Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

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

Nature Chemical Biology volume 16, pages 695–701 (2020)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

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.

References

  1. Brophy, J. A. & Voigt, C. A. Principles of genetic circuit design. Nat. Methods 11, 508–520 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Liao, C., Blanchard, A. E. & Lu, T. An integrative circuit-host modelling framework for predicting synthetic gene network behaviours. Nat. Microbiol. 2, 1658–1666 (2017).

    Article  CAS  PubMed  Google Scholar 

  3. Boo, A., Ellis, T. & Stan, G.-B. Host-aware synthetic biology. Curr. Opin. Syst. Biol. 14, 66–72 (2019).

    Article  Google Scholar 

  4. Lynch, M. & Marinov, G. K. The bioenergetic costs of a gene. Proc. Natl Acad. Sci. USA 112, 15690–15695 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Ceroni, F. et al. Burden-driven feedback control of gene expression. Nat. Methods 15, 387–393 (2018).

    Article  CAS  PubMed  Google Scholar 

  6. Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z. & Hwa, T. Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099–1102 (2010).

    Article  CAS  PubMed  Google Scholar 

  7. Weisse, A. Y., Oyarzun, D. A., Danos, V. & Swain, P. S. Mechanistic links between cellular trade-offs, gene expression, and growth. Proc. Natl Acad. Sci. USA 112, E1038–E1047 (2015).

    Article  CAS  PubMed  Google Scholar 

  8. Klumpp, S., Zhang, Z. & Hwa, T. Growth rate-dependent global effects on gene expression in bacteria. Cell 139, 1366–1375 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Qian, Y., Huang, H. H., Jimenez, J. I. & Del Vecchio, D. Resource competition shapes the response of genetic circuits. ACS Synth. Biol. 6, 1263–1272 (2017).

    Article  CAS  PubMed  Google Scholar 

  10. Erickson, D. W. et al. A global resource allocation strategy governs growth transition kinetics of Escherichia coli. Nature 551, 119–123 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Venturelli, O. S. et al. Programming mRNA decay to modulate synthetic circuit resource allocation. Nat. Commun. 8, 15128 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Klumpp, S. & Hwa, T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc. Natl Acad. Sci. USA 105, 20245–20250 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Lu, T. K., Khalil, A. S. & Collins, J. J. Next-generation synthetic gene networks. Nat. Biotechnol. 27, 1139–1150 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Purnick, P. E. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Kwok, R. Five hard truths for synthetic biology. Nature 463, 288–290 (2010).

    Article  CAS  PubMed  Google Scholar 

  16. Purcell, O., Jain, B., Karr, J. R., Covert, M. W. & Lu, T. K. Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Cardinale, S. & Arkin, A. P. Contextualizing context for synthetic biology–identifying causes of failure of synthetic biological systems. Biotechnol. J. 7, 856–866 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zhang, C., Tsoi, R. & You, L. Addressing biological uncertainties in engineering gene circuits. Integr. Biol. Quant. Biosci. Nano Macro 8, 456–464 (2016).

    Google Scholar 

  19. Arkin, A. P. A wise consistency: engineering biology for conformity, reliability, predictability. Curr. Opin. Chem. Biol. 17, 893–901 (2013).

    Article  CAS  PubMed  Google Scholar 

  20. Klumpp, S. & Hwa, T. Bacterial growth: global effects on gene expression, growth feedback and proteome partition. Curr. Opin. Biotechnol. 28, 96–102 (2014).

    Article  CAS  PubMed  Google Scholar 

  21. Tan, C., Marguet, P. & You, L. Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 5, 842–848 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Nevozhay, D., Adams, R. M., Van Itallie, E., Bennett, M. R. & Balazsi, G. Mapping the environmental fitness landscape of a synthetic gene circuit. PLoS Comput. Biol. 8, e1002480 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Deris, J. B. et al. The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science 342, 1237435 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Feng, J., Kessler, D. A., Ben-Jacob, E. & Levine, H. Growth feedback as a basis for persister bistability. Proc. Natl Acad. Sci. USA 111, 544–549 (2014).

    Article  CAS  PubMed  Google Scholar 

  25. Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).

    Article  CAS  PubMed  Google Scholar 

  26. Lou, C. et al. Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol. Syst. Biol. 6, 350–350 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Isaacs, F. J., Hasty, J., Cantor, C. R. & Collins, J. J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl Acad. Sci. USA 100, 7714–7719 (2003).

