1
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Jain A, Stavrakis S, deMello A. Droplet-based microfluidics and enzyme evolution. Curr Opin Biotechnol 2024; 87:103097. [PMID: 38430713 DOI: 10.1016/j.copbio.2024.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.
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Affiliation(s)
- Ankit Jain
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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2
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Hoshino M, Ota Y, Suyama T, Morishita Y, Tsuneda S, Noda N. Water-in-oil droplet-mediated method for detecting and isolating infectious bacteriophage particles via fluorescent staining. Front Microbiol 2023; 14:1282372. [PMID: 38125569 PMCID: PMC10731258 DOI: 10.3389/fmicb.2023.1282372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteriophages are the most abundant entities on Earth. In contrast with the number of phages considered to be in existence, current phage isolation and screening methods lack throughput. Droplet microfluidic technology has been established as a platform for high-throughput screening of biological and biochemical components. In this study, we developed a proof-of-concept method for isolating phages using water-in-oil droplets (droplets) as individual chambers for phage propagation and co-cultivating T2 phage and their host cell Escherichia coli within droplets. Liquid cultivation of microbes will facilitate the use of microbes that cannot grow on or degrade agar as host cells, ultimately resulting in the acquisition of phages that infect less known bacterial cells. The compartmentalizing characteristic of droplets and the use of a fluorescent dye to stain phages simultaneously enabled the enumeration and isolation of viable phage particles. We successfully recultivated the phages after simultaneously segregating single phage particles into droplets and inoculating them with their host cells within droplets. By recovering individual droplets into 96-well plates, we were able to isolate phage clones derived from single phage particles. The success rate for phage recovery was 35.7%. This study lays the building foundations for techniques yet to be developed that will involve the isolation and rupturing of droplets and provides a robust method for phage enumeration and isolation.
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Affiliation(s)
- Miu Hoshino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yuri Ota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- On-chip Biotechnologies Co., Ltd., Tokyo, Japan
| | - Tetsushi Suyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | | | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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3
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De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun 2023; 14:4788. [PMID: 37553326 PMCID: PMC10409775 DOI: 10.1038/s41467-023-40322-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Affiliation(s)
- Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - David B Morse
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte E Handford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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4
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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5
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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6
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Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
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Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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7
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Eenink BDG, Kaminski TS, Bornberg-Bauer E, Jose J, Hollfelder F, van Loo B. Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli. Microb Biotechnol 2022; 15:2845-2853. [PMID: 36099491 PMCID: PMC9618318 DOI: 10.1111/1751-7915.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
Directed evolution (DE) is a widely used method for improving the function of biomolecules via multiple rounds of mutation and selection. Microfluidic droplets have emerged as an important means to screen the large libraries needed for DE, but this approach was so far partially limited by the need to lyse cells, recover DNA, and retransform into cells for the next round, necessitating the use of a high‐copy number plasmid or oversampling. The recently developed live cell recovery avoids some of these limitations by directly regrowing selected cells after sorting. However, repeated sorting cycles used to further enrich the most active variants ultimately resulted in unfavourable recovery of empty plasmid vector‐containing cells over those expressing the protein of interest. In this study, we found that engineering of the original expression vector solved the problem of false positives (i.e. plasmids lacking an insert) cells containing empty vectors. Five approaches to measure activity of cell‐displayed enzymes in microdroplets were compared. By comparing various cell treatment methods prior to droplet sorting two things were found. Substrate encapsulation from the start, that is prior to expression of enzyme, showed no disadvantage to post‐induction substrate addition by pico‐injection with respect to recovery of true positive variants. Furthermore in‐droplet cell growth prior to induction of enzyme production improves the total amount of cells retrieved (recovery) and proportion of true positive variants (enrichment) after droplet sorting.
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Affiliation(s)
- Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | | | - Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, UK
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8
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Schlachter CR, O’Malley A, Grimes LL, Tomashek JJ, Chruszcz M, Lee LA. Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis. Molecules 2021; 27:87. [PMID: 35011319 PMCID: PMC8746622 DOI: 10.3390/molecules27010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfatases are ubiquitous enzymes that hydrolyze sulfate from sulfated organic substrates such as carbohydrates, steroids, and flavones. These enzymes can be exploited in the field of biotechnology to analyze sulfated metabolites in humans, such as steroids and drugs of abuse. Because genomic data far outstrip biochemical characterization, the analysis of sulfatases from published sequences can lead to the discovery of new and unique activities advantageous for biotechnological applications. We expressed and characterized a putative sulfatase (PyuS) from the bacterium Pedobacter yulinensis. PyuS contains the (C/S)XPXR sulfatase motif, where the Cys or Ser is post-translationally converted into a formylglycine residue (FGly). His-tagged PyuS was co-expressed in Escherichia coli with a formylglycine-generating enzyme (FGE) from Mycobacterium tuberculosis and purified. We obtained several crystal structures of PyuS, and the FGly modification was detected at the active site. The enzyme has sulfatase activity on aromatic sulfated substrates as well as phosphatase activity on some aromatic phosphates; however, PyuS did not have detectable activity on 17α-estradiol sulfate, cortisol 21-sulfate, or boldenone sulfate.
