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Cao Y, Qiu B, Ning X, Fan L, Qin Y, Yu D, Yang C, Ma H, Liao X, You C. Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis. Int J Mol Sci 2024; 25:6252. [PMID: 38892439 PMCID: PMC11173260 DOI: 10.3390/ijms25116252] [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: 04/02/2024] [Revised: 05/22/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Enzymes play a crucial role in various industrial production and pharmaceutical developments, serving as catalysts for numerous biochemical reactions. Determining the optimal catalytic temperature (Topt) of enzymes is crucial for optimizing reaction conditions, enhancing catalytic efficiency, and accelerating the industrial processes. However, due to the limited availability of experimentally determined Topt data and the insufficient accuracy of existing computational methods in predicting Topt, there is an urgent need for a computational approach to predict the Topt values of enzymes accurately. In this study, using phosphatase (EC 3.1.3.X) as an example, we constructed a machine learning model utilizing amino acid frequency and protein molecular weight information as features and employing the K-nearest neighbors regression algorithm to predict the Topt of enzymes. Usually, when conducting engineering for enzyme thermostability, researchers tend not to modify conserved amino acids. Therefore, we utilized this machine learning model to predict the Topt of phosphatase sequences after removing conserved amino acids. We found that the predictive model's mean coefficient of determination (R2) value increased from 0.599 to 0.755 compared to the model based on the complete sequences. Subsequently, experimental validation on 10 phosphatase enzymes with undetermined optimal catalytic temperatures shows that the predicted values of most phosphatase enzymes based on the sequence without conservative amino acids are closer to the experimental optimal catalytic temperature values. This study lays the foundation for the rapid selection of enzymes suitable for industrial conditions.
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Affiliation(s)
- Yinyin Cao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (Y.C.)
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
| | - Boyu Qiu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230022, China
| | - Xiao Ning
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmei Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (Y.C.)
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
| | - Chunhe Yang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (Y.C.)
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (B.Q.); (H.M.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Herman RA, Ayepa E, Zhang WX, Li ZN, Zhu X, Ackah M, Yuan SS, You S, Wang J. Molecular modification and biotechnological applications of microbial aspartic proteases. Crit Rev Biotechnol 2024; 44:388-413. [PMID: 36842994 DOI: 10.1080/07388551.2023.2171850] [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: 06/22/2022] [Revised: 12/13/2022] [Accepted: 01/07/2023] [Indexed: 02/28/2023]
Abstract
The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.
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Affiliation(s)
- Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- School of Materials Science and Engineering, Jiangsu University of Science and Technology, Zhenjiang, P. R. China
| | - Ellen Ayepa
- Oil Palm Research Institute, Council for Scientific and Industrial Research, Kusi, Ghana
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Zong-Nan Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Xuan Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuang-Shuang Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Zhang Y, Hu J, Wang J, Liu C, Liu X, Sun J, Song X, Wu Y. Purification and characteristics of a novel milk-clotting metalloprotease from Bacillus velezensis DB219. J Dairy Sci 2023; 106:6688-6700. [PMID: 37558047 DOI: 10.3168/jds.2023-23450] [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: 03/03/2023] [Accepted: 04/25/2023] [Indexed: 08/11/2023]
Abstract
Milk-clotting enzyme (MCE) is the essential active agents in dairy processing. The traditional MCE is mainly obtained from animal sources, in which calf rennet is the most widely used in cheese industry. Traditional MCE substitute is becoming necessary due to its limited production and increased cheese consumption. A novel traditional MCE substitute was produced from Bacillus velezensis DB219 in this study. The DB219 MCE exhibited a notable specific activity of 6,110 Soxhlet units/mg and 3.16-fold purification yield with 28.87% recovery through ammonium sulfate fractionation and DEAE-Sepharose Fast Flow. The purified DB219 MCE was a metalloprotease with a molecular weight of 36 kDa. The DB219 MCE was weak acid resistance and stable at pH 6.0 to 10.0 and temperature <45°C. The highest milk-clotting activity was observed in substrate at pH 5.5 added with 20 to 30 mM CaCl2. The Michaelis constant and maximal velocity for casein were 0.31 g/L and 14.22 μmol/min. The DB219 MCE preferred to hydrolyze β-casein instead of α-casein. The DB219 MCE hydrolyzed α-casein, β-casein, and κ-casein to generate significantly different peptides in comparison with calf rennet and ES6023 MCE (fungal MCE) through SDS-PAGE and reversed-phase HPLC analysis. The DB219 MCE mainly cleaved Thr124-Ile125 and Ser104-Phe105 bonds in κ-casein and had unique casein cleavage sites and peptide composition through LC-MS/MS analysis. The DB219 MCE was potential to be a new milk coagulant and enriched kinds of traditional MCE substitute.
