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Open AccessArticle

Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols

1
Laboratoire Gulliver, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
2
Laboratoire CBI, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Life 2020, 10(2), 17; https://doi.org/10.3390/life10020017
Received: 6 December 2019 / Revised: 21 January 2020 / Accepted: 25 January 2020 / Published: 13 February 2020
(This article belongs to the Section Evolutionary Biology)
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. View Full-Text
Keywords: directed evolution; enrichment factor; self-selection directed evolution; enrichment factor; self-selection
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Dramé-Maigné, A.; Zadorin, A.S.; Golovkova, I.; Rondelez, Y. Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols. Life 2020, 10, 17.

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