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Bretagne D, Pâris A, Matthews D, Fougère L, Burrini N, Wagner GK, Daniellou R, Lafite P. "Mix and match" auto-assembly of glycosyltransferase domains delivers biocatalysts with improved substrate promiscuity. J Biol Chem 2024; 300:105747. [PMID: 38354783 PMCID: PMC10937113 DOI: 10.1016/j.jbc.2024.105747] [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: 07/21/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Glycosyltransferases (GT) catalyze the glycosylation of bioactive natural products, including peptides and proteins, flavonoids, and sterols, and have been extensively used as biocatalysts to generate glycosides. However, the often narrow substrate specificity of wild-type GTs requires engineering strategies to expand it. The GT-B structural family is constituted by GTs that share a highly conserved tertiary structure in which the sugar donor and acceptor substrates bind in dedicated domains. Here, we have used this selective binding feature to design an engineering process to generate chimeric glycosyltransferases that combine auto-assembled domains from two different GT-B enzymes. Our approach enabled the generation of a stable dimer with broader substrate promiscuity than the parent enzymes that were related to relaxed interactions between domains in the dimeric GT-B. Our findings provide a basis for the development of a novel class of heterodimeric GTs with improved substrate promiscuity for applications in biotechnology and natural product synthesis.
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Affiliation(s)
- Damien Bretagne
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France; School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Arnaud Pâris
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France
| | - David Matthews
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Laëtitia Fougère
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France
| | - Nastassja Burrini
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Richard Daniellou
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France; Chaire de Cosmétologie, AgroParisTech, Orléans, France; Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Pierre Lafite
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans, Université d'Orléans, Orléans Cedex 2, France.
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2
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Zhu Q, Zheng Y, Zhang Z, Chen Y. Enzyme immobilization on covalent organic framework supports. Nat Protoc 2023; 18:3080-3125. [PMID: 37674094 DOI: 10.1038/s41596-023-00868-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/01/2023] [Indexed: 09/08/2023]
Abstract
Enzymes are natural catalysts with high catalytic activity, substrate specificity and selectivity. Their widespread utilization in industrial applications is limited by their sensitivity to harsh reaction conditions and difficulties relating to their removal and re-use after the reaction is complete. These limitations can be addressed by immobilizing the enzymes in solid porous supports. Covalent organic frameworks (COFs) are ideal candidate carriers because of their good biocompatibility, long-term water stability and large surface area. In post-synthetic immobilization, the enzyme is added to an existing COF; this has had limited success because of enzyme leaching and pore blockage by enzymes that are too large. Direct-immobilization methods-building the COF around the enzyme-allow tailored incorporation of proteins of any size and result in materials with lower levels of leaching and better mass transport of reactants and products. This protocol describes direct-immobilization methods that can be used to fabricate enzyme@COF (@ = engulfing) biocomposites with rationally programmed structures and functions. If COF construction requires harsh reaction conditions, the enzyme can be protected by using a removable metal-organic framework. Alternatively, a direct in situ approach, in which the enzyme and the COF monomers assemble under very mild conditions, can be used. Examples of both approaches are described: enzyme@COF-42-B/43-B capsules (enzymes including catalase, glucose oxidase, etc.) with ZIF-90 or ZPF-2 as protectors, and lipase@NKCOF-98/99 via in situ direct-immobilization methods (synthesis timing: 30-100 min). Example assays for physical and functional characterization of the COF and enzyme@COF materials are also described.
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Affiliation(s)
- Qianqian Zhu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, P.R. China
- College of Chemistry, Nankai University, Tianjin, P.R. China
| | - Yunlong Zheng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, P.R. China
- College of Pharmacy, Nankai University, Tianjin, P.R. China
| | - Zhenjie Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, P.R. China.
- College of Chemistry, Nankai University, Tianjin, P.R. China.
| | - Yao Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, P.R. China.
- College of Pharmacy, Nankai University, Tianjin, P.R. China.
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3
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Lu S, Deng H, Zhou C, Du Z, Guo X, Cheng Y, He X. Enhancement of β-Caryophyllene Biosynthesis in Saccharomyces cerevisiae via Synergistic Evolution of β-Caryophyllene Synthase and Engineering the Chassis. ACS Synth Biol 2023; 12:1696-1707. [PMID: 37224386 DOI: 10.1021/acssynbio.3c00024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
β-Caryophyllene is a plant-derived bicyclic sesquiterpene with multiple biological functions. β-Caryophyllene production by engineered Saccharomyces cerevisiae represents a promising technological route. However, the low catalytic activity of β-caryophyllene synthase (CPS) is one of the main restrictive factors for β-caryophyllene production. Here, directed evolution of the Artemisia annua CPS was performed, and variants of CPS enhancing the β-caryophyllene biosynthesis in S. cerevisiae were obtained, in which an E353D mutant enzyme presented large improvements in Vmax and Kcat. The Kcat/Km of the E353D mutant was 35.5% higher than that of wild-type CPS. Moreover, the E353D variant exhibited higher catalytic activity in much wider pH and temperature ranges. Thus, both the higher catalytic activity and the robustness of the E353D variant contribute to the 73.3% increase in β-caryophyllene production. Furthermore, the S. cerevisiae chassis was engineered by overexpressing genes related to β-alanine metabolism and MVA pathway to enhance the synthesis of the precursor, and ATP-binding cassette transporter gene variant STE6T1025N to improve the transmembrane transport of β-caryophyllene. The combined engineering of CPS and chassis resulted in 70.45 mg/L of β-caryophyllene after 48 h of cultivation in a test tube, which was 2.93-fold of that of the original strain. Finally, a β-caryophyllene yield of 594.05 mg/L was obtained by fed-batch fermentation, indicating the potential of β-caryophyllene production by yeast.
