1
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Cheung-Lee WL, Kolev JN, McIntosh JA, Gil AA, Pan W, Xiao L, Velásquez JE, Gangam R, Winston MS, Li S, Abe K, Alwedi E, Dance ZEX, Fan H, Hiraga K, Kim J, Kosjek B, Le DN, Marzijarani NS, Mattern K, McMullen JP, Narsimhan K, Vikram A, Wang W, Yan JX, Yang RS, Zhang V, Zhong W, DiRocco DA, Morris WJ, Murphy GS, Maloney KM. Engineering Hydroxylase Activity, Selectivity, and Stability for a Scalable Concise Synthesis of a Key Intermediate to Belzutifan. Angew Chem Int Ed Engl 2024; 63:e202316133. [PMID: 38279624 DOI: 10.1002/anie.202316133] [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: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Biocatalytic oxidations are an emerging technology for selective C-H bond activation. While promising for a range of selective oxidations, practical use of enzymes catalyzing aerobic hydroxylation is presently limited by their substrate scope and stability under industrially relevant conditions. Here, we report the engineering and practical application of a non-heme iron and α-ketoglutarate-dependent dioxygenase for the direct stereo- and regio-selective hydroxylation of a non-native fluoroindanone en route to the oncology treatment belzutifan, replacing a five-step chemical synthesis with a direct enantioselective hydroxylation. Mechanistic studies indicated that formation of the desired product was limited by enzyme stability and product overoxidation, with these properties subsequently improved by directed evolution, yielding a biocatalyst capable of >15,000 total turnovers. Highlighting the industrial utility of this biocatalyst, the high-yielding, green, and efficient oxidation was demonstrated at kilogram scale for the synthesis of belzutifan.
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Affiliation(s)
| | - Joshua N Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - John A McIntosh
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Agnieszka A Gil
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Weilan Pan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Li Xiao
- Modeling & Informatics, Discovery Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Juan E Velásquez
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rekha Gangam
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kotoe Abe
- Chemical Commercialization Technologies, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Embarek Alwedi
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zachary E X Dance
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Haiyang Fan
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Kaori Hiraga
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jungchul Kim
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Birgit Kosjek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Diane N Le
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Keith Mattern
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Karthik Narsimhan
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Ajit Vikram
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wei Wang
- API Process Research & Development (Biocatalysis), Shanghai STA Pharmaceutical Co., Ltd., Shanghai, 201507, China
| | - Jia-Xuan Yan
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rong-Sheng Yang
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Victoria Zhang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Wendy Zhong
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Daniel A DiRocco
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - William J Morris
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Kevin M Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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2
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Li M, Wang H, Yang Z, Zhang L, Zhu Y. DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences. Comput Struct Biotechnol J 2023; 21:5544-5560. [PMID: 38034401 PMCID: PMC10681957 DOI: 10.1016/j.csbj.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting temperature (Tm). However, due to the limited availability of experimentally determined Tm data and the insufficient accuracy of existing computational methods in predicting Tm, there is an urgent need for a computational approach to accurately forecast the Tm values of thermophilic proteins. Here, we present a deep learning-based model, called DeepTM, which exclusively utilizes protein sequences as input and accurately predicts the Tm values of target thermophilic proteins on a dataset consisting of 7790 thermophilic protein entries. On a test set of 1550 samples, DeepTM demonstrates excellent performance with a coefficient of determination (R2) of 0.75, Pearson correlation coefficient (P) of 0.87, and root mean square error (RMSE) of 6.24 ℃. We further analyzed the sequence features that determine the thermal stability of thermophilic proteins and found that dipeptide frequency, optimal growth temperature (OGT) of the host organisms, and the evolutionary information of the protein significantly affect its melting temperature. We compared the performance of DeepTM with recently reported methods, ProTstab2 and DeepSTABp, in predicting the Tm values on two blind test datasets. One dataset comprised 22 PET plastic-degrading enzymes, while the other included 29 thermally stable proteins of broader classification. In the PET plastic-degrading enzyme dataset, DeepTM achieved RMSE of 8.25 ℃. Compared to ProTstab2 (20.05 ℃) and DeepSTABp (20.97 ℃), DeepTM demonstrated a reduction in RMSE of 58.85% and 60.66%, respectively. In the dataset of thermally stable proteins, DeepTM (RMSE=7.66 ℃) demonstrated a 51.73% reduction in RMSE compared to ProTstab2 (RMSE=15.87 ℃). DeepTM, with the sole requirement of protein sequence information, accurately predicts the melting temperature and achieves a fully end-to-end prediction process, thus providing enhanced convenience and expediency for further protein engineering.
