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Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems

A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our abi...

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Autores principales: Yu, Timothy C., Liu, Winnie L., Brinck, Marcia S., Davis, Jessica E., Shek, Jeremy, Bower, Grace, Einav, Tal, Insigne, Kimberly D., Phillips, Rob, Kosuri, Sriram, Urtecho, Guillaume
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804116/
https://www.ncbi.nlm.nih.gov/pubmed/33436562
http://dx.doi.org/10.1038/s41467-020-20094-3
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author Yu, Timothy C.
Liu, Winnie L.
Brinck, Marcia S.
Davis, Jessica E.
Shek, Jeremy
Bower, Grace
Einav, Tal
Insigne, Kimberly D.
Phillips, Rob
Kosuri, Sriram
Urtecho, Guillaume
author_facet Yu, Timothy C.
Liu, Winnie L.
Brinck, Marcia S.
Davis, Jessica E.
Shek, Jeremy
Bower, Grace
Einav, Tal
Insigne, Kimberly D.
Phillips, Rob
Kosuri, Sriram
Urtecho, Guillaume
author_sort Yu, Timothy C.
collection PubMed
description A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.
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spelling pubmed-78041162021-01-21 Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems Yu, Timothy C. Liu, Winnie L. Brinck, Marcia S. Davis, Jessica E. Shek, Jeremy Bower, Grace Einav, Tal Insigne, Kimberly D. Phillips, Rob Kosuri, Sriram Urtecho, Guillaume Nat Commun Article A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics. Nature Publishing Group UK 2021-01-12 /pmc/articles/PMC7804116/ /pubmed/33436562 http://dx.doi.org/10.1038/s41467-020-20094-3 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Yu, Timothy C.
Liu, Winnie L.
Brinck, Marcia S.
Davis, Jessica E.
Shek, Jeremy
Bower, Grace
Einav, Tal
Insigne, Kimberly D.
Phillips, Rob
Kosuri, Sriram
Urtecho, Guillaume
Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title_full Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title_fullStr Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title_full_unstemmed Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title_short Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
title_sort multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for iptg-inducible systems
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804116/
https://www.ncbi.nlm.nih.gov/pubmed/33436562
http://dx.doi.org/10.1038/s41467-020-20094-3
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