCID: PMC10058486 DOI: 10.3390/microorganisms11030762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Anthracyclines are an important class of natural antitumor drugs. They have a conservative aromatic tetracycline backbone that is substituted with different deoxyglucoses. The deoxyglucoses are crucial for the biological activity of many bacterial natural products after the proper modification from glycosyltransferases (GTs). The difficulty in obtaining highly purified active GTs has prevented biochemical studies on natural product GTs. In this paper, a new Escherichia coli fusion plasmid pGro7′, which introduces the Streptomyces coelicolor chaperone genes groEL1, groES and groEL2, was constructed. The glycosyltransferase DnmS from Streptomyces peucetius ATCC 27952 was co-expressed with the plasmid pGro7′, and unprecedented high-efficiency and soluble expression of DnmS in the E. coli expression system was realized. Subsequently, the reverse glycosylation reaction characteristics of DnmS and DnmQ were verified. We found that DnmS and DnmQ had the highest enzyme activity when they participated in the reaction at the same time. These studies provide a strategy for the soluble expression of GTs in Streptomyces and confirm the reversibility of the catalytic reaction of GTs. This provides a powerful method for the production of active anthracyclines and to enhance the diversity of natural products.
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Affiliation(s)
- Liyan Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Huimin Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Guiguang Chen
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Hongliang Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Dengfeng Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- Institute of Biology, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (D.Y.); (L.P.)
| | - Lixia Pan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
- College of Food and Quality Engineering, Nanning University, Nanning 530200, China
- Correspondence: (D.Y.); (L.P.)
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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4
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Ni W, Wang Z, Zheng A, Zhao Y. Preparation and self-cleavage of fusion soluble farnesyl diphosphate synthase in E. coli. Prep Biochem Biotechnol 2023; 53:988-994. [PMID: 36639146 DOI: 10.1080/10826068.2022.2164591] [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: 01/15/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is a crucial protein in terpenoid production. However, its industrial application is limited owing to its low solubility in Escherichia coli. In this study, we focused on ispA encoding FPPS and designed a fusion expression system to reduce inclusion body (IB) formation. Among the chosen fusion tags, the GB1-domain (GB1) exhibited the highest ability to solubilize the recombinant protein. Increased rare tRNA abundance not only improved the GB1-FPPS yield but also increased its soluble level. A "one-step" method for the acquisition of soluble FPPS was also considered. By combining GB1-FPPS expression and Tobacco Etch Virus protease (TEVp) cleavage in vivo, a controllable GB1-FPPS "self-cleavage" system was constructed. Overall, this study provides an efficient approach for obtaining soluble forms of FPPS, which show great potential for use in the soluble expression of other homologous diphosphate synthase.
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Affiliation(s)
- Wenfeng Ni
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Zixuan Wang
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Aifang Zheng
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Ying Zhao
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
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5
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GroEL—A Versatile Chaperone for Engineering and a Plethora of Applications. Biomolecules 2022; 12:biom12050607. [PMID: 35625535 PMCID: PMC9138447 DOI: 10.3390/biom12050607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Chaperones play a vital role in the life of cells by facilitating the correct folding of other proteins and maintaining them in a functional state, being themselves, as a rule, more stable than the rest of cell proteins. Their functional properties naturally tempt investigators to actively adapt them for biotechnology needs. This review will mostly focus on the applications found for the bacterial chaperonin GroE and its counterparts from other organisms, in biotechnology or for research purposes, both in their engineered or intact versions.