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Affiliation(s)
- Yao Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Jiayun Hu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Jiaxin Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Chen Liu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Xiaofeng Liu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Juan Sun
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Xinjie Song
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Yuanfeng Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China.
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5
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Zhang Y, Wang J, He J, Liu X, Sun J, Song X, Wu Y. Characteristics and application in cheese making of newly isolated milk-clotting enzyme from Bacillus megaterium LY114. Food Res Int 2023; 172:113202. [PMID: 37689949 DOI: 10.1016/j.foodres.2023.113202] [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: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 09/11/2023]
Abstract
Milk-clotting enzyme (MCE) is a crucial active agent in cheese making. It is necessary to find traditional MCE substitutes due to the limited production of traditional MCE (e.g., calf rennet) and increased cheese consumption. Bacillus megaterium strain LY114 with good milk-clotting activity (MCA) (448 SU/mL) and a high MCA/proteolytic activity (PA) ratio (6.0) was isolated and identified from agricultural soil in Laiyang (Shandong, China) through 16S rRNA sequencing of 45 strains. The Bacillus megaterium LY114 MCE had a remarkable specific activity (7532 SU/mg) and displayed a 4.83-fold purification yield with 34.17% recovery through ammonium sulfate fractionation and DEAE-Sepharose Fast Flow. The purified LY114 MCE was a metalloprotease with a molecular weight of 30 kDa. LY114 MCE was stable at pH 5.0-7.0 and temperature <40 °C. The highest MCA appeared at a substrate pH of 5.5 with 30 mM CaCl2. The Michaelis constant (Km) and maximal velocity (Vm) for casein were 0.31 g/L and 14.16 μmol/min, respectively. LY114 MCE preferred to hydrolyze α-casein (α-CN) rather than β-casein (β-CN) and had unique α-CN, β-CN and κ-casein (κ-CN) cleavage sites. LY114 MCE hydrolyzed casein to generate significantly different peptides compared with calf rennet and fungal MCE as determined by SDS-PAGE analysis. Chemical index analysis and sensory evaluation confirmed the usefulness of LY114 MCE in cheese making. LY114 MCE had the potential to be used in dairy processing and enriched traditional MCE substitutes.
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Affiliation(s)
- Yao Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Jiaxin Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Jiamin He
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Xiaofeng Liu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Juan Sun
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Xinjie Song
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China
| | - Yuanfeng Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China.
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Yang Z, Huang Z, Wu Q, Tang X, Huang Z. Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst. Int J Mol Sci 2023; 24:ijms24108532. [PMID: 37239878 DOI: 10.3390/ijms24108532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The modern biotechnology industry has a demand for macromolecules that can function in extreme environments. One example is cold-adapted proteases, possessing advantages such as maintaining high catalytic efficiency at low temperature and low energy input during production and inactivation. Meanwhile, cold-adapted proteases are characterised by sustainability, environmental protection, and energy conservation; therefore, they hold significant economic and ecological value regarding resource utilisation and the global biogeochemical cycle. Recently, the development and application of cold-adapted proteases have gained gaining increasing attention; however, their applications potential has not yet been fully developed, which has seriously restricted the promotion and application of cold-adapted proteases in the industry. This article introduces the source, related enzymology characteristics, cold resistance mechanism, and the structure-function relationship of cold-adapted proteases in detail. This is in addition to discussing related biotechnologies to improve stability, emphasise application potential in clinical medical research, and the constraints of the further developing of cold-adapted proteases. This article provides a reference for future research and the development of cold-adapted proteases.
