Development and Application of an ACQUIRE Method for Direct Cloning of Superlarge Biosynthetic Gene Cluster

Here, we developed a direct cloning method that aims to capture superlarge biosynthetic gene clusters (BGCs) (e.g., >150 kb), namely, ACQUIRE (advanced Cas12a nuclease assisted precise and quick digestion of in-gel prepared genomic DNA in combination with the transformation-associated recombination in yeast). Following the ACQUIRE method, we successfully cloned three BGCs with the size from 94 kb to 180 kb, including the rifamycin BGC (rif, ∼94 kb, GC 73%) with an efficiency of 12.8% from the actinomycete Amycolatopsis mediterranei U32 and one superlarge polyketide synthase BGC (∼180 kb, GC 73%, with efficiency of ∼1.6%) from Amycolatopsis pretoriensis Y0289. Subsequently, we introduced the rif BGC into A. mediterranei U32 and generated high rifamycin producers. Therefore, the ACQUIRE method developed here greatly complements the current direct cloning toolbox and has an advantage to capture superlarge BGCs that can be harnessed for enhancement of antibiotic production or for genome mining of new natural products.