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Liu K, Li J, Liu M, Hou J. Molecular chaperone GroEL-GroES enhances the soluble expression of biologically active ovine growth hormone in the prokaryotic system. Protein Expr Purif 2022; 195-196:106097. [DOI: 10.1016/j.pep.2022.106097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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Ravitchandirane G, Bandhu S, Chaudhuri TK. Multimodal approaches for the improvement of the cellular folding of a recombinant iron regulatory protein in E. coli. Microb Cell Fact 2022; 21:20. [PMID: 35123481 PMCID: PMC8818239 DOI: 10.1186/s12934-022-01749-w] [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: 08/26/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Background During the recombinant protein expression, most heterologous proteins expressed in E. coli cell factories are generated as insoluble and inactive aggregates, which prohibit E. coli from being employed as an expression host despite its numerous advantages and ease of use. The yeast mitochondrial aconitase protein, which has a tendency to aggregate when expressed in E. coli cells in the absence of heterologous chaperones GroEL/ES was utilised as a model to investigate how the modulation of physiological stimuli in the host cell can increase protein solubility. The presence of folding modulators such as exogenous molecular chaperones or osmolytes, as well as process variables such as incubation temperature, inducer concentrations, growth media are all important for cellular folding and are investigated in this study. This study also investigated how the cell's stress response system activates and protects the proteins from aggregation. Results The cells exposed to osmolytes plus a pre-induction heat shock showed a substantial increase in recombinant aconitase activity when combined with modulation of process conditions. The concomitant GroEL/ES expression further assists the folding of these soluble aggregates and increases the functional protein molecules in the cytoplasm of the recombinant E. coli cells. Conclusions The recombinant E. coli cells enduring physiological stress provide a cytosolic environment for the enhancement in the solubility and activity of the recombinant proteins. GroEL/ES-expressing cells not only aided in the folding of recombinant proteins, but also had an effect on the physiology of the expression host. The improvement in the specific growth rate and aconitase production during chaperone GroEL/ES co-expression is attributed to the reduction in overall cellular stress caused by the expression host's aggregation-prone recombinant protein expression. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01749-w.
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Mital S, Christie G, Dikicioglu D. Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications. Microb Cell Fact 2021; 20:208. [PMID: 34717620 PMCID: PMC8557517 DOI: 10.1186/s12934-021-01698-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023] Open
Abstract
Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclusion bodies. Our analysis systematically reviews literature from 2010 to 2021 and details the methods and strategies researchers have utilized for expression of difficult to express (DtE), industrially relevant recombinant enzymes in E. coli expression strains. Our review identifies an absence of a coherent strategy with disparate practices being used to promote solubility. We discuss the potential to approach recombinant expression systematically, with the aid of modern bioinformatics, modelling, and ‘omics’ based systems-level analysis techniques to provide a structured, holistic approach. Our analysis also identifies potential gaps in the methods used to report metadata in publications and the impact on the reproducibility and growth of the research in this field.
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Affiliation(s)
- Suraj Mital
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Duygu Dikicioglu
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK.
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Fatima K, Naqvi F, Younas H. A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins. Cell Biochem Biophys 2021; 79:153-174. [PMID: 33634426 DOI: 10.1007/s12013-021-00970-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
The advancements in biotechnology over time have led to an increase in the demand of pure, soluble and functionally active proteins. Recombinant protein production has thus been employed to obtain high expression of purified proteins in bulk. E. coli is considered as the most desirable host for recombinant protein production due to its inexpensive and fast cultivation, simple nutritional requirements and known genetics. Despite all these benefits, recombinant protein production often comes with drawbacks, such as, the most common being the formation of inclusion bodies due to improper protein folding. Consequently, this can lead to the loss of the structure-function relationship of a protein. Apart from various strategies, one major strategy to resolve this issue is the use of molecular chaperones that act as folding modulators for proteins. Molecular chaperones assist newly synthesized, aggregated or misfolded proteins to fold into their native conformations. Chaperones have been widely used to improve the expression of various proteins which are otherwise difficult to produce in E. coli. Here, we discuss the structure, function, and role of major E. coli molecular chaperones in recombinant technology such as trigger factor, GroEL, DnaK and ClpB.
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Affiliation(s)
- Komal Fatima
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Fatima Naqvi
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Hooria Younas
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan.