    Article  CAS  PubMed  Google Scholar 

  28. Wu, F., Su, R. Q., Lai, Y. C. & Wang, X. Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination. eLife 6, e23702 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Zeng, W. et al. Rational design of an ultrasensitive quorum-sensing switch. ACS Synth. Biol. 6, 1445–1452 (2017).

    Article  CAS  PubMed  Google Scholar 

  30. Li, T. et al. Engineering of a genetic circuit with regulatable multistability. Integr. Biol. Quant. Biosci. Nano Macro 10, 474–482 (2018).

    Google Scholar 

  31. Wu, F., Menn, D. J. & Wang, X. Quorum-sensing crosstalk-driven synthetic circuits: from unimodality to trimodality. Chem. Biol. 21, 1629–1638 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Dong, H., Nilsson, L. & Kurland, C. G. Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction. J. Bacteriol. 177, 1497–1504 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Blanchard, A. E., Liao, C. & Lu, T. Circuit-host coupling induces multifaceted behavioral modulations of a gene switch. Biophys. J. 114, 737–746 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Andersen, J. B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ. Microbiol. 64, 2240–2246 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Gefen, O., Fridman, O., Ronin, I. & Balaban, N. Q. Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity. Proc. Natl Acad. Sci. USA 111, 556–561 (2014).

    Article  CAS  PubMed  Google Scholar 

  36. Litcofsky, K. D., Afeyan, R. B., Krom, R. J., Khalil, A. S. & Collins, J. J. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat. Methods 9, 1077–1080 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Menn, D., Sochor, P., Goetz, H., Tian, X. J. & Wang, X. Intracellular noise level determines ratio control strategy confined by speed-accuracy trade-off. ACS Synth. Biol. 8, 1352–1360 (2019).

    Article  CAS  PubMed  Google Scholar 

  38. Wu, M. et al. Engineering of regulated stochastic cell fate determination. Proc. Natl Acad. Sci. USA 110, 10610–10615 (2013).

    Article  CAS  PubMed  Google Scholar 

  39. Keren, L. et al. Noise in gene expression is coupled to growth rate. Genome Res. 25, 1893–1902 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wang, L., Xin, J. & Nie, Q. A critical quantity for noise attenuation in feedback systems. PLoS Comput. Biol. 6, e1000764 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Chen, M., Wang, L., Liu, C. C. & Nie, Q. Noise attenuation in the ON and OFF states of biological switches. ACS Synth. Biol. 2, 587–593 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Slager, J. & Veening, J. W. Hard-wired control of bacterial processes by chromosomal gene location. Trends Microbiol 24, 788–800 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C. & Voigt, C. A. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zhong, Z., Ravikumar, A. & Liu, C. C. Tunable expression systems for orthogonal DNA replication. ACS Synth. Biol. 7, 2930–2934 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Liu, C. C., Jewett, M. C., Chin, J. W. & Voigt, C. A. Toward an orthogonal central dogma. Nat. Chem. Biol. 14, 103–106 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Arzumanyan, G. A., Gabriel, K. N., Ravikumar, A., Javanpour, A. A. & Liu, C. C. Mutually orthogonal DNA replication systems in vivo. ACS Synth. Biol. 7, 1722–1729 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Darlington, A. P. S., Kim, J., Jimenez, J. I. & Bates, D. G. Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nat. Commun. 9, 695 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. An, W. & Chin, J. W. Synthesis of orthogonal transcription-translation networks. Proc. Natl Acad. Sci. USA 106, 8477–8482 (2009).

    Article  CAS  PubMed  Google Scholar 

  49. Zong, Y. et al. Insulated transcriptional elements enable precise design of genetic circuits. Nat. Commun. 8, 52 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Ferry, M. S., Razinkov, I. A. & Hasty, J. in Methods in Enzymology Vol. 497 (ed. Voigt, C.) 295–372 (Academic Press, 2011).

Download references

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.

Author information

Author notes

  1. These authors contributed equally: Rong Zhang, Jiao Li.

Authors and Affiliations

  1. School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA

    Rong Zhang, Jiao Li, Juan Melendez-Alvarez, Xingwen Chen, Patrick Sochor, Hanah Goetz, Qi Zhang, Xiao Wang & Xiao-Jun Tian

  2. Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China

    Jiao Li & Tian Ding

Authors
  1. Rong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Juan Melendez-Alvarez
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xingwen Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Patrick Sochor
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hanah Goetz
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Qi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tian Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xiao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Xiao-Jun Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–15 and Note.

Reporting Summary

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.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41589-020-0509-x

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing