Reconstructing the hydrogenobyrinic acid synthetic toolkit by combining cell-free systems and metabolic engineering

Hydrogenobyrinic acid (HBA) is a pivotal intermediate in the aerobic biosynthesis of cobalamin (vitamin B12), representing a stable, metal-free corrin precursor and a useful substrate for both biological and chemical derivatization. Despite its significance, efficient HBA production remains limited by the complexity of the native cobalamin pathway, which involves more than 30 enzymatic steps and tightly regulated gene clusters. In this study, we combined in vivo metabolic engineering and in vitro multienzyme screening to design, optimize, and validate an artificial HBA operon. A systematic strategy was employed to identify pathway bottlenecks by tuning ribosome-binding sites and introducing isoenzymes in Escherichia coli, followed by cell-free prototyping to further analyze and enhance catalytic steps. Integration of the two approaches revealed that the downstream enzymes CobF, CobK, CobL, and CobH are critical determinants of HBA yield. Guided by this insight, we constructed an optimized artificial operon (FKLHIGJM), which demonstrated superior performance both in whole-cell fermentation and in cell-free systems. Furthermore, we established a simple and efficient HBA biosynthetic platform in vitro using crude cell extracts derived from our optimized HBA operon, achieving an HBA titer of 37.01 ± 0.94 μM (32.59 ± 0.83 mg/L) HBA within 12 h. This performance represents a 12.2-fold improvement over the titer obtained with the originally designed operon in our initial cell-free system, and a 214.5-fold enhancement compared with the titer produced by recombinant E. coli fermentation using the originally designed operon. This work highlights the value of coupling metabolic engineering with cell-free strategies to advance artificial pathway design and sustainable cobalamin precursor production.