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Affiliation(s)
- Mengyu Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongzhao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhenwu Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Longgui Zhang
- SINOPEC Beijing Research Institute of Chemical Industry, Beijing 100013, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, China
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3
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Cui X, Yuan X, Li S, Hu X, Zhao J, Zhang G. Simultaneously improving the specific activity and thermostability of α-amylase BLA by rational design. Bioprocess Biosyst Eng 2022; 45:1839-1848. [PMID: 36136173 DOI: 10.1007/s00449-022-02790-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/10/2022] [Indexed: 11/02/2022]
Abstract
Higher activity and alkaline α-amylases are desired for textile desizing and detergent additive. Here, rational design was used to improve the specific activity and thermostability of the α-amylase BLA from Bacillus licheniformis. Seventeen mutants of BLA were designed based on sequence consensus analysis and folding free energy calculation, and characterized by measuring their respective activity and thermostability at pH 8.5. Among them, mutant Q360C exhibited nearly threefold improved activity than that of wild-type and retained a higher residual activity (75% vs 59% for wild-type) after preincubation at 70 ℃ for 30 min. The modeled structures and molecular dynamics simulations analysis demonstrated that the enhanced hydrophobic interaction near residue 360 and reduced disturbance to the conformation of catalytic residues are the possible reasons for the improved thermostability and activity of Q360C. The results suggest that 360th of BLA may act as a hotspot for engineering other enzymes in the GH13 superfamily.
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Affiliation(s)
- Xin Cui
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Xin Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Shunyi Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Xinlin Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China.
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China.
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4
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Zhang Z, Su W, Bao Y, Huang Q, Ye K, Liu P, Chu X. Modular reconstruction and optimization of the trans-4-hydroxy-L-proline synthesis pathway in Escherichia coli. Microb Cell Fact 2022; 21:159. [PMID: 35953819 PMCID: PMC9367115 DOI: 10.1186/s12934-022-01884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background In recent years, there has been a growing demand for microbial production of trans-4-hydroxy-L-proline (t4Hyp), which is a value-added amino acid and has been widely used in the fields of medicine, food, and cosmetics. In this study, a multivariate modular metabolic engineering approach was used to remove the bottleneck in the synthesis pathway of t4Hyp. Results Escherichia coli t4Hyp synthesis was performed using two modules: a α-ketoglutarate (α-KG) synthesis module (K module) and L-proline synthesis with hydroxylation module (H module). First, α-KG attrition was reduced, and then, L-proline consumption was inhibited. Subsequently, to improve the contribution to proline synthesis with hydroxylation, optimization of gene overexpression, promotor, copy number, and the fusion system was performed. Finally, optimization of the H and K modules was performed in combination to balance metabolic flow. Using the final module H1K4 in a shaking flask culture, 8.80 g/L t4Hyp was produced, which was threefold higher than that produced by the W0 strain. Conclusions These strategies demonstrate that a microbial cell factory can be systematically optimized by modular engineering for efficient production of t4Hyp. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01884-4.
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Affiliation(s)
- Zhenyu Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.,School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yunyun Bao
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Qianqian Huang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Kai Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
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5
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Savino S, Desmet T, Franceus J. Insertions and deletions in protein evolution and engineering. Biotechnol Adv 2022; 60:108010. [PMID: 35738511 DOI: 10.1016/j.biotechadv.2022.108010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Protein evolution or engineering studies are traditionally focused on amino acid substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion of amino acids is often overlooked, despite being one of the most common sources of genetic variation. Recent methodological advances and successful engineering stories have demonstrated that the time is ripe for greater emphasis on these mutations and their understudied effects. This review highlights the evolutionary importance and biotechnological relevance of insertions and deletions (indels). We provide a comprehensive overview of approaches that can be employed to include indels in random, (semi)-rational or computational protein engineering pipelines. Furthermore, we discuss the tolerance to indels at the structural level, address how domain indels can link the function of unrelated proteins, and feature studies that illustrate the surprising and intriguing potential of frameshift mutations.
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Affiliation(s)
- Simone Savino
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium..
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6
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Rational engineering of phospholipase C from Bacillus cereus HSL3 for simultaneous thermostability and activity improvement. J Biotechnol 2022; 355:1-9. [DOI: 10.1016/j.jbiotec.2022.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023]
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7
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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8
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Zhang Z, Liu P, Su W, Zhang H, Xu W, Chu X. Metabolic engineering strategy for synthetizing trans-4-hydroxy-L-proline in microorganisms. Microb Cell Fact 2021; 20:87. [PMID: 33882914 PMCID: PMC8061225 DOI: 10.1186/s12934-021-01579-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/13/2021] [Indexed: 11/14/2022] Open
Abstract
Trans-4-hydroxy-L-proline is an important amino acid that is widely used in medicinal and industrial applications, particularly as a valuable chiral building block for the organic synthesis of pharmaceuticals. Traditionally, trans-4-hydroxy-L-proline is produced by the acidic hydrolysis of collagen, but this process has serious drawbacks, such as low productivity, a complex process and heavy environmental pollution. Presently, trans-4-hydroxy-L-proline is mainly produced via fermentative production by microorganisms. Some recently published advances in metabolic engineering have been used to effectively construct microbial cell factories that have improved the trans-4-hydroxy-L-proline biosynthetic pathway. To probe the potential of microorganisms for trans-4-hydroxy-L-proline production, new strategies and tools must be proposed. In this review, we provide a comprehensive understanding of trans-4-hydroxy-L-proline, including its biosynthetic pathway, proline hydroxylases and production by metabolic engineering, with a focus on improving its production.
