Systematic CRISPRi screening reveals genetic modulators of E. coli isoprenoid production
Isoprenoid biosynthesis in E. coli is a promising source of high-value natural products. However, isoprenoid production imposes a substantial metabolic burden on cellular carbon and cofactor metabolism. In this project we used CRISPR interference (CRISPRi) with mismatched single guide RNAs (sgRNAs) to identify genes that modulate lycopene production (and upstream isoprenoid biosynthesis). Our method uses next generation sequencing to identify sgRNAs across hundreds of colonies picked into 96 well plates. This allows mapping of gene knockdown to biosynthetic phenotype with good throughput. In the context of our screen, genes whose repression increased lycopene yield were found across fatty acid, amino acid, central carbon, and isoprenoid metabolism as well as stress response pathways. This SRA project contains the NGS short read amplicon data used for sgRNA identification.