A quorum sensing-controlled type I CRISPRi toolkit for dynamically regulating metabolic flux

Abstract Synthetic biology advances have enabled dynamic metabolic regulation via quorum sensing (QS) and CRISPR systems. However, the integration of QS with CRISPR-based systems for dynamic control remains largely underexplored. Here, we developed a QS-controlled type I CRISPR interference (QICi) toolkit that modulates target gene expression in response to cell density. By streamlining CRISPR RNA (crRNA) vector construction and optimizing key QS components PhrQ and RapQ, we achieved a twofold enhancement in QICi efficacy. We subsequently implemented the optimized QICi to reprogram Bacillus subtilis for d-pantothenic acid (DPA) and riboflavin (RF) biosynthesis. Dynamic regulation of the citrate synthase gene citZ by QICi, coupled with pantoate pathway engineering, cofactor supply enhancement, and suppression of sporulation, elevated DPA titers to 14.97 g/l in 5-l fed-batch fermentations without precursor supplementation. QICi-mediated metabolic rewiring of key nodes boosted RF production by 2.49-fold. Together, our work provides a robust tool for reprogramming microbial metabolism and advancing sustainable biomanufacturing.