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10
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Gao Q, Shao J, Tang M, Xin Y, Zhang L. Promote the expression and corrected folding of an extremely stable N-demethylase by promoter reconstruction, native environment simulation and surface design. Int J Biol Macromol 2021; 178:434-443. [PMID: 33647338 DOI: 10.1016/j.ijbiomac.2021.02.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 01/10/2023]
Abstract
Thermomicrobium roseum sarcosine oxidase (TrSOX) was a N-demethylase with specific substrate chiral selectivity, outstanding thermostability and environmental resistance. To promote the expression of TrSOX in Bacillus subtilis W600, the HpaII promoter of pMA5 plasmid was replaced by constitutive or inducible promoters. Through orthogonal experiment, the expression process was optimized, B. subtilis W600 cells containing pMA5-Pxyl-trSOX plasmid were cultivated until OD600nm reached 2.0 and were then induced with 1.6% xylose at 37 °C for 2 h, and the native environment of T. roseum was simulated by heating at 80 °C, with the productivity of TrSOX increased from ~8.3 to ~66.7 μg/g wet cells; and the simulated high temperature was the key switch for the final folding. To reduce the surface hydrophobicity, a S320R mutant was built to form a hydrophilic lid around the entrance of the substrate pocket, and the yield of TrSOX (S320R) was ~163.0 μg/g wet cells, approximately 20 folds as that in the initial expression system. This mutant revealed the similar secondary structure, stability, resistance, chiral substrate selectivity and optimal reaction environment with wild type TrSOX; however, the N-demethylation activities for amino acid derivative substrates were dramatically increased, while those for hydrophobic non-amino acid compounds were repressed.
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Affiliation(s)
- Qiuyue Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China
| | - Jun Shao
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Mengwei Tang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China.
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China.
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Bhatwa A, Wang W, Hassan YI, Abraham N, Li XZ, Zhou T. Challenges Associated With the Formation of Recombinant Protein Inclusion Bodies in Escherichia coli and Strategies to Address Them for Industrial Applications. Front Bioeng Biotechnol 2021; 9:630551. [PMID: 33644021 PMCID: PMC7902521 DOI: 10.3389/fbioe.2021.630551] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Recombinant proteins are becoming increasingly important for industrial applications, where Escherichia coli is the most widely used bacterial host for their production. However, the formation of inclusion bodies is a frequently encountered challenge for producing soluble and functional recombinant proteins. To overcome this hurdle, different strategies have been developed through adjusting growth conditions, engineering host strains of E. coli, altering expression vectors, and modifying the proteins of interest. These approaches will be comprehensively highlighted with some of the new developments in this review. Additionally, the unique features of protein inclusion bodies, the mechanism and influencing factors of their formation, and their potential advantages will also be discussed.
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Affiliation(s)
- Arshpreet Bhatwa
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Weijun Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Yousef I. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Nadine Abraham
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Xiu-Zhen Li
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
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12
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Fu H, Liang Y, Zhong X, Pan Z, Huang L, Zhang H, Xu Y, Zhou W, Liu Z. Codon optimization with deep learning to enhance protein expression. Sci Rep 2020; 10:17617. [PMID: 33077783 PMCID: PMC7572362 DOI: 10.1038/s41598-020-74091-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/21/2020] [Indexed: 02/05/2023] Open
Abstract
Heterologous expression is the main approach for recombinant protein production ingenetic synthesis, for which codon optimization is necessary. The existing optimization methods are based on biological indexes. In this paper, we propose a novel codon optimization method based on deep learning. First, we introduce the concept of codon boxes, via which DNA sequences can be recoded into codon box sequences while ignoring the order of bases. Then, the problem of codon optimization can be converted to sequence annotation of corresponding amino acids with codon boxes. The codon optimization models for Escherichia Coli were trained by the Bidirectional Long-Short-Term Memory Conditional Random Field. Theoretically, deep learning is a good method to obtain the distribution characteristics of DNA. In addition to the comparison of the codon adaptation index, protein expression experiments for plasmodium falciparum candidate vaccine and polymerase acidic protein were implemented for comparison with the original sequences and the optimized sequences from Genewiz and ThermoFisher. The results show that our method for enhancing protein expression is efficient and competitive.
