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Wang B, Liu Y, Bai X, Tian H, Wang L, Feng M, Xia H. In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis. Commun Biol 2024; 7:628. [PMID: 38789612 PMCID: PMC11126579 DOI: 10.1038/s42003-024-06340-0] [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: 10/22/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Generating genetic diversity lies at the heart of directed evolution which has been widely used to engineer genetic parts and gene circuits in synthetic biology. With the ever-expanding application of directed evolution, different approaches of generating genetic diversity are required to enrich the traditional toolbox. Here we show in vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis (epADS). This approach comprises a three-step process which incorporates base errors randomly generated during chemical synthesis of oligonucleotides under specific conditions into the target DNA. Through this method, 200 ~ 4000 folds of diversification in fluorescent strength have been achieved in genes encoding fluorescent proteins. EpADS has also been successfully used to diversify regulatory genetic parts, synthetic gene circuits and even increase microbial tolerance to carbenicillin in a short time period. EpADS would be an alternative tool for directed evolution which may have useful applications in synthetic biology.
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Affiliation(s)
- Baowei Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
| | - Yang Liu
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xuelian Bai
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huijuan Tian
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lina Wang
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Miao Feng
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Hairong Xia
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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2
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Chen Y, Li M, Yan M, Chen Y, Saeed M, Ni Z, Fang Z, Chen H. Bacillus subtilis: current and future modification strategies as a protein secreting factory. World J Microbiol Biotechnol 2024; 40:195. [PMID: 38722426 DOI: 10.1007/s11274-024-03997-x] [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: 03/01/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.
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Affiliation(s)
- Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Miaomiao Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yong Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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3
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Sun B, Li Z, Peng Y, Wang F, Cheng Y, Liu Y, Ma L. Whole-Cell Display of Phospholipase D in Escherichia coli for High-Efficiency Extracellular Phosphatidylserine Production. Biomolecules 2024; 14:430. [PMID: 38672447 PMCID: PMC11048313 DOI: 10.3390/biom14040430] [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: 02/04/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Phospholipids are widely utilized in various industries, including food, medicine, and cosmetics, due to their unique chemical properties and healthcare benefits. Phospholipase D (PLD) plays a crucial role in the biotransformation of phospholipids. Here, we have constructed a super-folder green fluorescent protein (sfGFP)-based phospholipase D (PLD) expression and surface-display system in Escherichia coli, enabling the surface display of sfGFP-PLDr34 on the bacteria. The displayed sfGFP-PLDr34 showed maximum enzymatic activity at pH 5.0 and 45 °C. The optimum Ca2+ concentrations for the transphosphatidylation activity and hydrolysis activity are 100 mM and 10 mM, respectively. The use of displayed sfGFP-PLDr34 for the conversion of phosphatidylcholine (PC) and L-serine to phosphatidylserine (PS) showed that nearly all the PC was converted into PS at the optimum conditions. The displayed enzyme can be reused for up to three rounds while still producing detectable levels of PS. Thus, Escherichia coli/sfGFP-PLD shows potential for the feasible industrial-scale production of PS. Moreover, this system is particularly valuable for quickly screening higher-activity PLDs. The fluorescence of sfGFP can indicate the expression level of the fused PLD and changes that occur during reuse.
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Affiliation(s)
| | | | | | | | | | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (B.S.); (Z.L.); (Y.P.); (F.W.); (Y.C.)
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (B.S.); (Z.L.); (Y.P.); (F.W.); (Y.C.)
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4
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Guan A, Hou Y, Yang R, Qin J. Enzyme engineering for functional lipids synthesis: recent advance and perspective. BIORESOUR BIOPROCESS 2024; 11:1. [PMID: 38647956 PMCID: PMC10992173 DOI: 10.1186/s40643-023-00723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/24/2023] [Indexed: 04/25/2024] Open
Abstract
Functional lipids, primarily derived through the modification of natural lipids by various processes, are widely acknowledged for their potential to impart health benefits. In contrast to chemical methods for lipid modification, enzymatic catalysis offers distinct advantages, including high selectivity, mild operating conditions, and reduced byproduct formation. Nevertheless, enzymes face challenges in industrial applications, such as low activity, stability, and undesired selectivity. To address these challenges, protein engineering techniques have been implemented to enhance enzyme performance in functional lipid synthesis. This article aims to review recent advances in protein engineering, encompassing approaches from directed evolution to rational design, with the goal of improving the properties of lipid-modifying enzymes. Furthermore, the article explores the future prospects and challenges associated with enzyme-catalyzed functional lipid synthesis.
