Exploring sequence space in search of functional enzymes using microfluidic droplets.

Screening of enzyme mutants in monodisperse picoliter compartments, generated at kilohertz speed in microfluidic devices, is coming of age. After a decade of proof-of-principle experiments, workflows have emerged that combine existing microfluidic modules to assay reaction progress quantitatively and yield improved enzymes. Recent examples of the screening of libraries of randomised proteins and from metagenomic sources suggest that this approach is not only faster and cheaper, but solves problems beyond the feasibility scope of current methodologies. The establishment of new assays in this format - so far covering hydrolases, aldolases, polymerases and dehydrogenases - will enable the exploration of sequence space for new catalysts of natural and non-natural chemical transformations.

[1]  A. Griffiths,et al.  Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms. , 2014, Chemistry & biology.

[2]  A. Hatch,et al.  A general strategy for expanding polymerase function by droplet microfluidics , 2016, Nature Communications.

[3]  C. A. Smith,et al.  High-throughput screening of antibiotic-resistant bacteria in picodroplets. , 2016, Lab on a chip.

[4]  A. deMello,et al.  Ultrafast surface enhanced resonance Raman scattering detection in droplet-based microfluidic systems. , 2011, Analytical chemistry.

[5]  Fabienne Courtois,et al.  Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. , 2012, Chemistry & biology.

[6]  Florian Hollfelder,et al.  Microfluidic droplets: new integrated workflows for biological experiments. , 2010, Current opinion in chemical biology.

[7]  Alexander K. Price,et al.  hνSABR: Photochemical Dose–Response Bead Screening in Droplets , 2016, Analytical chemistry.

[8]  D. Baker,et al.  Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase , 2016, Nature Chemistry.

[9]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

[10]  Donald Hilvert,et al.  Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code , 2013, PLoS genetics.

[11]  R. Daniel,et al.  Metagenomic Analyses: Past and Future Trends , 2010, Applied and Environmental Microbiology.

[12]  Rafael Bargiela,et al.  Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends , 2015, Microbial biotechnology.

[13]  Karl-Erich Jaeger,et al.  Alternative hosts for functional (meta)genome analysis , 2014, Applied Microbiology and Biotechnology.

[14]  D. Weitz,et al.  Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity. , 2009, Lab on a chip.

[15]  R. Jensen Enzyme recruitment in evolution of new function. , 1976, Annual review of microbiology.

[16]  J. Nielsen,et al.  High-throughput screening for industrial enzyme production hosts by droplet microfluidics. , 2014, Lab on a chip.

[17]  Martin Fischlechner,et al.  One in a Million: Flow Cytometric Sorting of Single Cell-Lysate Assays in Monodisperse Picolitre Double Emulsion Droplets for Directed Evolution , 2014, Analytical chemistry.

[18]  E. Rees,et al.  Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets , 2017, Analytical chemistry.

[19]  Andrew D Griffiths,et al.  Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions , 2015, RNA.

[20]  Peter Karuso,et al.  Fluorescence anisotropy assay for the traceless kinetic analysis of protein digestion. , 2008, Analytical chemistry.

[21]  Alison M Stuart,et al.  Single-Fluorophore Detection in Femtoliter Droplets Generated by Flow Focusing. , 2015, ACS nano.

[22]  Martin Fischlechner,et al.  Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS) , 2016, Proceedings of the National Academy of Sciences.

[23]  A. Griffiths,et al.  High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics , 2016, Scientific Reports.

[24]  Yolanda Schaerli,et al.  Evolution of enzyme catalysts caged in biomimetic gel-shell beads. , 2014, Nature chemistry.

[25]  Adam Sciambi,et al.  Accurate microfluidic sorting of droplets at 30 kHz. , 2015, Lab on a chip.

[26]  F. Hollfelder,et al.  Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics , 2015, Nature Communications.

[27]  Donald Hilvert,et al.  A simple selection strategy for evolving highly efficient enzymes , 2007, Nature Biotechnology.

[28]  Miles A. Miller,et al.  Single cell multiplexed assay for proteolytic activity using droplet microfluidics. , 2016, Biosensors & bioelectronics.

[29]  Moritz Pott,et al.  Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting. , 2017, Protein engineering, design & selection : PEDS.

[30]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[31]  Philippe Marlière,et al.  Chemical evolution of a bacterium's genome. , 2011, Angewandte Chemie.

[32]  Huabing Yin,et al.  Raman-activated cell sorting based on dielectrophoretic single-cell trap and release. , 2015, Analytical chemistry.

[33]  Andrew D Griffiths,et al.  A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. , 2012, Lab on a chip.

[34]  Dick B Janssen,et al.  Quantifying the accessibility of the metagenome by random expression cloning techniques. , 2004, Environmental microbiology.

[35]  Jiseok Lim,et al.  Controlling molecular transport in minimal emulsions , 2016, Nature Communications.

[36]  Richard Wolfenden,et al.  Catalytic proficiency: the extreme case of S-O cleaving sulfatases. , 2012, Journal of the American Chemical Society.

[37]  David Baker,et al.  Evolution of a designed retro-aldolase leads to complete active site remodeling , 2013, Nature chemical biology.

[38]  D. Herschlag,et al.  Catalytic promiscuity and the evolution of new enzymatic activities. , 1999, Chemistry & biology.

[39]  Radivoje Prodanovic,et al.  A high-throughput cellulase screening system based on droplet microfluidics. , 2014, Biomicrofluidics.

[40]  Daniel Bratton,et al.  Development of quantitative cell-based enzyme assays in microdroplets. , 2008, Analytical chemistry.

[41]  M. Figge,et al.  Real-time image processing for label-free enrichment of Actinobacteria cultivated in picolitre droplets. , 2013, Lab on a chip.