1
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Du Y, Lv X, Feng C, Ma Y, Wang Y. Simultaneously Enhanced Catalytic Activity and Thermostability of a Baeyer-Villiger Monooxygenase from Oceanicola granulosus by Reshaping the Binding Pocket. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15778-15787. [PMID: 38951118 DOI: 10.1021/acs.jafc.4c02395] [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: 07/03/2024]
Abstract
Enzymatic oxygenation of various cyclic ketones into lactones via Baeyer-Villiger monooxygenases (BVMOs) could provide a promising route for synthesizing fragrances and pharmaceutical ingredients. However, unsatisfactory catalytic activity and thermostability restricted their applications in the pharmaceutical and food industries. In this study, we successfully improved the catalytic activity and thermostability of a Baeyer-Villiger monooxygenase (OgBVMO) from Oceanicola granulosus by reshaping the binding pocket. As a result, mutant OgBVMO-Re displayed a 1.0- to 6.4-fold increase in the activity toward branched cyclic ketones tested, accompanied by a 3 °C higher melting point, and a 2-fold longer half-life time (t1/2 (45 °C)). Molecular dynamics simulations revealed that reshaping the binding pocket achieved strengthened motion correlation between amino acid residues, appropriate size of the substrate-binding pocket, beneficial surface characteristics, lower energy barriers, and shorter nucleophilic distance. This study well demonstrated the trade-off between the enzyme activity and thermostability by reshaping the substrate-binding pocket, paving the way for further engineering other enzymes.
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Affiliation(s)
- Yu Du
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xiang Lv
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214129, China
| | - Chenhao Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yunjian Ma
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Co., Ltd, Foshan 528012, China
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2
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Wang B, Lei S, Li Q, Luo Y. Production of lactulose from lactose using a novel cellobiose 2-epimerase from Clostridium disporicum. Enzyme Microb Technol 2024; 179:110466. [PMID: 38889605 DOI: 10.1016/j.enzmictec.2024.110466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/17/2024] [Accepted: 06/01/2024] [Indexed: 06/20/2024]
Abstract
Lactulose is a semisynthetic nondigestive sugar derived from lactose, with wide applications in the food and pharmaceutical industries. Its biological production routes which use cellobiose 2-epimerase (C2E) as the key enzyme have attracted widespread attention. In this study, a set of C2Es from different sources were overexpressed in Escherichia coli to produce lactulose. We obtained a novel and highly efficient C2E from Clostridium disporicum (CDC2E) to synthesize lactulose from lactose. The effects of different heat treatment conditions, reaction pH, reaction temperature, and substrate concentrations were investigated. Under the optimum biotransformation conditions, the final concentration of lactulose was up to 1.45 M (496.3 g/L), with a lactose conversion rate of 72.5 %. This study provides a novel C2E for the biosynthesis of lactulose from low-cost lactose.
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Affiliation(s)
- Bohua Wang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, PR China; Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Province, Changde 415000, PR China; Hunan Provincial 3R Food Innovation and Entrepreneurship Education Center for General Universities, Changde 415000, PR China.
