1
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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2
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Singh S, Kumar Sharma P, Chaturvedi S, Kumar P, Deepak Nannaware A, Kalra A, Kumar Rout P. Biocatalyst for the synthesis of natural flavouring compounds as food additives: Bridging the gap for a more sustainable industrial future. Food Chem 2024; 435:137217. [PMID: 37832337 DOI: 10.1016/j.foodchem.2023.137217] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 10/15/2023]
Abstract
Biocatalysis entails the use of purified enzymes in the manufacturing of flavouring chemicals food industry as well as at the laboratory level. These biocatalysts can significantly accelerate organic chemical processes and improve product stereospecificity. The unique characteristics of biocatalyst helpful in synthesizing the environmentally friendly flavour and aroma compounds used as a food additive in foodstuffs. With methods like enzyme engineering on biotechnological interventions the efficient tuning of produce will fulfil the needs of food industry. This review summarizes the biosynthesis of different flavour and aroma component through microbial catalysts and using advanced techniques which are available for enzyme improvement. Also pointing out their benefits and drawbacks for specific technological processes necessary for successful industrial application of biocatalysts. The article covers the market scenario, cost economics, environmental safety and regulatory framework for the production of food flavoured chemicals by the bioprocess engineering.
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Affiliation(s)
- Suman Singh
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India
| | - Praveen Kumar Sharma
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India
| | - Shivani Chaturvedi
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India
| | - Prashant Kumar
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashween Deepak Nannaware
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Alok Kalra
- Crop Production and Protection Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India
| | - Prasant Kumar Rout
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Dai C, Tian JX, Chen YF, Ni YH, Cui L, Cao HX, Song LL, Xu SY, Wang YJ, Zheng YG. Computer-aided design to enhance the stability of aldo-keto reductase KdAKR. Biotechnol J 2024; 19:e2300637. [PMID: 38472092 DOI: 10.1002/biot.202300637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
The aldo-keto reductase (AKR) KdAKR from Kluyvermyces dobzhanskii can reduce t-butyl 6-chloro-(5S)-hydroxy-3-oxohexanoate ((5S)-CHOH) to t-butyl 6-chloro-(3R,5S)-dihydroxyhexanoate ((3R,5S)-CDHH), which is the key chiral intermediate of rosuvastatin. Herein, a computer-aided design that combined the use of PROSS platform and consensus design was employed to improve the stability of a previously constructed mutant KdAKRM6 . Experimental verification revealed that S196C, T232A, V264I and V45L produced improved thermostability and activity. The "best" mutant KdAKRM10 (KdAKRM6 -S196C/T232A/V264I/V45L) was constructed by combining the four beneficial mutations, which displayed enhanced thermostability. Its T50 15 and Tm values were increased by 10.2 and 10.0°C, respectively, and half-life (t1/2 ) at 40°C was increased by 17.6 h. Additionally, KdAKRM10 demonstrated improved resistance to organic solvents compared to that of KdAKRM6 . Structural analysis revealed that the increased number of hydrogen bonds and stabilized hydrophobic core contributed to the rigidity of KdAKRM10 , thus improving its stability. The results validated the feasibility of the computer-aided design strategy in improving the stability of AKRs.
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Affiliation(s)
- Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Jia-Xin Tian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Feng Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yue-Han Ni
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lei Cui
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Hai-Xing Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lin-Lin Song
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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4
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Cosgrove SC, Miller GJ, Bornadel A, Dominguez B. Realizing the Continuous Chemoenzymatic Synthesis of Anilines Using an Immobilized Nitroreductase. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:8556-8561. [PMID: 37323810 PMCID: PMC10265703 DOI: 10.1021/acssuschemeng.3c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/22/2023] [Indexed: 06/17/2023]
Abstract
The use of biocatalysis for classically synthetic transformations has seen an increase in recent years, driven by the sustainability credentials bio-based approaches can offer the chemical industry. Despite this, the biocatalytic reduction of aromatic nitro compounds using nitroreductase biocatalysts has not received significant attention in the context of synthetic chemistry. Herein, a nitroreductase (NR-55) is demonstrated to complete aromatic nitro reduction in a continuous packed-bed reactor for the first time. Immobilization on an amino-functionalized resin with a glucose dehydrogenase (GDH-101) permits extended reuse of the immobilized system, all operating at room temperature and pressure in aqueous buffer. By transferring into flow, a continuous extraction module is incorporated, allowing the reaction and workup to be continuously undertaken in a single operation. This is extended to showcase a closed-loop aqueous phase, permitting reuse of the contained cofactors, with a productivity of >10 gproduct gNR-55-1 and milligram isolated yields >50% for the product anilines. This facile method removes the need for high-pressure hydrogen gas and precious-metal catalysts and proceeds with high chemoselectivity in the presence of hydrogenation-labile halides. Application of this continuous biocatalytic methodology to panels of aryl nitro compounds could offer a sustainable approach to its energy and resource-intensive precious-metal-catalyzed counterpart.
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Affiliation(s)
- Sebastian C. Cosgrove
- School
of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gavin J. Miller
- School
of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Amin Bornadel
- Johnson
Matthey, 28 Cambridge
Science Park, Milton Rd, Cambridge CB4 0FP, United Kingdom
| | - Beatriz Dominguez
- Johnson
Matthey, 28 Cambridge
Science Park, Milton Rd, Cambridge CB4 0FP, United Kingdom
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5
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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6
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Special Issue on “Biocatalysis, Enzyme and Process Engineering”. Processes (Basel) 2023. [DOI: 10.3390/pr11030740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Biocatalysis entails the use of enzymes, which are catalytically active proteins, to speed up reactions so that products can be obtained swiftly and accurately [...]
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7
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Li C, Gao X, Qi H, Zhang W, Li L, Wei C, Wei M, Sun X, Wang S, Wang L, Ji Y, Mao S, Zhu Z, Tanokura M, Lu F, Qin HM. Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening. Angew Chem Int Ed Engl 2023; 62:e202216721. [PMID: 36658306 DOI: 10.1002/anie.202216721] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Biosynthesis of D-allulose has been achieved using ketose 3-epimerases (KEases), but its application is limited by poor catalytic performance. In this study, we redesigned a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator for real-time monitoring of D-allulose. An ultrahigh-throughput droplet-based microfluidic screening platform was further constructed by coupling with this D-allulose-detecting biosensor for the directed evolution of the KEases. Structural analysis of Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) revealed that a highly flexible helix/loop region exposes or occludes the catalytic center as an essential lid conformation regulating substrate recognition. We reprogrammed SfDAE using structure-guided rational design and directed evolution, in which a mutant M3-2 was identified with 17-fold enhanced catalytic efficiency. Our research offers a paradigm for the design and optimization of a biosensor-based microdroplet screening platform.
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Affiliation(s)
- Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Hongbin Qi
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Lei Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Cancan Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Meijing Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Xiaoxuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Shusen Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Liyan Wang
- Luoyang BIO-Industry Technology Innovation Center, Luoyang, 471000, Henan, China
| | - Yingbin Ji
- Luoyang BIO-Industry Technology Innovation Center, Luoyang, 471000, Henan, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
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Ölçücü G, Krauss U, Jaeger KE, Pietruszka J. Carrier‐Free Enzyme Immobilizates for Flow Chemistry. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Gizem Ölçücü
- Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße 52425 Jülich Germany
- Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences IBG-1: Biotechnology Wilhelm Johnen Straße 52425 Jülich Germany
| | - Ulrich Krauss
- Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße 52425 Jülich Germany
- Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences IBG-1: Biotechnology Wilhelm Johnen Straße 52425 Jülich Germany
| | - Karl-Erich Jaeger
- Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße 52425 Jülich Germany
- Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences IBG-1: Biotechnology Wilhelm Johnen Straße 52425 Jülich Germany
| | - Jörg Pietruszka
- Forschungszentrum Jülich GmbH Institute of Bio- and Geosciences IBG-1: Biotechnology Wilhelm Johnen Straße 52425 Jülich Germany
- Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Institute of Biorganic Chemistry Wilhelm Johnen Straße 52425 Jülich Germany
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9
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Ölçücü G, Baumer B, Küsters K, Möllenhoff K, Oldiges M, Pietruszka J, Jaeger KE, Krauss U. Catalytically Active Inclusion Bodies─Benchmarking and Application in Flow Chemistry. ACS Synth Biol 2022; 11:1881-1896. [PMID: 35500299 DOI: 10.1021/acssynbio.2c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In industries, enzymes are often immobilized to obtain stable preparations that can be utilized in batch and flow processes. In contrast to traditional immobilization methods that rely on carrier binding, various immobilization strategies have been recently presented that enable the simultaneous production and in vivo immobilization of enzymes. Catalytically active inclusion bodies (CatIBs) are a promising example for such in vivo enzyme immobilizates. CatIB formation is commonly induced by fusion of aggregation-inducing tags, and numerous tags, ranging from small synthetic peptides to protein domains or whole proteins, have been successfully used. However, since these systems have been characterized by different groups employing different methods, a direct comparison remains difficult, which prompted us to benchmark different CatIB-formation-inducing tags and fusion strategies. Our study highlights that important CatIB properties like yield, activity, and stability are strongly influenced by tag selection and fusion strategy. Optimization enabled us to obtain alcohol dehydrogenase CatIBs with superior activity and stability, which were subsequently applied for the first time in a flow synthesis approach. Our study highlights the potential of CatIB-based immobilizates, while at the same time demonstrating the robust use of CatIBs in flow chemistry.
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Affiliation(s)
- Gizem Ölçücü
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Benedikt Baumer
- Institute of Biorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Kira Küsters
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Kathrin Möllenhoff
- Mathematical Institute, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Jörg Pietruszka
- Institute of Biorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany
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10
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Fessner ND, Badenhorst CPS, Bornscheuer UT. Enzyme Kits to Facilitate the Integration of Biocatalysis into Organic Chemistry – First Aid for Synthetic Chemists. ChemCatChem 2022. [DOI: 10.1002/cctc.202200156] [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)
- Nico D. Fessner
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Christoffel P. S. Badenhorst
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Uwe T. Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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11
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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12
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Ogawa Y, Katsuyama Y, Ohnishi Y. Engineering of the Ligand Specificity of Transcriptional Regulator XylS by Deep Mutational Scanning. ACS Synth Biol 2022; 11:473-485. [PMID: 34964613 DOI: 10.1021/acssynbio.1c00564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deep mutational scanning is a method for protein engineering. Here, we applied it to alter the ligand specificity of the transcriptional regulator XylS from Pseudomonas putida to recognize p-toluic acid instead of the native ligand m-toluic acid. For this purpose, we used an antibiotic resistance gene-based dual screening system, which was constructed for the directed evolution of XylS toward the above-mentioned ligand specificity. We constructed a xylS mutant library in which each codon for the amino acid residue of the putative ligand-binding domain (residues 1-213, except 7th residue) was randomized to generate all possible single amino acid-substituted XylS variants and introduced it into Escherichia coli harboring the selection plasmid for the screening system. The cells were cultured in the presence of appropriate antibiotics and m-toluic acid or p-toluic acid, and the frequency of each mutation present in the library was examined using a next-generation sequencer before and after cultivation. Heatmaps showing the enrichment score of each XylS variant were obtained. By searching for a p-toluic-acid-specific heatmap pattern, we focused on G71 and H77. Analysis of the ligand specificities of G71- or H77-substituted XylS variants revealed that several G71-substituted XylS variants responded specifically to p-toluic acid. Thus, the 71st residue was found to be an unprecedented residue that is important for switching ligand specificity. Our study demonstrated the usefulness of deep mutational scanning in engineering the ligand specificity of a transcriptional regulator without structural information. We also discussed the advantages and disadvantages of deep mutational scanning compared with directed evolution.
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Affiliation(s)
- Yuki Ogawa
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Ismagilov I, Vosmerikov A, Korobitsyna L, Matus E, Kerzhentsev M, Stepanov A, Mihaylova E, Ismagilov Z. Promoters for Improvement of the Catalyst Performance in Methane Valorization Processes. EURASIAN CHEMICO-TECHNOLOGICAL JOURNAL 2021. [DOI: 10.18321/ectj1099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In this work, the introduction of modifying additives in the composition of catalysts is considered as an effective mode of improving functional characteristics of materials for two processes of methane conversion into valuable products – methane dehydroaromatization (DHA of CH4) into benzene and hydrogen and autothermal reforming of methane (ATR of CH4) into synthesis gas. The effect of type and content of promoters on the structural and electronic state of the active component as well as catalyst activity and stability against deactivation is discussed. For DHA of CH4 the operation mode of additives M = Ag, Ni, Fe in the composition of Mo-M/ZSM-5 catalysts was elucidated and correlated with the product yield and coke content. It was shown that when Ag serves as a promoter, the duration of the catalyst stable operation is enhanced due to a decrease in the rate of the coke formation. In the case of Ni and Fe additives, the Ni-Мо and Fe-Mo alloys are formed that retain the catalytic activity for a long time in spite of the carbon accumulation. For ATR of CH4, the influence of M = Pd, Pt, Re, Mo, Sn in the composition of Ni-M catalysts supported on La2O3 or Ce0.5Zr0.5O2/Al2O3 was elucidated. It was demonstrated that for Ni-M/La2O3 catalysts, Pd is a more efficient promoter that improves the reducibility of Ni cations and increases the content of active Nio centers. In the case of Ni-M/Ce0.5Zr0.5O2/Al2O3 samples, Re is considered the best promoter due to the formation of an alloy with anti-coking and anti-sintering properties. The use of catalysts with optimal promoter type and its content provides high efficiency of methane valorization processes.
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14
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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15
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Dutta K, Shityakov S, Khalifa I. New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. Front Bioeng Biotechnol 2021; 9:666858. [PMID: 34409018 PMCID: PMC8365754 DOI: 10.3389/fbioe.2021.666858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 01/29/2023] Open
Abstract
Today's environmental balance has been compromised by the unreasonable and sometimes dangerous actions committed by humans to maintain their dominance over the Earth's natural resources. As a result, oceans are contaminated by the different types of plastic trash, crude oil coming from mismanagement of transporting ships spilling it in the water, and air pollution due to increasing production of greenhouse gases, such as CO2 and CH4 etc., into the atmosphere. The lands, agricultural fields, and groundwater are also contaminated by the infamous chemicals viz., polycyclic aromatic hydrocarbons, pyrethroids pesticides, bisphenol-A, and dioxanes. Therefore, bioremediation might function as a convenient alternative to restore a clean environment. However, at present, the majority of bioremediation reports are limited to the natural capabilities of microbial enzymes. Synthetic biology with uncompromised supervision of ethical standards could help to outsmart nature's engineering, such as the CETCH cycle for improved CO2 fixation. Additionally, a blend of synthetic biology with machine learning algorithms could expand the possibilities of bioengineering. This review summarized current state-of-the-art knowledge of the data-assisted enzyme redesigning to actively promote new research on important enzymes to ameliorate the environment.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Medinipur, India
| | - Sergey Shityakov
- Department of Chemoinformatics, Infochemistry Scientific Center, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Saint-Petersburg, Russia
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
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16
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Bezsudnova EY, Nikolaeva AY, Bakunova AK, Rakitina TV, Suplatov DA, Popov VO, Boyko KM. Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum. PLoS One 2021; 16:e0255098. [PMID: 34324538 PMCID: PMC8320979 DOI: 10.1371/journal.pone.0255098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/11/2021] [Indexed: 11/28/2022] Open
Abstract
Creating biocatalysts for (R)-selective amination effectively is highly desirable in organic synthesis. Despite noticeable progress in the engineering of (R)-amine activity in pyridoxal-5'-phosphate-dependent transaminases of fold type IV, the specialization of the activity is still an intuitive task, as there is poor understanding of sequence-structure-function relationships. In this study, we analyzed this relationship in transaminase from Thermobaculum terrenum, distinguished by expanded substrate specificity and activity in reactions with L-amino acids and (R)-(+)-1-phenylethylamine using α-ketoglutarate and pyruvate as amino acceptors. We performed site-directed mutagenesis to create a panel of the enzyme variants, which differ in the active site residues from the parent enzyme to a putative transaminase specific to (R)-primary amines. The variants were examined in the overall transamination reactions and half-reaction with (R)-(+)-1-phenylethylamine. A structural analysis of the most prominent variants revealed a spatial reorganization in the active sites, which caused changes in activity. Although the specialization to (R)-amine transaminase was not implemented, we succeeded in understanding the role of the particular active site residues in expanding substrate specificity of the enzyme. We showed that the specificity for (R)-(+)-1-phenylethylamine in transaminase from T. terrenum arises without sacrificing the specificity for L-amino acids and α-ketoglutarate and in consensus with it.
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Affiliation(s)
- Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alena Yu. Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alina K. Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A. Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, Russian Federation
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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17
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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18
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Wang X, Bowman J, Tu S, Nykypanchuk D, Kuksenok O, Minko S. Polyethylene Glycol Crowder's Effect on Enzyme Aggregation, Thermal Stability, and Residual Catalytic Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8474-8485. [PMID: 34236863 DOI: 10.1021/acs.langmuir.1c00872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein stability and performance in various natural and artificial systems incorporating many other macromolecules for therapeutic, diagnostic, sensor, and biotechnological applications attract increasing interest with the expansion of these technologies. Here we address the catalytic activity of lysozyme protein (LYZ) in the presence of a polyethylene glycol (PEG) crowder in a broad range of concentrations and temperatures in aqueous solutions of two different molecular mass PEG samples (Mw = 3350 and 10000 g/mol). The phase behavior of PEG-protein solutions is examined by using dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS), while the enzyme denaturing is monitored by using an activity assay (AS) and circular dichroism (CD) spectroscopy. Molecular dynamic (MD) simulations are used to illustrate the effect of PEG concentration on protein stability at high temperatures. The results demonstrate that LYZ residual activity after 1 h incubation at 80 °C is improved from 15% up to 55% with the addition of PEG. The improvement is attributed to two underlying mechanisms. (i) Primarily, the stabilizing effect is due to the suppression of the enzyme aggregation because of the stronger PEG-protein interactions caused by the increased hydrophobicity of PEG and lysozyme at elevated temperatures. (ii) The MD simulations showed that the addition of PEG to some degree stabilizes the secondary structures of the enzyme by delaying unfolding at elevated temperatures. The more pronounced effect is observed with an increase in PEG concentration. This trend is consistent with CD and AS experimental results, where the thermal stability is strengthened with increasing of PEG concentration and molecular mass. The results show that the highest stabilizing effect is approached at the critical overlap concentration of PEG.
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Affiliation(s)
- Xue Wang
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
| | - Jeremy Bowman
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
| | - Sidong Tu
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
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19
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Impact of the Expression System on Recombinant Protein Production in Escherichia coli BL21. Front Microbiol 2021; 12:682001. [PMID: 34234760 PMCID: PMC8257044 DOI: 10.3389/fmicb.2021.682001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production for medical, academic, or industrial applications is essential for our current life. Recombinant proteins are obtained mainly through microbial fermentation, with Escherichia coli being the host most used. In spite of that, some problems are associated with the production of recombinant proteins in E. coli, such as the formation of inclusion bodies, the metabolic burden, or the inefficient translocation/transport system of expressed proteins. Optimizing transcription of heterologous genes is essential to avoid these drawbacks and develop competitive biotechnological processes. Here, expression of YFP reporter protein is evaluated under the control of four promoters of different strength (PT7lac, Ptrc, Ptac, and PBAD) and two different replication origins (high copy number pMB1′ and low copy number p15A). In addition, the study has been carried out with the E. coli BL21 wt and the ackA mutant strain growing in a rich medium with glucose or glycerol as carbon sources. Results showed that metabolic burden associated with transcription and translation of foreign genes involves a decrease in recombinant protein expression. It is necessary to find a balance between plasmid copy number and promoter strength to maximize soluble recombinant protein expression. The results obtained represent an important advance on the most suitable expression system to improve both the quantity and quality of recombinant proteins in bioproduction engineering.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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20
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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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21
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Lindenburg L, Hollfelder F. “NAD‐display”: Ultrahigh‐Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
- Current address: Genmab Uppsalalaan 15 3584 CT Utrecht The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
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22
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Gkantzou E, Chatzikonstantinou AV, Fotiadou R, Giannakopoulou A, Patila M, Stamatis H. Trends in the development of innovative nanobiocatalysts and their application in biocatalytic transformations. Biotechnol Adv 2021; 51:107738. [PMID: 33775799 DOI: 10.1016/j.biotechadv.2021.107738] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 12/22/2022]
Abstract
The ever-growing demand for cost-effective and innocuous biocatalytic transformations has prompted the rational design and development of robust biocatalytic tools. Enzyme immobilization technology lies in the formation of cooperative interactions between the tailored surface of the support and the enzyme of choice, which result in the fabrication of tremendous biocatalytic tools with desirable properties, complying with the current demands even on an industrial level. Different nanoscale materials (organic, inorganic, and green) have attracted great attention as immobilization matrices for single or multi-enzymatic systems. Aiming to unveil the potentialities of nanobiocatalytic systems, we present distinct immobilization strategies and give a thorough insight into the effect of nanosupports specific properties on the biocatalysts' structure and catalytic performance. We also highlight the development of nanobiocatalysts for their incorporation in cascade enzymatic processes and various types of batch and continuous-flow reactor systems. Remarkable emphasis is given on the application of such nanobiocatalytic tools in several biocatalytic transformations including bioremediation processes, biofuel production, and synthesis of bioactive compounds and fine chemicals for the food and pharmaceutical industry.
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Affiliation(s)
- Elena Gkantzou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Alexandra V Chatzikonstantinou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Renia Fotiadou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Archontoula Giannakopoulou
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Michaela Patila
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.
| | - Haralambos Stamatis
- Laboratory of Biotechnology, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.
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23
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Lindenburg L, Hollfelder F. "NAD-display": Ultrahigh-Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021; 60:9015-9021. [PMID: 33470025 PMCID: PMC8048591 DOI: 10.1002/anie.202013486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Indexed: 12/25/2022]
Abstract
NAD(H)‐utiliing enzymes have been the subject of directed evolution campaigns to improve their function. To enable access to a larger swath of sequence space, we demonstrate the utility of a cell‐free, ultrahigh‐throughput directed evolution platform for dehydrogenases. Microbeads (1.5 million per sample) carrying both variant DNA and an immobilised analogue of NAD+ were compartmentalised in water‐in‐oil emulsion droplets, together with cell‐free expression mixture and enzyme substrate, resulting in the recording of the phenotype on each bead. The beads’ phenotype could be read out and sorted for on a flow cytometer by using a highly sensitive fluorescent protein‐based sensor of the NAD+:NADH ratio. Integration of this “NAD‐display” approach with our previously described Split & Mix (SpliMLiB) method for generating large site‐saturation libraries allowed straightforward screening of fully balanced site saturation libraries of formate dehydrogenase, with diversities of 2×104. Based on modular design principles of synthetic biology NAD‐display offers access to sophisticated in vitro selections, avoiding complex technology platforms.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.,Current address: Genmab, Uppsalalaan 15, 3584 CT, Utrecht, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
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Hollmann F, Opperman DJ, Paul CE. Biocatalytic Reduction Reactions from a Chemist's Perspective. Angew Chem Int Ed Engl 2021; 60:5644-5665. [PMID: 32330347 PMCID: PMC7983917 DOI: 10.1002/anie.202001876] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 11/09/2022]
Abstract
Reductions play a key role in organic synthesis, producing chiral products with new functionalities. Enzymes can catalyse such reactions with exquisite stereo-, regio- and chemoselectivity, leading the way to alternative shorter classical synthetic routes towards not only high-added-value compounds but also bulk chemicals. In this review we describe the synthetic state-of-the-art and potential of enzymes that catalyse reductions, ranging from carbonyl, enone and aromatic reductions to reductive aminations.
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Affiliation(s)
- Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Diederik J. Opperman
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
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25
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Li G, Qin Y, Fontaine NT, Ng Fuk Chong M, Maria‐Solano MA, Feixas F, Cadet XF, Pandjaitan R, Garcia‐Borràs M, Cadet F, Reetz MT. Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation. Chembiochem 2021; 22:904-914. [PMID: 33094545 PMCID: PMC7984044 DOI: 10.1002/cbic.202000612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Indexed: 12/15/2022]
Abstract
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.
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Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Youcai Qin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Nicolas T. Fontaine
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Matthieu Ng Fuk Chong
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Miguel A. Maria‐Solano
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Xavier F. Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Rudy Pandjaitan
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Frederic Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Manfred T. Reetz
- Department of ChemistryPhilipps-Universität35032MarburgGermany) .
- Max-Planck-Institut fuer Kohlenforschung45470MülheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Avenue, Tianjin Airport Economic Area300308TianjinP. R. China
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26
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Ravikumar Y, Ponpandian LN, Zhang G, Yun J, Qi X. Harnessing -arabinose isomerase for biological production of -tagatose: Recent advances and its applications. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Eger E, Schrittwieser JH, Wetzl D, Iding H, Kuhn B, Kroutil W. Asymmetric Biocatalytic Synthesis of 1-Aryltetrahydro-β-carbolines Enabled by "Substrate Walking". Chemistry 2020; 26:16281-16285. [PMID: 33017078 PMCID: PMC7756766 DOI: 10.1002/chem.202004449] [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: 10/04/2020] [Indexed: 12/19/2022]
Abstract
Stereoselective catalysts for the Pictet-Spengler reaction of tryptamines and aldehydes may allow a simple and fast approach to chiral 1-substituted tetrahydro-β-carbolines. Although biocatalysts have previously been employed for the Pictet-Spengler reaction, not a single one accepts benzaldehyde and its substituted derivatives. To address this challenge, a combination of substrate walking and transfer of beneficial mutations between different wild-type backbones was used to develop a strictosidine synthase from Rauvolfia serpentina (RsSTR) into a suitable enzyme for the asymmetric Pictet-Spengler condensation of tryptamine and benzaldehyde derivatives. The double variant RsSTR V176L/V208A accepted various ortho-, meta- and para-substituted benzaldehydes and produced the corresponding chiral 1-aryl-tetrahydro-β-carbolines with up to 99 % enantiomeric excess.
