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

Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, View ORCID ProfileSriram Kosuri, View ORCID ProfileGuillaume Urtecho
doi: https://doi.org/10.1101/2020.01.31.928689
Timothy C. Yu
1Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
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Winnie L. Liu
2Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
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Marcia Brinck
3Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
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Jessica E. Davis
4Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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Jeremy Shek
4Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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Grace Bower
2Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
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Tal Einav
5Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
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Kimberly D. Insigne
6Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA, 90095, USA
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Rob Phillips
5Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
7Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
8Department of Applied Physics, California Institute of Technology, Pasadena, CA, 91125, USA
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Sriram Kosuri
4Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
9UCLA-DOE Institute for Genomics and Proteomics, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA
10Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA, 90095, USA
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  • ORCID record for Sriram Kosuri
  • For correspondence: sri@ucla.edu gurtecho@ucla.edu
Guillaume Urtecho
10Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA, 90095, USA
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  • ORCID record for Guillaume Urtecho
  • For correspondence: sri@ucla.edu gurtecho@ucla.edu
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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 8,269 rationally designed IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. Using these data, we fit a statistical mechanics model that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three novel 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.

Footnotes

  • ↵† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 02, 2020.
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Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
bioRxiv 2020.01.31.928689; doi: https://doi.org/10.1101/2020.01.31.928689
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Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
bioRxiv 2020.01.31.928689; doi: https://doi.org/10.1101/2020.01.31.928689

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