Deletion of bikaverin and fusarubin biosynthesis gene clusters via CRISPR/Cas9 system in Fusarium fujikuroi and its effect on GA3 biosynthesis

Gibberellic acid (GA3) is a critical plant hormone with significant agricultural applications, yet its production in Fusarium fujikuroi is constrained by competition for metabolic precursors, particularly acetyl-CoA, which is essential for GA3 biosynthesis. The genome of F. fujikuroi harbors numerous secondary metabolite biosynthetic gene clusters that divert acetyl-CoA away from the GA3 pathway, thereby limiting its yield. To address this challenge, we employed the CRISPR/Cas9 system to delete the bikaverin and fusarubin biosynthesis gene clusters, which are known to compete with GA3 biosynthesis for acetyl-CoA. This genetic intervention resulted in a substantial increase in GA3 production, with the ΔBIKΔFSR strain yielding 31.67 % more GA3 compared to the wild-type strain. Notably, the deletion of these gene clusters not only enhanced GA3 biosynthesis but also improved mycelial growth and carbon assimilation, as evidenced by increased consumption of reducing sugars during fermentation. We further employed qRT-PCR to assess comparative expression levels of genes associated with the glycohydrolysis, glycolysis, and the TCA pathway in engineered strain. Results indicated that removing by-product gene clusters enhances the glycohydrolase system, accelerating carbon assimilation. Given the presence of dozens of secondary metabolite biosynthetic gene clusters in the F. fujikuroi genome, the strategy reported here offers a promising avenue for further enhancing GA3 production by targeting additional non-essential gene clusters.