scholarly journals Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols

Life ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 17
Author(s):  
Adèle Dramé-Maigné ◽  
Anton S. Zadorin ◽  
Iaroslava Golovkova ◽  
Yannick Rondelez
Keyword(s):  
Directed Evolution ◽  
High Throughput ◽  
Quality Index ◽  
Selection Mechanisms ◽  
Self Replication ◽  
Initial Fraction

High-throughput, in vitro approaches for the evolution of enzymes rely on a random micro-encapsulation to link phenotypes to genotypes, followed by screening or selection steps. In order to optimise these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants of a library. Here, we introduce a new metric, the Selection Quality Index (SQI), which can be computed from a simple mock experiment, performed with a known initial fraction of active variants. In contrast to previous approaches, our index integrates the effect of random co-encapsulation, and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general protocol efficiency trends or reveal hidden selection mechanisms such as a counterintuitive form of beneficial poisoning in the compartmentalized self-replication protocol.

scholarly journals A Flow Cytometry–Based Screening System for Directed Evolution of Proteases

2011 ◽  
Vol 16 (3) ◽  
pp. 285-294 ◽  
Author(s):  
Ran Tu ◽  
Ronny Martinez ◽  
Radivoje Prodanovic ◽  
Mathias Klein ◽  
Ulrich Schwaneberg
Keyword(s):  
Flow Cytometry ◽  
Directed Evolution ◽  
High Throughput ◽  
Double Emulsion ◽  
Catalytic Efficiency ◽  
Small Population ◽  
Subtilis Strain ◽  
Screening System ◽  
Screening Technology

Proteases are industrially important enzymes but often have to be improved for their catalytic efficiency and stabilities to suit applications. Flow cytometry screening technology based on in vitro compartmentalization in double emulsion had been developed and applied on directed evolution of paraoxonase and β-galactosidase. Further advancements of flow cytometry–based screening technologies will enable an ultra-high throughput of variants offering novel opportunities in directed enzyme evolution under high mutational loads. For the industrially important enzyme class of proteases, a first flow cytometry–based screening system for directed protease evolution has been developed based on an extracellular protease-deficient Bacillus subtilis strain (WB800N), a model protease (subtilisin Carlsberg), and a water-in-oil-in-water double-emulsion technology. B. subtilis WB800N cells are encapsulated in double emulsion with a fluorogenic substrate (rhodamine 110–containing peptide), allowing the screening of protease variants in femtoliter compartments at high throughput. The protease screening technology was validated by employing an epPCR mutant library with a high mutational load and screened for increased resistance toward the inhibitor antipain dihydrochloride. A variant (K127R, T237P, M239I, I269V, Y310F, I372V) with an improved relative resistance was isolated from a small population of active variants, validating the reported protease flow cytometry screening technology for increased inhibitor resistance.

scholarly journals Directed Evolution of Enzymes based on in vitro Programmable Self-Replication

2021 ◽  
Author(s):  
Adèle Dramé-Maigné ◽  
Rocio Espada ◽  
Giselle McCallum ◽  
Rémi Sieskind ◽  
Yannick Rondelez
Keyword(s):  
Directed Evolution ◽  
Feedback Loop ◽  
Enzyme Engineering ◽  
Molecular Networks ◽  
Individual Variant ◽  
Activity Screening ◽  
Nicking Enzyme ◽  
Self Replication

High-throughput directed evolution, implemented in well-controlled in vitro conditions, provides a powerful route for enzyme engineering. Most existing technologies are based on activity screening and require the sequential observation and sorting of each individual variant. By contrast, approaches based on autonomous feedback loops, linking phenotype to genotype replication, enable autonomous selection without screening. However, these approaches are only possible in vivo, or applicable to very specific activities, such as polymerases or ligases. Here, we leverage synthetic molecular networks to create a programmable in vitro feedback loop linking a target enzymatic activity to gene amplification. After encapsulation and lysis of up to 10^7 transformed variants, the genes present in each droplet are amplified according to the activity of the encoded enzyme, resulting in the autonomous enrichment of interesting sequences. Applied to a nicking enzyme with thermal or kinetic selection pressures, this method reveals detailed mutational landscapes and provides improved variants.

scholarly journals In vitro optoacoustic flow cytometry with light scattering referencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Markus Seeger ◽  
Andre C. Stiel ◽  
Vasilis Ntziachristos
Keyword(s):  
Light Scattering ◽  
Directed Evolution ◽  
High Throughput ◽  
High Throughput Screening ◽  
Single Cells ◽  
Light Flux ◽  
Focal Volume ◽  
Optoacoustic Imaging ◽  
Excitation Light

AbstractMorphological and functional optoacoustic imaging is enhanced by dedicated transgene reporters, in analogy to fluorescence methods. The development of optoacoustic reporters using protein engineering and directed evolution would be accelerated by high-throughput in-flow screening for intracellular, genetically encoded, optoacoustic contrast. However, accurate characterization of such contrast is impeded because the optoacoustic signals depend on the cell’s size and position in the flow chamber. We report herein an optoacoustic flow cytometer (OA-FCM) capable of precise measurement of intracellular optoacoustic signals of genetically-encoded chromoproteins in flow. The novel system records light-scattering as a reference for the detected optoacoustic signals in order to account for cell size and position, as well as excitation light flux in the focal volume, which we use to reference the detected optoacoustic signals to enhance the system’s precision. The OA-FCM was calibrated using micrometer-sized particles to showcase the ability to assess in-flow objects in the size range of single-cells. We demonstrate the capabilities of our OA-FCM to identify sub-populations in a mixture of two E. coli stocks expressing different reporter-proteins with a precision of over 90%. High-throughput screening of optoacoustic labels could pave the way for identifying genetically encoded optoacoustic reporters by transferring working concepts of the fluorescence field such as directed evolution and activated cell sorting.

New Imidazole Inhibitors of Mycobacterial FtsZ: the Way from High-Throughput Molecular Screening in Grid up to in vitro Verification

2016 ◽  
Vol 12 (3) ◽  
pp. 43-55 ◽  
Author(s):  
P.A. Karpov ◽  
◽  
O.M. Demchuk ◽  
V.M. Britsun ◽  
D.I. Lytvyn ◽  
...  
Keyword(s):  
High Throughput ◽  
Molecular Screening ◽  
The Way

Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity

2019 ◽  
Author(s):  
Huifang Xu ◽  
Weinan Liang ◽  
Linlin Ning ◽  
Yuanyuan Jiang ◽  
Wenxia Yang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Fatty Acid ◽  
Directed Evolution ◽  
High Throughput ◽  
High Throughput Screening ◽  
Colorimetric Detection ◽  
Screening Method ◽  
Random Mutagenesis ◽  
Direct Production ◽  
Consumption Activity

P450 fatty acid decarboxylases (FADCs) have recently been attracting considerable attention owing to their one-step direct production of industrially important 1-alkenes from biologically abundant feedstock free fatty acids under mild conditions. However, attempts to improve the catalytic activity of FADCs have met with little success. Protein engineering has been limited to selected residues and small mutant libraries due to lack of an effective high-throughput screening (HTS) method. Here, we devise a catalase-deficient <i>Escherichia coli</i> host strain and report an HTS approach based on colorimetric detection of H<sub>2</sub>O<sub>2</sub>-consumption activity of FADCs. Directed evolution enabled by this method has led to effective identification for the first time of improved FADC variants for medium-chain 1-alkene production from both DNA shuffling and random mutagenesis libraries. Advantageously, this screening method can be extended to other enzymes that stoichiometrically utilize H<sub>2</sub>O<sub>2</sub> as co-substrate.

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