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Affiliation(s)
- Zhenyu Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Wenqian Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
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9
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Jiang L, Pang J, Yang L, Li W, Duan L, Zhang G, Luo Y. Engineering endogenous l-proline biosynthetic pathway to boost trans-4-hydroxy-l-proline production in Escherichia coli. J Biotechnol 2021; 329:104-117. [PMID: 33539894 DOI: 10.1016/j.jbiotec.2021.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
Non-proteinogenic trans-4-hydroxy-l-proline (t4HYP), a crucial naturally occurred amino acid, is present in most organisms. t4HYP is a regio- and stereo-selectively hydroxylated product of l-proline and a valuable building block for pharmaceutically important intermediates/ingredients synthesis. Microbial production of t4HYP has aroused extensive investigations because of its low-cost and environmentally benign features. Herein, we reported metabolic engineering of endogenous l-proline biosynthetic pathway to enhance t4HYP production in trace l-proline-producing Escherichia coli BL21(DE3) (21-S0). The genes responsible for by-product formation from l-proline, pyruvate, acetyl-CoA, and isocitrate in the biosynthetic network of 21-S0 were knocked out to channel the metabolic flux towards l-proline biosynthesis. PdhR was knocked out to remove its negative regulation and aceK was deleted to ensure isocitrate dehydrogenase's activity and to increase NADPH/NADP+ level. The other genes for l-proline biosynthesis were enhanced by integration of strong promoters and 5'-untranslated regions. The resulting engineered E. coli strains 21-S1 ∼ 21-S9 harboring a codon-optimized proline 4-hydroxylase-encoding gene (P4H) were grown and fermented. A titer of 4.82 g/L of t4HYP production in 21-S6 overexpressing P4H was obtained at conical flask level, comparing with the starting 21-S0 (26 mg/L). The present work paves an efficient metabolic engineering way for higher t4HYP production in E. coli.
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Affiliation(s)
- Liangzhen Jiang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; College of Pharmacy and Biological Engineering, Chengdu University, 2025 Chengluo Avenue, Chengdu 610106, People's Republic of China
| | - Jing Pang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Lixia Yang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Lili Duan
- College of Food Science and Technology, Sichuan Tourism University, 459 Hongling Road, Chengdu 610100, People's Republic of China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
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10
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Cui X, Li Z. High production of glutathione by in vitro enzymatic cascade after thermostability enhancement. AIChE J 2020. [DOI: 10.1002/aic.17055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiangwei Cui
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology East China University of Science and Technology Shanghai China
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11
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Chen X, Yi J, Liu J, Luo Q, Liu L. Enzymatic production of trans-4-hydroxy-l-proline by proline 4-hydroxylase. Microb Biotechnol 2020; 14:479-487. [PMID: 32618422 PMCID: PMC7936316 DOI: 10.1111/1751-7915.13616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/23/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Trans-4-hydroxy-l-proline (Hyp) is a useful chiral building block for production of many nutritional supplements and pharmaceuticals. However, it is still challenging for industrial production of Hyp due to heavy environmental pollution and low production efficiency. To establish a green and efficient process for Hyp production, the proline 4-hydroxylase (DsP4H) from Dactylosporangium sp. RH1 was overexpressed and functionally characterized in Escherichia coli BL21(DE3). The recombinant DsP4H with l-proline as a substrate exhibited Km , kcat and kcat /Km values up to 0.80 mM, 0.52 s-1 and 0.65 s-1 ·mM-1 respectively. Furthermore, DsP4H showed the highest activity at 35°C and pH 6.5 towards l-proline. The highest enzyme activity of 175.6 U mg-1 was achieved by optimizing culture parameters. Under the optimal transformation conditions in a 5-l fermenter, Hyp titre, conversion rate and productivity were up to 99.9 g l-1 , 99.9% and 2.77 g l-1 h-1 respectively. This strategy described here provides an efficient method for production of Hyp and thus has a great potential in industrial application.
