101
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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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102
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Chen X, Shen R, Liu S, Xiao X, Yan J, Zhang Y, Jiang Z, Nie B, Liu J. The sensitive detection of single-cell secreted lactic acid for glycolytic inhibitor screening with a microdroplet biosensor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3250-3259. [PMID: 32930188 DOI: 10.1039/d0ay00633e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Lactic acid (LA) plays an important role in the tumor metabolism and malignant progression of various cancers. Herein, we have developed a one-step, wash-free microfluidic approach with droplet biosensors for the sensitive detection of LA secreted by a single tumor cell. Our assay integrates the enzyme-assisted chemical conversion of LA in small-volume (4.2 nL) droplets for fluorescence signal readout. The microdroplet assay achieved a limit of detection of 1.02 μM and was more sensitive than the commercial ELISA kit by nearly two orders of magnitude. A good specificity has been demonstrated for this assay by testing various ions and biomolecules from the culture medium. This droplet assay allows us to acquire the profiles of the lactic acid secretion of tumor cells under the influence of glycolytic inhibitors at the single-cell level. It offers a useful research tool to study the cell-to-cell differences of LA secretion and glycolytic inhibitor screening for cancer research.
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Affiliation(s)
- Xuyue Chen
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Rui Shen
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Sidi Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Xiang Xiao
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Jun Yan
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Yiqiu Zhang
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Zhongyun Jiang
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Baoqing Nie
- School of Electronic and Information Engineering, Soochow University, Suzhou, Jiangsu Province 215006, China
| | - Jian Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu Province 215123, China.
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103
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Bowman EK, Alper HS. Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications. Trends Biotechnol 2020; 38:701-714. [DOI: 10.1016/j.tibtech.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022]
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104
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Payne EM, Holland-Moritz DA, Sun S, Kennedy RT. High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects. LAB ON A CHIP 2020; 20:2247-2262. [PMID: 32500896 DOI: 10.1039/d0lc00347f] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.
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Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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105
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Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins. Curr Opin Struct Biol 2020; 63:123-133. [PMID: 32615371 DOI: 10.1016/j.sbi.2020.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.
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106
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Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM. Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. LAB ON A CHIP 2020; 20:2062-2074. [PMID: 32417874 PMCID: PMC7670282 DOI: 10.1039/d0lc00261e] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics has made large impacts in diverse areas such as enzyme evolution, chemical product screening, polymer engineering, and single-cell analysis. However, while droplet reactions have become increasingly sophisticated, phenotyping droplets by a fluorescent signal and sorting them to isolate individual variants-of-interest at high-throughput remains challenging. Here, we present sdDE-FACS (s[combining low line]ingle d[combining low line]roplet D[combining low line]ouble E[combining low line]mulsion-FACS), a new method that uses a standard flow cytometer to phenotype, select, and isolate individual double emulsion droplets of interest. Using a 130 μm nozzle at high sort frequency (12-14 kHz), we demonstrate detection of droplet fluorescence signals with a dynamic range spanning 5 orders of magnitude and robust post-sort recovery of intact double emulsion (DE) droplets using 2 commercially-available FACS instruments. We report the first demonstration of single double emulsion droplet isolation with post-sort recovery efficiencies >70%, equivalent to the capabilities of single-cell FACS. Finally, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets via qPCR with little to no cross-contamination. sdDE-FACS marries the full power of droplet microfluidics with flow cytometry to enable a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis.
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Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California, USA.
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107
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Zhao X, Cebrián R, Fu Y, Rink R, Bosma T, Moll GN, Kuipers OP. High-Throughput Screening for Substrate Specificity-Adapted Mutants of the Nisin Dehydratase NisB. ACS Synth Biol 2020; 9:1468-1478. [PMID: 32374981 PMCID: PMC7309312 DOI: 10.1021/acssynbio.0c00130] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Microbial
lanthipeptides are formed by a two-step enzymatic introduction
of (methyl)lanthionine rings. A dehydratase catalyzes the dehydration
of serine and threonine residues, yielding dehydroalanine and dehydrobutyrine,
respectively. Cyclase-catalyzed coupling of the formed dehydroresidues
to cysteines forms (methyl)lanthionine rings in a peptide. Lanthipeptide
biosynthetic systems allow discovery of target-specific, lanthionine-stabilized
therapeutic peptides. However, the substrate specificity of existing
modification enzymes impose limitations on installing lanthionines
in non-natural substrates. The goal of the present study was to obtain
a lanthipeptide dehydratase with the capacity to dehydrate substrates
that are unsuitable for the nisin dehydratase NisB. We report high-throughput
screening for tailored specificity of intracellular, genetically encoded
NisB dehydratases. The principle is based on the screening of bacterially
displayed lanthionine-constrained streptavidin ligands, which have
a much higher affinity for streptavidin than linear ligands. The designed
NisC-cyclizable high-affinity ligands can be formed via mutant NisB-catalyzed
dehydration but less effectively via wild-type NisB activity. In Lactococcus lactis, a cell surface display precursor was
designed comprising DSHPQFC. The Asp residue preceding the serine
in this sequence disfavors its dehydration by wild-type NisB. The
cell surface display vector was coexpressed with a mutant NisB library
and NisTC. Subsequently, mutant NisB-containing bacteria that display
cyclized strep ligands on the cell surface were selected via panning
rounds with streptavidin-coupled magnetic beads. In this way, a NisB
variant with a tailored capacity of dehydration was obtained, which
was further evaluated with respect to its capacity to dehydrate nisin
mutants. These results demonstrate a powerful method for selecting
lanthipeptide modification enzymes with adapted substrate specificity.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Rick Rink
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Tjibbe Bosma
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Gert N. Moll
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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108
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Saucedo-Espinosa MA, Dittrich PS. In-Droplet Electrophoretic Separation and Enrichment of Biomolecules. Anal Chem 2020; 92:8414-8421. [DOI: 10.1021/acs.analchem.0c01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mario A. Saucedo-Espinosa
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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109
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Erdogan M, Fabritius A, Basquin J, Griesbeck O. Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells. Cell Chem Biol 2020; 27:610-621.e5. [PMID: 32142629 DOI: 10.1016/j.chembiol.2020.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/22/2019] [Accepted: 02/14/2020] [Indexed: 02/08/2023]
Abstract
Engineered proteins must be phenotypically selected for function in the appropriate physiological context. Here, we present a versatile approach that allows generating panels of mammalian cells that express diversified heterologous protein libraries in the cytosol or subcellular compartments under stable conditions and in a single-variant-per-cell manner. To this end we adapt CRISPR/Cas9 editing technology to diversify targeted stretches of a protein of interest in situ. We demonstrate the utility of the approach by in situ engineering and intra-lysosome specific selection of an extremely pH-resistant long Stokes shift red fluorescent protein variant. Tailoring properties to specific conditions of cellular sub-compartments or organelles of mammalian cells can be an important asset to optimize various proteins, protein-based tools, and biosensors for distinct functions.
