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Hao M, Huang A, Li B, Xin Y, Zhang L, Gu Z, Sun H, Li Y, Shi G. Preparation and characterization of a laccase-like enzyme from Thermomicrobium roseum. Int J Biol Macromol 2023; 242:124992. [PMID: 37211077 DOI: 10.1016/j.ijbiomac.2023.124992] [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: 03/22/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
In this study, a laccase-like gene from Thermomicrobium roseum DSM 5159 (TrLac-like) (NCBI: WP_012642205.1) was recombinantly expressed in Bacillus subtilis WB600. The optimum temperature and pH for TrLac-like were 50 °C and 6.0, respectively. TrLac-like showed high tolerance to mixed systems of water and organic solvents, indicating its potential for large-scale application in various industries. It showed 36.81 % similarity with YlmD from Geobacillus stearothermophilus (PDB:6T1B) in sequence alignment; therefore, 6T1B was employed as the template for homology modeling. To improve catalytic efficiency, amino acid substitutions within 5 Å of the inosine ligand were simulated to reduce the binding energy and promote substrate affinity. Single and double substitutions (44 and 18, respectively) were prepared, and the catalytic efficiency of the mutant A248D was increased to approximately 110-fold that of the wild type, while the thermal stability was maintained. Bioinformatics analysis revealed that the significant improvement in catalytic efficiency could be attributed to the formation of new hydrogen bonds between the enzyme and substrate. With a further decrease in the binding energy, the catalytic efficiency of the multiple mutant H129N/A248D was approximately 14-fold higher than that of the wild type but lower than that of the single mutant A248D. This is possibly because kcat also decreased with the decrease of Km; consequently, the substrate could not be released in time owing to the enzyme with the combination mutation not being able to release the substrate at a high rate.
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Affiliation(s)
- Mengyao Hao
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Aimin Huang
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Bingjie Li
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Yu Xin
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China.
| | - Liang Zhang
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China.
| | - ZhengHua Gu
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Haiyan Sun
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Youran Li
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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Li B, Sun Y, Zhu X, Qian S, Pu J, Guo Y, Wu H, Zhang L, Xin Y. Aggregation Interface and Rigid Spots Sustain the Stable Framework of a Thermophilic N-Demethylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5614-5629. [PMID: 37000489 DOI: 10.1021/acs.jafc.3c00877] [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: 06/19/2023]
Abstract
Enzymes from thermophilic microorganisms usually show high thermostability, which is of great potential in industrial application; to understand the structural logic of these enzymes is helpful for the construction of robust biocatalysts. In this study, based on the crystal structure of an N-demethylase─TrSOX─with outstanding thermostability from Thermomicrobium roseum, substitutions were introduced on the aggregation interface and rigid spots to reduce the aggregation ratio and the rigidity. Four substitutions on the aggregation interface─V162S, M308S, F170S, and V306S─considerably reduced the thermostability and slightly enhanced the catalytic efficiency. In addition, the thermostable framework was considerably disrupted in several multiple P → G substitutions in several local motifs (P129G/P134G, P237G/P259G, and P259G/P276G). These structural fluctuations were in good accordance with whole-structure or partial root-mean-square deviation, radius of gyration H-bonds, and solvent-accessible surface area values in molecular dynamics simulation. Furthermore, these key spots were introduced into an unstable homolog from Bacillus sp., resulting in a dramatical increase in the half-life at 60 °C from <10 to 1440 min. These results could help understand the natural stable framework of thermophilic enzymes, which could be references for the construction of robust enzymes in industrial applications.
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Affiliation(s)
- Bingjie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuqian Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Xinyi Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Siyu Qian
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Jiayang Pu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuwen Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Haobo Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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Najmi AA, Bischoff R, Permentier HP. N-Dealkylation of Amines. Molecules 2022; 27:molecules27103293. [PMID: 35630770 PMCID: PMC9146227 DOI: 10.3390/molecules27103293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 02/01/2023] Open
Abstract
N-dealkylation, the removal of an N-alkyl group from an amine, is an important chemical transformation which provides routes for the synthesis of a wide range of pharmaceuticals, agrochemicals, bulk and fine chemicals. N-dealkylation of amines is also an important in vivo metabolic pathway in the metabolism of xenobiotics. Identification and synthesis of drug metabolites such as N-dealkylated metabolites are necessary throughout all phases of drug development studies. In this review, different approaches for the N-dealkylation of amines including chemical, catalytic, electrochemical, photochemical and enzymatic methods will be discussed.