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Affiliation(s)
- Zhengfeng Yang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650000, China
| | - Zhendi Huang
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
| | - Qian Wu
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
| | - Xianghua Tang
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
| | - Zunxi Huang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650000, China
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650000, China
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Wang X, Dong T, Zhou Q, Tong L, Zheng J, Qin X, Wang X, Wang Y, Yao B, Huang H, Luo H. Improving the Activity and Stability of Serine Protease ThAPT3 by Alleviating Self-Cleavage and Its Application in Deproteinization of Shrimp Shells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7777-7790. [PMID: 37161941 DOI: 10.1021/acs.jafc.3c01618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The self-cleavage properties of proteases result in low activity and instability, which limit their industrial application. In this study, the serine protease ThAPT3 from Torrubiella hemipterigena was successfully expressed in Komagataella phaffii. We investigated the self-degradation mechanism of ThAPT3 and presented a rational strategy to alleviate self-cleavage. A major self-degradation site (Leu238-Met239) and a primary autolysis region were identified. The autolysis regions (loop18, α8-helix, and loop19) were redesigned and optimized using loop transplantation, energy calculations, surface cavity optimization, and loop anchoring. A triple-superposition mutant, ThAPT3-M9 (M239GKDGAVAAGLC250 → M239TLNRTTAANAC250/A251E/A254Q/R259L/A267E/S280N), was obtained. Compared to the wild type, the autolysis of M9 was significantly alleviated, and its half-life at 60 °C was increased approximately 39-fold (from 1.6 to 62.4 min). The optimal temperature and specific activity of M9 increased by 5 °C (from 60 to 65 °C) and 62% (4985 vs 3078 U/mg), respectively. M9 showed significant advantages in shrimp shell deproteinization.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiao Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Guo Y, Zhou J, Jia W, Gao H, Zhang H, Zhang C. Characterization of a Novel Milk-Clotting Aspartic Protease from Penicillium sp. and Structural Explanation for its High Milk-Clotting Index. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37017929 DOI: 10.1021/acs.jafc.2c07303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A novel milk-clotting enzyme isolated from Penicillium sp. ACCC 39790 (PsMCE) was prepared by heterologous expression. The recombinant PsMCE had an apparent molecular mass of 45 kDa and exhibited maximum casein hydrolysis activity at pH 4.0 and 50 °C. The PsMCE activity was enhanced by calcium ions and strongly inhibited by pepstatin A. Through hydrolysis pattern and cleavage site analyses, the milk-clotting activity of PsMCE was related to its specific hydrolysis between Phe105 and Met106 in the κ-casein proteins. The structural basis of PsMCE was characterized using homology modeling, molecular docking, and interactional analysis. The P1' region of PsMCE is critical for its selective binding to the hydrolytic site in κ-casein, and the hydrophobic forces play a decisive role in the specific cleavage of Phe105 and Met106. These interactional analyses between PsMCE and the ligand peptide clarified the fundamentals of its high milk-clotting index (MCI). PsMCE could be applied in cheese making due to its thermolability and high MCI value as a potential milk-clotting enzyme.
