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Sheng Y, Yang J, Wang C, Sun X, Yan L. Microbial nattokinase: from synthesis to potential application. Food Funct 2023; 14:2568-2585. [PMID: 36857725 DOI: 10.1039/d2fo03389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Nattokinase (NK) is an alkaline serine protease with strong thrombolytic activity produced by Bacillus spp. or Pseudomonas spp. It is a potential therapeutic agent for thrombotic diseases because of its safety, economy, and lack of side effects. Herein, a comprehensive summary and analysis of the reports surrounding NK were presented, and the physical-chemical properties and producers of NK were first described. The process and mechanism of NK synthesis were summarized, but these are vague and not specific enough. Further results may be achieved if detection techniques such as multi-omics are used to explore the process of NK synthesis. The purification of NK has problems such as a complicated operation and low recovery rate, which were found when summarizing the techniques to improve the quality of finished products. If multiple simple and efficient precipitation methods and purification materials are combined to purify NK, it may be possible to solve the current challenges. Additionally, the application potential of NK in biomedicine was reviewed, but functional foods with NK are challenging for acceptance in daily life due to their unpleasant odor. Accordingly, multi-strain combination fermentation or food flavoring agents can improve the odor of fermented foods and increase people's acceptance of them. Finally, the possible future directions focused on NK studies were proposed and provided suggestions for subsequent researchers.
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Affiliation(s)
- Yanan Sheng
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China.
| | - Jiani Yang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Changyuan Wang
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China.
| | - Xindi Sun
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Lei Yan
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China.
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
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Li Y, Wu Y, Liu Y, Li J, Du G, Lv X, Liu L. A genetic toolkit for efficient production of secretory protein in Bacillus subtilis. BIORESOURCE TECHNOLOGY 2022; 363:127885. [PMID: 36064082 DOI: 10.1016/j.biortech.2022.127885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Bacillus subtilis is a microbial cell factory widely used to produce recombinant proteins, but the expression of heterologous proteins is often severely hampered. This study constructed a genetic toolkit for improving the secretory efficiency of heterologous proteins in Bacillus subtilis. First, the protease-deficient hosts were reconstructed. Then, two endogenous constitutive promoters, Phag and PspovG, were screened. Next, a method called systemic combinatorial optimization of ribosome binding site (RBS) equipped with signal peptide (SCORES) was designed for optimizing the secretion and translation of the heterologous protein. Finally, Serratia marcescens nonspecific endonuclease (SMNE), which causes cell death by degrading nucleic acids, was expressed. The enzyme activity in the shake flask reached 7.5 × 106 U/L, which was 7.5-times that of the control RBS and signal peptide combination (RS0). This study not only expanded on the synthetic biology toolbox in B. subtilis but also provided strategies to create a prokaryotic protein expression system.
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Affiliation(s)
- Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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Sharma C, Nigam A, Singh R. Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1. PeerJ 2021; 9:e11570. [PMID: 34141495 PMCID: PMC8183432 DOI: 10.7717/peerj.11570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as-Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (-21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.
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Affiliation(s)
- Chhavi Sharma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
| | - Arti Nigam
- Department of Microbiology, Institute of Home Economics, Delhi University South Campus, Delhi, India
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
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Yang M, Wu J, Huang Q, Jia Y. Probing the Role of Catalytic Triad on the Cleavage between Intramolecular Chaperone and NK Mature Peptide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2348-2353. [PMID: 33569954 DOI: 10.1021/acs.jafc.0c07238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many proteases require the assistance of an intramolecular chaperone (IMC) that is essential for protein folding. Subtilisin is produced as a precursor that requires its N-terminal propeptide to act as an IMC to chaperone the folding of its subtilisin domain. During the precursor folding, the cleavage of the peptide bond between the IMC and the subtilisin domain is the most important and rate-limiting step, which leads to the structural reorganization of the subtilisin domain and IMC's degradation. It is speculated that the cleavage is fulfilled by the nucleophilic attack of Ser221, with the assistance of Asp32 positioning the correct tautomer of His64 and His64 accepting a proton from Ser221. In this study, our results suggested that there was a different mechanism of cleavage of the peptide bond between the IMC and the subtilisin domain in nattokinase (NK), and the role of the NK catalytic triad on the cleavage was not consistent with the classical theory. This finding suggested that members of the subtilisin family had evolved different mechanisms to acquire their own active subtilisin efficiently.