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Xin Y, Shen C, Tang M, Guo Z, Shi Y, Gu Z, Shao J, Zhang L. Recreating the natural evolutionary trend in key microdomains provides an effective strategy for engineering of a thermomicrobial N-demethylase. J Biol Chem 2022; 298:101656. [PMID: 35124004 PMCID: PMC8892156 DOI: 10.1016/j.jbc.2022.101656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/10/2023] Open
Abstract
N-demethylases have been reported to remove the methyl groups on primary or secondary amines, which could further affect the properties and functions of biomacromolecules or chemical compounds; however, the substrate scope and the robustness of N-demethylases have not been systematically investigated. Here we report the recreation of natural evolution in key microdomains of the Thermomicrobium roseum sarcosine oxidase (TrSOX), an N-demethylase with marked stability (melting temperature over 100 °C) and enantioselectivity, for enhanced substrate scope and catalytic efficiency on -C-N- bonds. We obtained the structure of TrSOX by crystallization and X-ray diffraction (XRD) for the initial framework. The natural evolution in the nonconserved residues of key microdomains—including the catalytic loop, coenzyme pocket, substrate pocket, and entrance site—was then identified using ancestral sequence reconstruction (ASR), and the substitutions that accrued during natural evolution were recreated by site-directed mutagenesis. The single and double substitution variants catalyzed the N-demethylation of N-methyl-L-amino acids up to 1800- and 6000-fold faster than the wild type, respectively. Additionally, these single substitution variants catalyzed the terminal N-demethylation of non-amino-acid compounds and the oxidation of the main chain -C-N- bond to a -C=N- bond in the nitrogen-containing heterocycle. Notably, these variants retained the enantioselectivity and stability of the initial framework. We conclude that the variants of TrSOX are of great potential use in N-methyl enantiomer resolution, main-chain Schiff base synthesis, and alkaloid modification or degradation.
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Gao Q, Shao J, Tang M, Xin Y, Zhang L. Promote the expression and corrected folding of an extremely stable N-demethylase by promoter reconstruction, native environment simulation and surface design. Int J Biol Macromol 2021; 178:434-443. [PMID: 33647338 DOI: 10.1016/j.ijbiomac.2021.02.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 01/10/2023]
Abstract
Thermomicrobium roseum sarcosine oxidase (TrSOX) was a N-demethylase with specific substrate chiral selectivity, outstanding thermostability and environmental resistance. To promote the expression of TrSOX in Bacillus subtilis W600, the HpaII promoter of pMA5 plasmid was replaced by constitutive or inducible promoters. Through orthogonal experiment, the expression process was optimized, B. subtilis W600 cells containing pMA5-Pxyl-trSOX plasmid were cultivated until OD600nm reached 2.0 and were then induced with 1.6% xylose at 37 °C for 2 h, and the native environment of T. roseum was simulated by heating at 80 °C, with the productivity of TrSOX increased from ~8.3 to ~66.7 μg/g wet cells; and the simulated high temperature was the key switch for the final folding. To reduce the surface hydrophobicity, a S320R mutant was built to form a hydrophilic lid around the entrance of the substrate pocket, and the yield of TrSOX (S320R) was ~163.0 μg/g wet cells, approximately 20 folds as that in the initial expression system. This mutant revealed the similar secondary structure, stability, resistance, chiral substrate selectivity and optimal reaction environment with wild type TrSOX; however, the N-demethylation activities for amino acid derivative substrates were dramatically increased, while those for hydrophobic non-amino acid compounds were repressed.
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Affiliation(s)
- Qiuyue Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China
| | - Jun Shao
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Mengwei Tang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China.
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, PR China.
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Fang Y, Zhou Y, Xin Y, Shi Y, Guo Z, Li Y, Gu Z, Ding Z, Shi G, Zhang L. Preparation and characterization of a novel thermostable lipase from Thermomicrobium roseum. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01486b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this study, a hypothetical lipase gene from Thermomicrobium roseum DSM 5159 (GenBank: ACM04789.1) was recombinantly expressed in two system and characterized.
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Affiliation(s)
- Yakun Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yanjie Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yu Xin
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yi Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zitao Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zhenghua Gu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
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