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Affiliation(s)
- Surui Lu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Hong Deng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chenyao Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfei Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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4
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Shi CY, Zhan YF, Liu Y, Zhang ZP, Shen XY, Wu CK, Bai ZY, Zhang ZA, Wang J. Hydrophobic effects enhance xylooligosaccharides production from mulberry branch using xylanase-methacrylate conjugate-catalyzed hydrolysis. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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5
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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Fu X, Hong K, Wang H, Zhang C, Lu W. Screening and Remodeling of Enone Oxidoreductase for High Production of 2(or 5)-Ethyl-5(or 2)-methyl-4-hydroxy-3(2H)-Furanone in Saccharomyces Cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9888-9897. [PMID: 35925879 DOI: 10.1021/acs.jafc.2c03306] [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: 06/15/2023]
Abstract
Owing to its unique fragrance, 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone (HEMF) is widely used as a food flavoring agent and has high demand. Enone oxidoreductase is a vital enzyme involved in HEMF production. In this study, an enone oxidoreductase from Naumovozyma dairenensis CBS 421 (NDEO) was used for HEMF production for the first time. The mutant NDEOT183W,K290W was obtained through semirational protein engineering, which increased the HEMF yield by 75.2%. Finally, the engineered strain BM4 produced the highest HEMF yield, 194.42 mg L-1 in 132 h. Our study revealed that HEMF production can be improved in Saccharomyces cerevisiae and that this is an efficient method to improve the activity of enone oxidoreductase, which is important for the industrial synthesis of furanone.
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Affiliation(s)
- Xiaomeng Fu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Kunqiang Hong
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Haibin Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin 300350, PR China
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7
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Abstract
Lipases are versatile enzymes widely used in the pharmaceutical, cosmetic, and food industries. They are green biocatalysts with a high potential for industrial use compared to traditional chemical methods. In recent years, lipases have been used to synthesize a wide variety of molecules of industrial interest, and extraordinary results have been reported. In this sense, this review describes the important role of lipases in the synthesis of phytosterol esters, which have attracted the scientific community’s attention due to their beneficial effects on health. A systematic search for articles and patents published in the last 20 years with the terms “phytosterol AND esters AND lipase” was carried out using the Scopus, Web of Science, Scielo, and Google Scholar databases, and the results showed that Candida rugosa lipases are the most relevant biocatalysts for the production of phytosterol esters, being used in more than 50% of the studies. The optimal temperature and time for the enzymatic synthesis of phytosterol esters mainly ranged from 30 to 101 °C and from 1 to 72 h. The esterification yield was greater than 90% for most analyzed studies. Therefore, this manuscript presents the new technological approaches and the gaps that need to be filled by future studies so that the enzymatic synthesis of phytosterol esters is widely developed.
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8
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Gao J, Le S, Thayumanavan S. Enzyme Catalysis in Non‐Native Environment with Unnatural Selectivity Using Polymeric Nanoreactors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jingjing Gao
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
- Center for Nanomedicine and Division of Engineering in Medicine Department of Anesthesiology Brigham and Women's Hospital Boston MA 02115 USA
- Harvard Medical School Boston MA 02115 USA
| | - Stephanie Le
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - S. Thayumanavan
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
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9
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Gao J, Le S, Thayumanavan S. Enzyme Catalysis in Non-Native Environment with Unnatural Selectivity Using Polymeric Nanoreactors. Angew Chem Int Ed Engl 2021; 60:27189-27194. [PMID: 34510672 DOI: 10.1002/anie.202109477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Indexed: 11/10/2022]
Abstract
The utilization of enzymes for catalysis in organic solvents, while exhibiting selectivity to different substrates, is a big challenge. We report an amphiphilic random copolymer system that self-assembles with enzymes in an organic solvent to form nanoreactors. These encapsulated enzymes are not denatured and they do preserve the catalytic activity. The cross-linkable functional groups in the hydrophobic compartments of the polymers offer to control accessibility to the enzyme. This varied accessibility due to the polymer host, rather than the enzyme itself, endows the nanoreactor with an unnatural selectivity. The findings here highlight the significant potential of simple polymer-based enzyme nanoreactors to execute selective organic reactions under non-native conditions.
