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Pu Z, Cao J, Wu W, Song Z, Yang L, Wu J, Yu H. Reconstructing dynamics correlation network to simultaneously improve activity and stability of 2,3-butanediol dehydrogenase by design of distal interchain disulfide bonds. Int J Biol Macromol 2024; 267:131415. [PMID: 38582485 DOI: 10.1016/j.ijbiomac.2024.131415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The complete enzyme catalytic cycle includes substrate binding, chemical reaction and product release, in which different dynamic conformations are adopted. Due to the complex relationship among enzyme activity, stability and dynamics, the directed evolution of enzymes for improved activity or stability commonly leads to a trade-off in stability or activity. It hence remains a challenge to engineer an enzyme to have both enhanced activity and stability. Here, we have attempted to reconstruct the dynamics correlation network involved with active center to improve both activity and stability of a 2,3-butanediol dehydrogenase (2,3-BDH) by introducing inter-chain disulfide bonds. A computational strategy was first applied to evaluate the effect of introducing inter-chain disulfide bond on activity and stability of three 2,3-BDHs, and the N258C mutation of 2,3-BDH from Corynebacterium glutamicum (CgBDH) was proved to be effective in improving both activity and stability. In the results, CgBDH-N258C showed a different unfolding curve from the wild type, with two melting temperatures (Tm) of 68.3 °C and 50.8 °C, 19.7 °C and 2 °C higher than 48.6 °C of the wild type. Its half-life was also improved by 14.8-fold compared to the wild type. Catalytic efficiency (kcat/Km) of the mutant was increased by 7.9-fold toward native substrate diacetyl and 8.8-fold toward non-native substrate 2,5-hexanedione compared to the wild type. Molecular dynamics simulations revealed that an interaction network formed by Cys258, Arg162, Ala144 and the catalytic residues was reconstructed in the mutant and the dynamics change caused by the disulfide bond could be propagated through the interactions network. This improved the enzyme stability and activity by decreasing the flexibility and locking more "reactive" pose, respectively. Further construction of mutations including A144G showing a 44-fold improvement in catalytic efficiency toward meso-2,3-BD confirmed the role of modifying dynamics correlation network in tunning enzyme activity and selectivity. This study provided important insights into the relationship among dynamics, enzyme catalysis and stability, and will be useful in the designing new enzymes with co-evolution of stability, activity and selectivity.
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Affiliation(s)
- Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Jiawen Cao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China.
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Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023; 69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [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: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.
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Affiliation(s)
- Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zijian Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
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Chen S, Fu J, Yu B, Wang L. Development of a Conjugation-Based Genome Editing System in an Undomesticated Bacillus subtilis Strain for Poly-γ-glutamic Acid Production with Diverse Molecular Masses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7734-7743. [PMID: 37186794 DOI: 10.1021/acs.jafc.3c01505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) is a biodegradable polymer produced by microorganisms. Biosynthesizing γ-PGA with diverse molecular masses (Mw) is an urgent industrial technical problem to be solved. Bacillus subtilis KH2, a high-Mw γ-PGA producer, is an ideal candidate for de novo production of γ-PGA with diverse Mw values. However, the inability to transfer DNA to this strain has limited its industrial use. In this study, a conjugation-based genetic operating system was developed in strain KH2. This system enabled us to modify the promoter of γ-PGA hydrolase PgdS in strain KH2 chromosome to de novo biosynthesize γ-PGA with diverse Mws. The conjugation efficiency was improved to 1.23 × 10-4 by establishing a plasmid replicon sharing strategy. A further increase to 3.15 × 10-3 was achieved after knocking out two restriction endonucleases. To demonstrate the potential of our newly established system, the pgdS promoter was replaced by different phase-dependent promoters. A series of strains producing γ-PGA with specific Mws of 411.73, 1356.80, 2233.30, and 2411.87 kDa, respectively, were obtained. The maximum yield of γ-PGA was 23.28 g/L. Therefore, we have successfully constructed ideal candidate strains for efficient γ-PGA production with a specific Mw value, which provides an important research basis for sustainable production of desirable γ-PGA.
