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

doi:10.1038/s41467-020-20094-3

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

Journal Article · 11 January 2021 · Nature Communications

DOI: https://doi.org/10.1038/s41467-020-20094-3 · OSTI ID:1756903

Yu, Timothy C.; Liu, Winnie L.;

; Davis, Jessica E.;

; Bower, Grace;

; Insigne, Kimberly D.; Phillips, Rob;

;

Abstract 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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Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-02ER63421

OSTI ID:: 1756903

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 12; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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

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