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Affiliation(s)
- Mutlu Erdogan
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany.
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110
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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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111
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“Development and application of analytical detection techniques for droplet-based microfluidics”-A review. Anal Chim Acta 2020; 1113:66-84. [DOI: 10.1016/j.aca.2020.03.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 01/03/2023]
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112
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Li J, Amatuni A, Renata H. Recent advances in the chemoenzymatic synthesis of bioactive natural products. Curr Opin Chem Biol 2020; 55:111-118. [PMID: 32086167 PMCID: PMC7237303 DOI: 10.1016/j.cbpa.2020.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 01/18/2023]
Abstract
The field of organic chemistry has recently witnessed a rapid rise in the use of chemoenzymatic strategies for the synthesis of complex molecules. Under this paradigm, biocatalytic methods and contemporary synthetic methods are used synergistically in a multistep approach toward a target molecule. In light of the unparalleled regioselectivity and stereoselectivity of enzymatic transformations and the reaction diversity of contemporary organic chemistry, chemoenzymatic strategies hold enormous potential for streamlining access to important bioactive molecules. This review covers recent demonstrations of chemoenzymatic approaches in chemical synthesis, with special emphasis on the preparation of medicinally relevant natural products.
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Affiliation(s)
- Jian Li
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Alexander Amatuni
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.
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113
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Ali M, Ishqi HM, Husain Q. Enzyme engineering: Reshaping the biocatalytic functions. Biotechnol Bioeng 2020; 117:1877-1894. [DOI: 10.1002/bit.27329] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Misha Ali
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
| | | | - Qayyum Husain
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
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114
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Karamitros CS, Morvan M, Vigne A, Lim J, Gruner P, Beneyton T, Vrignon J, Baret JC. Bacterial Expression Systems for Enzymatic Activity in Droplet-Based Microfluidics. Anal Chem 2020; 92:4908-4916. [PMID: 31909981 DOI: 10.1021/acs.analchem.9b04969] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Functional screenings in droplet-based microfluidics require the analysis of various types of activities of individual cells. When screening for enzymatic activities, the link between the enzyme of interest and the information-baring molecule, the DNA, must be maintained to relate phenotypes to genotypes. This linkage is crucial in directed evolution experiments or for the screening of natural diversity. Micro-organisms are classically used to express enzymes from nucleic acid sequences. However, little information is available regarding the most suitable expression system for the sensitive detection of enzymatic activity at the single-cell level in droplet-based microfluidics. Here, we compare three different expression systems for l-asparaginase (l-asparagine amidohydrolase, EC 3.5.1.1), an enzyme of therapeutic interest that catalyzes the conversion of l-asparagine to l-aspartic acid and ammonia. We developed three expression vectors to produce and localize l-asparaginase (l-ASNase) in E. coli either in the cytoplasm, on the surface of the inner membrane (display), or in the periplasm. We show that the periplasmic expression is the most optimal strategy combining both a good yield and a good accessibility for the substrate without the need for lysing the cells. We suggest that periplasmic expression may provide a very efficient platform for screening applications at the single-cell level in microfluidics.
