Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed “SCRaMbLE-in”) to tackle both challenges simultaneously. SCRaMbLE-in includes an in-vitro recombinase toolkit to rapid prototype and diversify gene expression at the pathway level and an in-vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis. A set of loxP mutant pairs was identified to maximize the efficiency of the in-vitro diversification. Exemplar pathways of β-carotene and violacein were successfully assembled, diversified and integrated using this SCRaMbLE-in method. High throughput sequencing was performed on selected engineered strains to reveal the resulting genotype-to-phenotype relationships. The SCRaMbLE-in method proves to be a rapid, efficient and universal method to fast track the cycle of engineering biology.