| | - Song Lei
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, PR China; Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Province, Changde 415000, PR China; Hunan Provincial 3R Food Innovation and Entrepreneurship Education Center for General Universities, Changde 415000, PR China
| | - Qingqin Li
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, PR China
| | - Yushuang Luo
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde 415000, PR China
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3
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Chen Q, Wu J, Wu Y, Wang Z, Zeng M, He Z, Chen J, Mu W. Rational Design of Loop Dynamics for a Barrel-Shaped Enzyme by Introducing Disulfide Bonds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13856-13868. [PMID: 38848490 DOI: 10.1021/acs.jafc.4c03493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Loop dynamics redesign is an important strategy to manipulate protein function. Cellobiose 2-epimerase (CE) and other members of its superfamily are widely used for diverse industrial applications. The structural feature of the loops connecting barrel helices contributes greatly to the differences in their functional characteristics. Inspired by the in-silico mutation with molecular dynamics (MD) simulation analysis, we propose a strategy for identifying disulfide bond mutation candidates based on the prediction of protein flexibility and residue-residue interaction. The most beneficial mutant with the newly introduced disulfide bond would simultaneously improve both its thermostability and its reaction propensity to the targeting isomerization product. The ratio of the isomerization/epimerization catalytic rate was improved from 4:103 to 9:22. MD simulation and binding free energy calculations were applied to provide insights into molecular recognition upon mutations. The comparative analysis of enzyme/substrate binding modes indicates that the altered catalytic reaction pathway is due to less efficient binding of the native product. The key residue responsible for the observed phenotype was identified by energy decomposition and was further confirmed by the mutation experiment. The rational design of the key loop region might be a promising strategy to alter the catalytic behavior of all (α/α)6-barrel-like proteins.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Junhao Wu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Yanchang Wu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Zhaojun Wang
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Maomao Zeng
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Zhiyong He
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Jie Chen
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi Jiangsu 214122, P. R. China
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4
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Zhang W, Xiong S, Ni D, Huang Z, Ding J, Mu W. Engineering Bacillus subtilis for highly efficient production of functional disaccharide lactulose from lactose. Int J Biol Macromol 2024; 271:132478. [PMID: 38772465 DOI: 10.1016/j.ijbiomac.2024.132478] [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] [Received: 01/05/2024] [Revised: 05/05/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
Bioconversion of lactose to functional lactose derivatives attracts increasing attention. Lactulose is an important high-value lactose derivative, which has been widely used in pharmaceutical, nutraceutical, and food industries. Lactulose can be enzymatically produced from lactose by cellobiose 2-epimerase (CEase). Several studies have already focused on the food-grade expression of CEase, but they are all aimed at the biosynthesis of epilactose. Herein, we reported for the first time the biosynthesis of lactulose using the recombinant food-grade Bacillus subtilis. Lactulose biosynthesis was optimized by varying lactulose-producing CEases and expression vectors. Caldicellulosiruptor saccharolyticus CEase and pP43NMK were determined to be the optimal CEase and expression vector. Fine-tuning of CEase expression was investigated by screening a beneficial N-terminal coding sequence. After fed-batch cultivation, the highest fermentation isomerization activity reached 11.6 U/mL. Lactulose was successfully produced by the broth of the engineered B. subtilis with a yield of 52.1 %.
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Affiliation(s)
- Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Suchun Xiong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China.
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5
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Huang Z, Ni D, Chen Z, Zhu Y, Zhang W, Mu W. Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37485919 DOI: 10.1080/10408398.2023.2238054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.
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Affiliation(s)
- Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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6
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Tian Y, Kong H, Ban X, Li C, Gu Z, Li Z. Distribution of Aromatic Amino Acid Residues in Substrate-Binding Regions Modulates Substrate Specificity of Microbial Debranching Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37463425 DOI: 10.1021/acs.jafc.3c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Debranching enzymes (DBEs) directly hydrolyze α-1,6-glucosidic linkages in glycogen, starch, and related polysaccharides, making them important in the starch processing industry. However, the ambiguous substrate specificity usually restricts synergistic catalysis with other amylases for improving starch utilization. Herein, a glycogen-debranching enzyme from Saccharolobus solfataricus (SsGDE) and two isoamylases from Pseudomonas amyloderamosa (PaISO) and Chlamydomonas reinhardtii (CrISO) were used to investigate the molecular mechanism of substrate specificity. Along with the structure-based computational analysis, the aromatic residues in the substrate-binding region of DBEs played an important role in binding substrates. The aromatic residues in SsGDE appeared clustered, contributing to a small substrate-binding region. In contrast, the aromatic residues in isoamylase were distributed dispersedly, forming a large active site. The distinct characteristics of substrate-binding regions in SsGDE and isoamylase might explain their substrate preferences for maltodextrin and amylopectin, respectively. By modulating the substrate-binding region of SsGDE, variants Y323F and V375F were obtained with significantly enhanced activities, and the activities of Y323F and V375F increased by 30 and 60% for amylopectin, and 20 and 23% for DE4 maltodextrin, respectively. This study revealed the molecular mechanisms underlying the substrate specificity for SsGDE and isoamylases, providing a route for engineering enzymes to achieve higher catalytic performance.
