Convenient synthesis and delivery of a megabase-scale designer accessory chromosome empower biosynthetic capacity.

Synthetic biology confers new functions to hosts by introducing exogenous genetic elements, yet rebuilding complex traits that are based on large-scale genetic information remains challenging. Here, we developed a CRISPR/Cas9-mediated haploidization method that bypasses the natural process of meiosis. Based on the programmed haploidization in yeast, we further developed an easy-to-use method designated HAnDy (Haploidization-based DNA Assembly and Delivery in yeast) that enables efficient assembly and delivery of large DNA, with no need for any fussy in vitro manipulations. Using HAnDy, a de novo designed 1.024 Mb synthetic accessory chromosome (synAC) encoding 542 exogenous genes was parallelly assembled and then directly transferred to six phylogenetically diverse yeasts. The synAC significantly promotes hosts' adaptations and increases the scope of the metabolic network, which allows the emergence of valuable compounds. Our approach should facilitate the assembly and delivery of large-scale DNA for expanding and deciphering complex biological functions.

Enhancement and mapping of tolerance to salt stress and 5-fluorocytosine in synthetic yeast strains via SCRaMbLE.

Varied environmental stress can affect cell growth and activity of the cellular catalyst. Traditional path of adaptive evolution generally takes a long time to achieve a tolerance phenotype, meanwhile, it is a challenge to dissect the underlying genetic mechanism. Here, using SCRaMbLE, a genome scale tool to generate random structural variations, a total of 222 evolved yeast strains with enhanced environmental tolerances were obtained in haploid or diploid yeasts containing six synthetic chromosomes. Whole genome sequencing of the evolved strains revealed that these strains generated different structural variants. Notably, by phenotypic-genotypic analysis of the SCRaMbLEd strains, we find that a deletion of gene YFR009W (GCN20) can improve salt tolerance of Saccharomyces cerevisiae, and a deletion of gene YER056C can improve 5-flucytosine tolerance of Saccharomyces cerevisiae. This study shows applications of SCRaMbLE to accelerate phenotypic evolution for varied environmental stress and to explore relationships between structural variations and evolved phenotypes.