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Affiliation(s)
- Christos S Karamitros
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D37077 Goettingen, Germany.,Aeglea Biotherapeutics, 901 S MoPac Expy #250, Austin, Texas 78746, United States
| | - Mickaël Morvan
- Université de Bordeaux, CNRS, CRPP, UMR5031, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Aurélie Vigne
- Université de Bordeaux, CNRS, CRPP, UMR5031, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Jiseok Lim
- School of Mechanical Engineering, Yeungnam University, 280 Daehak-ro, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea
| | - Philipp Gruner
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, D37077 Goettingen, Germany
| | - Thomas Beneyton
- Université de Bordeaux, CNRS, CRPP, UMR5031, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Jérémy Vrignon
- Université de Bordeaux, CNRS, CRPP, UMR5031, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Jean-Christophe Baret
- Université de Bordeaux, CNRS, CRPP, UMR5031, 115 Avenue Albert Schweitzer, 33600 Pessac, France.,Institut Universitaire de France, 1 Rue Descartes, 75005 Paris, France
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115
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Anagnostidis V, Sherlock B, Metz J, Mair P, Hollfelder F, Gielen F. Deep learning guided image-based droplet sorting for on-demand selection and analysis of single cells and 3D cell cultures. LAB ON A CHIP 2020; 20:889-900. [PMID: 31989120 DOI: 10.1039/d0lc00055h] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Uncovering the heterogeneity of cellular populations and multicellular constructs is a long-standing goal in fields ranging from antimicrobial resistance to cancer research. Emerging technology platforms such as droplet microfluidics hold the promise to decipher such heterogeneities at ultra-high-throughput. However, there is a lack of methods able to rapidly identify and isolate single cells or 3D cell cultures. Here we demonstrate that deep neural networks can accurately classify single droplet images in real-time based on the presence and number of micro-objects including single mammalian cells and multicellular spheroids. This approach also enables the identification of specific objects within mixtures of objects of different types and sizes. The training sets for the neural networks consisted of a few hundred images manually picked and augmented to up to thousands of images per training class. Training required less than 10 minutes using a single GPU, and yielded accuracies of over 90% for single mammalian cell identification. Crucially, the same model could be used to classify different types of objects such as polystyrene spheres, polyacrylamide beads and MCF-7 cells. We applied the developed method for the selection of 3D cell cultures generated with Hek293FT cells encapsulated in agarose gel beads, highlighting the potential of the technology for the selection of objects with a high diversity of visual appearances. The real-time sorting of single droplets was in-line with droplet generation and occurred at rates up to 40 per second independently of image size up to 480 × 480 pixels. The presented microfluidic device also enabled storage of sorted droplets to allow for downstream analyses.
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Affiliation(s)
| | - Benjamin Sherlock
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Jeremy Metz
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, 80 Tennis Court, Cambridge, CB2 1QW, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court, Cambridge, CB2 1QW, UK
| | - Fabrice Gielen
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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116
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Hengoju S, Wohlfeil S, Munser AS, Boehme S, Beckert E, Shvydkiv O, Tovar M, Roth M, Rosenbaum MA. Optofluidic detection setup for multi-parametric analysis of microbiological samples in droplets. BIOMICROFLUIDICS 2020; 14:024109. [PMID: 32547676 PMCID: PMC7148121 DOI: 10.1063/1.5139603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/27/2020] [Indexed: 05/03/2023]
Abstract
High-throughput microbiological experimentation using droplet microfluidics is limited due to the complexity and restricted versatility of the available detection techniques. Current detection setups are bulky, complicated, expensive, and require tedious optical alignment procedures while still mostly limited to fluorescence. In this work, we demonstrate an optofluidic detection setup for multi-parametric analyses of droplet samples by easily integrating micro-lenses and embedding optical fibers for guiding light in and out of the microfluidic chip. The optofluidic setup was validated for detection of absorbance, fluorescence, and scattered light. The developed platform was used for simultaneous detection of multiple parameters in different microbiological applications like cell density determination, growth kinetics, and antibiotic inhibition assays. Combining the high-throughput potential of droplet microfluidics with the ease, flexibility, and simplicity of optical fibers results in a powerful platform for microbiological experiments.
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Affiliation(s)
| | - S. Wohlfeil
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - A. S. Munser
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - S. Boehme
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - E. Beckert
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - O. Shvydkiv
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - M. Tovar
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - M. Roth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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117
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Goto H, Kanai Y, Yotsui A, Shimokihara S, Shitara S, Oyobiki R, Fujiwara K, Watanabe T, Einaga Y, Matsumoto Y, Miki N, Doi N. Microfluidic screening system based on boron-doped diamond electrodes and dielectrophoretic sorting for directed evolution of NAD(P)-dependent oxidoreductases. LAB ON A CHIP 2020; 20:852-861. [PMID: 31984406 DOI: 10.1039/c9lc01263j] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the development of a micro total analysis system (μTAS) based on electrochemical measurements and dielectrophoretic sorting for screening of NAD(P)-dependent oxidoreductases. In this system, the activity of enzymes immobilized on microbeads, together with their encoding DNA, can be measured with a boron-doped diamond (BDD) electrode in each compartment (∼30 nL) of the microfluidic system. The 30 nL droplets containing microbead-displayed genes of enzymes with higher activity can then be recovered by dielectrophoretic sorting. Previously, we developed the NAD(P)H-measuring device containing the BDD electrode for high-throughput measurement of the activity of NAD(P)-dependent oxidoreductases. In this study, we fabricated an encapsulating device and a droplet-sorting device for nanoliter-size droplets, for the first time, and then combined these three devices to construct a μTAS for directed evolution of NAD(P)-dependent oxidoreductases. We confirmed that this system works by proof-of-principle experiments and successfully applied this system for screening of randomized libraries of NAD-dependent dehydrogenases.
