A CRISPR-Cas9 System for Knock-out and Knock-in of High Molecular Weight DNA Enables Module-Swapping of the Pikromycin Synthase in its Native Host

Background: Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA. Results: We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI - pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin. Conclusion: Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.