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Vasina M, Vanacek P, Damborsky J, Prokop Z. Exploration of enzyme diversity: High-throughput techniques for protein production and microscale biochemical characterization. Methods Enzymol 2020; 643:51-85. [PMID: 32896287 DOI: 10.1016/bs.mie.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are being increasingly utilized for acceleration of industrially and pharmaceutically critical chemical reactions. The strong demand for finding robust and efficient biocatalysts for these applications can be satisfied via the exploration of enzyme diversity. The first strategy is to mine the natural diversity, represented by millions of sequences available in the public genomic databases, by using computational approaches. Alternatively, metagenomic libraries can be targeted experimentally or computationally to explore the natural diversity of a specific environment. The second strategy, known as directed evolution, is to generate man-made diversity in the laboratory using gene mutagenesis and screen the constructed library of mutants. The selected hits must be experimentally characterized in both strategies, which currently represent the rate-limiting step in the process of diversity exploration. The traditional techniques used for biochemical characterization are time-demanding, cost, and sample volume ineffective, and low-throughput. Therefore, the development and implementation of high-throughput experimental methods are essential for discovering novel enzymes. This chapter describes the experimental protocols employing the combination of robust production and high-throughput microscale biochemical characterization of enzyme variants. We validated its applicability against the model enzyme family of haloalkane dehalogenases. These protocols can be adapted to other enzyme families, paving the way towards the functional characterization and quick identification of novel biocatalysts.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.
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Gul I, Bogale TF, Chen Y, Yang X, Fang R, Feng J, Gao H, Tang L. A paper-based whole-cell screening assay for directed evolution-driven enzyme engineering. Appl Microbiol Biotechnol 2020; 104:6013-6022. [DOI: 10.1007/s00253-020-10615-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/06/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
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Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
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Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
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Buryska T, Vasina M, Gielen F, Vanacek P, van Vliet L, Jezek J, Pilat Z, Zemanek P, Damborsky J, Hollfelder F, Prokop Z. Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Anal Chem 2019; 91:10008-10015. [PMID: 31240908 DOI: 10.1021/acs.analchem.9b01839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Functional annotation of novel proteins lags behind the number of sequences discovered by the next-generation sequencing. The throughput of conventional testing methods is far too low compared to sequencing; thus, experimental alternatives are needed. Microfluidics offer high throughput and reduced sample consumption as a tool to keep up with a sequence-based exploration of protein diversity. The most promising droplet-based systems have a significant limitation: leakage of hydrophobic compounds from water compartments to the carrier prevents their use with hydrophilic reagents. Here, we present a novel approach of substrate delivery into microfluidic droplets and apply it to high-throughput functional characterization of enzymes that convert hydrophobic substrates. Substrate delivery is based on the partitioning of hydrophobic chemicals between the oil and water phases. We applied a controlled distribution of 27 hydrophobic haloalkanes from oil to reaction water droplets to perform substrate specificity screening of eight model enzymes from the haloalkane dehalogenase family. This droplet-on-demand microfluidic system reduces the reaction volume 65 000-times and increases the analysis speed almost 100-fold compared to the classical test tube assay. Additionally, the microfluidic setup enables a convenient analysis of dependences of activity on the temperature in a range of 5 to 90 °C for a set of mesophilic and hyperstable enzyme variants. A high correlation between the microfluidic and test tube data supports the approach robustness. The precision is coupled to a considerable throughput of >20 000 reactions per day and will be especially useful for extending the scope of microfluidic applications for high-throughput analysis of reactions including compounds with limited water solubility.
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Affiliation(s)
- Tomas Buryska
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Fabrice Gielen
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom.,Living Systems Institute , University of Exeter , Exeter EX4 4QD , United Kingdom
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Liisa van Vliet
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Jan Jezek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Zdenek Pilat
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Pavel Zemanek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Florian Hollfelder
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
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5
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Beier A, Damborsky J, Prokop Z. Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andy Beier
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk University Kamenice 5 A 625 00 Brno Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital Pekarska 53 656 91 Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk University Kamenice 5 A 625 00 Brno Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital Pekarska 53 656 91 Brno Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk University Kamenice 5 A 625 00 Brno Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital Pekarska 53 656 91 Brno Czech Republic
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