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Affiliation(s)
- Jingjing Gao
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA.,Center for Nanomedicine and Division of Engineering in Medicine, Department of Anesthesiology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Stephanie Le
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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10
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Zhang FR, Wan NW, Ma JM, Cui BD, Han WY, Chen YZ. Enzymatic Kinetic Resolution of Bulky Spiro-Epoxyoxindoles via Halohydrin Dehalogenase-Catalyzed Enantio- and Regioselective Azidolysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fang-Rui Zhang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Jin-Mei Ma
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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11
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Revolutionizing enzyme engineering through artificial intelligence and machine learning. Emerg Top Life Sci 2021; 5:113-125. [PMID: 33835131 DOI: 10.1042/etls20200257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022]
Abstract
The combinatorial space of an enzyme sequence has astronomical possibilities and exploring it with contemporary experimental techniques is arduous and often ineffective. Multi-target objectives such as concomitantly achieving improved selectivity, solubility and activity of an enzyme have narrow plausibility under approaches of restricted mutagenesis and combinatorial search. Traditional enzyme engineering approaches have a limited scope for complex optimization due to the requirement of a priori knowledge or experimental burden of screening huge protein libraries. The recent surge in high-throughput experimental methods including Next Generation Sequencing and automated screening has flooded the field of molecular biology with big-data, which requires us to re-think our concurrent approaches towards enzyme engineering. Artificial Intelligence (AI) and Machine Learning (ML) have great potential to revolutionize smart enzyme engineering without the explicit need for a complete understanding of the underlying molecular system. Here, we portray the role and position of AI techniques in the field of enzyme engineering along with their scope and limitations. In addition, we explain how the traditional approaches of directed evolution and rational design can be extended through AI tools. Recent successful examples of AI-assisted enzyme engineering projects and their deviation from traditional approaches are highlighted. A comprehensive picture of current challenges and future avenues for AI in enzyme engineering are also discussed.
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12
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Madhavan A, Arun KB, Binod P, Sirohi R, Tarafdar A, Reshmy R, Kumar Awasthi M, Sindhu R. Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology. BIORESOURCE TECHNOLOGY 2021; 325:124617. [PMID: 33450638 DOI: 10.1016/j.biortech.2020.124617] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| | - Ranjna Sirohi
- The Center for Energy and Environmental Sustainability, Lucknow 226 010, Uttar Pradesh, India
| | - Ayon Tarafdar
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India.
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13
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Liang W, Wied P, Carraro F, Sumby CJ, Nidetzky B, Tsung CK, Falcaro P, Doonan CJ. Metal–Organic Framework-Based Enzyme Biocomposites. Chem Rev 2021; 121:1077-1129. [DOI: 10.1021/acs.chemrev.0c01029] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Weibin Liang
- Department of Chemistry and Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Peter Wied
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Francesco Carraro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Christopher J. Sumby
- Department of Chemistry and Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Chia-Kuang Tsung
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Christian J. Doonan
- Department of Chemistry and Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia 5005, Australia
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14
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Abstract
In the past years, several serine hydrolases such as cutinases, esterases and lipases have shown the ability to degrade not only natural polymers but also synthetic polyesters, even aromatic representatives like polyethylene terephthalate (PET). Hence, cutinases and related ester hydrolases have become very important to be applied in the biocatalytic plastic recycling as green alternative to chemical recycling as well as to the functionalization of polyester surfaces in order to change superficial properties like hydrophobicity or hydrophilicity. Sorption characteristics of the enzymes to the polymers have turned out to be a crucial process for efficient polymer hydrolysis. Hence, special attention was paid on tuning the sorption of the enzymes to the hydrophobic polymers. Engineering of the enzyme surface, fusion of hydrophobic substrate-binding domains or truncation of domains hindering the access of the polymer to the enzyme has led to significant improvement of sorption processes and consequently increased activity on the bulky substrate. Finally, the combination of engineering approaches has proved that they can bring additional advantages in improving the enzyme activity when used in a synergistic manner.
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Affiliation(s)
- Doris Ribitsch
- Institute for Environmental Biotechnology, IFA Tulln, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria.
| | - Georg M Guebitz
- Institute for Environmental Biotechnology, IFA Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
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15
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Yu Y, Rasool A, Liu H, Lv B, Chang P, Song H, Wang Y, Li C. Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool. Metab Eng 2020; 62:72-83. [DOI: 10.1016/j.ymben.2020.08.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 12/19/2022]
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16
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Hydrolysis of Glycosyl Thioimidates by Glycoside Hydrolase Requires Remote Activation for Efficient Activity. Catalysts 2019. [DOI: 10.3390/catal9100826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chemoenzymatic synthesis of glycosides relies on efficient glycosyl donor substrates able to react rapidly and efficiently, yet with increased stability towards chemical or enzymatic hydrolysis. In this context, glycosyl thioimidates have previously been used as efficient donors, in the case of hydrolysis or thioglycoligation. In both cases, the release of the thioimidoyl aglycone was remotely activated through a protonation driven by a carboxylic residue in the active site of the corresponding enzymes. A recombinant glucosidase (DtGly) from Dictyoglomus themophilum, previously used in biocatalysis, was also able to use such glycosyl thioimidates as substrates. Yet, enzymatic kinetic values analysis, coupled to mutagenesis and in silico modelling of DtGly/substrate complexes demonstrated that the release of the thioimidoyl moiety during catalysis is only driven by its leaving group ability, without the activation of a remote protonation. In the search of efficient glycosyl donors, glycosyl thioimidates are attractive and efficient. Their utility, however, is limited to enzymes able to promote leaving group release by remote activation.