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Affiliation(s)
- Yujie Guo
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Jiaojiao Zhou
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Jia
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongwei Gao
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongru Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunhui Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Silva RDS, Segura WD, Oliveira RS, Xander P, Batista WL. Characterization of Aspartic Proteases from Paracoccidioides brasiliensis and Their Role in Fungal Thermo-Dimorphism. J Fungi (Basel) 2023; 9:jof9030375. [PMID: 36983543 PMCID: PMC10053120 DOI: 10.3390/jof9030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is the most prevalent systemic mycosis in Latin America and is caused by fungi from the Paracoccidioides genus. The infection begins after inhalation of the fungal propagules and their thermo-dimorphic shift to yeast form. Proteases play an important role in the host invasion process and immune modulation in many pathogenic microorganisms. Aspartyl proteases are virulence factors in many human fungal pathogens that play an important role in the host invasion process morphogenesis, cellular function, immunity, and nutrition. In the present study, we characterized the modulation of acid proteases from Paracoccidioides brasiliensis. We detected four aspartyl proteases in P. brasiliensis with high homology to aspartic protease from Saccharomyces cerevisiae Pep4. Furthermore, we demonstrated that Pepstatin A can inhibit dimorphic switching (mycelium→yeast) in P. brasiliensis. In addition, these genes were modulated during thermo-dimorphism (M→Y transition) in the presence or absence of carbon and nitrogen sources and during growth at pH 4 during 24 and 48 h. We also observed that P. brasiliensis increase the secretion of aspartic proteases when cultivated at pH 4, and these acid proteases cleave BSA, collagen, and hemoglobin. These data suggest that aspartyl proteases are modulated by environmental conditions and during fungal thermo-dimorphism. Thus, this work brings new possibilities for studying the role of aspartyl proteases in the host-pathogen relationship and P. brasiliensis biology.
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Affiliation(s)
- Rafael de Souza Silva
- Departamento Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
| | - Wilson Dias Segura
- Departamento Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
| | - Reinaldo Souza Oliveira
- Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema 09913-030, SP, Brazil
| | - Patricia Xander
- Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema 09913-030, SP, Brazil
| | - Wagner Luiz Batista
- Departamento Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
- Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema 09913-030, SP, Brazil
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10
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Wei M, Chen P, Zheng P, Tao X, Yu X, Wu D. Purification and characterization of aspartic protease from Aspergillus niger and its efficient hydrolysis applications in soy protein degradation. Microb Cell Fact 2023; 22:42. [PMID: 36864487 PMCID: PMC9983247 DOI: 10.1186/s12934-023-02047-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Adding acid protease to feed can enhance protein digestibility, boost feed utilization, and stimulate the growth of animals in breading industry. In order to obtain an acid protease with high hydrolysis efficiency to plant protein, in this study, an aspartic protease from Aspergillus niger was heterologous expressed in Pichia pastoris (P. pastoris). The enzymatic properties and application in soybean protein degradation were also studied. RESULTS In our investigation, the high aspartic protease (Apa1) activity level of 1500 U/mL was achieved in 3 L bioreactor. After dialysis and anion exchange chromatography, the total enzyme activity and specific enzyme activity were 9412 U and 4852 U/mg, respectively. The molecular weight of the purified protease was 50 kDa, while the optimal pH and temperature were 3.0 and 50 °C, respectively. It was stable at pH 2.0-5.0 and 30-60 °C. Apa1 was used to hydrolyze soybean isolate protein (SPI) at 40 °C and pH 3.0, and a high hydrolysis degree (DH) of 61.65% was achieved. In addition, the molecular weight distribution of SPI hydrolysis products was studied, the result showed that the hydrolysis products were primarily oligopeptides with molecular weights of 189 Da or below. CONCLUSIONS In this study, Apa1 was successfully expressed in P. pastoris and high expression level was obtained. In addition, the highest protein hydrolysis rate to SPI degradation so far was achieved. The acid protease in this study provides a new protease that is suitable for the feed industry, which will be very helpful to improve the feed utilization and promote the development of the breeding industry.
