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A fast, robust, and tunable synthetic gene oscillator

One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to “design specs” generated from computational modeling(1–6). This approach provides a systematic framework for exploring how a given regulator...

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Autores principales: Stricker, Jesse, Cookson, Scott, Bennett, Matthew R., Mather, William H., Tsimring, Lev S., Hasty, Jeff
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791529/
https://www.ncbi.nlm.nih.gov/pubmed/18971928
http://dx.doi.org/10.1038/nature07389
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author Stricker, Jesse
Cookson, Scott
Bennett, Matthew R.
Mather, William H.
Tsimring, Lev S.
Hasty, Jeff
author_facet Stricker, Jesse
Cookson, Scott
Bennett, Matthew R.
Mather, William H.
Tsimring, Lev S.
Hasty, Jeff
author_sort Stricker, Jesse
collection PubMed
description One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to “design specs” generated from computational modeling(1–6). This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behavior. Several fundamental gene circuits have been developed using this approach, including toggle switches(7) and oscillators(8–10), and these have been applied in novel contexts such as triggered biofilm development(11) and cellular population control(12). Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust, and persistent, with tunable oscillatory periods as fast as 13 minutes. The oscillator was designed using a previously modeled network architecture comprising linked positive and negative feedback loops(1,13). Using a microfluidic platform tailored for single-cell microscopy, we precisely control environmental conditions and monitor oscillations in individual cells through multiple cycles. Experiments reveal remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibited large-amplitude fluorescence oscillations throughout observation runs. The oscillatory period can be tuned by altering inducer levels, temperature, and media source. Computational modeling demonstrates that the key design principle for constructing a robust oscillator is a time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. The positive feedback loop increases the robustness of the oscillations and allows for greater tunability. Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction.
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spelling pubmed-67915292019-10-14 A fast, robust, and tunable synthetic gene oscillator Stricker, Jesse Cookson, Scott Bennett, Matthew R. Mather, William H. Tsimring, Lev S. Hasty, Jeff Nature Article One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to “design specs” generated from computational modeling(1–6). This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behavior. Several fundamental gene circuits have been developed using this approach, including toggle switches(7) and oscillators(8–10), and these have been applied in novel contexts such as triggered biofilm development(11) and cellular population control(12). Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust, and persistent, with tunable oscillatory periods as fast as 13 minutes. The oscillator was designed using a previously modeled network architecture comprising linked positive and negative feedback loops(1,13). Using a microfluidic platform tailored for single-cell microscopy, we precisely control environmental conditions and monitor oscillations in individual cells through multiple cycles. Experiments reveal remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibited large-amplitude fluorescence oscillations throughout observation runs. The oscillatory period can be tuned by altering inducer levels, temperature, and media source. Computational modeling demonstrates that the key design principle for constructing a robust oscillator is a time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. The positive feedback loop increases the robustness of the oscillations and allows for greater tunability. Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction. 2008-10-29 2008-11-27 /pmc/articles/PMC6791529/ /pubmed/18971928 http://dx.doi.org/10.1038/nature07389 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Stricker, Jesse
Cookson, Scott
Bennett, Matthew R.
Mather, William H.
Tsimring, Lev S.
Hasty, Jeff
A fast, robust, and tunable synthetic gene oscillator
title A fast, robust, and tunable synthetic gene oscillator
title_full A fast, robust, and tunable synthetic gene oscillator
title_fullStr A fast, robust, and tunable synthetic gene oscillator
title_full_unstemmed A fast, robust, and tunable synthetic gene oscillator
title_short A fast, robust, and tunable synthetic gene oscillator
title_sort fast, robust, and tunable synthetic gene oscillator
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791529/
https://www.ncbi.nlm.nih.gov/pubmed/18971928
http://dx.doi.org/10.1038/nature07389
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