Enhancing and stabilizing a high-yield industrial Rhodobacter sphaeroides strain for coenzyme Q 10 production

Abstract Strengthening high-yield phenotypes while maintaining physiological and genetic stability presents a significant challenge in the improvement of high-yield industrial strains (HIS). Coenzyme Q 10 (CoQ 10 ), a crucial quinone electron carrier in the electron transport chain, is widely used in the prevention and treatment of cardiovascular diseases. In this study, the established HIS Rhodobacter sphaeroides HY01, employed for CoQ 10 production, was engineered to enhance productivity while ensuring strain stability. Comparative omics identified the PrrAB two-component system as an oxygen-responsive regulator that links CoQ 10 biosynthesis to photosynthetic pathways. Mutagenesis of PrrA, guided by AlphaFold3 modeling and fluorescence screening, introduced mutations that led to a 37.5% increase in CoQ 10 production. To address phenotypic reversion due to metabolic burden, genome-scale CRISPR interference (CRISPRi) screening identified key genes involved in DNA repair and stress adaptation. Deletions of these genes generated a stable strain that achieved 3.6 g/L CoQ 10 in a 50- L pilot-scale fed-batch fermentation, surpassing previous reports. This study reveals PrrAB-mediated flux partitioning for redox homeostasis and provides a framework for stabilizing burdened phenotypes in photosynthetic microbes, advancing the sustainable production of redox-active metabolites. Bullet points Identified the PrrAB two-component system as a critical global regulator of CoQ 10 biosynthesis in Rhodobacter sphaeroides . PrrA was evolved through fluorescence-based screening and rational protein engineering, significantly enhancing CoQ 10 biosynthesis in industrial high-yield strain. Genome-scale CRISPRi screening identified genes affecting R. sphaeroides HY01 stability enabling targeted modifications to stabilize high-yield CoQ 10 phenotype. Achieved record 3.6 g/L CoQ 10 yield in 50-L pilot-scale bioreactors enhancing microbial productivity stabilizing high-yield phenotypes advancing strain engineering.