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Affiliation(s)
- Haruna Goto
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Yuki Kanai
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Arisa Yotsui
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Shota Shimokihara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Shunya Shitara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Ryo Oyobiki
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Takeshi Watanabe
- Department of Electrical Engineering and Electronics, Aoyama Gakuin University, Sagamihara 252-5258, Japan
| | - Yasuaki Einaga
- Department of Chemistry, Keio University, Yokohama 223-8522, Japan
| | - Yoshinori Matsumoto
- Department of Applied Physics and Physico-Informatics, Keio University, Yokohama 223-8522, Japan
| | - Norihisa Miki
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
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118
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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: 142] [Impact Index Per Article: 35.5] [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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119
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Holland-Moritz DA, Wismer MK, Mann BF, Farasat I, Devine P, Guetschow ED, Mangion I, Welch CJ, Moore JC, Sun S, Kennedy RT. Mass Activated Droplet Sorting (MADS) Enables High-Throughput Screening of Enzymatic Reactions at Nanoliter Scale. Angew Chem Int Ed Engl 2020; 59:4470-4477. [PMID: 31868984 DOI: 10.1002/anie.201913203] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/21/2019] [Indexed: 01/02/2023]
Abstract
Microfluidic droplet sorting enables the high-throughput screening and selection of water-in-oil microreactors at speeds and volumes unparalleled by traditional well-plate approaches. Most such systems sort using fluorescent reporters on modified substrates or reactions that are rarely industrially relevant. We describe a microfluidic system for high-throughput sorting of nanoliter droplets based on direct detection using electrospray ionization mass spectrometry (ESI-MS). Droplets are split, one portion is analyzed by ESI-MS, and the second portion is sorted based on the MS result. Throughput of 0.7 samples s-1 is achieved with 98 % accuracy using a self-correcting and adaptive sorting algorithm. We use the system to screen ≈15 000 samples in 6 h and demonstrate its utility by sorting 25 nL droplets containing transaminase expressed in vitro. Label-free ESI-MS droplet screening expands the toolbox for droplet detection and recovery, improving the applicability of droplet sorting to protein engineering, drug discovery, and diagnostic workflows.
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Affiliation(s)
| | - Michael K Wismer
- Scientific Engineering and Design, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Benjamin F Mann
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Iman Farasat
- Janssen R&D, 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Paul Devine
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Erik D Guetschow
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Ian Mangion
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | | | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Shuwen Sun
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Robert T Kennedy
- Dept. of Chemistry, University of Michigan, 930 N University, Ann Abor, MI, 48109, USA
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120
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Holland‐Moritz DA, Wismer MK, Mann BF, Farasat I, Devine P, Guetschow ED, Mangion I, Welch CJ, Moore JC, Sun S, Kennedy RT. Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913203] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michael K. Wismer
- Scientific Engineering and Design Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - Benjamin F. Mann
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Iman Farasat
- Janssen R&D 1400 McKean Rd. Spring House PA 19477 USA
| | - Paul Devine
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Erik D. Guetschow
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Ian Mangion
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | | | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Shuwen Sun
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Robert T. Kennedy
- Dept. of Chemistry University of Michigan 930 N University Ann Abor MI 48109 USA
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121
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van Loo B, Heberlein M, Mair P, Zinchenko A, Schüürmann J, Eenink BDG, Holstein JM, Dilkaute C, Jose J, Hollfelder F, Bornberg-Bauer E. High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets. ACS Synth Biol 2019; 8:2690-2700. [PMID: 31738524 DOI: 10.1021/acssynbio.9b00274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of an ultra high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure, we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Compartmentalization of the fluorescent reaction product with living E. coli cells autodisplaying the sulfatase variants ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1 variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.
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Affiliation(s)
- Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Anastasia Zinchenko
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Jan Schüürmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Bernard D. G. Eenink
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Josephin M. Holstein
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Carina Dilkaute
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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122
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Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019; 412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
Abstract
The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.
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123
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Huang R, Chen H, Upp DM, Lewis JC, Zhang YHPJ. A High-Throughput Method for Directed Evolution of NAD(P) +-Dependent Dehydrogenases for the Reduction of Biomimetic Nicotinamide Analogues. ACS Catal 2019; 9:11709-11719. [PMID: 34765284 DOI: 10.1021/acscatal.9b03840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineering flavin-free NAD(P)+-dependent dehydrogenases to reduce biomimetic nicotinamide analogues (mNAD+s) is of importance for eliminating the need for costly NAD(P)+ in coenzyme regeneration systems. Current redox dye-based screening methods for engineering the mNAD+ specificity of dehydrogenases are frequently encumbered by a background signal from endogenous NAD(P) and intracellular reducing compounds, making the detection of low mNAD+-based activities a limiting factor for directed evolution. Here, we develop a high-throughput screening method, NAD(P)-eliminated solid-phase assay (NESPA), which can reliably identify mNAD+-active mutants of dehydrogenases with a minimal background signal. This method involves (1) heat lysis of colonies to permeabilize the cell membrane, (2) colony transfer onto filter paper, (3) washing to remove endogenous NAD(P) and reducing compounds, (4) enzyme-coupled assay for mNADH-dependent color production, and (5) digital imaging of colonies to identify mNAD+-active mutants. This method was used to improve the activity of 6-phosphogluconate dehydrogenase on nicotinamide mononucleotide (NMN+). The best mutant obtained after six rounds of directed evolution exhibits a 50-fold enhancement in catalytic efficiency (k cat/K M) and a specific activity of 17.7 U/mg on NMN+, which is comparable to the wild-type enzyme on its natural coenzyme, NADP+. The engineered dehydrogenase was then used to construct an NMNH regeneration system to drive an ene-reductase catalysis. A comparable level of turnover frequency and product yield was observed using the engineered system relative to NADPH regeneration by using the wild-type dehydrogenase. NESPA provides a simple and accurate readout of mNAD+-based activities and the screening at high-throughput levels (approximately tens of thousands per round), thus opening up an avenue for the evolution of dehydrogenases with specific activities on mNAD+s similar to the levels of natural enzyme/coenzyme pairs.