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Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Juyang Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Shaoxing Baiyin Biotechnology Co. Ltd, Shaoxing, 312000, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
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12
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Hara R, Kino K. Enzymatic reactions and microorganisms producing the various isomers of hydroxyproline. Appl Microbiol Biotechnol 2020; 104:4771-4779. [PMID: 32291491 DOI: 10.1007/s00253-020-10603-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023]
Abstract
Hydroxyproline is an industrially important compound with applications in the pharmaceutical, nutrition, and cosmetic industries. trans-4-Hydroxy-L-proline is recognized as the most abundant of the eight possible isomers (hydroxy group at C-3 or C-4, cis- or trans-configuration, and L- or D-form). However, little attention has been paid to the rare isomers, probably due to their limited availability. This mini-review provides an overview of recent advances in microbial and enzymatic processes to develop practical production strategies for various hydroxyprolines. Here, we introduce three screening strategies, namely, activity-, sequence-, and metabolite-based approaches, allowing identification of diverse proline-hydroxylating enzymes with different product specificities. All naturally occurring hydroxyproline isomers can be produced by using suitable hydroxylases in a highly regio- and stereo-selective manner. Furthermore, crystal structures of relevant hydroxylases provide much insight into their functional roles. Since hydroxylases acting on free L-proline belong to the 2-oxoglutarate-dependent dioxygenase superfamily, cellular metabolism of Escherichia coli coupled with a hydroxylase is a valuable source of 2-oxoglutarate, which is indispensable as a co-substrate in L-proline hydroxylation. Further, microbial hydroxyproline 2-epimerase may serve as a highly adaptable tool to convert L-hydroxyproline into D-hydroxyproline. KEY POINTS: • Proline hydroxylases serve as powerful tools for selectivel-proline hydroxylation. • Engineered Escherichia coli are a robust platform for hydroxyproline production. • Hydroxyproline epimerase convertsl-hydroxyproline intod-hydroxyproline.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan. .,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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13
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Mao S, Cheng X, Zhu Z, Chen Y, Li C, Zhu M, Liu X, Lu F, Qin HM. Engineering a thermostable version of D-allulose 3-epimerase from Rhodopirellula baltica via site-directed mutagenesis based on B-factors analysis. Enzyme Microb Technol 2019; 132:109441. [PMID: 31731964 DOI: 10.1016/j.enzmictec.2019.109441] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/05/2019] [Accepted: 10/04/2019] [Indexed: 12/19/2022]
Abstract
D-allulose has received increasing attention due to its excellent physiological properties and commercial potential. The D-allulose 3-epimerase from Rhodopirellula baltica (RbDAEase) catalyzes the conversion of D-fructose to D-allulose. However, its poor thermostability has hampered its industrial application. Site-directed mutagenesis based on homologous structures in which the residuals on high flexible regions were substituted according to B-factors analysis, is an effective way to improve the thermostability and robustness of an enzyme. RbDAEase showed substrate specificity toward D-allulose with a Km of 58.57 mM and kcat of 1849.43 min-1. It showed a melting temperature (Tm) of 45.7 °C and half-life (t1/2) of 52.3 min at pH 8.0, 60 °C with 1 mM Mn2+. The Site-directed mutation L144 F strengthened the thermostability to a Δt1/2 of 50.4 min, ΔTm of 12.6 °C, and ΔT5060 of 22 °C. It also improved the conversion rate to 28.6%. Structural analysis reveals that a new hydrophobic interaction was formed by the mutation. Thus, site-directed mutagenesis based on B-factors analysis would be an efficient strategy to enhance the thermostability of designed ketose 3-epimerases.
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Affiliation(s)
- Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Xiaotao Cheng
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Ying Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Menglu Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Xin Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China.
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, PR China.
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14
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Zhao J, Liu C, Guo X, Wang J, Liu H, Zheng P, Sun J, Ma Y. Efficient production of trans-3-hydroxyproline by a bacterial trans-3-proline hydroxylase and characterization of enzymatic properties. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Abstract
C–H functionalization is a chemically challenging but highly desirable transformation. 2-oxoglutarate-dependent oxygenases (2OGXs) are remarkably versatile biocatalysts for the activation of C–H bonds. In nature, they have been shown to accept both small and large molecules carrying out a plethora of reactions, including hydroxylations, demethylations, ring formations, rearrangements, desaturations, and halogenations, making them promising candidates for industrial manufacture. In this review, we describe the current status of 2OGX use in biocatalytic applications concentrating on 2OGX-catalyzed oxyfunctionalization of amino acids and synthesis of antibiotics. Looking forward, continued bioinformatic sourcing will help identify additional, practical useful members of this intriguing enzyme family, while enzyme engineering will pave the way to enhance 2OGX reactivity for non-native substrates.
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