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17
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Duan J, Li B, Qin Y, Dong Y, Ren J, Li G. Recent progress in directed evolution of stereoselective monoamine oxidases. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0272-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMonoamine oxidases (MAOs) use molecular dioxygen as oxidant to catalyze the oxidation of amines to imines. This type of enzyme can be employed for the synthesis of primary, secondary, and tertiary amines by an appropriate deracemization protocol. Consequently, MAOs are an attractive class of enzymes in biocatalysis. However, they also have limitations in enzyme-catalyzed processes due to the often-observed narrow substrate scope, low activity, or poor/wrong stereoselectivity. Therefore, directed evolution was introduced to eliminate these obstacles, which is the subject of this review. The main focus is on recent efforts concerning the directed evolution of four MAOs: monoamine oxidase (MAO-N), cyclohexylamine oxidase (CHAO),D-amino acid oxidase (pkDAO), and 6-hydroxy-D-nicotine oxidase (6-HDNO).
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18
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Borkowska M, Białas W, Kubiak M, Celińska E. Rapid micro-assays for amylolytic activities determination: customization and validation of the tests. Appl Microbiol Biotechnol 2019; 103:2367-2379. [PMID: 30675636 PMCID: PMC6420461 DOI: 10.1007/s00253-018-09610-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 02/07/2023]
Abstract
High-throughput function-based screening techniques remain the major bottleneck in the novel biocatalysts development pipeline. In the present study, we customized protocols for amylolytic activity determination (Somogyi-Nelson and starch-iodine tests) to micro-volume thermalcycler-based assays (linearity range 60-600 μM of reducing sugar, R2 = 0.9855; 0-2 mg/mL of starch, R2 = 0.9921, respectively). Exploitation of a thermalcycler enabled rapid and accurate temperature control, further reduction of reagents and samples volumes, and limited evaporation of the reaction mixtures, meeting several crucial requirements of an adequate enzymatic assay. In the optimized micro-volume Somogyi-Nelson protocol, we were able to reduce the time required for high-temperature heating sixfold (down to 5 min) and further increase sensitivity of the assay (tenfold), when compared to the previous MTP-based protocol. The optimized microassays have complementary scope of specificities: micro-starch-iodine test for endoglucanases, micro-Somogyi-Nelson test for exoglucanases. Due to rapid, micro-volume and high-throughput character, the methods can complement toolbox assisting development of novel biocatalysts and analysis of saccharides-containing samples.
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Affiliation(s)
- Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Monika Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
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Bio-production of Baccatin III, an Important Precursor of Paclitaxel by a Cost-Effective Approach. Mol Biotechnol 2018; 60:492-505. [DOI: 10.1007/s12033-018-0090-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Liu C, Zhang K, Cao W, Zhang G, Chen G, Yang H, Wang Q, Liu H, Xian M, Zhang H. Genome mining of 2-phenylethanol biosynthetic genes from Enterobacter sp. CGMCC 5087 and heterologous overproduction in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:305. [PMID: 30455734 PMCID: PMC6223000 DOI: 10.1186/s13068-018-1297-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/22/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND 2-Phenylethanol (2-PE) is a higher aromatic alcohol that is widely used in the perfumery, cosmetics, and food industries and is also a potentially valuable next-generation biofuel. In our previous study, a new strain Enterobacter sp. CGMCC 5087 was isolated to produce 2-PE from glucose through the phenylpyruvate pathway. RESULTS In this study, candidate genes for 2-PE biosynthesis were identified from Enterobacter sp. CGMCC 5087 by draft whole-genome sequence, metabolic engineering, and shake flask fermentation. Subsequently, the identified genes encoding the 2-keto acid decarboxylase (Kdc) and alcohol dehydrogenase (Adh) enzymes from Enterobacter sp. CGMCC 5087 were introduced into E. coli BL21(DE3) to construct a high-efficiency microbial cell factory for 2-PE production using the prokaryotic phenylpyruvate pathway. The enzymes Kdc4427 and Adh4428 from Enterobacter sp. CGMCC 5087 showed higher performances than did the corresponding enzymes ARO10 and ADH2 from Saccharomyces cerevisiae, respectively. The E. coli cell factory was further improved by overexpressing two upstream shikimate pathway genes, aroF/aroG/aroH and pheA, to enhance the metabolic flux of the phenylpyruvate pathway, which resulted in 2-PE production of 260 mg/L. The combined overexpression of tktA and ppsA increased the precursor supply of erythrose-4-phosphate and phosphoenolpyruvate, which resulted in 2-PE production of 320 mg/L, with a productivity of 13.3 mg/L/h. CONCLUSIONS The present study achieved the highest titer of de novo 2-PE production of in a recombinant E. coli system. This study describes a new, efficient 2-PE producer that lays foundation for the industrial-scale production of 2-PE and its derivatives in the future.