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Affiliation(s)
- Yixiong Tian
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
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7
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Jia DX, Yu H, Wang F, Jin LQ, Liu ZQ, Zheng YG. Computer-aided design of novel cellobiose 2-epimerase for efficient synthesis of lactulose using lactose. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02896-z. [PMID: 37450268 DOI: 10.1007/s00449-023-02896-z] [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: 03/06/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Cellobiose 2-epimerase (CE) is ideally suited to synthesize lactulose from lactose, but the poor thermostability and catalytic efficiency restrict enzymatic application. Herein, a non-characterized CE originating from Caldicellulosiruptor morganii (CmCE) was discovered in the NCBI database. Then, a smart mutation library was constructed based on FoldX ΔΔG calculation and modeling structure analysis, from which a positive mutant D226G located within the α8/α9 loop exhibited longer half-lives at 65-75 °C as well as lower Km and higher kcat/Km values compared with CmCE. Molecular modeling demonstrated that the improvement of D226G was largely attributed to the rigidification of the flexible loop, the compactness of the catalysis pocket and the increment of substrate-binding capability. Finally, the yield of synthesizing lactulose catalyzed by D226G reached 45.5%, higher than the 35.9% achieved with CmCE. The disclosed effect of the flexible loop on enzymatic stability and catalysis provides insight to redesign efficient CEs to biosynthesize lactulose.
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Affiliation(s)
- Dong-Xu Jia
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Hai Yu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Fan Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
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8
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Zhao L, Ma Z, Wang Q, Hu M, Zhang J, Chen L, Shi G, Ding Z. Engineering the Thermostability of Sucrose Synthase by Reshaping the Subunit Interaction Contributes to Efficient UDP-Glucose Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3832-3841. [PMID: 36795895 DOI: 10.1021/acs.jafc.2c08642] [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: 06/18/2023]
Abstract
The restricted availability of UDP-glucose, an essential precursor that targets oligo/polysaccharide and glycoside synthesis, makes its practical application difficult. Sucrose synthase (Susy), which catalyzes one-step UDP-glucose synthesis, is a promising candidate. However, due to poor thermostability of Susy, mesophilic conditions are required for synthesis, which slow down the process, limit productivity, and prevent scaled and efficient UDP-glucose preparation. Here, we obtained an engineered thermostable Susy (mutant M4) from Nitrosospira multiformis through automated prediction and greedy accumulation of beneficial mutations. The mutant improved the T1/2 value at 55 °C by 27-fold, resulting in UDP-glucose synthesis at 37 g/L/h of space-time yield that met industrial biotransformation standards. Furthermore, global interaction between mutant M4 subunits was reconstructed by newly formed interfaces according to molecular dynamics simulations, with residue Trp162 playing an important role in strengthening the interface interaction. This work enabled effective, time-saving UDP-glucose production and paved the way for rational thermostability engineering of oligomeric enzymes.
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Affiliation(s)
- Liting Zhao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongbao Ma
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Qiong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Manfeng Hu
- School of Science, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jingxiang Zhang
- School of Science, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Lei Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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9
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Wang L, Gu J, Zhao W, Wang M, Ng KR, Lyu X, Yang R. Reshaping the Binding Pocket of Cellobiose 2-Epimerase for Improved Substrate Affinity and Isomerization Activity for Enabling Green Synthesis of Lactulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15879-15893. [PMID: 36475670 DOI: 10.1021/acs.jafc.2c06980] [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: 06/17/2023]
Abstract
Enzymatic isomerization of lactose into lactulose via cellobiose 2-epimerase (CE) could provide an eco-friendly route for the industrial production of lactulose, a valuable food prebiotic. However, poor substrate affinity for lactose and preference for epimerization over isomerization hinder this application. Previous studies on CE improvement have focused on random mutagenesis or active site rational design; little is known about the relationship between substrate binding and enzyme efficacy, which was hence the subject of this study. First, residues 372W and 308W were identified as key for disaccharide recognition in CEs based on crystal structure alignment of the N-acetyl-glucosamine 2-epimerase superfamily and site-directed mutation. This binding domain was then reshaped through site saturation mutagenesis, resulting in seven mutants with enhanced isomerization activity. The optimal mutant CsCE/Q371E had significantly enhanced substrate affinity (Km, 269.65 mM vs Km, 417.5 mM), reduced epimerization activity, and 3.3-fold increased isomerization activity over the original CsCE. Molecular dynamics simulation further revealed that substituting Gln-371 with Glu strengthened the hydrogen-bonding network and altered the active site-substrate interactions, increasing the substrate stability and shifting the catalytic direction. This study uncovered new information about the substrate binding region and its mechanisms and impact on CE catalytic performance, paving the way for potential commercial applications.