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Affiliation(s)
- Mengyuan Wei
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Pengcheng Chen
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Pu Zheng
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xiumei Tao
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaowei Yu
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Dan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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11
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High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like model. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Liu X, Wu Y, Guan R, Jia G, Ma Y, Zhang Y. Advances in research on calf rennet substitutes and their effects on cheese quality. Food Res Int 2021; 149:110704. [PMID: 34600696 DOI: 10.1016/j.foodres.2021.110704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022]
Abstract
Milk coagulation is an important step in cheese production, and milk-clotting enzymes (MCEs) play a major role in this process. Calf rennet is the most widely used MCE in the cheese industry. The use of calf rennet substitutes is becoming necessary due to the limited availability of calf rennet and the increase in cheese consumption. The objective of this review is to summarize the latest findings on calf rennet substitutes (animal MCEs, plant-derived MCEs, recombinant MCEs and microbial MCEs) and their application in cheese production. Special emphasis has been placed on aspects of the effects of these substitutes on hydrolysis, functional peptides, cheese variety and cheese yield. The advantages and disadvantages of different calf rennet substitutes are discussed, in which microbial MCEs have the advantages of less expensive production, greater biochemical diversity, easier genetic modification, etc. In particular, some of these MCEs have suitable characteristics for cheese production and are considered to be the most potential calf rennet substitutes. Moreover, challenges and future perspectives are presented to provide inspiration for the development of excellent calf rennet substitutes.
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Affiliation(s)
- Xiaofeng Liu
- College of Food Science and Technology, Zhejiang University of Technology, Zhejiang, Hangzhou 310014, China; Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yuanfeng Wu
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Rongfa Guan
- College of Food Science and Technology, Zhejiang University of Technology, Zhejiang, Hangzhou 310014, China
| | - Guochao Jia
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Henan, Zhengzhou 450044, China
| | - YuChen Ma
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yao Zhang
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China.
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Purushothaman K, Bhat SK, Siddappa S, Singh SA, Subbaiah R, Marathe GK, Rao G Appu Rao A. Aspartic protease-pepstatin A interactions: Structural insights on the thermal inactivation mechanism. Biochimie 2021; 189:26-39. [PMID: 34116131 DOI: 10.1016/j.biochi.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022]
Abstract
Aspartic proteases are the targets for structure-based drug design for their role in physiological processes and pharmaceutical applications. Structural insights into the thermal inactivation mechanism of an aspartic protease in presence and absence of bound pepstatin A have been obtained by kinetics of thermal inactivation, CD, fluorescence spectroscopy and molecular dynamic simulations. The irreversible thermal inactivation of the aspartic protease comprised of loss of tertiary and secondary structures succeeded by the loss of activity, autolysis and aggregation The enthalpy and entropy of thermal inactivation of the enzyme in presence of pepstatin A increased from 81.2 to 148.5 kcal mol-1, and from 179 to 359 kcal mol-1 K-1 respectively. Pepstatin A shifted the mid-point of thermal inactivation of the protease from 58 °C to 77 °C. The association constant (K) for pepstatin A with aspartic protease was 2.5 ± 0.3 × 10 5 M-1 and ΔGo value was -8.3 kcal mol-1. Molecular dynamic simulation studies were able to delineate the role of pepstatin A in stabilizing backbone conformation and side chain interactions. In the Cα-backbone, the short helical segments and the conserved glycines were part of the most unstable segments of the protein. Understanding the mechanism of thermal inactivation has the potential to develop re-engineered thermostable proteases.