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Affiliation(s)
- Ailin Guan
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Yue Hou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Run Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China.
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Liu Z, Chen S, Wu J. Advances in ultrahigh-throughput screening technologies for protein evolution. Trends Biotechnol 2023; 41:1168-1181. [PMID: 37088569 DOI: 10.1016/j.tibtech.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023]
Abstract
Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.
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Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China.
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Zhang P, Gong JS, Xie ZH, Su C, Zhang XM, Rao ZM, Xu ZH, Shi JS. Efficient secretory expression of phospholipase D for the high-yield production of phosphatidylserine and phospholipid derivates from soybean lecithin. Synth Syst Biotechnol 2023; 8:273-280. [PMID: 37033293 PMCID: PMC10073938 DOI: 10.1016/j.synbio.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Phospholipase D (PLD) is an essential biocatalyst for the biological production of phosphatidylserine and phospholipid modification. However, the efficient heterologous expression of PLD is limited by its cell toxicity. In this study, a PLD was secretory expressed efficiently in Bacillus subtilis with an activity around 100 U/mL. A secretory expression system containing the signal peptide SPEstA and the dual-promoter PHpaII-SrfA was established, and the extracellular PLD activity further reached 119.22 U/mL through scale-up fermentation, 191.30-fold higher than that of the control. Under optimum reaction conditions, a 61.61% conversion ratio and 21.07 g/L of phosphatidylserine production were achieved. Finally, the synthesis system of PL derivates was established, which could efficiently synthesis novel PL derivates. The results highlight that the secretory expression system constructed in this study provides a promising PLD producing strain in industrial application, and laid the foundation for the biosynthesis of phosphatidylserine and other PL derivates. As far as we know, this work reports the highest level of extracellular PLD expression to date and the enzymatic production of several PL derivates for the first time.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
- Corresponding author. Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China.
| | - Zhi-Hao Xie
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Xiao-Mei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Zhi-Ming Rao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, PR China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
- Corresponding author. Lihu Avenue No. 1800, Jiangnan University, Wuxi, 214122, PR China.
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Yin C, Zhang H, Mao X. Cellulose nanofibril-stabilized Pickering emulsion as a high-performance interfacial biocatalysis system for the synthesis of phosphatidylserine. Food Chem 2023; 399:133865. [DOI: 10.1016/j.foodchem.2022.133865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022]
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Zhang H, Secundo F, Sun J, Mao X. Advances in enzyme biocatalysis for the preparation of functional lipids. Biotechnol Adv 2022; 61:108036. [PMID: 36130694 DOI: 10.1016/j.biotechadv.2022.108036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/02/2022]
Abstract
Functional lipids, mainly ω-3 polyunsaturated fatty acids (n-3 PUFAs) such as eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3), are known to have a variety of health benefits. Lipases and phospholipases are widely used to prepare different forms of structured lipids, since biocatalytic methods can be carried out under mild conditions, preserving the quality of the products. On the other hand, many processes still are conducted at high temperatures and with organic solvents, which are conditions unfavorable for the production of nutritional products. This article gives an updated overview of enzyme biocatalysis methods for the preparation of different derivatives containing n-3 PUFAs, including specific reactions, enzyme immobilization research for high-efficiency catalysis, and enzyme engineering technologies (higher selectivity, stability, and activity). Furthermore, advanced control strategies of biocatalytic processes and reactors are presented. The future prospect and opportunities for marine functional lipids are also discussed. Therefore, the obtainment of enzymes endowed with superior properties and the development of optimized processes, still have to be pursued to achieve greener bio-catalyzed processes.
