A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover

David S. Glass; Anat Bren; Elizabeth Vaisbourd; Avi Mayo; Uri Alon

doi:10.1016/j.cell.2024.01.024

A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover

David S. Glass^*, Anat Bren, Elizabeth Vaisbourd, Avi Mayo, Uri Alon

^*Corresponding author for this work

Department of Molecular Cell Biology

Research output: Contribution to journal › Article › peer-review

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Abstract

Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.

Original language	English
Pages (from-to)	931-944.e12
Journal	Cell
Volume	187
Issue number	4
Early online date	5 Feb 2024
DOIs	https://doi.org/10.1016/j.cell.2024.01.024
Publication status	Published - 15 Feb 2024

Bibliographical note

The authors would like to thank H. Kim, T. Milo, V. Jayaraman, Y. Yang, M. Raz, S. Kostinski, D. Lipton, S. Miyara, J. Elkahal, J. Glass, and the Alon lab for helpful feedback and comments on the manuscript. Funding was provided by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 856587) and by the Israel Science Foundation (grant agreement no. 1966/22). D.S.G. was funded as a member of the Zuckerman Postdoctoral Scholars Program. U.A. is the incumbent of the Abisch-Frenkel Professional Chair.

Author contributions
Conceptualization, D.S.G., A.B., and U.A.; methodology, D.S.G., E.V., and A.B.; investigation, D.S.G., E.V., A.B., and A.M.; visualization, D.S.G., E.V., and A.B.; funding acquisition, D.S.G., A.B., and U.A.; supervision, U.A.; writing – original draft, D.S.G. and U.A.; writing – review & editing, D.S.G., U.A., A.B., E.V., and A.M.

All Science Journal Classification (ASJC) codes

General Biochemistry,Genetics and Molecular Biology

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10.1016/j.cell.2024.01.024Licence: CC BY-NC-ND

ua_Cell_SyntheticDifferentiationCircuitinEColi_PV_2024Final published version, 2.76 MBLicence: CC BY-NC-ND

Cite this

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title = "A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover",

abstract = "Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.",

author = "Glass, {David S.} and Anat Bren and Elizabeth Vaisbourd and Avi Mayo and Uri Alon",

note = "The authors would like to thank H. Kim, T. Milo, V. Jayaraman, Y. Yang, M. Raz, S. Kostinski, D. Lipton, S. Miyara, J. Elkahal, J. Glass, and the Alon lab for helpful feedback and comments on the manuscript. Funding was provided by the European Research Council (ERC) under the European Union{\textquoteright}s Horizon 2020 research and innovation program (grant agreement no. 856587) and by the Israel Science Foundation (grant agreement no. 1966/22). D.S.G. was funded as a member of the Zuckerman Postdoctoral Scholars Program. U.A. is the incumbent of the Abisch-Frenkel Professional Chair. Author contributions Conceptualization, D.S.G., A.B., and U.A.; methodology, D.S.G., E.V., and A.B.; investigation, D.S.G., E.V., A.B., and A.M.; visualization, D.S.G., E.V., and A.B.; funding acquisition, D.S.G., A.B., and U.A.; supervision, U.A.; writing – original draft, D.S.G. and U.A.; writing – review & editing, D.S.G., U.A., A.B., E.V., and A.M.",

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N2 - Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.

AB - Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.

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A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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