Discovery and green metabolic engineering of a self-sufficient genistein pathway in Paenibacillus jilinensis

Abstract

Genistein, a plant-derived isoflavone with pharmaceutical value, is conventionally obtained through ecologically detrimental extraction processes that rely on large-scale plant harvesting and hazardous solvents. Here, we report the discovery of native genistein biosynthesis in the Paenibacillus jilinensis, which inherently produces 5.7 mg L⁻¹ genistein via the phenylalanine branch of the phenylpropanoid pathway. This pathway mirrors plant flavonoid synthesis but operates through seven bacterial enzymes (PjPAL, PjC4H, Pj4CL, PjCHS, PjCHI, PjIFS, and PjHID) with about 30% sequence homology to the corresponding protein sequences in plants, suggesting evolutionary convergence. To leverage this native capability for sustainable production, we constructed a genome-scale metabolic model (GSMM YPG26) with 1636 reactions and 717 genes to rationally optimize carbon flux. Metabolic engineering elevated genistein titers by 9.3-fold to 52.8 mg L⁻¹ without introducing heterologous plant genes. Green-chemistry analysis further showed that P. jilinensis-ΔGLN achieves 92% less waste than soybean extraction and up to one order of magnitude better than state-of-the-art E. coli and yeast systems. It is crucial that this bacterial platform requires only a basic culture medium for sustained production, and eliminates dependence on medicinal plants. Our findings reveal P. jilinensis as a naturally gifted genistein producer and a green chassis for industrial isoflavone synthesis, aligning with green chemistry goals of waste prevention and bio-based process innovation.