Abstract
Microbial cell factories offer a sustainable route to plant-derived natural products, but yield drift and strain degeneration persist. Growth-coupled biosynthesis can continuously enrich high producers, yet specific product-responsive biosensors remain scarce and their population-level effects are unclear. Here, we describe a rapid transcriptome-mining workflow that, as proof-of-concept, delivers yeast biosensors for glycyrrhetinic acid and medicarpin. By fine-tuning PDR5 promoter, we expand the dynamic range of the glycyrrhetinic acid sensor and wire it to an essential gene, establishing a growth-addiction circuit that increases titer by 46.8 % after subculture. Single-cell transcriptome reveals that the evolved strain population exhibits a completely different division of labor compared to the initial strain. Coupling does not eliminate phenotypic heterogeneity; instead, it amplifies a dedicated sub-population marked by discrete transcriptional signatures. Deletion of genes highly expressed in non-producing cells or enrichment of high-producing cell clusters can further boost population-level production. This study provides both a generalizable biosensor-discovery platform and single-cell-guided strategies for stabilizing and optimizing natural-product cell factories.
Data availability
Source data are provided with this paper. The bulk RNA-seq data generated in this study have been deposited in the NCBI database under BioProject accession codes PRJNA1146062, PRJNA1415461 and PRJNA1436984. The single-cell RNA-seq data generated in this study have been deposited in the NCBI database under BioProject accession code PRJNA1415668. All other data supporting the findings of this study are available from the corresponding author upon reasonable request. The request will be responded within 2 weeks. Source data are provided with this paper.
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Acknowledgements
This work was supported by the National Key Research and Development Program of China (2024YFA0919600 to L.Q.) and the Natural Science Foundation of China (22138006 to C.L., 22278240 to L.Q., 22478031 to B.L., 22478032 to H.J., 22178024 to B.H.).
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L.Q. and C.L conceived the project. B.Y. and L.Q. developed and engineered the GA biosensor, carried out the strain fermentation and parameter determination, and wrote the manuscript. L.Q. and Q.L. facilitated strain evolution. H.Z. and W.S. validated the experiment results. R.H. and Y.T. analyzed and verified the single-cell RNA-seq result, and developed the medicarpin biosensor. X.L. and B.H. conducted the structure simulation of the transcription factor complex. H.J., B.L., and C.L revised the manuscript and supervised the study.
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Qin, L., Yang, B., Huang, R. et al. Design of the biosensor-dependent coupling system stabilizes the high-synthesis phenotype of cell factory. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71801-5
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DOI: https://doi.org/10.1038/s41467-026-71801-5
