Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments

ABSTRACT Protein engineering aims to find top functional sequences in a vast design space. For such an expensive “black-box” function optimization problem, Bayesian optimization is a principled sample-efficient approach, which is guided by a surrogate model of the objective function. Unfortunately, Bayesian optimization is computationally intractable with the vast search space. Even worse, it proposes sequences sequentially, making it incompatible with batched wet-lab measurement. Here, we report a scalable and batched method, Bayesian Optimization-guided EVOlutionary (BO-EVO) algorithm, to guide multiple rounds of robotic experiments to explore protein fitness landscapes of combinatorial mutagenesis libraries. We first examined various design specifications based on an empirical landscape of protein G domain B1. Then, BO-EVO was successfully generalized to another empirical landscape of an Escherichia coli kinase PhoQ, as well as simulated NK landscapes with up to moderate epistasis. This approach was then applied to guide robotic library creation and screening to engineer enzyme specificity of RhlA, a key biosynthetic enzyme for rhamnolipid biosurfactants. A 4.8-fold improvement in producing a target rhamnolipid congener was achieved after examining less than 1% of all possible mutants after 4 iterations. Overall, BO-EVO proves to be an efficient and general approach to guide combinatorial protein engineering without prior knowledge.