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An excitable gene regulatory circuit induces transient cellular differentiation

Nature volume 440, pages 545–550 (2006)Cite this article

Abstract

Certain types of cellular differentiation are probabilistic and transient1,2,3. In such systems individual cells can switch to an alternative state and, after some time, switch back again. In Bacillus subtilis, competence is an example of such a transiently differentiated state associated with the capability for DNA uptake from the environment. Individual genes and proteins underlying differentiation into the competent state have been identified4,5, but it has been unclear how these genes interact dynamically in individual cells to control both spontaneous entry into competence and return to vegetative growth. Here we show that this behaviour can be understood in terms of excitability in the underlying genetic circuit. Using quantitative fluorescence time-lapse microscopy, we directly observed the activities of multiple circuit components simultaneously in individual cells, and analysed the resulting data in terms of a mathematical model. We find that an excitable core module containing positive and negative feedback loops can explain both entry into, and exit from, the competent state. We further tested this model by analysing initiation in sister cells, and by re-engineering the gene circuit to specifically block exit. Excitable dynamics driven by noise naturally generate stochastic and transient responses6, thereby providing an ideal mechanism for competence regulation.

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Figure 1: Stress response in B. subtilis and the core competence circuit.
Figure 2: Activities of P comK and P comG promoters are highly correlated during competence.
Figure 3: Promoter activities of P comS and P comG are anti-correlated during competence.
Figure 4: Modelling of the core competence network reveals an excitable system.
Figure 5: Competence lock through feedback bypass.

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Acknowledgements

We thank U. Alon, D. Dubnau, J. Dworkin, A. Eldar, J. Ferrell, R. Kishony, B. Lazazzera, R. Losick, A. Raj, B. Shraiman, D. Sprinzak, M. Surette and members of the laboratory for comments. G.M.S. is supported by the Caltech Center for Biological Circuit Design. J.G.-O. acknowledges financial support from the Generalitat de Catalunya and the Ministerio de Educacion y Ciencia (Spain). M.B.E. acknowledges support from the Searle Scholars Program and the Burroughs Wellcome Fund CASI program.

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Authors and Affiliations

  1. Division of Biology and Department of Applied Physics, California Institute of Technology, California, 91125, Pasadena, USA

    Gürol M. Süel, Louisa M. Liberman & Michael B. Elowitz

  2. Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Colom 11, E-08222, Terrassa, Spain

    Jordi Garcia-Ojalvo

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Correspondence to Michael B. Elowitz.

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Supplementary information

Supplementary Notes

This file contains the Supplementary Methods, Supplementary Discussion and Supplementary Figures The discussion concerns the analysis of the dynamical model and of competence excursions in sister cells and additional figures showing experimental data on growth rate and media comparison. (PDF 1678 kb)

Supplementary Movie 1

Movie of a B. subtilis microcolony under nutrient limitation conditions, showing PcomK and PcomG activities in blue and red colors, respectively. Simultaneous activation of comK and comG during competence results in a magenta color in the only cell of the microcolony that becomes competent. (MOV 2918 kb)

Supplementary Movie 2

Movie of a B. subtilis microcolony under nutrient limitation conditions, showing PcomG and PcomS activities in red and green colors, respectively. comS is expressed in all cells, but only one becomes competent. The two promoter activities are negatively correlated during competence. (MOV 3175 kb)

Supplementary Movie 3

Movie of a microcolony of FeBy B. subtilis cells incorporating a feedback bypass, under nutrient limitation conditions. PcomG and PcomS activities are shown in red and green colors, respectively. Competence is locked on due to the feedback bypass. (MOV 2540 kb)

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Süel, G., Garcia-Ojalvo, J., Liberman, L. et al. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440, 545–550 (2006). https://doi.org/10.1038/nature04588

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