Development of gene silencing with dCas13d in Streptomyces spp.

After the end of the antibiotic “Golden Age”, the discovery of antimicrobial natural products with unique mechanisms of actions has drastically decreased while at the same time antimicrobial resistance has been on the rise. Advancements in next-generation sequencing has unlocked hundreds of thousands of microbial genomes, offering the opportunities to study some of the most prolific antibiotic-producing taxa such as Streptomyces spp. in greater detail. To fully capitalise on this potential, robust functional genomics tools are essential for developing our understanding of these powerful organisms.

Existing functional genomics tools for Streptomyces spp. are effective but are not without flaws. Recently, dCas13d, a programmable, RNA-targeting Cas protein has emerged as a promising candidate for genetic study with the ability to knock down an individual gene at the translational level, showing a reduced impact on other genes present within an operon. This work lays the foundation for establishing dCas13d in Streptomyces albidoflavus J1074 by constructing the first integrative, customisable and codon optimised dCas13d plasmid and confirming its activity against an artificial gene. Although further study is needed, it is possible that dCas13d may become a key component of the Streptomyces spp. functional genomics toolkit in the future.