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Affiliation(s)
- Rui Huang
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Hui Chen
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David M. Upp
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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124
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Droplet barcoding: tracking mobile micro-reactors for high-throughput biology. Curr Opin Biotechnol 2019; 60:205-212. [DOI: 10.1016/j.copbio.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/07/2019] [Indexed: 01/09/2023]
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125
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
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126
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Zhao Y, Zhang W, Zhao Y, Campbell RE, Harrison DJ. A single-phase flow microfluidic cell sorter for multiparameter screening to assist the directed evolution of Ca 2+ sensors. LAB ON A CHIP 2019; 19:3880-3887. [PMID: 31641712 DOI: 10.1039/c9lc00779b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a single-phase flow microfluidic cell sorter with a two-point detection system capable of two-parameter screening to assist with directed evolution of a fluorescent protein based Ca2+ sensor expressed in bacterial cells. The new cell sorting system utilizes two fluorescence microscopes to obtain signals at two different points along a flow path in which a change in concentration of the analyte, Ca2+, is induced. The two detectors thus determine the magnitude of fluorescence change of the sensor following the reaction, along with the overall brightness of the sensor. A design for a 3D focusing flow was configured to enhance the spatial control of cells and signal pair-matching. The cell sorter screens the sensors at a moderate throughput, 10 cells per s and 105 cells per round, enriching top variants for the subsequent manual screening with higher accuracy. Our new μFACS greatly accelerates the directed evolution of genetically encoded Ca2+ sensors compared to the previous version with single point detection for brightness-based screening. Two rounds of directed evolution led to a variant, named Y-GECO2f, which exhibits a 26% increase in brightness and a greater than 300% larger Ca2+-dependent fluorescence change in vitro relative to the variant before evolution.
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Affiliation(s)
- Yufeng Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Wei Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Yongxin Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada. and Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - D Jed Harrison
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
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127
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Chen J, Vestergaard M, Shen J, Solem C, Dufva M, Jensen PR. Droplet-based microfluidics as a future tool for strain improvement in lactic acid bacteria. FEMS Microbiol Lett 2019. [DOI: 10.1093/femsle/fny258s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
ABSTRACTStrain development is frequently used to improve the performance and functionality of industrially important microbes. As traditional mutagenesis screen is especially utilized by the food industry to improve strains used in food fermentation, high-throughput and cost-effective screening tools are important in mutant selection. The emerging droplet-based microfluidics technology miniaturizes the volume for cell cultivation and phenotype interrogation down to the picoliter scales, which facilitates screening of microbes for improved phenotypical properties tremendously. In this mini review, we present recent application of the droplet-based microfluidics in microbial strain improvement with a focus on its potential use in the screening of lactic acid bacteria.
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Affiliation(s)
- Jun Chen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Mike Vestergaard
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jing Shen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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128
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Jusková P, Schmid YRF, Stucki A, Schmitt S, Held M, Dittrich PS. "Basicles": Microbial Growth and Production Monitoring in Giant Lipid Vesicles. ACS APPLIED MATERIALS & INTERFACES 2019; 11:34698-34706. [PMID: 31454223 PMCID: PMC7462352 DOI: 10.1021/acsami.9b12169] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 05/03/2023]
Abstract
We present an optimized protocol to encapsulate bacteria inside giant unilamellar lipid vesicles combined with a microfluidic platform for real-time monitoring of microbial growth and production. The microfluidic device allows us to immobilize the lipid vesicles and record bacterial growth and production using automated microscopy. Moreover, the lipid vesicles retain hydrophilic molecules and therefore can be used to accumulate products of microbial biosynthesis, which we demonstrate here for a riboflavin-producing bacterial strain. We show that stimulation as well as inhibition of bacterial production can be performed through the liposomal membrane simply by passive diffusion of inducing or antibiotic compounds, respectively. The possibility to introduce as well as accumulate compounds in liposomal cultivation compartments represents great advantage over the current state of the art systems, emulsion droplets, and gel beads. Additionally, the encapsulation of bacteria and monitoring of individual lipid vesicles have been accomplished on a single microfluidic device. The presented system paves the way toward highly parallel microbial cultivation and monitoring as required in biotechnology, basic research, or drug discovery.
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Affiliation(s)
- Petra Jusková
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Yannick R. F. Schmid
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ariane Stucki
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Steven Schmitt
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Held
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Petra S. Dittrich
- Department
of Biosystems Science and Engineering, Bioanalytics Group, and Department of
Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
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129
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130
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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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131
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Chiu FWY, Stavrakis S. High-throughput droplet-based microfluidics for directed evolution of enzymes. Electrophoresis 2019; 40:2860-2872. [PMID: 31433062 PMCID: PMC6899980 DOI: 10.1002/elps.201900222] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023]
Abstract
Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.
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Affiliation(s)
- Flora W Y Chiu
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
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132
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Grösche M, Zoheir AE, Stegmaier J, Mikut R, Mager D, Korvink JG, Rabe KS, Niemeyer CM. Microfluidic Chips for Life Sciences-A Comparison of Low Entry Manufacturing Technologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901956. [PMID: 31305015 DOI: 10.1002/smll.201901956] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/12/2019] [Indexed: 06/10/2023]
Abstract
Microfluidic water-in-oil droplets are a versatile tool for biological and biochemical applications due to the advantages of extremely small monodisperse reaction vessels in the pL-nL range. A key factor for the successful dissemination of this technology to life science laboratory users is the ability to produce microfluidic droplet generators and related accessories by low-entry barrier methods, which enable rapid prototyping and manufacturing of devices with low instrument and material costs. The direct, experimental side-by-side comparison of three commonly used additive manufacturing (AM) methods, namely fused deposition modeling (FDM), inkjet printing (InkJ), and stereolithography (SLA), is reported. As a benchmark, micromilling (MM) is used as an established method. To demonstrate which of these methods can be easily applied by the non-expert to realize applications in topical fields of biochemistry and microbiology, the methods are evaluated with regard to their limits for the minimum structure resolution in all three spatial directions. The suitability of functional SLA and MM chips to replace classic SU-8 prototypes is demonstrated on the basis of representative application cases.