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Affiliation(s)
- Shengbao Chen
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaming Fu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Wang
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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He H, Yu Q, Ding Z, Zhang L, Shi G, Li Y. Biotechnological and food synthetic biology potential of platform strain: Bacillus licheniformis. Synth Syst Biotechnol 2023; 8:281-291. [PMID: 37090063 PMCID: PMC10119484 DOI: 10.1016/j.synbio.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/01/2023] Open
Abstract
Bacillus licheniformis is one of the most characteristic Gram-positive bacteria. Its unique genetic background and safety characteristics make it have important biologic applications in the food industry, including, the biosynthesis of high value-added bioproducts, probiotic functions, biological treatment of wastes derived from food production, etc. In this review, these recent advances are summarized and presented systematically for the first time. In addition, we highlight synthetic biology strategies as a potential driver of developing this strain for wider and more efficient application in the food industry. Finally, we present the current challenges faced and provide our unique perspective on relevant future research directions. In summary, this review will provide an illuminating and comprehensive perspective that will allow an in-depth understanding of B. licheniformis and promote its more effective development in the food industry.
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Eliminating host-guest incompatibility via enzyme mining enables the high-temperature production of N-acetylglucosamine. iScience 2022; 26:105774. [PMID: 36636338 PMCID: PMC9829697 DOI: 10.1016/j.isci.2022.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/09/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The host-guest incompatibility between a production host and non-native enzymes has posed an arduous challenge for synthetic biology, particularly between mesophile-derived enzymes and a thermophilic chassis. In the present study, we develop a thermophilic enzyme mining strategy comprising an automated co-evolution-based screening pipeline (http://cem.sjtu.edu.cn), computation-based enzyme characterization, and gene synthesis-based function validation. Using glucosamine-6-phosphate acetyltransferase (GNA1) as an example, we successfully mined four novel GNA1s with excellent thermostabilities and catalytic performances. Calculation and analysis based on AlphaFold2-generated structures were also conducted to uncover the mechanism underlying their excellent properties. Finally, our mined GNA1s were used to enable the high-temperature N-acetylglucosamine (GlcNAc) production with high titers of up to 119.3 g/L, with the aid of systems metabolic engineering and temperature programming. This study demonstrates the effectiveness of the enzyme mining strategy, highlighting the application prospects of mining new enzymes from massive databases and providing an effective solution for tackling host-guest incompatibility.
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Chi H, Wang Y, Xia B, Zhou Y, Lu Z, Lu F, Zhu P. Enhanced Thermostability and Molecular Insights for l-Asparaginase from Bacillus licheniformis via Structure- and Computation-Based Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14499-14509. [PMID: 36341695 DOI: 10.1021/acs.jafc.2c05712] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
l-Asparaginase has gained much attention for effectively treating acute lymphoblastic leukemia (ALL) and mitigating carcinogenic acrylamide in fried foods. Due to high-dose dependence for clinical treatment and low mitigation efficiency for thermal food processes caused by poor thermal stability, a method to achieve thermostable l-asparaginase has become a critical bottleneck. In this study, a rational design including free energy combined with structural and conservative analyses was applied to engineer the thermostability of l-asparaginase from Bacillus licheniformis (BlAsnase). Two enhanced thermostability mutants D172W and E207A were screened out by site-directed saturation mutagenesis. The double mutant D172W/E207A exhibited highly remarkable thermostability with a 65.8-fold longer half-life at 55 °C and 5 °C higher optimum reaction temperature and melting temperature (Tm) than those of wild-type BlAsnase. Further, secondary structure, sequence, molecular dynamics (MD), and 3D-structure analysis revealed that the excellent thermostability of the mutant D172W/E207A was on account of increased hydrophobicity and decreased flexibility, highly rigid structure, hydrophobic interactions, and favorable electrostatic potential. As the first report of rationally designing l-asparaginase with improved thermostability from B. licheniformis, this study offers a facile and efficient process to improve the thermostability of l-asparaginase for industrial applications.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yilian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Bingjie Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yawen Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
