Systemic engineering and global regulation enabling high-level bilirubin biosynthesis

Bilirubin biosynthesis has long been constrained by low yields and poorly understood bottlenecks. Here, we report a fully in vitro pathway that converts heme to bilirubin with the titer of 1.7 g/L and 95.8%. Systematically, enzyme screening and mechanistic analysis reveal the hidden challenge: Fe²⁺-induced oxidative degradation of intermediates. We show that Fe²⁺ coordinates with deprotonated intermediates to trigger oxidative ring-opening degradation via O₂-mediated radical mechanism, as supported by DFT calculations indicating reduced HOMO-LUMO gap in Fe²⁺-ligand complexes. The degradation is mitigated through competitive iron chelation and protonation state modulation, improving yield to 80.1%. Furthermore, we have resolved heme-CO complexes blocking O₂ activation at heme oxygenase by introducing a carbon monoxide dehydrogenase to remove CO and restore enzyme activity. Coupled with NADPH-recycling via formate dehydrogenase, these interventions enable efficient, scalable bilirubin synthesis with a 20-fold improvement. Our work shows controlling inhibitory byproducts is critical for stabilizing heme-related pathways and as a generalizable framework for synthetic biology.