Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

  1. William T Ireland
  2. Suzannah M Beeler
  3. Emanuel Flores-Bautista
  4. Nicholas S McCarty
  5. Tom Röschinger
  6. Nathan M Belliveau
  7. Michael J Sweredoski
  8. Annie Moradian
  9. Justin B Kinney
  10. Rob Phillips  Is a corresponding author
  1. California Institute of Technology, United States
  2. California Institute of Technology, United States
  3. Cold Spring Harbor Laboratory, United States

Abstract

Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈ 65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively-parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than 100 E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.

Data availability

Sequencing data has been deposited in the SRA under accession no.PRJNA599253 and PRJNA603368Mass spectrometry data is deposited in the CalTech data repository at doi:10.22002/d1.1336Model files and inferred information footprints are deposited in the CalTech data repository at doi:10.22002/D1.1331Processed sequencing data sets and analysis software are available in the GitHub repository available at https://doi.org/10.5281/zenodo.3953312

The following data sets were generated

Article and author information

Author details

  1. William T Ireland

    Physics, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0971-2904
  2. Suzannah M Beeler

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1930-4827
  3. Emanuel Flores-Bautista

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Nicholas S McCarty

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Tom Röschinger

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Nathan M Belliveau

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1536-1963
  7. Michael J Sweredoski

    Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0878-3831
  8. Annie Moradian

    Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0407-2031
  9. Justin B Kinney

    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1897-3778
  10. Rob Phillips

    Department of Bioengineering, California Institute of Technology, Pasadena, United States
    For correspondence
    phillips@pboc.caltech.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3082-2809

Funding

National Institutes of Health (Director's Pioneer Award)

  • Rob Phillips

National Institutes of Health (National Research Service Award,5T32GM007616-38)

  • Suzannah M Beeler

National Institutes of Health (Maximizing Investigators Research Award)

  • Rob Phillips

Howard Hughes Medical Institute (International Student Research Fellowship)

  • Nathan M Belliveau

National Institutes of Health (1S10OD02001301)

  • Annie Moradian

National Institutes of Health (1S10OD02001301)

  • Michael J Sweredoski

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Armita Nourmohammad, University of Washington, United States

Publication history

  1. Received: January 20, 2020
  2. Accepted: September 18, 2020
  3. Accepted Manuscript published: September 21, 2020 (version 1)
  4. Version of Record published: October 16, 2020 (version 2)

Copyright

© 2020, Ireland et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. William T Ireland
  2. Suzannah M Beeler
  3. Emanuel Flores-Bautista
  4. Nicholas S McCarty
  5. Tom Röschinger
  6. Nathan M Belliveau
  7. Michael J Sweredoski
  8. Annie Moradian
  9. Justin B Kinney
  10. Rob Phillips
(2020)
Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time
eLife 9:e55308.
https://doi.org/10.7554/eLife.55308
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