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Chen H, Liu R, Cai S, Zhang Y, Zhu C, Yu H, Li S. Intermediate product control in cascade reaction for one-pot production of ε-caprolactone by Escherichia coli. Biotechnol J 2024; 19:e2300210. [PMID: 38403458 DOI: 10.1002/biot.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 02/27/2024]
Abstract
ε-Caprolactone is an important non-toxic compound for polymer synthesis like polycaprolactone which has been widely used in drug delivery and degradable plastics. To meet the demand for a green economy, a bi-enzymatic cascade, consisting of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO), was designed and introduced into Escherichia coli to synthesize ε-caprolactone from cyclohexanol with a self-sufficient NADPH-cofactor regeneration system. To further improve the catalytic efficiency, a carbonyl group-dependent colorimetric method using inexpensive 2,4-dinitrophenylhydrazine (DNPH) was developed for assay of cyclohexanone, an intermediate production of cascade reaction. It can be used to screen mutant strains with high catalytic efficiency from high-throughput library by detecting the absorbance value in microtiter plates (MTP) instead of gas chromatography (GC) analysis. Moreover, an RBS combinatorial library was constructed for balancing the expression of ADH and CHMO from two independent transcriptional units. After the high-throughput screening based on intermediate product control, an optimal variant with higher substrate tolerance and long-term stability was obtained from RBS combinatorial library. Through a fed-batch process, ε-caprolactone production reached 148.2 mM after 70 h of reaction under the optimized conditions, which was the highest yield achieved to date.
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Affiliation(s)
- Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ran Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shengliang Cai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingjiao Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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2
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Biler M, Crean RM, Schweiger AK, Kourist R, Kamerlin SCL. Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. J Am Chem Soc 2020; 142:20216-20231. [PMID: 33180505 PMCID: PMC7735706 DOI: 10.1021/jacs.0c10701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity, and selectivity of this enzyme are only poorly understood to date, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the nonconverted or poorly converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering.
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Affiliation(s)
- Michal Biler
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Rory M. Crean
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Anna K. Schweiger
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
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3
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Mügge C, Kourist R. Practical Considerations Regarding the Choice of the Best High-Throughput Assay. Methods Mol Biol 2018; 1685:189-208. [PMID: 29086310 DOI: 10.1007/978-1-4939-7366-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
All protein engineering studies include the stage of identifying and characterizing variants within a mutant library by employing a suitable assay or selection method. A large variety of different assay approaches for different enzymes have been developed in the last few decades, and the throughput performance of these assays vary considerably. Thus, the concept of a protein engineering study must be adapted to the available assay methods. This introductory review chapter describes different assay concepts on selected examples, including selection and screening approaches, detection of pH and cosubstrate changes, coupled enzyme assays, methods using surrogate substrates and selective derivatization. The given examples should guide and inspire the reader when choosing and developing own high-throughput screening approaches.
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Affiliation(s)
- Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Robert Kourist
- Institute of Molecular Biotechnology, TU Graz, Petersgasse 14, A8010, Graz, Austria.
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Schartner J, Güldenhaupt J, Katharina Gaßmeyer S, Rosga K, Kourist R, Gerwert K, Kötting C. Highly stable protein immobilizationviamaleimido-thiol chemistry to monitor enzymatic activity. Analyst 2018; 143:2276-2284. [DOI: 10.1039/c8an00301g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining a novel protein immobilisation method with multivariate curve resolution enables the direct observation of biocatalysis by ATR-FTIR spectroscopy.
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Affiliation(s)
- Jonas Schartner
- Department of Biophysics
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
| | - Jörn Güldenhaupt
- Department of Biophysics
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
| | | | - Katharina Rosga
- Department of Biophysics
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
| | - Klaus Gerwert
- Department of Biophysics
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
| | - Carsten Kötting
- Department of Biophysics
- Ruhr-Universität Bochum
- 44801 Bochum
- Germany
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5
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From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution. Appl Microbiol Biotechnol 2017; 102:559-567. [PMID: 29181567 DOI: 10.1007/s00253-017-8568-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 01/17/2023]
Abstract
With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.
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Miyamoto K, Kourist R. Arylmalonate decarboxylase—a highly selective bacterial biocatalyst with unknown function. Appl Microbiol Biotechnol 2016; 100:8621-31. [PMID: 27566691 DOI: 10.1007/s00253-016-7778-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 08/02/2016] [Indexed: 11/24/2022]
Affiliation(s)
- Kenji Miyamoto
- Department for Biosciences and Bioinformatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, 44780, Bochum, Germany.
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Maimanakos J, Chow J, Gaßmeyer SK, Güllert S, Busch F, Kourist R, Streit WR. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. Front Microbiol 2016; 7:1332. [PMID: 27610105 PMCID: PMC4996985 DOI: 10.3389/fmicb.2016.01332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
Arylmalonate Decarboxylases (AMDases, EC 4.1.1.76) are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta-, and Gamma-proteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the tripartite tricarboxylate transporters family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99%) of the (R)-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes.
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Affiliation(s)
- Janine Maimanakos
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Sarah K Gaßmeyer
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Simon Güllert
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Florian Busch
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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Directed evolution of mandelate racemase by a novel high-throughput screening method. Appl Microbiol Biotechnol 2016; 101:1063-1072. [DOI: 10.1007/s00253-016-7790-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/24/2016] [Accepted: 08/03/2016] [Indexed: 12/30/2022]
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9
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Gaßmeyer SK, Wetzig J, Mügge C, Assmann M, Enoki J, Hilterhaus L, Zuhse R, Miyamoto K, Liese A, Kourist R. Arylmalonate Decarboxylase-Catalyzed Asymmetric Synthesis of Both Enantiomers of Optically Pure Flurbiprofen. ChemCatChem 2016. [DOI: 10.1002/cctc.201501205] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Jasmin Wetzig
- Chiracon GmbH; Im Biotechnologiepark 14943 Luckenwalde Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
| | - Miriam Assmann
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Junichi Enoki
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
| | - Lutz Hilterhaus
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Ralf Zuhse
- Chiracon GmbH; Im Biotechnologiepark 14943 Luckenwalde Germany
| | - Kenji Miyamoto
- Department for Biosciences and Bioinformatics; Keio University; 3-14-1 Hiyoshi Yokohama 223-8522 Japan
| | - Andreas Liese
- Institute for Technical Biocatalysis; Hamburg University of Technology TUHH; Denickestr. 15 21071 Hamburg Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology; Ruhr-University Bochum; 44780 Bochum Germany
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10
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Busch F, Enoki J, Hülsemann N, Miyamoto K, Bocola M, Kourist R. Semiempirical QM/MM calculations reveal a step-wise proton transfer and an unusual thiolate pocket in the mechanism of the unique arylpropionate racemase AMDase G74C. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01964h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Semiempirical calculations on the mechanism of the arylpropionate racemase AMDase G74C reveal a step-wise mechanism involving a planar-enedionate intermediate.
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Affiliation(s)
- F. Busch
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - J. Enoki
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - N. Hülsemann
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
| | - K. Miyamoto
- Department of Bioscience and Informatics
- Keio University
- Yokohama
- Japan
| | - M. Bocola
- Institute of Biotechnology
- RWTH Aachen
- 52062 Aachen
- Germany
| | - R. Kourist
- Faculty of Biology and Biotechnology
- Ruhr-University Bochum
- 44801 Bochum
- Germany
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