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Dutschei T, Zühlke MK, Welsch N, Eisenack T, Hilkmann M, Krull J, Stühle C, Brott S, Dürwald A, Reisky L, Hehemann JH, Becher D, Schweder T, Bornscheuer UT. Metabolic engineering enables Bacillus licheniformis to grow on the marine polysaccharide ulvan. Microb Cell Fact 2022; 21:207. [PMID: 36217189 PMCID: PMC9549685 DOI: 10.1186/s12934-022-01931-0] [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: 06/28/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Marine algae are responsible for half of the global primary production, converting carbon dioxide into organic compounds like carbohydrates. Particularly in eutrophic waters, they can grow into massive algal blooms. This polysaccharide rich biomass represents a cheap and abundant renewable carbon source. In nature, the diverse group of polysaccharides is decomposed by highly specialized microbial catabolic systems. We elucidated the complete degradation pathway of the green algae-specific polysaccharide ulvan in previous studies using a toolbox of enzymes discovered in the marine flavobacterium Formosa agariphila and recombinantly expressed in Escherichia coli. Results In this study we show that ulvan from algal biomass can be used as feedstock for a biotechnological production strain using recombinantly expressed carbohydrate-active enzymes. We demonstrate that Bacillus licheniformis is able to grow on ulvan-derived xylose-containing oligosaccharides. Comparative growth experiments with different ulvan hydrolysates and physiological proteogenomic analyses indicated that analogues of the F. agariphila ulvan lyase and an unsaturated β-glucuronylhydrolase are missing in B. licheniformis. We reveal that the heterologous expression of these two marine enzymes in B. licheniformis enables an efficient conversion of the algal polysaccharide ulvan as carbon and energy source. Conclusion Our data demonstrate the physiological capability of the industrially relevant bacterium B. licheniformis to grow on ulvan. We present a metabolic engineering strategy to enable ulvan-based biorefinery processes using this bacterial cell factory. With this study, we provide a stepping stone for the development of future bioprocesses with Bacillus using the abundant marine renewable carbon source ulvan. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01931-0.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Marie-Katherin Zühlke
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Norma Welsch
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Tom Eisenack
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Maximilian Hilkmann
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Carlo Stühle
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Stefan Brott
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Alexandra Dürwald
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute for Microbiology, University of Greifswald, 17487, Greifswald, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
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Immobilization of Alcohol Dehydrogenase, Acetaldehyde Lyase, and NADH Oxidase for Cascade Enzymatic Conversion of Ethanol to Acetoin. ENERGIES 2022. [DOI: 10.3390/en15124242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Acetoin, a four-carbon hydroxyl-keto compound, is used in the food, pharmaceutical, and chemical industries. The cascade enzymatic production is considered a promising and efficient method to produce acetoin. However, the stability and compatibility of the enzymes under the same catalytic conditions are challenges that need to be resolved. In this work, alcohol dehydrogenase, acetaldehyde lyase, and NADH oxidase were selected to work at the same conditions to efficiently convert ethanol into acetoin. These three enzymes were immobilized on epoxy-modified magnetic nanomaterials to obtain highly stable biocatalysts. The stability and the immobilization conditions, including temperature, pH, enzyme–carrier ratio, and immobilization time, were optimized to obtain the immobilized enzymes with a high catalytic activity. The cascade reactions catalyzed by the immobilized enzymes yielded a high conversion of 90%, suggesting that the use of immobilized enzymes is a promising way to produce acetoin.