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Affiliation(s)
- Maximilian Grösche
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Ahmed E Zoheir
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- RWTH Aachen University, Institute of Imaging and Computer Vision, Kopernikusstraße 16, 52074, Aachen, Germany
| | - Ralf Mikut
- Karlsruhe Institute of Technology (KIT), Institute for Automation and Applied Informatics (IAI), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Dario Mager
- Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Jan G Korvink
- Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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133
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Affiliation(s)
- Yajie Wang
- Institute for Sustainability, Energy, and Environment University of Illinois at Urbana‐Champaign Urbana Illinois
| | - Xiaowei Yu
- Department of Chemical and Biomolecular Engineering University of Illinois at Urbana‐Champaign Urbana Illinois
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering University of Illinois at Urbana‐Champaign Urbana Illinois
- Department of Chemistry University of Illinois at Urbana‐Champaign Urbana Illinois
- Department of Bioengineering University of Illinois at Urbana‐Champaign Urbana Illinois
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois
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134
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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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135
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Saleski TE, Kerner AR, Chung MT, Jackman CM, Khasbaatar A, Kurabayashi K, Lin XN. Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metab Eng 2019; 54:232-243. [PMID: 31034921 DOI: 10.1016/j.ymben.2019.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 12/12/2022]
Abstract
Microbes can be engineered to synthesize a wide array of bioproducts, yet production phenotype evaluation remains a frequent bottleneck in the design-build-test cycle where strain development requires iterative rounds of library construction and testing. Here, we present Syntrophic Co-culture Amplification of Production phenotype (SnoCAP). Through a metabolic cross-feeding circuit, the production level of a target molecule is translated into highly distinguishable co-culture growth characteristics, which amplifies differences in production into highly distinguishable growth phenotypes. We demonstrate SnoCAP with the screening of Escherichia coli strains for production of two target molecules: 2-ketoisovalerate, a precursor of the drop-in biofuel isobutanol, and L-tryptophan. The dynamic range of the screening can be tuned by employing an inhibitory analog of the target molecule. Screening based on this framework requires compartmentalization of individual producers with the sensor strain. We explore three formats of implementation with increasing throughput capability: confinement in microtiter plates (102-104 assays/experiment), spatial separation on agar plates (104-105 assays/experiment), and encapsulation in microdroplets (105-107 assays/experiment). Using SnoCAP, we identified an efficient isobutanol production strain from a random mutagenesis library, reaching a final titer that is 5-fold higher than that of the parent strain. The framework can also be extended to screening for secondary metabolite production using a push-pull strategy. We expect that SnoCAP can be readily adapted to the screening of various microbial species, to improve production of a wide range of target molecules.
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Affiliation(s)
- Tatyana E Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Alissa R Kerner
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Meng Ting Chung
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Corine M Jackman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Azzaya Khasbaatar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Katsuo Kurabayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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136
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137
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Schütz SS, Beneyton T, Baret JC, Schneider TM. Rational design of a high-throughput droplet sorter. LAB ON A CHIP 2019; 19:2220-2232. [PMID: 31157806 DOI: 10.1039/c9lc00149b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The high-throughput selection of individual droplets is an essential function in droplet-based microfluidics. Fluorescence-activated droplet sorting is achieved using electric fields triggered at rates up to 30 kHz, providing the ultra-high throughput relevant in applications where large libraries of compounds or cells must be analyzed. To achieve such sorting frequencies, electrodes have to create an electric field distribution that generates maximal actuating forces on the droplet while limiting the induced droplet deformation and avoid disintegration. We propose a metric characterizing the performance of an electrode design relative to the theoretical optimum and analyze existing devices using full 3D simulations of the electric fields. By combining parameter optimization with numerical simulation we derive rational design guidelines and propose optimized electrode configurations. When tested experimentally, the optimized design show significantly better performance than the standard designs.
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Affiliation(s)
- Simon S Schütz
- Emergent Complexity in Physical Systems Laboratory (ECPS), École Polytechnique Fédérale de Lausanne (EPFL), Station 9, 1015 Lausanne, Switzerland.
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138
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Recent Advances in Droplet-based Microfluidic Technologies for Biochemistry and Molecular Biology. MICROMACHINES 2019; 10:mi10060412. [PMID: 31226819 PMCID: PMC6631694 DOI: 10.3390/mi10060412] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
Recently, droplet-based microfluidic systems have been widely used in various biochemical and molecular biological assays. Since this platform technique allows manipulation of large amounts of data and also provides absolute accuracy in comparison to conventional bioanalytical approaches, over the last decade a range of basic biochemical and molecular biological operations have been transferred to drop-based microfluidic formats. In this review, we introduce recent advances and examples of droplet-based microfluidic techniques that have been applied in biochemistry and molecular biology research including genomics, proteomics and cellomics. Their advantages and weaknesses in various applications are also comprehensively discussed here. The purpose of this review is to provide a new point of view and current status in droplet-based microfluidics to biochemists and molecular biologists. We hope that this review will accelerate communications between researchers who are working in droplet-based microfluidics, biochemistry and molecular biology.