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Affiliation(s)
- Hongguang Fu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yanbing Liang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xiuqin Zhong
- University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - ZhiLing Pan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Huang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - HaiLin Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Xu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Wei Zhou
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zhong Liu
- Chengdu Institute of Computer Applications, Chinese Academy of Sciences, Chengdu, 610041, China
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Fu Z, Fan G, Zhu Y, Teng C, Li H, Liu Q, Yang R, Li X. Soluble expression of a novel feruloyl esterase from Burkholderia pyrrocinia B1213 in Escherichia coli and optimization of production conditions. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1803129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Zhilei Fu
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Guangsen Fan
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Yuting Zhu
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Chao Teng
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Hehe Li
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Qian Liu
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, College of Biochemical Engineering, Beijing Union University, Beijing, PR China
| | - Ran Yang
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
| | - Xiuting Li
- Laboratory of Food Microbiology and Enzyme Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, PR China
- Laboratory of Food Microbiology and Enzyme Engineering, School of Food and Health, Beijing Technology and Business University, Beijing, PR China
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Yao D, Fan J, Han R, Xiao J, Li Q, Xu G, Dong J, Ni Y. Enhancing soluble expression of sucrose phosphorylase in Escherichia coli by molecular chaperones. Protein Expr Purif 2020; 169:105571. [DOI: 10.1016/j.pep.2020.105571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
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15
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Deng J, Li J, Ma M, Zhao P, Ming F, Lu Z, Shi J, Fan Q, Liang Q, Jia J, Li J, Zhang S, Zhang L. Co-expressing GroEL-GroES, Ssa1-Sis1 and Bip-PDI chaperones for enhanced intracellular production and partial-wall breaking improved stability of porcine growth hormone. Microb Cell Fact 2020; 19:35. [PMID: 32070347 PMCID: PMC7027120 DOI: 10.1186/s12934-020-01304-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/09/2020] [Indexed: 12/18/2022] Open
Abstract
Porcine growth hormone (pGH) is a class of peptide hormones secreted from the pituitary gland, which can significantly improve growth and feed utilization of pigs. However, it is unstable and volatile in vitro. It needs to be encapsulated in liposomes when feeding livestock, whose high cost greatly limits its application in pig industry. Therefore we attempted to express pGH as intracellular soluble protein in Pichia pastoris and feed these yeasts with partial wall-breaking for swine, which could release directly pGH in intestine tract in case of being degraded in intestinal tract with low cost. In order to improve the intracellular soluble expression of pGH protein in Pichia pastoris and stability in vitro, we optimized the pGH gene, and screened molecular chaperones from E. coli and Pichia pastoris respectively for co-expressing with pGH. In addition, we had also explored conditions of mechanical crushing and fermentation. The results showed that the expression of intracellular soluble pGH protein was significantly increased after gene optimized and co-expressed with Ssa1-Sis1 chaperone from Pichia pastoris. Meanwhile, the optimal conditions of partial wall-breaking and fermentation of Pichia pastoris were confirmed, the data showed that the intracellular expression of the optimized pGH protein co-expressed with Ssa1-Sis1 could reach 340 mg/L with optimal conditions of partial wall-breaking and fermentation. Animal experiments verified that the optimized pGH protein co-expression with Ssa1-Sis1 had the best promoting effects on the growth of piglets. Our study demonstrated that Ssa1-Sis1 could enhance the intracellular soluble expression of pGH protein in Pichia pastoris and that partial wall-breaking of yeast could prevent pGH from degradation in vitro, release targetedly in the intestine and play its biological function effectively. Our study could provide a new idea to cut the cost effectively, establishing a theoretical basis for the clinic application of unstable substances in vitro.
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Affiliation(s)
- Jinbo Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jiaoqing Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Miaopeng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Peijing Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Feiping Ming
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Zhipeng Lu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Juqing Shi
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Qin Fan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Qianyi Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Junhao Jia
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jiayi Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Shuxia Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Linghua Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China.
