Engineering substrate channeling with synthetic biomolecular condensates for improved ectoine biosynthesis

Ectoine is a compatible solute originally discovered in desert microorganisms and serves as a key weapon for microbes to cope with extreme environmental threats, such as drought and high salinity. Owing to its exceptional water-binding capacity and protective properties, ectoine is extensively used in biomedicine, cosmetics, and industrial biocatalysis. To overcome the efficiency bottleneck of heterologous ectoine biosynthesis in non-halophilic strains, we introduced a synthetic biomolecular condensate system that has been successfully employed in protein overexpression to enhance ectoine formation in pathways constructed with biosynthetic ancestral enzymes in the engineering of Vibrio natriegens. First, the ancestral core metabolic enzymes EctA, EctB, and EctC were reconstructed using an integrated bioinformatics process, and the selected ancestral enzymes were analyzed using molecular dynamics simulations. Subsequently, ectoine biosynthesis via 27 combinatory pathways involving core metabolic enzymes was systematically evaluated. The Pum2-ELP fusion protein system was then introduced to construct membraneless biomolecular condensates within the cells. Such a design was justified by the report that the interaction between the tandem PRS tags at the 3' ends of mRNAs of metabolic enzymes and Pum2 in the condensate of Pum2-ELP could recruit ribosomes and metabolic enzymes into the condensates, enabling substrate channeling in the biosynthetic pathway because of the physical approximation of the relevant components. The experimental results demonstrated that the optimal hybrid pathway exhibited synergistic catalytic efficiency. Upon introducing the Pum2-ELP system, the ectoine yield increased by approximately 1.7 folds, which should be ascribed to the substrate channeling effect. In a 5-L bioreactor batch fermentation, the engineered strain achieved a final titer of ∼50 g/L within 24 h, reaching a high volumetric productivity of 2.08 g/(L·h). This study demonstrates that integrating evolution-derived ancestral metabolic enzymes with engineered spatial assembly can significantly optimize metabolic flux, providing an efficient platform strategy for the rapid and high-titer industrial production of ectoine and other high-value compatible solutes under controlled fermentation conditions.