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Affiliation(s)
- Changqing Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenyan Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ge Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Guoqiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Haiyan Yang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Haobao Liu
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
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Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
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Madhavan A, Sindhu R, Binod P, Sukumaran RK, Pandey A. Strategies for design of improved biocatalysts for industrial applications. BIORESOURCE TECHNOLOGY 2017; 245:1304-1313. [PMID: 28533064 DOI: 10.1016/j.biortech.2017.05.031] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/28/2017] [Accepted: 05/05/2017] [Indexed: 05/07/2023]
Abstract
Biocatalysts are creating increased interest among researchers due to their unique properties. Several enzymes are efficiently produced by microorganisms. However, the use of natural enzymes as biocatalysts is hindered by low catalytic efficiency and stability during various industrial processes. Many advanced enzyme technologies have been developed to reshape the existing natural enzymes to reduce these limitations and prospecting of novel enzymes. Frequently used enzyme technologies include protein engineering by directed evolution, immobilisation techniques, metagenomics etc. This review summarizes recent and emerging advancements in the area of enzyme technologies for the development of novel biocatalysts and further discusses the future directions in this field.
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Affiliation(s)
- Aravind Madhavan
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre For Biotechnology, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
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23
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Yin H, Pijning T, Meng X, Dijkhuizen L, van Leeuwen SS. Engineering of the Bacillus circulans β-Galactosidase Product Specificity. Biochemistry 2017; 56:704-711. [PMID: 28092444 PMCID: PMC5330655 DOI: 10.1021/acs.biochem.7b00032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/22/2022]
Abstract
Microbial β-galactosidase enzymes are widely used as biocatalysts in industry to produce prebiotic galactooligosaccharides (GOS) from lactose. GOS mixtures are used as beneficial additives in infant formula to mimic the prebiotic effects of human milk oligosaccharides (hMOS). The structural variety in GOS mixtures is significantly lower than in hMOS. Since this structural complexity is considered as the basis for the multiple biological functions of hMOS, it is important to broaden the variety of GOS structures. In this study, residue R484 near +1 subsite of the C-terminally truncated β-galactosidase from Bacillus circulans (BgaD-D) was subjected to site saturation mutagenesis. Especially the R484S and R484H mutant enzymes displayed significantly altered enzyme specificity, leading to a new type of GOS mixture with altered structures and linkage types. The GOS mixtures produced by these mutant enzymes contained 14 structures that were not present in the wild-type enzyme GOS mixture; 10 of these are completely new structures. The GOS produced by these mutant enzymes contained a combination of (β1 → 3) and (β1 → 4) linkages, while the wild-type enzyme has a clear preference toward (β1 → 4) linkages. The yield of the trisaccharide β-d-Galp-(1 → 3)-β-d-Galp-(1 → 4)-d-Glcp produced by mutants R484S and R484H increased 50 times compared to that of the wild-type enzyme. These results indicate that residue R484 is crucial for the linkage specificity of BgaD-D. This is the first study showing that β-galactosidase enzyme engineering results in an altered GOS linkage specificity and product mixture. The more diverse GOS mixtures produced by these engineered enzymes may find industrial applications.
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Affiliation(s)
- Huifang Yin
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tjaard Pijning
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xiangfeng Meng
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Microbial Physiology and Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University
of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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24
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Zhao J, Frauenkron-Machedjou VJ, Kardashliev T, Ruff AJ, Zhu L, Bocola M, Schwaneberg U. Amino acid substitutions in random mutagenesis libraries: lessons from analyzing 3000 mutations. Appl Microbiol Biotechnol 2017; 101:3177-3187. [DOI: 10.1007/s00253-016-8035-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/26/2016] [Accepted: 11/26/2016] [Indexed: 12/27/2022]
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25
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Overexpression of pyrroloquinoline quinone biosynthetic genes affects l -sorbose production in Gluconobacter oxydans WSH-003. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Modulating Mobility: a Paradigm for Protein Engineering? Appl Biochem Biotechnol 2016; 181:83-90. [PMID: 27449223 DOI: 10.1007/s12010-016-2200-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/17/2016] [Indexed: 12/30/2022]
Abstract
Proteins are highly mobile structures. In addition to gross conformational changes occurring on, for example, ligand binding, they are also subject to constant thermal motion. The mobility of a protein varies through its structure and can be modulated by ligand binding and other events. It is becoming increasingly clear that this mobility plays an important role in key functions of proteins including catalysis, allostery, cooperativity, and regulation. Thus, in addition to an optimum structure, proteins most likely also require an optimal dynamic state. Alteration of this dynamic state through protein engineering will affect protein function. A dramatic example of this is seen in some inherited metabolic diseases where alternation of residues distant from the active site affects the mobility of the protein and impairs function. We postulate that using molecular dynamics simulations, experimental data or a combination of the two, it should be possible to engineer the mobility of active sites. This may be useful in, for example, increasing the promiscuity of enzymes. Thus, a paradigm for protein engineering is suggested in which the mobility of the active site is rationally modified. This might be combined with more "traditional" approaches such as altering functional groups in the active site.
