NSF-SNSF: Continuous evolution of artificial catalysts into life-sustaining enzymes

University Of California-Irvine, Irvine CA

Investigators

Abstract

This project will use a state-of-the-art rapid gene evolution system to change relatively simple enzymes into enzymes with advanced capabilities that extend beyond those found in nature. In doing this, this project will help us understand how enzymes upgrade their performance over long periods of time, provide blueprints for enzyme design, and contribute to synthetic biology, and potentially biotechnology, medicine, agriculture and the bioeconomy. Like most processes involving long natural evolutionary timescales, the emergence of complex enzymes from what were presumably simple biocatalysts early in life's history has not been directly observed. The investigators have developed a powerful synthetic evolution system called orthogonal DNA replication (OrthoRep) that drives the in vivo continuous evolution of chosen genes at mutation rates one million-fold higher than those of the host genome. OrthoRep compresses gene evolution processes that naturally take thousands to millions of years into weeks-long laboratory experiments involving just the passaging of cells. The investigators propose using OrthoRep to prospectively evolve “simple” primitive catalysts into “advanced” biological enzymes. The simple catalysts from which we will start evolution are artificial metalloenzymes (ArMs), chosen because they mimic the putative organization of primordial enzymes in early life where catalytic performance is predominantly localized to a cofactor attached to a protein scaffold. They will evolve ArMs into advanced enzymes, guided by the hypothesis that the evolutionary emergence and optimization of interconnected amino acid networks coupling the active site to sectors across an entire protein is responsible for the exceptional performance of modern enzymes. This collaborative US/Switzerland project is supported by the US National Science Foundation (NSF) and the Swiss National Science Foundation (S-NSF), where NSF funds the US investigator and S-NSF funds the partners in Switzerland. Within NSF, the project is co-funded by Office of International Science and Engineering, and the Systems and Synthetic Biology Program in the Division of Molecular and Cellular Biosciences. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.