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

Nat Commun. 2021 Jan 12;12(1):325. doi: 10.1038/s41467-020-20094-3.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Biophysical Phenomena
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / drug effects
  • Escherichia coli / metabolism
  • Fluorescence
  • Genes, Reporter
  • Isopropyl Thiogalactoside / pharmacology*
  • Logic*
  • Mutation / genetics
  • Operator Regions, Genetic / genetics
  • Promoter Regions, Genetic*
  • Protein Binding
  • Reproducibility of Results
  • Thermodynamics
  • Transcription Factors / metabolism

Substances

  • Transcription Factors
  • Isopropyl Thiogalactoside
  • DNA-Directed RNA Polymerases