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Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci 2024; 33:e5097. [PMID: 39145402 PMCID: PMC11325166 DOI: 10.1002/pro.5097] [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: 04/20/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 08/16/2024]
Abstract
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostability. Although an increasing number of tools can assist with this task, significant amounts of time and resources are often wasted owing to inadequate consideration. To enhance the accuracy and efficiency of designing disulfide bonds for protein thermostability improvement, we initially collected disulfide bond and protein thermostability data from extensive literature sources. Thereafter, we extracted various sequence- and structure-based features and constructed machine-learning models to predict whether disulfide bonds can improve protein thermostability. Among all models, the neighborhood context model based on the Adaboost-DT algorithm performed the best, yielding "area under the receiver operating characteristic curve" and accuracy scores of 0.773 and 0.714, respectively. Furthermore, we also found AlphaFold2 to exhibit high superiority in predicting disulfide bonds, and to some extent, the coevolutionary relationship between residue pairs potentially guided artificial disulfide bond design. Moreover, several mutants of imine reductase 89 (IR89) with artificially designed thermostable disulfide bonds were experimentally proven to be considerably efficient for substrate catalysis. The SS-bond data have been integrated into an online server, namely, ThermoLink, available at guolab.mpu.edu.mo/thermoLink.
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Affiliation(s)
- Ran Xu
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Qican Pan
- Zelixir Biotech Company Ltd, Shanghai, China
| | | | - Yilin Ye
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Minghui Xin
- School of Physics, Shandong University, Jinan, China
| | - Zechen Wang
- School of Physics, Shandong University, Jinan, China
| | - Sheng Wang
- Zelixir Biotech Company Ltd, Shanghai, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Liangzhen Zheng
- Zelixir Biotech Company Ltd, Shanghai, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Sun J, He X, LE Y, Al-Tohamy R, Ali SS. Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120081. [PMID: 38237330 DOI: 10.1016/j.jenvman.2024.120081] [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: 11/25/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 02/04/2024]
Abstract
Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.
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Affiliation(s)
- Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Xing He
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yilin LE
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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Wu Q, Zhang C, Dong W, Lu H, Yang Y, Li W, Xu Y, Li X. Simultaneously Enhanced Thermostability and Catalytic Activity of Xylanase from Streptomyces rameus L2001 by Rigidifying Flexible Regions in Loop Regions of the N-Terminus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12785-12796. [PMID: 37590476 DOI: 10.1021/acs.jafc.3c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The GH11 xylanase XynA from Streptomyces rameus L2001 has favorable hydrolytic properties. However, its poor thermal stability hinders its widespread application in industry. In this study, mutants Mut1 and Mut2 were constructed by rationally combining the mutations 11YHDGYF16, 23AP24/23SP24, and 32GP33. The residual enzyme activity of these combinational mutants was more than 85% when incubated at 80 and 90 °C for 12 h, and thus are the most thermotolerant xylanases known to date. The reduced flexibility of the N-terminus, increased overall rigidity, as well as the surface net charge of Mut1 and Mut2 may be partially responsible for the improved thermal stability. In addition, the specific activity and catalytic efficiency of Mut1 and Mut2 were improved compared with those of wild-type XynA. The broader catalytic cleft and enhanced flexibility of the "thumb" of Mut1 and Mut2 may be partially responsible for the improved specific activity and catalytic efficiency.
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Affiliation(s)
- Qiuhua Wu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Chengnan Zhang
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Wenqi Dong
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Yue Yang
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiuting Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
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Liu S, Tian L, Cong Y, Shi Q, Wang L, Lu Y, Wang L, Yang G. Recent advances in polygalacturonase: Industrial applications and challenges. Carbohydr Res 2023; 528:108816. [PMID: 37094533 DOI: 10.1016/j.carres.2023.108816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
This review focuses on the applications of polygalacturonase (PG), one of the most commercially produced enzymes on the biocatalyst market, in the food, beverage, feed, textile, and paper industries. Most PGs are acidic mesophilic enzymes, as shown by a summary of their biochemical properties. However, the acidic PGs discovered to date are insufficiently effective for industrial applications. The sequence and structural characteristics of thermophilic PGs are analyzed based on the results of extensive discussions regarding the catalytic mechanism and structural characteristics of PGs with shared right-handed parallel β-helical structures. In addition, the molecular modification methods for obtaining thermostable PGs are systematically presented. Notably, the demand for alkaline heat-resistant PGs has increased significantly concurrent with the biomanufacturing industry development. Therefore, this review also provides a theoretical guideline for mining heat-resistant PG gene resources and modifying PG thermostability.