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Affiliation(s)
- Elisabeth Eger
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/II8010GrazAustria
| | - Joerg H. Schrittwieser
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/II8010GrazAustria
| | - Dennis Wetzl
- Process Chemistry & CatalysisF. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070BaselSwitzerland
| | - Hans Iding
- Process Chemistry & CatalysisF. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070BaselSwitzerland
| | - Bernd Kuhn
- Pharma Research & Early DevelopmentF. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070BaselSwitzerland
| | - Wolfgang Kroutil
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/II8010GrazAustria
- Field of Excellence BioHealth—University of Graz8010GrazAustria
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28
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Chen M. Unleashing the Power of Biocatalysts. Chembiochem 2020; 22:317-318. [PMID: 33174653 DOI: 10.1002/cbic.202000540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/14/2020] [Indexed: 11/08/2022]
Abstract
Biocatalysis is a continuously expanding subfield in chemical biology. Herein, I describe two categories of biocatalysts, the LEGO-brick-like and game-console-like type, both of which can streamline the synthetic routes to therapeutics. A multi-disciplinary approach to expand the biocatalytic toolkit will open up opportunities to develop new therapeutics.
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Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, 90095, USA
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29
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Hollmann F, Opperman DJ, Paul CE. Biokatalytische Reduktionen aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frank Hollmann
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Diederik J. Opperman
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Caroline E. Paul
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
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30
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Feng J, Li R, Zhang S, Bu Y, Chen Y, Cui Y, Lin B, Chen Y, Tao Y, Wu B. Bioretrosynthesis of Functionalized N-Heterocycles from Glucose via One-Pot Tandem Collaborations of Designed Microbes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001188. [PMID: 32995125 PMCID: PMC7507072 DOI: 10.1002/advs.202001188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/29/2020] [Indexed: 05/10/2023]
Abstract
The design of multistrain systems has markedly expanded the prospects of using long biosynthetic pathways to produce natural compounds. However, the cooperative use of artificially engineered microbes to synthesize xenobiotic chemicals from renewable carbohydrates is still in its infancy. Here, a microbial system is developed for the production of high-added-value N-heterocycles directly from glucose. Based on a retrosynthetic analysis, eleven genes are selected, systematically modulated, and overexpressed in three Escherichia coli strains to construct an artificial pathway to produce 5-methyl-2-pyrazinecarboxylic acid, a key intermediate in the production of the important pharmaceuticals Glipizide and Acipimox. Via one-pot tandem collaborations, the designed microbes remarkably realize high-level production of 5-methyl-2-pyrazinecarboxylic acid (6.2 ± 0.1 g L-1) and its precursor 2,5-dimethylpyrazine (7.9 ± 0.7 g L-1). This study is the first application of cooperative microbes for the total biosynthesis of functionalized N-heterocycles and provides new insight into integrating bioretrosynthetic principles with synthetic biology to perform complex syntheses.
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Affiliation(s)
- Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Shasha Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yifan Bu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yanchun Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Yihua Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
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31
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Van Roy W, Woronoff G, Jimenez Valencia AM, Stakenborg T, Clarke WA. Analytical description of the lag phase in coupled-enzyme substrate assays. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Krüger A, Schäfers C, Busch P, Antranikian G. Digitalization in microbiology - Paving the path to sustainable circular bioeconomy. N Biotechnol 2020; 59:88-96. [PMID: 32750680 DOI: 10.1016/j.nbt.2020.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022]
Abstract
The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.
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Affiliation(s)
- Anna Krüger
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Christian Schäfers
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Philip Busch
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
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33
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Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily. Structure 2020; 28:635-642.e3. [DOI: 10.1016/j.str.2020.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 03/02/2020] [Accepted: 03/23/2020] [Indexed: 11/19/2022]
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34
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Zhou J, McCandlish DM. Minimum epistasis interpolation for sequence-function relationships. Nat Commun 2020; 11:1782. [PMID: 32286265 PMCID: PMC7156698 DOI: 10.1038/s41467-020-15512-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 03/12/2020] [Indexed: 12/17/2022] Open
Abstract
Massively parallel phenotyping assays have provided unprecedented insight into how multiple mutations combine to determine biological function. While such assays can measure phenotypes for thousands to millions of genotypes in a single experiment, in practice these measurements are not exhaustive, so that there is a need for techniques to impute values for genotypes whose phenotypes have not been directly assayed. Here, we present an imputation method based on inferring the least epistatic possible sequence-function relationship compatible with the data. In particular, we infer the reconstruction where mutational effects change as little as possible across adjacent genetic backgrounds. The resulting models can capture complex higher-order genetic interactions near the data, but approach additivity where data is sparse or absent. We apply the method to high-throughput transcription factor binding assays and use it to explore a fitness landscape for protein G.
