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Topology-dependent interference of synthetic gene circuit function by growth feedback

Abstract

Growth-mediated feedback between synthetic gene circuits and host organisms leads to diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity. However, the range of possible impacts of growth feedback on gene circuits remains underexplored. Here we mathematically and experimentally demonstrated that growth feedback affects the functions of memory circuits in a network topology-dependent way. Specifically, the memory of the self-activation switch is quickly lost due to the growth-mediated dilution of the circuit products. Decoupling of growth feedback reveals its memory, manifested by its hysteresis property across a broad range of inducer concentration. On the contrary, the toggle switch is more refractory to growth-mediated dilution and can retrieve its memory after the fast-growth phase. The underlying principle lies in the different dependence of active and repressive regulations in these circuits on the growth-mediated dilution. Our results unveil the topology-dependent mechanism on how growth-mediated feedback influences the behaviors of gene circuits.

Fig. 1: Theoretical analysis reveals bistability, but experimental data shows no hysteresis.
Fig. 2: Growth-mediated feedback disguises the bistability of the SA circuit.
Fig. 3: Decoupling of growth feedback reveals the bistability of the SA circuit.
Fig. 4: The toggle switch is refractory to memory loss from the growth-mediated feedback.

Data availability

All data produced or analyzed for this study are included in the published article and its supplementary information files or are available from the corresponding authors upon reasonable request.

Code availability

All the equations and parameters of the mathematical models can be found in the Supplementary Note.

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Acknowledgements

We thank X. Fu, T. Hong, G. Yao, J. Xing, W. Shou and T. Hwa for valuable comments. This project was supported by the ASU School of Biological and Health Systems Engineering, NSF grant (no. EF-1921412 to X-J.T.) and NIH grant (no. GM106081 to X.W.). H.G. and J.M.-A. were also supported by the Arizona State University Dean’s Fellowship.

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X.-J.T. conceived the study. X.-J.T., R.Z. and X.W. designed the study. R.Z., J.L., P.S. and X.C. performed experiments. J.M.-A., H.G., and X.-J.T. performed model studies. R.Z., X.-J.T., Q.Z., T.D. and X.W. analyzed the data. R.Z. and X.-J.T. wrote the manuscript. H.G. and X.W. edited the manuscript.

Corresponding authors

Correspondence to Xiao Wang or Xiao-Jun Tian.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–15 and Note.

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Supplementary Video 1

A time-lapse video showing the dynamics of GFP in the AraC self-activation circuit under the condition without l-ara and fresh medium for 14 h and conditioned medium for 7 h thereafter.

Supplementary Video 2

A time-lapse video showing the dynamics of GFP in the AraC self-activation circuit under the condition with a high dose of l-ara and fresh medium condition for 14 h and conditioned medium for 7 h thereafter.

Supplementary Video 3

A time-lapse video showing the dynamics of GFP in the toggle switch circuit under the condition without aTc and fresh medium for 16 h and conditioned medium for 10 h thereafter.

Supplementary Video 4

A time-lapse video showing the dynamics of GFP in the toggle switch circuit under the condition with 2 ng ml−1 aTc and fresh medium for 16 h and conditioned medium for 10 h thereafter.

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Zhang, R., Li, J., Melendez-Alvarez, J. et al. Topology-dependent interference of synthetic gene circuit function by growth feedback. Nat Chem Biol 16, 695–701 (2020). https://doi.org/10.1038/s41589-020-0509-x

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