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Affiliation(s)
- Haiyang Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Francesco Secundo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, v. Mario Bianco 9, Milan 20131, Italy
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Abstract
In recent years, structured phospholipids (SPLs), which are modified phospholipids (PLs), have attracted more attention due to their great potential for application in the field of pharmacy, food, cosmetics, and health. SPLs not only possess enhanced chemical, physical and nutritional properties, but also present superior bioavailability in comparison with other lipid forms, such as triacylglycerols, which make SPLs become more competitive carriers to increase the absorption of the specific fatty acids in the body. Compared with chemical-mediated SPLs, the process of enzyme-mediated SPLs has the advantages of high product variety, high substrate selectivity, and mild operation conditions. Both lipases and phospholipases can be used in the enzymatic production of SPLs, and the main reaction type contains esterification, acidolysis, and transesterification. During the preparation, reaction medium, acyl migration, water content/activity, substrates and enzymes, and some other parameters have significant effects on the production and purity of the desired PLs products. In this paper, the progress in enzymatic modification of PLs over the last 20 years is reviewed. Reaction types and characteristic parameters are summarized in detail and the parameters affecting acyl migration are first discussed to give the inspiration to optimize the enzyme-mediated SPLs preparation. To expand the application of enzyme-mediated SPLs in the future, the prospect of further study on SPLs is also proposed at the end of the paper.
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Li Z, Li W, Wang Y, Chen Z, Nakanishi H, Xu X, Gao XD. Establishment of a Novel Cell Surface Display Platform Based on Natural "Chitosan Beads" of Yeast Spores. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7479-7489. [PMID: 35678723 DOI: 10.1021/acs.jafc.2c01983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cell surface display technology, which expresses and anchors proteins on the surface of microbial cells, has broad application prospects in many fields, such as protein library screening, biocatalysis, and biosensor development. However, traditional cell surface display systems have disadvantages: the molecular weight of phage display proteins cannot be too large; bacterial display lacks the post-translational modification process for eukaryotic proteins; yeast display is prone to excessive protein glycosylation and misfolding of multisubunit proteins; and the compatibility of Bacillus subtilis spore display needs to be further improved. Therefore, it is extremely valuable to develop an efficient surface display platform with strong universality and stress resistance properties. Although yeast surface display systems have been extensively investigated, the establishment of a surface display platform using yeast spores has rarely been reported. In this study, a novel cell surface display platform based on natural "chitosan beads" of yeast spores was developed. The target protein in fusion with the chitosan affinity protein (CAP) exhibited strong binding capability with "chitosan beads" of yeast spores in vitro and in vivo. Moreover, this protein display system showed highly preferable enzymatic properties and stability. As an example, the displayed LXYL-P1-2-CAP demonstrated high thermostability and reusability (60% of the initial activity after seven cycles of reuse), high storage stability (75% of original activity after 8 weeks), and excellent tolerance to a concentration up to 75% (v/v) organic reagents. To prove the practicability of this surface display system, the semisynthesis of paclitaxel intermediate was demonstrated and its highest conversion rate was 92% using 0.25 mM substrate. This study provides a novel and useful platform for the surface display of proteins, especially for multimeric macromolecular proteins of eukaryotic origin.
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Affiliation(s)
- Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wanjie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Xiangyang Xu
- Zaozhuang Jienuo Enzyme Co., Ltd., Zaozhuang 277100, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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Qi N, Liu J, Song W, Liu J, Gao C, Chen X, Guo L, Liu L, Wu J. Rational Design of Phospholipase D to Improve the Transphosphatidylation Activity for Phosphatidylserine Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6709-6718. [PMID: 35616637 DOI: 10.1021/acs.jafc.2c02212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Phosphatidylserine (PS) has been widely used in the fields of food and medicine, among others, owing to its unique chemical structure and health benefits. However, the phospholipase D (PLD)-mediated enzymatic production of PS remains a challenge due to the low transphosphatidylation activity of PLD. Therefore, in the present study, we designed a maltose-binding protein (MBP) tag and a PLD co-expression method to achieve the expression of soluble PLD in Escherichia coli. A "reconstruct substrate pocket" strategy was then proposed based on the catalytic mechanism and molecular dynamics simulation, expanding the substrate pocket and manipulating the coordination of l-Ser within the active site. The best mutant (SrMBPPLDMu6) exhibited a 2.04-fold higher transphosphatidylation/hydrolysis ratio than the wild-type Furthermore, under optimal conditions, Mu6 produced 58.6 g/L PS with 77.2% conversion, within 12 h on a 3 L scale, which demonstrates the potential of the proposed method for industrial application.
