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Rapid Mutation & Continuous Directed Evolution in Vivo; Continuous Directed Evolution

Ahmed Badran
Broad Institute of MIT and Harvard
Primer: Impact of Mutagenesis Efficiency and Selection Stringency Modulation During Continuous Directed Evolution

Abstract: The development and application of methods for the laboratory evolution of biomolecules has rapidly progressed over the last few decades. Advancements in continuous microbe culturing and selection design have facilitated the development of new technologies that enable the continuous directed evolution of proteins and nucleic acids. These technologies have the potential to support the extremely rapid evolution of biomolecules with tailor-made functional properties. Continuous evolution methods must support all of the key steps of laboratory evolution — translation of genes into gene products, selection or screening, replication of genes encoding the most fit gene products, and mutation of surviving genes — in a self-sustaining manner that requires little or no researcher intervention. In this presentation, I will describe the basis and applications of our Phage-Assisted Continuous Evolution (PACE) platform, focusing on the impact of mutagenesis efficiency and selection stringency modulation during directed evolution campaigns. Through these tools, we aspire to enable researchers to address increasingly complex biological questions and to access biomolecules with novel or even unprecedented properties.

Chang Liu 
UC Irvine
Meeting: Synthetic Genetic Systems for Rapid Mutation and Continuous Evolution in vivo

Abstract: We are interested in building genetic systems that have extremely high mutation rates in order to speed up the evolution of target proteins and enzymes in vivo as well as to record transient information, such as lineage relationships or exposure to biological stimuli, as durable genetic information in situ. I will primarily discuss our work on building OrthoRep, a highly error-prone orthogonal DNA replication system that mutates user-selected genes at a base pair substitution (bps) rate of 1e-5 without any increase in the genomic mutation rate (1e-10 bps). This ~100,000-fold mutational acceleration allows for the rapid continuous evolution of target biomolecules entirely in vivo using a simple serial passaging process amenable to extensive repetition. I will discuss the application of OrthoRep in exploring drug resistance and evolving useful enzymes and proteins. I will also comment on the value of scalable continuous evolution in searching for and understanding old and new biomolecular function.