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139
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Kan A, Joshi NS. Towards the directed evolution of protein materials. MRS COMMUNICATIONS 2019; 9:441-455. [PMID: 31750012 PMCID: PMC6867688 DOI: 10.1557/mrc.2019.28] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/22/2019] [Indexed: 05/06/2023]
Abstract
Protein-based materials have emerged as a powerful instrument for a new generation of biological materials, with many chemical and mechanical capabilities. Through the manipulation of DNA, researchers can design proteins at the molecular level, engineering a vast array of structural building blocks. However, our capability to rationally design and predict the properties of such materials is limited by the vastness of possible sequence space. Directed evolution has emerged as a powerful tool to improve biological systems through mutation and selection, presenting another avenue to produce novel protein materials. In this prospective review, we discuss the application of directed evolution for protein materials, reviewing current examples and developments that could facilitate the evolution of protein for material applications.
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Affiliation(s)
- Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Neel S. Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
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140
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Tan ZL, Zheng X, Wu Y, Jian X, Xing X, Zhang C. In vivo continuous evolution of metabolic pathways for chemical production. Microb Cell Fact 2019; 18:82. [PMID: 31088458 PMCID: PMC6518619 DOI: 10.1186/s12934-019-1132-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
Microorganisms have long been used as chemical plant to convert simple substrates into complex molecules. Various metabolic pathways have been optimised over the past few decades, but the progresses were limited due to our finite knowledge on metabolism. Evolution is a knowledge-free genetic randomisation approach, employed to improve the chemical production in microbial cell factories. However, evolution of large, complex pathway was a great challenge. The invention of continuous culturing systems and in vivo genetic diversification technologies have changed the way how laboratory evolution is conducted, render optimisation of large, complex pathway possible. In vivo genetic diversification, phenotypic selection, and continuous cultivation are the key elements in in vivo continuous evolution, where any human intervention in the process is prohibited. This approach is crucial in highly efficient evolution strategy of metabolic pathway evolution.
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Affiliation(s)
- Zheng Lin Tan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
- Laboratory of Future Interdisciplinary Research and Science Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xingjin Jian
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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141
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Žnidaršič‐Plazl P. The Promises and the Challenges of Biotransformations in Microflow. Biotechnol J 2019; 14:e1800580. [DOI: 10.1002/biot.201800580] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/11/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Polona Žnidaršič‐Plazl
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVečna pot 113, SI‐1000 Ljubljana Slovenia
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142
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Qin Y, Wu L, Wang J, Han R, Shen J, Wang J, Xu S, Paguirigan AL, Smith JL, Radich JP, Chiu DT. A Fluorescence-Activated Single-Droplet Dispenser for High Accuracy Single-Droplet and Single-Cell Sorting and Dispensing. Anal Chem 2019; 91:6815-6819. [PMID: 31050286 DOI: 10.1021/acs.analchem.9b01017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ability to sort and dispense droplets accurately is essential to droplet-based single-cell analysis. Here, we describe a fluorescence-activated single-droplet dispenser (FASD) that is analogous to a conventional fluorescence-activated cell sorter, but sorts droplets containing single cells within an oil emulsion. The FASD system uses cytometric detection and electrohydrodynamic actuation-based single-droplet manipulation, allowing droplet isolation and dispensing with high efficiency and accuracy. The system is compatible with multiwell plates and can be integrated with existing microfluidic devices and large-scale screening systems. By enabling sorting based on single-cell reactions such as PCR, this platform will help expand the basis of cell sorting from mainly protein biomarkers to nucleic acid sequences and secreted biomolecules.
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Affiliation(s)
- Yuling Qin
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jingang Wang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Rui Han
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jingyu Shen
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jiasi Wang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Shihan Xu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Amy L Paguirigan
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Jordan L Smith
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Jerald P Radich
- Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , Washington 98109 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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143
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Fluorescent nucleic acid probe in droplets for bacterial sorting (FNAP-sort) as a high-throughput screening method for environmental bacteria with various growth rates. PLoS One 2019; 14:e0214533. [PMID: 30995251 PMCID: PMC6469844 DOI: 10.1371/journal.pone.0214533] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/14/2019] [Indexed: 11/25/2022] Open
Abstract
We have developed a new method for selectively sorting droplets containing growing bacteria using a fluorescence resonance energy transfer (FRET)-based RNA probe. Bacteria and the FRET-based RNA probe are encapsulated into nanoliter-scale droplets, which are incubated to allow for cell growth. The FRET-based RNA probe is cleaved by RNase derived from the bacteria propagated in the droplets, resulting in an increase in fluorescence intensity. The fluorescent droplets containing growing bacteria are distinguishable from quenching droplets, which contain no cells. We named this method FNAP-sort based on the use of a fluorescent nucleic acid probe in droplets for bacterial sorting. Droplets containing the FRET-based RNA probe and four species of pure cultures, which grew in the droplets, were selectively enriched on the basis of fluorescence emission. Furthermore, fluorescent droplets were sorted from more than 500,000 droplets generated using environmental soil bacteria and the FRET-based RNA probe on days 1, 3, and 7 with repeated incubation and sorting. The bacterial compositions of sorted droplets differed on days 1, 3, and 7; moreover, on day 7, the bacterial composition of the fluorescent droplets was drastically different from that of the quenching droplets. We believe that FNAP-sort is useful for high-throughput cultivation and sorting of environmental samples containing bacteria with various growth rates, including slow-growing microbes that require long incubation times.