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Affiliation(s)
- Na Qi
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianmin Liu
- Shandong Huishilai Biotechnology Co., Ltd., Jinan, Shandong 250098, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
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Pei Y, Zhao S, Chen X, Zhang J, Ni H, Sun M, Lin H, Liu X, Chen H, Yang S. Bacillus velezensis EEAM 10B Strengthens Nutrient Metabolic Process in Black Soldier Fly Larvae (Hermetia illucens) via Changing Gut Microbiome and Metabolic Pathways. Front Nutr 2022; 9:880488. [PMID: 35662952 PMCID: PMC9161358 DOI: 10.3389/fnut.2022.880488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Insects are a potential alternative protein source to solve the food shortage crisis. Previous studies have illustrated that probiotics can improve the substrate conversion efficiency of insects and increase insect protein content. However, the effects of probiotics on insect physiology and nutrient metabolism are still not well understood. Here, the black soldier fly larvae (BSFL), Hermetia illucens (Diptera: Stratiomyidae), was used as a study subject to deeply investigate the specific interaction among a novel probiotic, Bacillus velezensis EEAM 10B (10B), intestinal microbiota, and the host. In this study, the effects of 10B on the survival and physiology of BSFL were first analyzed. It shows that 10B significantly elevated the substrate conversion rate, average dry weight, and protein content of BSFL by 5%, 0.13 g/pc, and 8%, respectively. Then, we assessed the effect of 10B on the microbial community composition in the gut and frass of BSFL using Illumina Miseq sequencing. It shows that 10B significantly altered the microbial composition of the gut, but not that of the frass. Pearson’s correlation analysis further showed that the Bacillus, unclassified_of_Caloramatoraceae, and Gracilibacillus were positively correlated with the survival rate, crude protein content, and substrate conversion rate of BSFL. To further investigate the effect of 10B on host metabolism, metabolic analyses on germ-free BSFL, monobacterial intestinal BSFL, and natural BSFL were also performed. The results proved that 10B (i) played a vital role in the survival of BSFL; and (ii) regulated the amino acid synthetic and metabolic process of BSFL, thus leading to the rise of the protein content of BSFL. In addition, vitamin backfill assays verified that the BSFL survival rate was significantly improved by supplying the germ-free BSFL with riboflavin, which further suggests that 10B determines the survival of BSFL via delivering riboflavin. Overall, this study provides a reference for understanding the comprehensive contribution of a specific probiotic to its host.
