Genome Combination Improvement Strategy Promotes Efficient Spinosyn Biosynthesis in Saccharopolyspora spinosa

Spinosyns are secondary metabolites produced by Saccharopolyspora spinosa known for their potent insecticidal properties and broad pesticidal spectrum. We report significant advancements in spinosyn biosynthesis achieved through a genome combination improvement strategy in S. spinosa. By integrating modified genome shuffling with ultraviolet mutation and multiomics analysis, we developed a high-yield spinosyn strain designated as YX2. The levels of most proteins and metabolites linked to primary metabolism and spinosyn biosynthesis were greater in this strain than those in S. spinosa. Based on these insights, we overexpressed 15 relevant functional genes to enhance the conversion of fatty acids into acetyl-coenzyme A. Notably, the overexpression of acd (YX2_3432) significantly increased the spinosyn yield, reaching 1120 ± 108 mg/L, which is about 12 times higher than that produced by S. spinosa. This study presents a valuable and straightforward strategy that can be broadly applied to enhance the production of secondary metabolites in actinomycetes.