The Sc2.0 project has set out to synthesise the Saccharomyces cerevisiae genome, with each chromosome redesigned along agreed principles. In this collection of papers, the researchers involved show how SCRaMbLE—Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution—can be used to rapidly reorganise the genome.
Synthetic biology aims to redesign and reconstruct biological systems for new, useful end goals. One of the ambitious projects currently underway is Sc2.0: the design and synthesis of a complete eukaroyotic genome - Saccharomyces cerevisiae.
This collection highlights the experimental work published in Nature Communications on redesigning the S. cerevisiae genome along with commentary from the community about the potential applications and implications of this work for synthetic biology, biotechnology and our understanding of the genome.
Commentary and Perspectives
Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.
Self-propagating drives allow for non-Mendelian inheritance. Here the authors use CRISPR to build a chromosome drive, showing elimination of entire chromosomes, endoreduplication of desired chromosomes and enabling preferential transmissions of complex genetic traits on a chromosomal scale in yeast.
Improved betulinic acid biosynthesis using synthetic yeast chromosome recombination and semi-automated rapid LC-MS screening
SCRaMbLE can lead to great genetic diversity for product biosynthesis but is limited by screening methods. Here the authors develop a rapid workflow using automation, ultra-fast LC/MS and barcoded nanopore sequencing to identify best performing strains.
Genome structural variation can play an important functional role in phenotypic diversity. Here the authors use the SCRaMbLE system on a ring synthetic chromosome V to generate complex rearrangements distinct from a rearranged linear chromosome.
The SCRaMbLE system integrated into Sc2.0’s synthetic yeast chromosome project allows rapid strain evolution. Here the authors use a genetic logic gate to control induction of recombination in a haploid and diploid yeast carrying synthetic chromosomes.
The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.
SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.
Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods
Pathway optimization and chassis engineering are usually carried out in a step-wise and trial-and-error manner. Here the authors present ’SCRaMbLE-in’ that combines in-vitro pathway rapid prototyping with in-vivo genome integration and optimization.
SCRaMbLE allows for the rapid and large scale rearrangement of genetic data in yeast carrying synthetic chromosomes. Here the authors demonstrate an in vitro use of the method to generate DNA libraries for optimization of biochemical reactions.
The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.
The International Synthetic Yeast Sc2.0 project has built Cre recombinase sites into synthetic chromosomes, enabling rapid genome evolution. Here the authors demonstrate L-SCRaMbLE, a light-controlled recombinase tool with improved control over recombination events.