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Affiliation(s)
- Juannan Zhou
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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35
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Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
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36
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
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37
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
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38
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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39
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Wang JB, Huang Q, Peng W, Wu P, Yu D, Chen B, Wang B, Reetz MT. P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species? J Am Chem Soc 2020; 142:2068-2073. [PMID: 31927987 PMCID: PMC7307895 DOI: 10.1021/jacs.9b13061] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/15/2022]
Abstract
While the mechanism of the P450-catalyzed oxidative hydroxylation of organic compounds has been studied in detail for many years, less is known about sulfoxidation. Depending upon the structure of the respective substrate, heme-Fe═O (Cpd I), heme-Fe(III)-OOH (Cpd 0), and heme-Fe(III)-H2O2 (protonated Cpd 0) have been proposed as reactive intermediates. In the present study, we consider the transformation of isosteric substrates via sulfoxidation and oxidative hydroxylation, respectively, catalyzed by regio- and enantioselective mutants of P450-BM3 which were constructed by directed evolution. 1-Thiochromanone and 1-tetralone were used as the isosteric substrates because, unlike previous studies involving fully flexible compounds such as thia-fatty acids and fatty acids, respectively, these compounds are rigid and cannot occur in a multitude of different conformations and binding modes in the large P450-BM3 binding pocket. The experimental results comprising activity and regio- and enantioselectivity, flanked by molecular dynamics computations within a time scale of 300 ns and QM/MM calculations of transition-state energies, unequivocally show that heme-Fe═O (Cpd I) is the common catalytically active intermediate in both sulfoxidation and oxidative hydroxylation.
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Affiliation(s)
- Jian-bo Wang
- Key Laboratory
of Phytochemistry R&D of Hunan Province, College of Chemistry
and Chemical Engineering and Key Laboratory of Chemical Biology and Traditional
Chinese Medicine Research (Ministry of Education), College of Chemistry
and Chemical Engineering, Hunan Normal University, 410081 Changsha, People’s Republic of China
| | - Qun Huang
- Key Laboratory
of Phytochemistry R&D of Hunan Province, College of Chemistry
and Chemical Engineering and Key Laboratory of Chemical Biology and Traditional
Chinese Medicine Research (Ministry of Education), College of Chemistry
and Chemical Engineering, Hunan Normal University, 410081 Changsha, People’s Republic of China
| | - Wei Peng
- State Key
Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, College
of Chemistry and Chemical Engineering, Xiamen
University, Xiamen 360015, P. R. China
| | - Peng Wu
- State Key
Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, College
of Chemistry and Chemical Engineering, Xiamen
University, Xiamen 360015, P. R. China
| | - Da Yu
- Key Laboratory
of Phytochemistry R&D of Hunan Province, College of Chemistry
and Chemical Engineering and Key Laboratory of Chemical Biology and Traditional
Chinese Medicine Research (Ministry of Education), College of Chemistry
and Chemical Engineering, Hunan Normal University, 410081 Changsha, People’s Republic of China
| | - Bo Chen
- Key Laboratory
of Phytochemistry R&D of Hunan Province, College of Chemistry
and Chemical Engineering and Key Laboratory of Chemical Biology and Traditional
Chinese Medicine Research (Ministry of Education), College of Chemistry
and Chemical Engineering, Hunan Normal University, 410081 Changsha, People’s Republic of China
| | - Binju Wang
- State Key
Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, College
of Chemistry and Chemical Engineering, Xiamen
University, Xiamen 360015, P. R. China
| | - Manfred T. Reetz
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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40
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Woodley JM. Advances in biological conversion technologies: new opportunities for reaction engineering. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00422j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction engineering needs to embrace biological conversion technologies, on the road to identify more sustainable routes for chemical manufacture.
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Affiliation(s)
- John M. Woodley
- Department of Chemical and Biochemical Engineering
- Technical University of Denmark (DTU)
- DK-2800 Kgs. Lyngby
- Denmark
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41
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Heine T, Scholtissek A, Hofmann S, Koch R, Tischler D. Accessing Enantiopure Epoxides and Sulfoxides: Related Flavin‐Dependent Monooxygenases Provide Reversed Enantioselectivity. ChemCatChem 2019. [DOI: 10.1002/cctc.201901353] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas Heine
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Anika Scholtissek
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Sarah Hofmann
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Rainhard Koch
- Engineering & TechnologyBayer AG Leverkusen 51368 Germany
| | - Dirk Tischler
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
- Microbial BiotechnologyRuhr University Bochum Bochum 44780 Germany
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42
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Debon A, Pott M, Obexer R, Green AP, Friedrich L, Griffiths AD, Hilvert D. Ultrahigh-throughput screening enables efficient single-round oxidase remodelling. Nat Catal 2019. [DOI: 10.1038/s41929-019-0340-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Seel CJ, Gulder T. Biocatalysis Fueled by Light: On the Versatile Combination of Photocatalysis and Enzymes. Chembiochem 2019; 20:1871-1897. [PMID: 30864191 DOI: 10.1002/cbic.201800806] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Enzymes catalyze a plethora of highly specific transformations under mild and environmentally benign reaction conditions. Their fascinating performances attest to high synthetic potential that is often hampered by operational obstacles such as in vitro cofactor supply and regeneration. Exploiting light and combining it with biocatalysis not only helps in overcoming these drawbacks, but the fruitful liaison of these two fields of "green chemistry" also offers opportunities to unlock new synthetic reactivities. In this review we provide an overview of the wide variety of photo-biocatalysis, ranging from the photochemical delivery of electrons required in redox biocatalysis and photochemical cofactor and reagent (re)generation to direct photoactivation of enzymes enabling reactions unknown in nature. We highlight synthetically relevant transformations such as asymmetric reactions facilitated by the combination of light as energy source and enzymes' catalytic power.
