Context and control in modular synthetic genomes
The international project to construct a synthetic version of the yeast genome (Sc2.0) has been one of the highest visibility research projects in synthetic biology in the last decade. As this draws to a close, Sc2.0 partners are now beginning to use the tools and knowledge of synthetic yeast genome assembly to ask new questions of biology and genomics, and develop new biotechnologies. As a milestone towards custom, modular genome, we are now using synthetic genome workflows with multiplex CRISPR to examine and exploit Synthetic Genome Modules (SGMs), where sets of genes that encode a common function are relocated from their native genomic loci into new synthetic defragmented or refactored gene clusters in the chromosomes. Following success using our SGM method to fine-tune pheromone sensing for biosensor cells, we are now employing it to the explore the minimal gene set for the cell cycle. This new work is revealing how changes in the genomic context of a gene can lead to changes in its expression levels and alter the regulatory control it has within a complex gene network. This highlights the importance of choosing the correct arrangements of genes when designing synthetic chromosomes, offering a new challenge for developing ‘design rules’. As well as gene arrangement, gene content is also critical for synthetic genomes, and using our cell cycle SGM we are able to use combinatorial screening to determine the minimal gene content for robust function.