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27
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Zhu L, Wang W, Zhao H, Xu M, Tada S, Uzawa T, Liu M, Ito Y. A dual functional peptide carrying in vitro selected catalytic and binding activities. Org Biomol Chem 2016; 13:9808-12. [PMID: 26272651 DOI: 10.1039/c5ob01271f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When minimal functional sequences are used, it is possible to integrate multiple functions on a single peptide chain, like a "single stroke drawing". Here a dual functional peptide was designed by combining in vitro selected catalytic and binding activities. For catalytic activity, we performed in vitro selection for a peptide aptamer binding to hemin by using ribosome display and isolated a peptide that had peroxidase activity in the presence of hemin. By combining the selected catalytic peptide with a peptide antigen, which can be recognized by an antibody, an enzyme-antibody conjugate-like peptide was obtained. This study demonstrates a successful strategy to create dual functionalized peptide chains for use in immunoassays.
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Affiliation(s)
- Liping Zhu
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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28
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US132 Cyclodextrin Glucanotransferase Engineering by Random Mutagenesis for an Anti-Staling Purpose. Mol Biotechnol 2016; 58:551-7. [PMID: 27271016 DOI: 10.1007/s12033-016-9952-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The use of the cyclodextrin glucanotransferase (CGTase) of the US132 strain, which is an effective anti-staling agent, has been hampered by its high cyclization activity. Since that random mutagenesis using error-prone PCR is nowadays a method of choice for enzymes engineering, we have optimized this method by adjusting manganese concentration in order to obtain a high percentage of active CGTase mutants. Therefore, the amplification of the gene encoding the US132 CGTase was performed using a MnCl2 concentration ranging between 0 and 0.5 mM. The finding showed that a manganese concentration of 0.04 mM allowed for 90 % of active mutants. A simple method to rapidly screen the obtained mutants was also developed. After the examination of a small library (of less than 1000 clones), the active mutant named MJ13 was selected for a significant decrease in the cyclization activity, thereby showing a remarkable change in the enzyme specificity towards starch dextrinizing. Sequence analysis showed that MJ13 is a triple mutant with two mutations in the catalytic domain (K47E and S382P) and one substitution in the starch binding domain (N655S).
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29
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Kaushik M, Sinha P, Jaiswal P, Mahendru S, Roy K, Kukreti S. Protein engineering andde novodesigning of a biocatalyst. J Mol Recognit 2016; 29:499-503. [DOI: 10.1002/jmr.2546] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/16/2016] [Accepted: 04/01/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Prashant Sinha
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
| | - Pragya Jaiswal
- Cluster Innovation Centre; University of Delhi; Delhi 110 007 India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry; University of Delhi; Delhi 110007 India
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30
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Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 2016; 6:1853-1869. [PMID: 27774349 DOI: 10.1021/acscatal.5b02158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a dynamic model of the HDVr reaction mechanism involving a conformational switch between multiple non-canonical G25:U20 base pair conformations in the active site. These local nucleobase dynamics play an important role in catalysis by modulating the metal binding environments of two Mg2+ ions that support catalysis at different steps of the reaction pathway. The first ion plays a structural role by inducing a base pair flip necessary to obtain the catalytic fold in which C75 moves towards to the scissile phosphate in the active site. Ejection of this ion then permits a second ion to bind elsewhere in the active site and facilitate nucleophile activation. The simulations collectively describe a mechanistic scenario that is consistent with currently available experimental data from crystallography, phosphorothioate substitutions, and chemical probing studies. Avenues for further experimental verification are suggested.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- Argonne National Laboratory, Argonne, Illinois 60439, United State
| | - Michael E. Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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31
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Cloning and characterization of a novel thermostable esterase from Bacillus gelatini KACC 12197. Protein Expr Purif 2015; 116:90-7. [DOI: 10.1016/j.pep.2015.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/07/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
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32
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Moridi N, Corvini PF, Shahgaldian P. Reversible Supramolecular Surface Attachment of Enzyme–Polymer Conjugates for the Design of Biocatalytic Filtration Membranes. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Negar Moridi
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
| | - Philippe F.‐X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
- School of the Environment, Nanjing University, 210093 Nanjing (China)
| | - Patrick Shahgaldian
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
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33
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Sang J, Wu R, Guo P, Du J, Xu S, Wang J. Affinity-tuned peroxidase-like activity of hydrogel-supported Fe3O4nanozyme through alteration of crosslinking concentration. J Appl Polym Sci 2015. [DOI: 10.1002/app.43065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jilong Sang
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
| | - Ronglan Wu
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
| | - Pingping Guo
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
| | - Juan Du
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
| | - Shimei Xu
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
| | - Jide Wang
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uyghur Autonomous Region, College of Chemistry and Chemical Engineering; Xinjiang University; Urumqi Xinjiang 830046 People's Republic of China
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34