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Affiliation(s)
- Catharina J Seel
- Department of Chemistry and Catalysis Research Center (CRC), Technical University Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tanja Gulder
- Department of Chemistry and Catalysis Research Center (CRC), Technical University Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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44
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Murugayah SA, Gerth ML. Engineering quorum quenching enzymes: progress and perspectives. Biochem Soc Trans 2019; 47:793-800. [PMID: 31064863 PMCID: PMC6599154 DOI: 10.1042/bst20180165] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Quorum sensing is a key contributor to the virulence of many important plant, animal and human pathogens. The disruption of this signalling-a process referred to as 'quorum quenching'-is a promising new approach for controlling microbial pathogens. In this mini-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability, specificity and activities of quorum quenching enzymes. Finally, we grapple with some of the issues around these approaches-including the disconnect between in vitro biochemistry and potential in vivo applications.
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Affiliation(s)
- Shereen A Murugayah
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Monica L Gerth
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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45
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Peters C, Buller R. Linear enzyme cascade for the production of (-)-iso-isopulegol. ACTA ACUST UNITED AC 2019; 74:63-70. [PMID: 30645192 DOI: 10.1515/znc-2018-0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/09/2018] [Indexed: 01/31/2023]
Abstract
Biocatalysis has developed enormously in the last decade and now offers solutions for the sustainable production of chiral and highly functionalised asset molecules. Products generated by enzymatic transformations are already being used in the food, feed, chemical, pharmaceutical and cosmetic industry, and the accessible compound panoply is expected to expand even further. In particular, the combination of stereo-selective enzymes in linear cascade reactions is an elegant strategy toward enantiomeric pure compounds, as it reduces the number of isolation and purification steps and avoids accumulation of potentially unstable intermediates. Here, we present the set-up of an enzyme cascade to selectively convert citral to (-)-iso-isopulegol by combining an ene reductase and a squalene hopene cyclase. In the initial reaction step, the ene reductase YqjM from Bacillus subtilis selectively transforms citral to (S)-citronellal, which is subsequently cyclised exclusively to (-)-iso-isopulegol by a mutant of the squalene hopene cyclase from Alicyclobacillus acidocaldarius (AacSHC). With this approach, we can convert citral to an enantiopure precursor for isomenthol derivatives.
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Affiliation(s)
- Christin Peters
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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46
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Ahan RE, Saltepe B, Apaydin O, Seker UOS. Cellular Biocatalysts Using Synthetic Genetic Circuits for Prolonged and Durable Enzymatic Activity. Chembiochem 2019; 20:1799-1809. [DOI: 10.1002/cbic.201800767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/08/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Recep Erdem Ahan
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Behide Saltepe
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Onur Apaydin
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Urartu Ozgur Safak Seker
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
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47
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Li G, Dong Y, Reetz MT. Can Machine Learning Revolutionize Directed Evolution of Selective Enzymes? Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900149] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural Sciences Beijing 100081 People's Republic of China
| | - Yijie Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural Sciences Beijing 100081 People's Republic of China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie der Philipps-Universität Hans-Meerwein-Strasse 35032 Marburg Germany
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48
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Abstract
The aromatic N-oxides have received increased attention over the last few years due to their potential application in medicine, agriculture and organic chemistry. As a green alternative in their synthesis, the biocatalytic method employing whole cells of Escherichia coli bearing phenol monooxygenase like protein PmlABCDEF (from here on – PML monooxygenase) has been introduced. In this work, site-directed mutagenesis was used to study the contributions of active site neighboring residues I106, A113, G109, F181, F200, F209 to the regiospecificity of N-oxidation. Based on chromogenic indole oxidation screening, a collection of PML mutants with altered catalytic properties was created. Among the tested mutants, the A113G variant acquired the most distinguishable N-oxidations capacity. This new variant of PML was able to produce dioxides (quinoxaline-1,4-dioxide, 2,5-dimethylpyrazine-1,4-dioxide) and specific mono-N-oxides (2,3,5-trimethylpyrazine-1-oxide) that were unachievable using the wild type PML. This mutant also featured reshaped regioselectivity as N-oxidation shifted towards quinazoline-1-oxide compared to quinazoline-3-oxide that is produced by the wild type PML.
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49
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Jin X, Park OJ, Hong SH. Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. Appl Microbiol Biotechnol 2019; 103:2947-2958. [PMID: 30790000 PMCID: PMC6449208 DOI: 10.1007/s00253-019-09690-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022]
Abstract
The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
- Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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50
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Shift in Bacillus sp. JR3 esterase LipJ activity profile after addition of essential residues from family I.5 thermophilic lipases. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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