A CRISPR interference platform for functional genomics in Streptomyces species

Antimicrobial resistance is a global problem and the majority of antibiotics are based on microbial natural products produced by Streptomyces bacteria. Although the first genome sequence for a Streptomyces species became available in 2002, a tenable approach for conducting genome-wide functional genomic studies still does not exist. The fact that such a basic line of scientific inquiry is still not possible is a major roadblock preventing high-level study of these industrially important microorganisms.

In this project, you will use CRISPR interference on a genome-wide scale. You will design and construct a library of CRISPRi sgRNA clones and move the library to S. albidoflavus, monitoring library construction and entry into S. albidoflavus by Illumina amplicon sequencing. You have an opportunity to learn the ‘rules of life’ for Streptomyces species by using your sgRNA library to assess gene essentiality, which will involve calculating a fitness score for each gene, which is based on the abundance of sgRNA sequences determined by Illumina amplicon sequence. At the end of the project, you will become an expert in CRISPR biology and the analysis of next generation sequencing data. The platform you construct will enable enhanced strain breeding, making medicines less expensive and more widely available.