Evolutionary stabilisation of stressful metabolism via integrated biocomputing and essential-gene metabolic locking circuits

Lu, Z.; Barry, C.; Tominaga, M.; Phan, A.; Jahanian, A.; Collier, T. R.; Wendrick, N. A.; Evans, S.; McDonnell, L.; Netzel, G.; McCubbin, T.; John, S.; da Roza, P. A.; Xu, X.; Wang, C.; Ishii, J.; Behrendorff, J.; Beliaev, A. S.; Vickers, C. E.; Peng, B.

doi:10.64898/2026.09.01.748751

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bioRxiv · 10.64898/2026.09.01.748751

Evolutionary stabilisation of stressful metabolism via integrated biocomputing and essential-gene metabolic locking circuits

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Abstract

Synthetic genetic circuits enable microbial differentiation from growth to production, yet metabolic burden, imbalance and toxicity frequently drive strain degeneration. Yeast strains engineered to produce different terpene products exhibited divergent genetic responses to metabolic stresses, but commonly underwent progressive loss of induction of synthetic GAL regulatory circuits, either across the entire population or within subpopulations. Using di- and tri-input biocomputing circuits, the essential glutamine synthetase gene GLN1 was coupled to GAL induction, thereby enabling stabilisation and evolutionary adaptation of the synthetic genetic circuits and stressful heterologous terpene synthetic pathways. The integrated biocomputing and metabolic coupling circuit systems not only prevent strain degeneration but also enable interrogation of non-degenerative evolutionary shifts, providing a platform for metabolic engineering optimisation.

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Lu, Z., Barry, C., Tominaga, M., Phan, A., Jahanian, A., Collier, T. R., Wendrick, N. A., Evans, S., McDonnell, L., Netzel, G., McCubbin, T., John, S., da Roza, P. A., Xu, X., Wang, C., Ishii, J., Behrendorff, J., Beliaev, A. S., Vickers, C. E., Peng, B.. 2026-09-03. Evolutionary stabilisation of stressful metabolism via integrated biocomputing and essential-gene metabolic locking circuits. https://doi.org/10.64898/2026.09.01.748751

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