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Affiliation(s)
- Lu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiali Gu
- College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingming Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kuan Rei Ng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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10
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Tian Y, Ban X, Li C, Gu Z, Li Z. Modulation of Flexible Loops in Catalytic Cavities Reveals the Thermal Activation Mechanism of a Glycogen-Debranching Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13358-13366. [PMID: 36217266 DOI: 10.1021/acs.jafc.2c04487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Some thermophilic enzymes not only exhibit high thermostability at high temperatures but also have an activation effect by thermal incubation. However, the correlations between temperature-induced structural modulation and thermal activation are still unclear. In this study, we selected a thermophilic glycogen-debranching enzyme from Saccharolobus solfataricus STB09 (SsGDE), which was a promising starch-debranching enzyme with a thermal activation property at temperatures ranging from 50 to 70 °C, to explore the thermal activation mechanism. Molecular dynamics simulations were performed for SsGDE at 30, 50, or 70 °C to reveal the temperature dependence of structure modulation and catalytic function. The results revealed that four loops (loop1 313-337, loop2 399-418, loop3 481-513, and loop4 540-574) in SsGDE were reshaped, which made the catalytic cavity more open. The internal residues, including the catalytic triad Asp3631, Glu399, and Asp471, could be exposed, due to the structural modulation, to exert catalytic functions. We proposed that the thermal activation effect of SsGDE was closely associated with the temperature-induced modulation of the catalytic cavity, which paved the way for further engineering enzymes to achieve higher catalytic performance and stability.
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Affiliation(s)
- Yixiong Tian
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, China
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Wang M, Wang L, Lyu X, Hua X, Goddard JM, Yang R. Lactulose production from lactose isomerization by chemo-catalysts and enzymes: Current status and future perspectives. Biotechnol Adv 2022; 60:108021. [PMID: 35901861 DOI: 10.1016/j.biotechadv.2022.108021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/02/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Lactulose, a semisynthetic nondigestive disaccharide with versatile applications in the food and pharmaceutical industries, has received increasing interest due to its significant health-promoting effects. Currently, industrial lactulose production is exclusively carried out by chemical isomerization of lactose via the Lobry de Bruyn-Alberda van Ekenstein (LA) rearrangement, and much work has been directed toward improving the conversion efficiency in terms of lactulose yield and purity by using new chemo-catalysts and integrated catalytic-purification systems. Lactulose can also be produced by an enzymatic route offering a potentially greener alternative to chemo-catalysis with fewer side products. Compared to the controlled trans-galactosylation by β-galactosidase, directed isomerization of lactose with high isomerization efficiency catalyzed by the most efficient lactulose-producing enzyme, cellobiose 2-epimerase (CE), has gained much attention in recent decades. To further facilitate the industrial translation of CE-based lactulose biotransformation, numerous studies have been reported on improving biocatalytic performance through enzyme mediated molecular modification. This review summarizes recent developments in the chemical and enzymatic production of lactulose. Related catalytic mechanisms are also highlighted and described in detail. Emerging techniques that aimed at advancing lactulose production, such as the boronate affinity-based technique and molecular biological techniques, are reviewed. Finally, perspectives on challenges and opportunities in lactulose production and purification are also discussed.
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Affiliation(s)
- Mingming Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China; Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Lu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiao Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Julie M Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China.
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