Genome Combination Improvement Strategy Promotes Efficient Spinosyn Biosynthesis in <i>Saccharopolyspora spinosa</i>

Spinosyns are secondary metabolites produced by <i>Saccharopolyspora spinosa</i> 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 <i>S. spinosa</i>. 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 <i>S. spinosa</i>. 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 <i>acd</i> (YX2_3432) significantly increased the spinosyn yield, reaching 1120 ± 108 mg/L, which is about 12 times higher than that produced by <i>S. spinosa</i>. This study presents a valuable and straightforward strategy that can be broadly applied to enhance the production of secondary metabolites in actinomycetes.