Development of a genome-reduced Escherichia coli chassis for highly efficient biochemical production

Abstract

Synthetic biology aims to design and construct biological system with novel and better functionalities. One fascinating approach to accomplish the goal is a streamlined genome, often referred as minimal genome, with fewer number of non-essential genes. A number of Escherichia coli strains harboring minimal genomes have been constructed by sequential genome reduction mostly without growth retardation in rich media. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. However, when genome-reduced strains are grown in minimal medium, their growth rate is often reduced. The decreased growth rate has been attributed to our limited understanding of some bacterial genome processes, such as synthetic lethality and interactions between interconnected cellular components, making it difficult to be applied in practical use. In this study, I utilized systems biology approach to re-optimize growth performance of a genome-reduced E. coli and developed an efficient chassis for efficient bio-production using a novel synthetic biology tool. First, I deployed adaptive laboratory evolution (ALE) to allow re-optimization of the perturbations during genome reduction. The evolved strain exhibited a comparable growth rate to wild-type E. coli. Next, multi-omic analysis of the evolved strain was performed to elucidate the cause of growth retardation and design principles for downstream applications. The analysis revealed transcriptome- and translatome-wide changes that remodel metabolism and growth. Lastly, I developed a novel synthetic biology tool and implemented it into the evolved strain to improve bio-production. The engineered strain showed superior capability of producing various biochemicals and proteins than other E. coli strains. Taken together, the comprehensive analysis of a genome-reduced strain provides valuable insight for cellular design and the engineered genome-reduced strain is a promising chassis for biochemical production.