Multiplexed Characterization of Rationally Designed Promoter Architectures Deconstructs Combinatorial Logic for IPTG-inducible Systems

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Jan 13

PMID 33436562

Citations 21

Authors

Timothy C Yu

Winnie L Liu

Marcia S Brinck

Jessica E Davis

Jeremy Shek

Grace Bower

Tal Einav

Kimberly D Insigne

Rob Phillips

Sriram Kosuri

Guillaume Urtecho

Affiliations

Soon will be listed here.

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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