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Affiliation(s)
- Caleb R. Schlachter
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - Andrea O’Malley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - Linda L. Grimes
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - John J. Tomashek
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - L. Andrew Lee
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
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9
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Min KH, Shin JW, Ki MR, Kim SH, Kim KH, Pack SP. Bio-inspired formation of silica particles using the silica-forming peptides found by silica-binding motif sequence, RRSSGGRR. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Manteca A, Gadea A, Van Assche D, Cossard P, Gillard-Bocquet M, Beneyton T, Innis CA, Baret JC. Directed Evolution in Drops: Molecular Aspects and Applications. ACS Synth Biol 2021; 10:2772-2783. [PMID: 34677942 PMCID: PMC8609573 DOI: 10.1021/acssynbio.1c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/29/2022]
Abstract
The process of optimizing the properties of biological molecules is paramount for many industrial and medical applications. Directed evolution is a powerful technique for modifying and improving biomolecules such as proteins or nucleic acids (DNA or RNA). Mimicking the mechanism of natural evolution, one can enhance a desired property by applying a suitable selection pressure and sorting improved variants. Droplet-based microfluidic systems offer a high-throughput solution to this approach by helping to overcome the limiting screening steps and allowing the analysis of variants within increasingly complex libraries. Here, we review cases where successful evolution of biomolecules was achieved using droplet-based microfluidics, focusing on the molecular processes involved and the incorporation of microfluidics to the workflow. We highlight the advantages and limitations of these microfluidic systems compared to low-throughput methods and show how the integration of these systems into directed evolution workflows can open new avenues to discover or improve biomolecules according to user-defined conditions.
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Affiliation(s)
- Aitor Manteca
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Alejandra Gadea
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | | | - Pauline Cossard
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Mélanie Gillard-Bocquet
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thomas Beneyton
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | - C. Axel Innis
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Jean-Christophe Baret
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
- Institut
Universitaire de France, F-75231 Paris, France
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11
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Buchholz PCF, van Loo B, Eenink BDG, Bornberg-Bauer E, Pleiss J. Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation. J R Soc Interface 2021; 18:20210389. [PMID: 34727710 DOI: 10.1098/rsif.2021.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
| | - Bert van Loo
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK.,Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
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12
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Directed Evolution Methods for Enzyme Engineering. Molecules 2021; 26:molecules26185599. [PMID: 34577070 PMCID: PMC8470892 DOI: 10.3390/molecules26185599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/22/2022] Open
Abstract
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades to accomplish this goal. In this review such methods and their specific attributes are examined.
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13
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Alex Wong CF, van Vliet L, Bhujbal SV, Guo C, Sletmoen M, Stokke BT, Hollfelder F, Lale R. A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution. ACS Synth Biol 2021; 10:1882-1894. [PMID: 34260196 PMCID: PMC8383311 DOI: 10.1021/acssynbio.1c00084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Water-in-oil emulsion
droplets are an attractive format for ultrahigh-throughput
screening in functional metagenomics and directed evolution applications
that allow libraries with more than 107 members to be characterized
in a day. Single library members are compartmentalized in droplets
that are generated in microfluidic devices and tested for the presence
of target biocatalysts. The target proteins can be produced intracellularly,
for example, in bacterial hosts in-droplet cell lysis is therefore
necessary to allow the enzymes to encounter the substrate to initiate
an activity assay. Here, we present a titratable lysis-on-demand (LoD)
system enabling the control of the cell lysis rate in Escherichia
coli. We demonstrate that the rate of cell lysis can be controlled
by adjusting the externally added inducer concentration. This LoD
system is evaluated both at the population level (by optical density
measurements) and at the single-cell level (on single-cell arrays
and in alginate microbeads). Additionally, we validate the LoD system
by droplet screening of a phosphotriesterase expressed from E. coli, with cell lysis triggered by inducer concentrations
in the μM range. The LoD system yields sufficient release of
the intracellularly produced enzymes to bring about a detectable quantity
of product (measured by fluorescence in flow cytometry of double emulsions),
while leaving viable cells for the downstream recovery of the genetic
material.
