Dynamic regulation is an effective strategy for fine-tuning metabolic pathways in order to maximize target product synthesis. However, achieving dynamic and autonomous up- and down-regulation of the metabolic modules of interest simultaneously, still remains a great challenge. In this work, we created an autonomous dual-control (ADC) system, by combining CRISPRi-based NOT gates with novel biosensors of a key metabolite in the pathway of interest. By sensing the levels of the intermediate glucosamine-6-phosphate (GlcN6P) and self-adjusting the expression levels of the target genes accordingly with the GlcN6P biosensor and ADC system enabled feedback circuits, the metabolic flux towards the production of the high value nutraceutical N-acetylglucosamine (GlcNAc) could be balanced and optimized in Bacillus subtilis. As a result, the GlcNAc titer in a 15-l fed-batch bioreactor increased from 59.9 g/l to 97.1 g/l with acetoin production and 81.7 g/l to 131.6 g/l without acetoin production, indicating the robustness and stability of the synthetic circuits in a large bioreactor system. Remarkably, this self-regulatory methodology does not require any external level of control such as the use of inducer molecules or switching fermentation/environmental conditions. Moreover, the proposed programmable genetic circuits may be expanded to engineer other microbial cells and metabolic pathways.

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Metabolic engineering facilitates chemical biosynthesis by rewiring cellular resources to produce target compounds. However, an imbalance between cell growth and bioproduction often reduces production efficiency. Genetic code expansion (GCE)-based orthogonal translation systems incorporating non-canonical amino acids (ncAAs) into proteins by reassigning non-canonical codons to ncAAs qualify for balancing cellular metabolism. Here, GCE-based cell growth and biosynthesis balance engineering (GCE-CGBBE) is developed, which is based on titrating expression of cell growth and metabolic flux determinant genes by constructing ncAA-dependent expression patterns. We demonstrate GCE-CGBBE in genome-recoded Escherichia coli Δ321AM by precisely balancing glycolysis and N-acetylglucosamine production, resulting in a 4.54-fold increase in titer. GCE-CGBBE is further expanded to non-genome-recoded Bacillus subtilis to balance growth and N-acetylneuraminic acid bioproduction by titrating essential gene expression, yielding a 2.34-fold increase in titer. Moreover, the development of ncAA-dependent essential gene expression regulation shows efficient biocontainment of engineered B. subtilis to avoid unintended proliferation in nature.

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N-acetylneuraminic acid (NeuAc), which has been widely used as a nutraceutical and pharmaceutical intermediate, plays an important role in improving brain development and cognition while enhancing immunity. Bacillus subtilis, generally regarded as a food-safe microorganism, is suitable for developing as a chassis cell for efficient NeuAc synthesis. However, accumulated intermediates can lead to metabolic bottlenecks for NeuAc synthesis. To eliminate the accumulated byproduct N-acetylglucosamine (GlcNAc), the UDP-GlcNAc epimerase pathway without GlcNAc production was first reconstructed and optimized in B. subtilis, resulting in the NeuAc titer increase of 5.9 g/L with GlcNAc elimination. In addition, to reduce another accumulated byproduct N-acetylmannosamine (ManNAc), the directed evolution of N-acetylneuraminic acid synthase and the enhancement of phosphoenolpyruvate supply was implemented. Using this strategy, ManNAc decreased by 46.3%, and the NeuAc titer increased by 54.9%, reaching 7.9 g/L. Finally, the maximum titer of NeuAc in a 3-L fermenter reached 21.8 g/L with a productivity of 0.34 g/L/h.