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Meng W, Ma C, Xu P, Gao C. Biotechnological production of chiral acetoin. Trends Biotechnol 2022; 40:958-973. [DOI: 10.1016/j.tibtech.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
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Abstract
The growing need for industrial production of bio-based acetoin and 2,3-butanediol (2,3-BD) is due to both environmental concerns, and their widespread use in the food, pharmaceutical, and chemical industries. Acetoin is a common spice added to many foods, but also a valuable reagent in many chemical syntheses. Similarly, 2,3-BD is an indispensable chemical on the platform in the production of synthetic rubber, printing inks, perfumes, antifreeze, and fuel additives. This state-of-the-art review focuses on representatives of the genus Bacillus as prospective producers of acetoin and 2,3-BD. They have the following important advantages: non-pathogenic nature, unpretentiousness to growing conditions, and the ability to utilize a huge number of substrates (glucose, sucrose, starch, cellulose, and inulin hydrolysates), sugars from the composition of lignocellulose (cellobiose, mannose, galactose, xylose, and arabinose), as well as waste glycerol. In addition, these strains can be improved by genetic engineering, and are amenable to process optimization. Bacillus spp. are among the best acetoin producers. They also synthesize 2,3-BD in titer and yield comparable to those of the pathogenic producers. However, Bacillus spp. show relatively lower productivity, which can be increased in the course of challenging future research.
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Xu M, Guo J, Li T, Zhang C, Peng X, Xing K, Qin S. Antibiotic Effects of Volatiles Produced by Bacillus tequilensis XK29 against the Black Spot Disease Caused by Ceratocystis fimbriata in Postharvest Sweet Potato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13045-13054. [PMID: 34705454 DOI: 10.1021/acs.jafc.1c04585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Black spot disease caused by Ceratocystis fimbriata is destructive to the production, transportation, and storage of sweet potato. The antifungal effects of Bacillus tequilensis XK29 against C. fimbriata through volatile organic compounds (VOCs) were evaluated in this study. The activated carbon assay proved that XK29 could exert antibiotic effects through volatiles. By optimizing the wheat seed weight, inoculation method, concentration, volume, and time, the antifungal activity of XK29 was significantly improved. XK29 fumigation inhibited spore formation and germination and changed the cell morphology of C. fimbriata. During the storage of sweet potato tuber roots, XK29 effectively controlled black spot disease and reduced the weight loss and malondialdehyde content. Metabolomic analysis revealed that 21 volatile compounds were released from XK29. Isovaleric acid, isobutyric acid, and 2-methylbutanoic acid effectively inhibited the growth of C. fimbriata. These results indicate that B. tequilensis XK29 has a good potential to be developed as a microbial fumigation agent.
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Affiliation(s)
- Mingjie Xu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
| | - Jianheng Guo
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
| | - Tengjie Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
- Wanbang Biopharmaceuticals Group Co., Ltd., Xuzhou 221001, Jiangsu, P.R. China
| | - Chunmei Zhang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
| | - Xue Peng
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
| | - Ke Xing
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
| | - Sheng Qin
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, P.R. China
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Enhanced In Vitro Cascade Catalysis of Glycerol into Pyruvate and Acetoin by Integration with Dihydroxy Acid Dehydratase from Paralcaligenes ureilyticus. Catalysts 2021. [DOI: 10.3390/catal11111282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently, an in vitro enzymatic cascade was constructed to transform glycerol into the high-value platform chemical pyruvate. However, the low activity of dihydroxy acid dehydratase from Sulfolobus solfataricus (SsDHAD) limited the efficiency. In this study, the enzymatic reduction of pyruvate catalyzed by d-lactate dehydrogenase from Pseudomonas aeruginosa PAO1 was used to assay the activities of dihydroxy acid dehydratases. Dihydroxy acid dehydratase from Paralcaligenes ureilyticus (PuDHT) was identified as the most efficient candidate for glycerate dehydration. After the optimization of the catalytic temperature for the enzymatic cascade, comprising alditol oxidase from Streptomyces coelicolor A3, PuDHT, and catalase from Aspergillus niger, 20.50 ± 0.27 mM of glycerol was consumed in 4 h to produce 18.95 ± 0.97 mM of pyruvate with a productivity 12.15-fold higher than the previous report using SsDHAD. The enzymatic cascade was further coupled with the pyruvate decarboxylase from Zymomonas mobile for the production of another platform compound, acetoin. Acetoin at a concentration of 8.52 ± 0.12 mM was produced from 21.62 ± 0.19 mM of glycerol with a productivity of 1.42 ± 0.02 mM h−1.