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Affiliation(s)
- Che Fai Alex Wong
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Liisa van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Swapnil Vilas Bhujbal
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Chengzhi Guo
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marit Sletmoen
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Bjørn Torger Stokke
- Department of Physics, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Rahmi Lale
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
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14
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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: 115] [Impact Index Per Article: 38.3] [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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15
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Bouzetos E, Ganar KA, Mastrobattista E, Deshpande S, van der Oost J. (R)evolution-on-a-chip. Trends Biotechnol 2021; 40:60-76. [PMID: 34049723 DOI: 10.1016/j.tibtech.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 01/17/2023]
Abstract
Billions of years of Darwinian evolution has led to the emergence of highly sophisticated and diverse life forms on Earth. Inspired by natural evolution, similar principles have been adopted in laboratory evolution for the fast optimization of genes and proteins for specific applications. In this review, we highlight state-of-the-art laboratory evolution strategies for protein engineering, with a special emphasis on in vitro strategies. We further describe how recent progress in microfluidic technology has allowed the generation and manipulation of artificial compartments for high-throughput laboratory evolution experiments. Expectations for the future are high: we foresee a revolution on-a-chip.
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Affiliation(s)
- Evgenios Bouzetos
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Ketan Ashok Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Enrico Mastrobattista
- Pharmaceutics Division, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
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16
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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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17
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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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18
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Zurek PJ, Hours R, Schell U, Pushpanath A, Hollfelder F. Growth amplification in ultrahigh-throughput microdroplet screening increases sensitivity of clonal enzyme assays and minimizes phenotypic variation. LAB ON A CHIP 2021; 21:163-173. [PMID: 33242058 DOI: 10.1039/d0lc00830c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microfluidic ultrahigh-throughput screening of enzyme activities provides information on libraries with millions of variants in a day. Each individual library member is represented by a recombinant single cell, compartmentalised in an emulsion droplet, in which an activity assay is carried out. Key to the success of this approach is the precision and sensitivity of the assay. Assay quality is most profoundly challenged when initially weak, promiscuous activities are to be enhanced in early rounds of directed evolution or when entirely novel catalysts are to be identified from metagenomic sources. Implementation of measures to widen the dynamic range of clonal assays would increase the chances of finding and generating new biocatalysts. Here, we demonstrate that the assay sensitivity and DNA recovery can be improved by orders of magnitude by growth of initially singly compartmentalised cells in microdroplets. Homogeneous cell growth is achieved by continuous oxygenation and recombinant protein expression is regulated by diffusion of an inducer from the oil phase. Reaction conditions are adjusted by directed droplet coalescence to enable full control of buffer composition and kinetic incubation time, creating level playing field conditions for library selections. The clonal amplification multiplies the product readout because more enzyme is produced per compartment. At the same time, phenotypic variation is reduced by measuring monoclonal populations rather than single cells and recovery efficiency is increased. Consequently, this workflow increases the efficiency of lysate-based microfluidic enzyme assays and will make it easier for protein engineers to identify or evolve new enzymes for applications in synthetic and chemical biology.
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Affiliation(s)
- Paul Jannis Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK.
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19
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Gargiulo S, Soumillion P. Directed evolution for enzyme development in biocatalysis. Curr Opin Chem Biol 2020; 61:107-113. [PMID: 33385931 DOI: 10.1016/j.cbpa.2020.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.
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Affiliation(s)
- Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium.
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20
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Neun S, Zurek PJ, Kaminski TS, Hollfelder F. Ultrahigh throughput screening for enzyme function in droplets. Methods Enzymol 2020; 643:317-343. [PMID: 32896286 DOI: 10.1016/bs.mie.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Water-in-oil droplets, made and handled in microfluidic devices, provide a new experimental format, in which ultrahigh throughput experiments can be conducted faster and with minimal reagent consumption. An increasing number of studies have emerged that applied this approach to directed evolution and metagenomic screening of enzyme catalysts. Here, we review the considerations necessary to implement robust workflows, based on choices of device design, detection modes, emulsion formulations and substrates, and scope out which enzyme classes have become amenable to droplet screening.
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Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Zurek
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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