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16
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Yurkova MS, Savvin OI, Zenin VA, Fedorov AN. Design and Characterization of a Methionineless Variant of Thermostable Chaperon GroEL from Thermus thermophilus. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819020157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Soluble expression of Thermomicrobium roseum sarcosine oxidase and characterization of N-demethylation activity. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Ni W, Liu H, Wang P, Wang L, Sun X, Wang H, Zhao G, Zheng Z. Evaluation of multiple fused partners on enhancing soluble level of prenyltransferase NovQ in Escherichia coli. Bioprocess Biosyst Eng 2018; 42:465-474. [DOI: 10.1007/s00449-018-2050-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/23/2018] [Indexed: 01/18/2023]
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19
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Preparation, reconstruction, and characterization of a predicted Thermomicrobium roseum sarcosine oxidase. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Zhou Y, Lu Z, Wang X, Selvaraj JN, Zhang G. Genetic engineering modification and fermentation optimization for extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol 2017; 102:1545-1556. [DOI: 10.1007/s00253-017-8700-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 02/06/2023]
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21
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Liu X, Zhang L, Feng X, Lv B, Li C. Biosynthesis of Glycyrrhetinic Acid-3-O-monoglucose Using Glycosyltransferase UGT73C11 from Barbarea vulgaris. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b03391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiaochen Liu
- Institute for Biotransformation and
Synthetic Biosystem, Department of Biological Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Liang Zhang
- Institute for Biotransformation and
Synthetic Biosystem, Department of Biological Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Xudong Feng
- Institute for Biotransformation and
Synthetic Biosystem, Department of Biological Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Bo Lv
- Institute for Biotransformation and
Synthetic Biosystem, Department of Biological Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Chun Li
- Institute for Biotransformation and
Synthetic Biosystem, Department of Biological Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
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22
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Chen L, Sun P, Li Y, Yan M, Xu L, Chen K, Ouyang P. A fusion protein strategy for soluble expression of Stevia glycosyltransferase UGT76G1 in Escherichia coli. 3 Biotech 2017; 7:356. [PMID: 29038773 DOI: 10.1007/s13205-017-0943-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
The UDP-glucosyltransferase UGT76G1 from Stevia rebaudiana converts stevioside to rebaudioside A via a one-step glycosylation reaction, which increases the amount of sweet-tasting rebaudioside A and decreases the amount of stevioside that has a bitter aftertaste. This enzyme could, therefore, conceivably be used to improve the organoleptic properties of steviol glycosides and offer a cost-effective preparation of high-purity rebaudioside A. Producing soluble enzymes by overexpression is a prerequisite for large-scale biocatalysis. However, most of the UGT76G1 overexpressed in Escherichia coli is in inclusion bodies. In this study, three N-terminal fusion partners, 3'-phosphoadenosine-5'-phosphatase (CysQ), 2-keto-3-deoxy-6-phosphogluconate aldolase (EDA) and N-utilisation substance A (NusA), were tested to improve UGT76G1 expression and solubility in E. coli. Compared with the fusion-free protein, the solubility of UGT76G1 was increased 40% by fusion with CysQ, and the glucosyltransferase activity of the crude extract was increased 82%. This successful CysQ fusion strategy could be applied to enhance the expression and solubility of other plant-derived glucosyltransferases and presumably other unrelated proteins in the popular, convenient and cost-effective E. coli host.
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Affiliation(s)
- Liangliang Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
| | - Ping Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
| | - Yan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
- Yichang Key Laboratory of Biocatalysis, China Three Gorges University, Yichang, 443002 China
| | - Ming Yan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
| | - Lin Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
| | - Kequan Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
| | - Pingkai Ouyang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 China
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23
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Wang Y, Shu T, Fan P, Zhang H, Turunen O, Xiong H, Yu L. Characterization of a recombinant alkaline thermostable β-mannanase and its application in eco-friendly ramie degumming. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Cai R, Chen C, Li Y, Sun K, Zhou F, Chen K, Jia H. Improved soluble bacterial expression and properties of the recombinant flavonoid glucosyltransferase UGT73G1 from Allium cepa. J Biotechnol 2017. [PMID: 28627388 DOI: 10.1016/j.jbiotec.2017.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Glycosylation of quercetin using flavonol-specific glycosyltransferases offers an alternate method for isoquercitrin production. Obtaining sufficient quantities of bioactive enzymes is an important prerequisite for highly effective biocatalysis and biotransformation. In this study, a codon-optimized gene for the flavonoid glucosyltransferase UGT73G1 from Allium cepa was heterologously expressed in the preferred prokaryotic expression host Escherichia coli. By combining expression as a fusion protein with 6-histidine tags with coexpression with molecular chaperones, increased soluble expression of UGT73G1 was achieved in E. coli. Two-terminal 6-histidine tags contributed more to the expression than molecular chaperones, as demonstrated by comparison of specific activities in crude extracts obtained from the recombinant E. coli strains. Studies of the catalytic properties of purified UGT73G1 indicated that its activity was significantly promoted by Mn2+ and Mg2+, while it was strongly inhibited by Cu2+. These expression strategies enhanced the solubility and activity of the overexpressed protein and enabled characterization of this plant-derived glucosyltransferase expressed in a prokaryotic host.
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Affiliation(s)
- Ruxin Cai
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Caihong Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; Yichang Key Laboratory of Biocatalysis, China Three Gorges University, Yichang 443002, China.
| | - Kaiyan Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Fangfang Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Kequan Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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