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Wang CY, Liu LC, Wu YC, Zhang YX. Identification and Validation of Four Novel Promoters for Gene Engineering with Broad Suitability across Species. J Microbiol Biotechnol 2021; 31:1154-1162. [PMID: 34226414 PMCID: PMC9706022 DOI: 10.4014/jmb.2103.03049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022]
Abstract
The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (Pk.rtufB, Pk.r1, Pk.r2, and Pk.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with Pk.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by Pk.r1 and Pk.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.
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Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Ying-Cai Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China,Corresponding author Phone: +86-024-43520921 E-mail:
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Bae SJ, Kim S, Park HJ, Kim J, Jin H, Kim BG, Hahn JS. High-yield production of (R)-acetoin in Saccharomyces cerevisiae by deleting genes for NAD(P)H-dependent ketone reductases producing meso-2,3-butanediol and 2,3-dimethylglycerate. Metab Eng 2021; 66:68-78. [PMID: 33845171 DOI: 10.1016/j.ymben.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/19/2021] [Accepted: 04/04/2021] [Indexed: 01/09/2023]
Abstract
Acetoin is widely used in food and cosmetics industries as a taste and fragrance enhancer. To produce (R)-acetoin in Saccharomyces cerevisiae, acetoin biosynthetic genes encoding α-acetolactate synthase (AlsS) and α-acetolactate decarboxylase (AlsD) from Bacillus subtilis and water-forming NADH oxidase (NoxE) from Lactococcus lactis were integrated into delta-sequences in JHY605 strain, where the production of ethanol, glycerol, and (R,R)-2,3-butanediol (BDO) was largely eliminated. We further improved acetoin production by increasing acetoin tolerance by adaptive laboratory evolution, and eliminating other byproducts including meso-2,3-BDO and 2,3-dimethylglycerate, a newly identified byproduct. Ara1, Ypr1, and Ymr226c (named Ora1) were identified as (S)-alcohol-forming reductases, which can reduce (R)-acetoin to meso-2,3-BDO in vitro. However, only Ara1 and Ypr1 contributed to meso-2,3-BDO production in vivo. We elucidate that Ora1, having a substrate preference for (S)-acetoin, reduces (S)-α-acetolactate to 2,3-dimethylglycerate, thus competing with AlsD-mediated (R)-acetoin production. By deleting ARA1, YPR1, and ORA1, 101.3 g/L of (R)-acetoin was produced with a high yield (96% of the maximum theoretical yield) and high stereospecificity (98.2%).
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Affiliation(s)
- Sang-Jeong Bae
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sujin Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, 33 Samyang-ro 144-gil, Dobong-gu, Seoul, 01369, Republic of Korea
| | - Joonwon Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyunbin Jin
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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15
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Paulino BN, Sales A, Felipe L, Pastore GM, Molina G, Bicas JL. Recent advances in the microbial and enzymatic production of aroma compounds. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.09.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Subramanian V, Lunin VV, Farmer SJ, Alahuhta M, Moore KT, Ho A, Chaudhari YB, Zhang M, Himmel ME, Decker SR. Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:186. [PMID: 33292448 PMCID: PMC7656694 DOI: 10.1186/s13068-020-01820-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. RESULTS Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh (SmBdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34-2.87 µmol/min/mg). The SmBdh crystal structure was determined through crystallization with cofactor (NAD+) and substrate (acetoin) molecules bound in the active site. Active SmBdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. SmBdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae (EcBdh) enzyme resulted in reduction of SmBdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the EcBdh to mimic the SmBdh structure resulted in ~ 70% increase in its activity. CONCLUSIONS This study has demonstrated that SmBdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. SmBdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.