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144
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Lin GM, Warden-Rothman R, Voigt CA. Retrosynthetic design of metabolic pathways to chemicals not found in nature. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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145
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Microfluidics for cell factory and bioprocess development. Curr Opin Biotechnol 2019; 55:95-102. [DOI: 10.1016/j.copbio.2018.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022]
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146
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Scheler O, Postek W, Garstecki P. Recent developments of microfluidics as a tool for biotechnology and microbiology. Curr Opin Biotechnol 2019; 55:60-67. [DOI: 10.1016/j.copbio.2018.08.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
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147
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Ahmadi F, Samlali K, Vo PQN, Shih SCC. An integrated droplet-digital microfluidic system for on-demand droplet creation, mixing, incubation, and sorting. LAB ON A CHIP 2019; 19:524-535. [PMID: 30633267 DOI: 10.1039/c8lc01170b] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Droplet microfluidics is a technique that has the ability to compartmentalize reactions in sub nano- (or pico-) liter volumes that can potentially enable millions of distinct biological assays to be performed on individual cells. In a typical droplet microfluidic system, droplets are manipulated by pressure-based flows. This has limited the fluidic operations that can be performed in these devices. Digital microfluidics is an alternative microfluidic paradigm with precise control and manipulation over individual droplets. Here, we implement an integrated droplet-digital microfluidic (which we call 'ID2M') system in which common fluidic operations (i.e. droplet generation, cell encapsulation, droplet merging and mixing, droplet trapping and incubation, and droplet sorting) can be performed. With the addition of electrodes, we have been able to create droplets on-demand, tune their volumes on-demand, and merge and mix several droplets to produce a dilution series. Moreover, this device can trap and incubate droplets for 24 h that can consequently be sorted and analyzed in multiple n-ary channels (as opposed to typical binary channels). The ID2M platform has been validated as a robust on-demand screening system by sorting fluorescein droplets of different concentration with an efficiency of ∼96%. The utility of the new system is further demonstrated by culturing and sorting tolerant yeast mutants and wild-type yeast cells in ionic liquid based on their growth profiles. This new platform for both droplet and digital microfluidics has the potential to be used for screening different conditions on-chip and for applications like directed evolution.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada.
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148
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Hasan S, Geissler D, Wink K, Hagen A, Heiland JJ, Belder D. Fluorescence lifetime-activated droplet sorting in microfluidic chip systems. LAB ON A CHIP 2019; 19:403-409. [PMID: 30604804 DOI: 10.1039/c8lc01278d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a highly efficient microfluidic fluorescence lifetime-activated droplet sorting (FLADS) approach as a novel technology for droplet manipulation in lab-on-a-chip devices. In a proof-of-concept study, we successfully applied the approach to sort droplets containing two different fluorescent compounds on the basis of their corresponding fluorescence lifetime. Towards this end, a technical set-up was developed enabling on-the-fly fluorescence lifetime determination of passing droplets. The herein developed LabVIEW program enabled fast triggering of a downstream dielectrophoretic force sorting functionality depending on average fluorescence lifetimes of individual droplets. The approach worked reliably at individual substrate concentrations from 1 nM to 1 mM. This not only allowed reliable sorting of droplets containing species with different fluorescence lifetimes but also enabled differentiation of mixtures in individual droplets.
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Affiliation(s)
- Sadat Hasan
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany.
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149
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Haidas D, Bachler S, Köhler M, Blank LM, Zenobi R, Dittrich PS. Microfluidic Platform for Multimodal Analysis of Enzyme Secretion in Nanoliter Droplet Arrays. Anal Chem 2019; 91:2066-2073. [PMID: 30571917 DOI: 10.1021/acs.analchem.8b04506] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-throughput screening of cell-secreted proteins is essential for various biotechnological applications. In this article, we show a microfluidic approach to perform the analysis of cell-secreted proteins in nanoliter droplet arrays by two complementary methods, fluorescence microscopy and mass spectrometry. We analyzed the secretion of the enzyme phytase, a phosphatase used as an animal feed additive, from a low number of yeast cells. Yeast cells were encapsulated in nanoliter volumes by droplet microfluidics and deposited on spatially defined spots on the surface of a glass slide mounted on the motorized stage of an inverted fluorescence microscope. During the following incubation for several hours to produce phytase, the droplets can be monitored by optical microscopy. After addition of a fluorogenic substrate at a defined time, the relative concentration of phytase was determined in every droplet. Moreover, we demonstrate the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to monitor the multistep conversion of the native substrate phytic acid by phytase secreted in 7 nL droplets containing 50-100 cells. Our method can be adapted to various other protocols. As the droplets are easily accessible, compounds such as assay reagents or matrix molecules can be added to all or to selected droplets only, or part of the droplet volume could be removed. Hence, this platform is a versatile tool for questions related to cell secretome analysis.
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Affiliation(s)
- Dominik Haidas
- Department of Biosystems Science and Engineering , ETH Zürich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Simon Bachler
- Department of Biosystems Science and Engineering , ETH Zürich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Martin Köhler
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Lars M Blank
- Institute of Applied Microbiology, Aachen Biology and Biotechnology , RWTH Aachen University , Worringer Weg 1 , 52074 Aachen , Germany
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering , ETH Zürich , Mattenstrasse 26 , 4058 Basel , Switzerland
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150
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