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Affiliation(s)
- Yaxin Pei
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Sijie Zhao
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Xiang Chen
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Jiran Zhang
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Hongyuhang Ni
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Mengxiao Sun
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Hui Lin
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Xinyu Liu
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Hongge Chen
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
| | - Sen Yang
- Department of Microbiology, School of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou, China
- *Correspondence: Sen Yang,
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Zhang P, Gong JS, Qin J, Li H, Hou HJ, Zhang XM, Xu ZH, Shi JS. Phospholipids (PLs) know-how: exploring and exploiting phospholipase D for its industrial dissemination. Crit Rev Biotechnol 2021; 41:1257-1278. [PMID: 33985392 DOI: 10.1080/07388551.2021.1921690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/26/2020] [Accepted: 02/24/2021] [Indexed: 10/21/2022]
Abstract
Owing to their numerous nutritional and bioactive functions, phospholipids (PLs), which are major components of biological membranes in all living organisms, have been widely applied as nutraceuticals, food supplements, and cosmetic ingredients. To date, PLs are extracted solely from soybean or egg yolk, despite the diverse market demands and high cost, owing to a tedious and inefficient manufacturing process. A microbial-based manufacturing process, specifically phospholipase D (PLD)-based biocatalysis and biotransformation process for PLs, has the potential to address several challenges associated with the soybean- or egg yolk-based supply chain. However, poor enzyme properties and inefficient microbial expression systems for PLD limit their wide industrial dissemination. Therefore, sourcing new enzyme variants with improved properties and developing advanced PLD expression systems are important. In the present review, we systematically summarize recent achievements and trends in the discovery, their structural properties, catalytic mechanisms, expression strategies for enhancing PLD production, and its multiple applications in the context of PLs. This review is expected to assist researchers to understand current advances in this field and provide insights for further molecular engineering efforts toward PLD-mediated bioprocessing.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Jiufu Qin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Hai-Juan Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Xiao-Mei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, P. R. China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, P. R. China
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14
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Zhang H, Li X, Liu Q, Sun J, Secundo F, Mao X. Construction of a Super-Folder Fluorescent Protein-Guided Secretory Expression System for the Production of Phospholipase D in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6842-6849. [PMID: 34124889 DOI: 10.1021/acs.jafc.1c02089] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phospholipids (PLs) are one of the main ingredients in food and nutraceutical, cosmetics, agriculture, and pharmaceutical products. Phospholipase D (PLD) is a crucial enzyme for the biocatalytic synthesis or modification of PLs. Here, to prepare PLD more efficiently, we constructed a PLD expression and secretion system in Bacillus subtilis and developed an environmentally friendly reaction system. A nonclassical secretory pathway where a super-folder green fluorescent protein plays as an N-terminal guide protein was introduced. This expression system can not only achieve rapid screening of high-level expression strains but can also achieve the secretion of the target proteins. Under optimal fermentation conditions, the enzyme activity of the culture medium was 0.35 U/mL, which was 2.05-fold that of the Sec secretion pathway strains. Meanwhile, the effects of several organic solvents in the biphasic reaction media were compared. The results showed that when using cyclopentyl methyl ether as the organic phase, the final conversion rate reached 96.9%. It has shown good application potential in the synthesis of phosphatidylserine, laid the foundation for the synthesis and application of other rare and high-value PLs, and provided a reference for the production of other biocatalysts.
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Affiliation(s)
- Haiyang Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xuehan Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Qi Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Francesco Secundo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, v. Mario Bianco 9, Milan 20131, Italy
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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15
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Su H, Gao L, Sun J, Mao X. Engineering a carbohydrate binding module to enhance chitinase catalytic efficiency on insoluble chitinous substrate. Food Chem 2021; 355:129462. [PMID: 33848938 DOI: 10.1016/j.foodchem.2021.129462] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/25/2020] [Accepted: 02/22/2021] [Indexed: 11/15/2022]
Abstract
Development of a high-performance chitinase for efficient biotransformation of insoluble chitinous substrate would be highly valuable in industry. In this study, the chitin-binding domains (ChBDs) of chitinase SaChiA4 were successfully modified to improve the enzymatic activity. The engineered substitution variant R-SaChiA4, which had the exogenous ChBD of chitinase ChiA1 from Bacillus circulans WL-12 (ChBDChiA1) substituted for its original ChBDChiA4, increased its activity by nearly 54% (28.0 U/mg) towards chitin powder, and by 49% towards colloidal chitin, compared with the wild-type. The substrate-binding assay demonstrated that the ChBD could enhance the capacity of enzymatic hydrolysis by promoting substrate affinity, and molecular dynamics simulations indicated that this could be due to hydrophobic interactions in different substrate binding modes. This work advances the understanding of the role of the ChBD, and provides a step towards the achievement of industrial-scale hydrolysis and utilization of insoluble chitin.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Li Gao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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16
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High-level soluble expression of phospholipase D from Streptomyces chromofuscus in Escherichia coli by combinatorial optimization. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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17
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Dong H, Zhang W, Zhou S, Huang J, Wang P. Engineering bioscaffolds for enzyme assembly. Biotechnol Adv 2021; 53:107721. [PMID: 33631185 DOI: 10.1016/j.biotechadv.2021.107721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 12/27/2022]
Abstract
With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN 55108, USA.
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