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Moridi N, Corvini PF, Shahgaldian P. Reversible Supramolecular Surface Attachment of Enzyme–Polymer Conjugates for the Design of Biocatalytic Filtration Membranes. Angew Chem Int Ed Engl 2015; 54:14800-4. [DOI: 10.1002/anie.201507020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Negar Moridi
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
| | - Philippe F.‐X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
- School of the Environment, Nanjing University, 210093 Nanjing (China)
| | - Patrick Shahgaldian
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
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35
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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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36
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Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
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Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
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37
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Improved enantioselectivity of thermostable esterase from Archaeoglobus fulgidus toward (S)-ketoprofen ethyl ester by directed evolution and characterization of mutant esterases. Appl Microbiol Biotechnol 2015; 99:6293-301. [PMID: 25661815 DOI: 10.1007/s00253-015-6422-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/27/2014] [Accepted: 01/19/2015] [Indexed: 01/07/2023]
Abstract
Thermostable esterases have potential applications in various biotechnology industries because of their resistance to high temperature and organic solvents. In a previous study, we isolated an esterase from Archaeoglobus fulgidus DSM 4304 (Est-AF), which showed high thermostability but low enantioselectivity toward (S)-ketoprofen ethyl ester. (R)-ketoprofenor (S)-ketoprofenis produced by esterase hydrolysis of the ester bond of (R,S)-ketoprofen ethyl ester and (S)-ketoprofen has better pharmaceutical activity and lower side effects than (R)-ketoprofen. Therefore, we have generated mutants of Est-AF that retained high thermostability whilst improving enantioselectivity. A library of Est-AF mutants was created by error-prone polymerase chain reaction, and mutants with improved enantioselectivity were isolated by site-saturation mutagenesis. The regions of Est-AF containing amino acid mutations were analyzed by homology modeling of its three-dimensional structure, and structure-based explanations for the changes in enantioselectivity are proposed. Finally, we isolated two mutants showing improved enantioselectivity over Est-AF (ee% = -16.2 ± 0.2 and E = 0.7 ± 0.0): V138G (ee% = 35.9 ± 1.0 and E = 3.0 ± 0.1) and V138G/L200R (ee% = 89.2 ± 0.2 and E = 19.5 ± 0.5). We also investigated various characteristics of these mutants and found that the mutants showed similar thermostability and resistance to additives or organic solvents to Est-AF, without a significant trade-off between activity and stability.
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38
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Ilie A, Agudo R, Roiban GD, Reetz MT. P450-catalyzed regio- and stereoselective oxidative hydroxylation of disubstituted cyclohexanes: creation of three centers of chirality in a single CH-activation event. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.11.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Zhang G, Qi F, Jia H, Zou C, Li C. Advances in bioprocessing for efficient bio manufacture. RSC Adv 2015. [DOI: 10.1039/c5ra07699d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The strategies involving molecular, cellular and community levels for improving various bioprocesses are reviewed with specific examples presented.
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Affiliation(s)
- Genlin Zhang
- School of Life Sciences
- Beijing Institute of Technology
- Beijing 100081
- China
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan
| | - Feng Qi
- School of Life Sciences
- Beijing Institute of Technology
- Beijing 100081
- China
- College of Life Sciences/Engineering Research Center of Industrial Microbiology
| | - Haiyang Jia
- School of Life Sciences
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Changling Zou
- School of Physics
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Chun Li
- School of Life Sciences
- Beijing Institute of Technology
- Beijing 100081
- China
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40
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Dudley QM, Karim AS, Jewett MC. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 2015; 10:69-82. [PMID: 25319678 PMCID: PMC4314355 DOI: 10.1002/biot.201400330] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/24/2014] [Accepted: 08/22/2014] [Indexed: 12/20/2022]
Abstract
Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
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Affiliation(s)
| | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- Member, Institute for Bionanotechnology in Medicine, Northwestern University, Chicago, IL, USA
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41
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Luan ZJ, Li FL, Dou S, Chen Q, Kong XD, Zhou J, Yu HL, Xu JH. Substrate channel evolution of an esterase for the synthesis of cilastatin. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00085h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Error-prone PCR and site-directed mutagenesis around substrate channel were employed for improving an esterase (RhEst1) activity towards Cilastatin building block. RhEst1A147I/V148F/G254A showed 20 times higher activity than the native enzyme in whole cell biotransformation.
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Affiliation(s)
- Zheng-Jiao Luan
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Fu-Long Li
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Shuai Dou
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Xu-Dong Kong
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Centre for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- China
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42
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Agudo R, Roiban GD, Lonsdale R, Ilie A, Reetz MT. Biocatalytic route to chiral acyloins: P450-catalyzed regio- and enantioselective α-hydroxylation of ketones. J Org Chem 2014; 80:950-6. [PMID: 25495724 DOI: 10.1021/jo502397s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
P450-BM3 and mutants of this monooxygenase generated by directed evolution are excellent catalysts for the oxidative α-hydroxylation of ketones with formation of chiral acyloins with high regioselectivity (up to 99%) and enantioselectivity (up to 99% ee). This constitutes a new route to a class of chiral compounds that are useful intermediates in the synthesis of many kinds of biologically active compounds.