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Affiliation(s)
- Siyi Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Linfang Tian
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Yuting Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Qianqian Shi
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Lianshun Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Yanan Lu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Li Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Guojun Yang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China.
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Dong R, Liao M, Liu X, Penttinen L, Hakulinen N, Qin X, Wang X, Huang H, Luo H, Yao B, Bai Y, Tu T. Effectiveness of ruminal xylanase with an extra proline-rich C-terminus on lignocellulosic biomass degradation. BIORESOURCE TECHNOLOGY 2023; 372:128695. [PMID: 36731612 DOI: 10.1016/j.biortech.2023.128695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The efficient degradation of plant polysaccharides in agricultural waste requires xylanases with high catalytic activity. In this study, the C-terminal proline-rich GH10 xylanase XynA from sheep rumen was investigated using product analysis, structural characterization, truncated and site-directed mutagenesis, molecular dynamics simulation, and application evaluation, revealing that the proline-rich C-terminus contributes to the interaction at the substrate-binding pocket to reduce the binding free energy. Compared to the C-terminally truncated enzyme XynA-Tr, XynA has a more favorable conformation for proton transfer and affinity attack, facilitating the degradation of oligomeric and beechwood xylan without altering the hydrolysis pattern. Moreover, both the reduced sugar yield and weight loss of the pretreated wheat bran, corn cob, and corn stalk hydrolyzed by XynA for 12 h increased by more than 30 %. These findings are important to better understand the relationship between enzyme activities and their terminal regions and suggest candidate materials for lignocellulosic biomass utilization.
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Affiliation(s)
- Ruyue Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Min Liao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Leena Penttinen
- Department of Chemistry, Joensuu Campus, University of Eastern Finland, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, Joensuu Campus, University of Eastern Finland, FIN-80101 Joensuu, Finland
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhou X, Xu Z, Li Y, He J, Zhu H. Improvement of the Stability and Activity of an LPMO Through Rational Disulfide Bonds Design. Front Bioeng Biotechnol 2022; 9:815990. [PMID: 35111741 PMCID: PMC8801915 DOI: 10.3389/fbioe.2021.815990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/23/2021] [Indexed: 11/18/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) oxidatively break down the glycosidic bonds of crystalline polysaccharides, significantly improving the saccharification efficiency of recalcitrant biomass, and have broad application prospects in industry. To meet the needs of industrial applications, enzyme engineering is needed to improve the catalytic performance of LPMOs such as enzyme activity and stability. In this study, we engineered the chitin-active CjLPMO10A from Cellvibrio japonicus through a rational disulfide bonds design. Compared with the wild-type, the variant M1 (N78C/H116C) exhibited a 3-fold increase in half-life at 60°C, a 3.5°C higher T5015, and a 7°C rise in the apparent Tm. Furthermore, the resistance of M1 to chemical denaturation was significantly improved. Most importantly, the introduction of the disulfide bond improved the thermal and chemical stability of the enzyme without causing damage to catalytic activity, and M1 showed 1.5 times the specific activity of the wild-type. Our study shows that the stability and activity of LPMOs could be improved simultaneously by selecting suitable engineering sites reasonably, thereby improving the industrial adaptability of the enzymes, which is of great significance for applications.
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Yang LL, Shi HL, Liu F, Wang Z, Chen KL, Chen WS, Niu XR, Kan YC, Yao LG, Tang CD. Gene cloning of a highly active phytase from Lactobacillus plantarum and further improving its catalytic activity and thermostability through protein engineering. Enzyme Microb Technol 2022; 156:109997. [DOI: 10.1016/j.enzmictec.2022.109997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
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