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Affiliation(s)
- Manli Yang
- Beijing Key Laboratory of Plants Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Jingyu Wu
- Beijing Key Laboratory of Plants Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick NJ08901, United States
| | - Yan Jia
- Beijing Key Laboratory of Plants Resource Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
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Moula Ali AM, Bavisetty SCB. Purification, physicochemical properties, and statistical optimization of fibrinolytic enzymes especially from fermented foods: A comprehensive review. Int J Biol Macromol 2020; 163:1498-1517. [PMID: 32781120 DOI: 10.1016/j.ijbiomac.2020.07.303] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Fibrinolytic enzymes are proteases responsible for cleavage of fibrin mesh in thrombus clots, which are the primary causative agents in cardiovascular diseases. Developing safe, effective and cheap thrombolytic agents are important for prevention and cure of thrombosis. Although a wide variety of sources have been discovered for fibrinolytic enzymes, only few of them have been employed in clinical and therapeutic applications due to the drawbacks such as high cost of production, low stability of enzyme or therapeutic side effects. However, the discovery of new fibrinolytic enzymes requires complex purification stages and characterization, which gives an insight into their diverse modes of action. Post-discovery, approaches such as a) statistical optimization for fermentative bioprocessing and b) genetic engineering are advantageous in providing economic viability by finding simple and cost-effective medium, strain development with sufficient nutrient supplements for stable and high-level production of recombinant enzyme. This review provides a comprehensive understanding of different sources, purification techniques, production through genetic engineering approaches and statistical optimization of fermentation parameters as proteases have a wide variety of industrial and biotechnological applications making 60% of total enzyme market worldwide. New strategies targeting increased enzyme yields, non-denaturing environments, improved stability, enzyme activity and strain improvement have been discussed.
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Affiliation(s)
- Ali Muhammed Moula Ali
- Department of Food Science and Technology, Faculty of Food-Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Sri Charan Bindu Bavisetty
- Department of Fermentation Technology, Faculty of Food-Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
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Zhang K, Su L, Wu J. Recent Advances in Recombinant Protein Production byBacillus subtilis. Annu Rev Food Sci Technol 2020; 11:295-318. [DOI: 10.1146/annurev-food-032519-051750] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacillus subtilis has become a widely used microbial cell factory for the production of recombinant proteins, especially those associated with foods and food processing. Recent advances in genetic manipulation and proteomic analysis have been used to greatly improve protein production in B. subtilis. This review begins with a discussion of genome-editing technologies and application of the CRISPR–Cas9 system to B. subtilis. A summary of the characteristics of crucial legacy strains is followed by suggestions regarding the choice of origin strain for genetic manipulation. Finally, the review analyzes the genes and operons of B. subtilis that are important for the production of secretory proteins and provides suggestions and examples of how they can be altered to improve protein production. This review is intended to promote the engineering of this valuable microbial cell factory for better recombinant protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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8
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Jia Y, Cao X, Deng Y, Bao W, Tang C, Ding H, Zheng Z, Zou G. Four residues of propeptide are essential for precursor folding of nattokinase. Acta Biochim Biophys Sin (Shanghai) 2014; 46:957-64. [PMID: 25267722 DOI: 10.1093/abbs/gmu093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Subtilisin propeptide functions as an intramolecular chaperone that guides precursor folding. Nattokinase, a member of subtilisin family, is synthesized as a precursor consisting of a signal peptide, a propeptide, and a subtilisin domain, and the mechanism of its folding remains to be understood. In this study, the essential residues of nattokinase propeptide which contribute to precursor folding were determined. Deletion analysis showed that the conserved regions in propeptide were important for precursor folding. Single-site and multi-site mutagenesis studies confirmed the role of Tyr10, Gly13, Gly34, and Gly35. During stage (i) and (ii) of precursor folding, Tyr10 and Gly13 would form the part of interface with subtilisin domain. While Gly34 and Gly35 connected with an α-helix that would stabilize the structure of propeptide. The quadruple Ala mutation, Y10A/G13A/G34A/G35A, resulted in a loss of the chaperone function for the propeptide. This work showed the essential residues of propeptide for precursor folding via secondary structure and kinetic parameter analyses.
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Affiliation(s)
- Yan Jia
- Beijing Key Laboratory of Plants Resource Research and Development, School of Science, Beijing Technology and Business University, Beijing 100048, China
| | - Xinhua Cao
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Deng
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Bao
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Changyan Tang
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hanjing Ding
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongliang Zheng
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Guolin Zou
- State Key Laboratory of Virology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Dang X, Pan G, Li T, Lin L, Ma Q, Geng L, He Y, Zhou Z. Characterization of a subtilisin-like protease with apical localization from microsporidian Nosema bombycis. J Invertebr Pathol 2013. [DOI: 10.1016/j.jip.2012.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Congyu K, Wujuan S, Qunzheng Z, Xindu G. Refolding of urea-denaturedα-chymotrypsin by protein-folding liquid chromatography. Biomed Chromatogr 2012; 27:433-9. [DOI: 10.1002/bmc.2810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 08/01/2012] [Accepted: 08/01/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ke Congyu
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Sun Wujuan
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Zhang Qunzheng
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Geng Xindu
- Institute of Modern Separation Science, Shaanxi Key Laboratory of Modern Separation Science; Northwest University; Xi'an; 710069; China
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Yongjun C, Wei B, Shujun J, Meizhi W, Yan J, Yan Y, Zhongliang Z, Goulin Z. Directed evolution improves the fibrinolytic activity of nattokinase from Bacillus natto. FEMS Microbiol Lett 2011; 325:155-61. [DOI: 10.1111/j.1574-6968.2011.02423.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Cai Yongjun
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Bao Wei
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Jiang Shujun
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Weng Meizhi
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Jia Yan
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Yin Yan
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Zheng Zhongliang
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Zou Goulin
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
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