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Affiliation(s)
- Kavya Purushothaman
- Kaypeeyes Biotech Private Limited, R&D Center, Hebbal Industrial Area, Mysuru, 570016, Karnataka, India; Department of Studies in Biochemistry, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India
| | - Sagar Krishna Bhat
- Kaypeeyes Biotech Private Limited, R&D Center, Hebbal Industrial Area, Mysuru, 570016, Karnataka, India
| | - Shiva Siddappa
- Department of Studies in Biochemistry, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India
| | - Sridevi Annapurna Singh
- Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysuru, 570020, Karnataka, India
| | - Roopashree Subbaiah
- Department of Biochemistry, Yuvaraja College, University of Mysore, 570020, India
| | - Gopal Kedihithlu Marathe
- Department of Studies in Biochemistry, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India; Department of Studies in Molecular Biology, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India
| | - Appu Rao G Appu Rao
- Kaypeeyes Biotech Private Limited, R&D Center, Hebbal Industrial Area, Mysuru, 570016, Karnataka, India.
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Niu C, Wan X. Engineering a Trypsin-Resistant Thermophilic α-Galactosidase to Enhance Pepsin Resistance, Acidic Tolerance, Catalytic Performance, and Potential in the Food and Feed Industry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10560-10573. [PMID: 32829638 DOI: 10.1021/acs.jafc.0c02175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
α-Galactosidase has potential applications, and attempts to improve proteolytic resistance of enzymes have important values. We use a novel strategy for genetic manipulation of a pepsin-sensitive region specific for a pepsin-sensitive but trypsin-resistant high-temperature-active Gal27B from Neosartorya fischeri to screen mutants with enhanced pepsin resistance. All enzymes were produced in Pichia pastoris to identify the roles of loop 4 (Gal27B-A23) and its key residue at position 156 (Gly156Arg/Pro/His) in pepsin resistance. Gal27B-A23 and Gly156Arg/Pro/His elevated pepsin resistance, thermostability, stability at low pH, activity toward raffinose (5.3-6.9-fold) and stachyose (about 1.3-fold), and catalytic efficiencies (up to 4.9-fold). Replacing the pepsin cleavage site Glu155 with Gly improved pepsin resistance but had no effect on pepsin resistance when Arg/Pro/His was at position 156. Thus, pepsin resistance could appear to occur through steric hindrance between the residue at the altered site and neighboring pepsin active site. In the presence of pepsin or trypsin, all mutations increased the ability of Gal27B to hydrolyze galactosaccharides in soybean flour (up to 9.6- and 4.3-fold, respectively) and promoted apparent metabolizable energy and nutrient digestibility in soybean meal for broilers (1.3-1.8-fold). The high activity and tolerance to heat, low pH, and protease benefit food and feed industry in a cost-effective way.
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Affiliation(s)
- Canfang Niu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
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Zhu M, Zhang L, Yang F, Cha Y, Li S, Zhuo M, Huang S, Li J. A Recombinant β-Mannanase from Thermoanaerobacterium aotearoense SCUT27: Biochemical Characterization and Its Thermostability Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:818-825. [PMID: 31845578 DOI: 10.1021/acs.jafc.9b06246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Mannanase was expressed in Thermoanaerobacterium aotearoense SCUT27 induced by locust bean gum (LBG). The open reading frame encoding a GH26 β-mannanase was identified and encoded a preprotein of 515 amino acids with a putative signal peptide. The enzyme without a signal sequence (Man25) was overexpressed in Escherichia coli with a specific activity of 1286.2 U/mg. Moreover, a facile method for β-mannanase activity screening was established based on agar plates. The optimum temperature for the purified Man25 using LBG as a substrate was 55 °C. The catalytic activity and thermostability of Man25 displayed a strong dependence on calcium ions. Through saturation mutagenesis at the putative Ca2+ binding sites in Man25, the best mutant ManM3-3 (D143A) presented improvements in thermostability with 3.6-fold extended half-life at 55 °C compared with that of the wild-type. The results suggest that mutagenesis at metal binding sites could be an efficient approach to increase enzyme thermostability.
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Affiliation(s)
- Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology , Guangdong Academy of Sciences , Guangzhou 510070 , China
| | | | - Fang Yang
- Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou 510642 , China
| | | | | | | | | | - Jianjun Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology , Guangdong Academy of Sciences , Guangzhou 510070 , China
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