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Affiliation(s)
- Rubén Agudo
- Department of Chemistry, Philipps-Universität Marburg , Hans-Meerwein Strasse, 35032 Marburg, Germany
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43
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Luque A, Sebai SC, Sauveplane V, Ramaen O, Pandjaitan R. In vivo evolution of metabolic pathways: Assembling old parts to build novel and functional structures. Bioengineered 2014; 5:347-56. [PMID: 25482082 PMCID: PMC4601399 DOI: 10.4161/bioe.34347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In our recent article "In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells" we proposed a useful alternative to directed evolution methods that permits the generation of yeast cell libraries containing recombinant metabolic pathways from counterpart genes. The methodology was applied to generate single mosaic genes and intragenic mosaic pathways. We used flavonoid metabolism genes as a working model to assembly and express evolved pathways in DNA repair deficient cells. The present commentary revises the principles of gene and pathway mosaicism and explores the scope and perspectives of our results as an additional tool for synthetic biology.
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44
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Zhang ZG, Lonsdale R, Sanchis J, Reetz MT. Extreme Synergistic Mutational Effects in the Directed Evolution of a Baeyer–Villiger Monooxygenase as Catalyst for Asymmetric Sulfoxidation. J Am Chem Soc 2014; 136:17262-72. [DOI: 10.1021/ja5098034] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhi-Gang Zhang
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Richard Lonsdale
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Joaquin Sanchis
- Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, 3052
VIC, Australia
| | - Manfred T. Reetz
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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45
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Li XJ, Zheng RC, Ma HY, Huang JF, Zheng YG. Key residues responsible for enhancement of catalytic efficiency of Thermomyces lanuginosus lipase Lip revealed by complementary protein engineering strategy. J Biotechnol 2014; 188:29-35. [DOI: 10.1016/j.jbiotec.2014.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/25/2014] [Accepted: 08/01/2014] [Indexed: 01/13/2023]
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46
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47
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Agudo R, Reetz MT. Designer cells for stereocomplementary de novo enzymatic cascade reactions based on laboratory evolution. Chem Commun (Camb) 2014; 49:10914-6. [PMID: 24135920 DOI: 10.1039/c3cc46229c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Designer cells for a synthetic cascade reaction harnessing selective redox reactions were devised, featuring two successive regioselective P450-catalyzed CH-activating oxidations of 1-cyclohexene carboxylic acid methyl ester followed by stereoselective olefin-reduction catalysed by (R)- or (S)-selective mutants of an enoate reductase.
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Affiliation(s)
- Rubén Agudo
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Str., 35032 Marburg, Germany
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48
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In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells. Metab Eng 2014; 23:123-35. [DOI: 10.1016/j.ymben.2014.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 01/27/2014] [Accepted: 02/12/2014] [Indexed: 12/29/2022]
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49
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Ma BD, Kong XD, Yu HL, Zhang ZJ, Dou S, Xu YP, Ni Y, Xu JH. Increased Catalyst Productivity in α-Hydroxy Acids Resolution by Esterase Mutation and Substrate Modification. ACS Catal 2014. [DOI: 10.1021/cs401183e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bao-Di Ma
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xu-Dong Kong
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui-Lei Yu
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhi-Jun Zhang
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Shuai Dou
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yan-Peng Xu
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yan Ni
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- Laboratory of Biocatalysis
and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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50
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Rodrigues RC, Barbosa O, Ortiz C, Berenguer-Murcia Á, Torres R, Fernandez-Lafuente R. Amination of enzymes to improve biocatalyst performance: coupling genetic modification and physicochemical tools. RSC Adv 2014. [DOI: 10.1039/c4ra04625k] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Improvement of the features of an enzyme is in many instances a pre-requisite for the industrial implementation of these exceedingly interesting biocatalysts.
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Affiliation(s)
- Rafael C. Rodrigues
- Biocatalysis and Enzyme Technology Lab
- Institute of Food Science and Technology
- Federal University of Rio Grande do Sul
- Porto Alegre, Brazil
| | - Oveimar Barbosa
- Escuela de Química
- Grupo de investigación en Bioquímica y Microbiología (GIBIM)
- Edificio Camilo Torres 210
- Universidad Industrial de Santander
- Bucaramanga, Colombia
| | - Claudia Ortiz
- Escuela de Bacteriología y Laboratorio Clínico
- Universidad Industrial de Santander
- Bucaramanga, Colombia
| | - Ángel Berenguer-Murcia
- Instituto Universitario de Materiales
- Departamento de Química Inorgánica
- Universidad de Alicante
- Ap. 99-03080 Alicante, Spain
| | - Rodrigo Torres
- Escuela de Química
- Grupo de investigación en Bioquímica y Microbiología (GIBIM)
- Edificio Camilo Torres 210
- Universidad Industrial de Santander
- Bucaramanga, Colombia
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