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Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols.

ABSTRACT: 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.

SUBMITTER: Drame-Maigne A

PROVIDER: S-EPMC7175308 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols.

Dramé-Maigné Adèle A Zadorin Anton S AS Golovkova Iaroslava I Rondelez Yannick Y

Life (Basel, Switzerland) 20200213 2

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 activ ...[more]

PMID: 32069848

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