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Affiliation(s)
- Venkataramanan Subramanian
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Samuel J Farmer
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Kyle T Moore
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Angela Ho
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Yogesh B Chaudhari
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
- Biodiversity and Ecosystem Research, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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17
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Guo ZW, Ou XY, Liang S, Gao HF, Zhang LY, Zong MH, Lou WY. Recruiting a Phosphite Dehydrogenase/Formamidase-Driven Antimicrobial Contamination System in Bacillus subtilis for Nonsterilized Fermentation of Acetoin. ACS Synth Biol 2020; 9:2537-2545. [PMID: 32786356 DOI: 10.1021/acssynbio.0c00312] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Microbial contamination, especially in large-scale processes, is partly a life-or-death issue for industrial fermentation. Therefore, the aim of this research was to create an antimicrobial contamination system in Bacillus subtilis 168 (an ideal acetoin producer for its safety and acetoin synthesis potential). First, introduction of the formamidase (FmdA) from Helicobacter pylori and the phosphite dehydrogenase (PtxD) from Pseudomonas stutzeri enabled the engineered Bacillus subtilis to simultaneously assimilate formamide and phosphite as nitrogen (N) and phosphorus (P) sources. Thus, the engineered B. subtilis became the dominant population in a potentially contaminated system, while contaminated microbes were starved of key nutrients. Second, stepwise metabolic engineering via chromosome-based overexpression of the relevant glycolysis and acetoin biosynthesis genes led to a 1.12-fold increment in acetoin titer compared with the starting host. Finally, with our best acetoin producer, 25.56 g/L acetoin was synthesized in the fed-batch fermentation, with a productivity of 0.33 g/L/h and a yield of 0.37 g/g under a nonsterilized and antibiotic-free system. More importantly, our work fulfills many key criteria of sustainable chemistry since sterilization is abolished, contributing to the simplified fermentation operation with lower energy consumption and cost.
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Affiliation(s)
- Ze-Wang Guo
- School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, Guangdong, China
| | - Xiao-Yang Ou
- School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, Guangdong, China
| | - Shan Liang
- School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, Guangdong, China
| | - Hui-Fang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Liao-Yuan Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Min-Hua Zong
- School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, Guangdong, China
| | - Wen-Yong Lou
- School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, Guangdong, China
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18
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Lu L, Mao Y, Kou M, Cui Z, Jin B, Chang Z, Wang Z, Ma H, Chen T. Engineering central pathways for industrial-level (3R)-acetoin biosynthesis in Corynebacterium glutamicum. Microb Cell Fact 2020; 19:102. [PMID: 32398078 PMCID: PMC7216327 DOI: 10.1186/s12934-020-01363-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Acetoin, especially the optically pure (3S)- or (3R)-enantiomer, is a high-value-added bio-based platform chemical and important potential pharmaceutical intermediate. Over the past decades, intense efforts have been devoted to the production of acetoin through green biotechniques. However, efficient and economical methods for the production of optically pure acetoin enantiomers are rarely reported. Previously, we systematically engineered the GRAS microorganism Corynebacterium glutamicum to efficiently produce (3R)-acetoin from glucose. Nevertheless, its yield and average productivity were still unsatisfactory for industrial bioprocesses. RESULTS In this study, cellular carbon fluxes in the acetoin producer CGR6 were further redirected toward acetoin synthesis using several metabolic engineering strategies, including blocking anaplerotic pathways, attenuating key genes of the TCA cycle and integrating additional copies of the alsSD operon into the genome. Among them, the combination of attenuation of citrate synthase and inactivation of phosphoenolpyruvate carboxylase showed a significant synergistic effect on acetoin production. Finally, the optimal engineered strain CGS11 produced a titer of 102.45 g/L acetoin with a yield of 0.419 g/g glucose at a rate of 1.86 g/L/h in a 5 L fermenter. The optical purity of the resulting (3R)-acetoin surpassed 95%. CONCLUSION To the best of our knowledge, this is the highest titer of highly enantiomerically enriched (3R)-acetoin, together with a competitive product yield and productivity, achieved in a simple, green processes without expensive additives or substrates. This process therefore opens the possibility to achieve easy, efficient, economical and environmentally-friendly production of (3R)-acetoin via microbial fermentation in the near future.
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Affiliation(s)
- Lingxue Lu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yufeng Mao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengyun Kou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhenzhen Cui
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Biao Jin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhishuai Chang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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