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

Ireland, William T. and Beeler, Suzannah M. and Flores-Bautista, Emanuel and McCarty, Nicholas S. and Röschinger, Tom and Belliveau, Nathan M. and Sweredoski, Michael J. and Moradian, Annie and Kinney, Justin B. and Phillips, Rob (2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife, 2020 (9). Art. No. e55308. ISSN 2050-084X. PMCID PMC7567609. https://resolver.caltech.edu/CaltechAUTHORS:20200121-102719123

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.7554/eLife.55308DOIArticle
https://doi.org/10.22002/d1.1336DOIData
https://doi.org/10.22002/D1.1331DOIData
https://doi.org/10.5281/zenodo.3953312DOIData
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7567609/PubMed CentralArticle
https://arxiv.org/abs/2001.07396arXivDiscussion Paper
https://doi.org/10.1101/2020.01.18.910323DOIDiscussion Paper
ORCID:
AuthorORCID
Ireland, William T.0000-0003-0971-2904
Beeler, Suzannah M.0000-0002-1930-4827
McCarty, Nicholas S.0000-0003-4479-284X
Röschinger, Tom0000-0002-4900-3216
Belliveau, Nathan M.0000-0002-1536-1963
Sweredoski, Michael J.0000-0003-0878-3831
Moradian, Annie0000-0002-0407-2031
Kinney, Justin B.0000-0003-1897-3778
Phillips, Rob0000-0003-3082-2809
Additional Information:© 2020 Ireland et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Received: 20 January 2020; Accepted: 18 September 2020; Published: 21 September 2020. We are grateful to Rachel Banks, Stephanie Barnes, Curt Callan, Griffin Chure, Ana Duarte, Vahe Galstyan, Hernan Garcia, Soichi Hirokawa, Thomas Lecuit, Heun Jin Lee, Madhav Mani, Muir Morrison, Steve Quake, Manuel Razo-Mejia, Gabe Salmon, and Guillaume Urtecho for useful discussion and feedback on the manuscript. Guillaume Urtecho and Sri Kosuri have been instrumental in providing key advice and protocols at various stages in the development of this work. We would like to thank Jost Vielmetter and Nina Budaeva for providing access to their Cell Disruptor. Brett Lomenick provided crucial help and advice with protein preparation. We also thank Igor Antoshechkin for his help with sequencing at the Caltech Genomics Facility. We are deeply grateful for support from NIH Grants DP1 OD000217 (Director’s Pioneer Award) and 1R35 GM118043-01 Maximizing Investigators Research Award) which made it possible to undertake this multi-year project. N.M.B. was supported by an HHMI International Student Research Fellowship. S.M.B was supported by the NIH Institutional National Research Service Award (5T32GM007616-38) provided through Caltech. The Proteome Exploration Laboratory is supported by, the Beckman Institute, and NIH 1S10OD02001301. Author contributions: William T Ireland, Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Suzannah M Beeler, Conceptualization, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Emanuel Flores-Bautista, Software, Formal analysis, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Nicholas S McCarty, Resources, Software, Writing - review and editing; Tom Röschinger, Data curation, Software, Writing - review and editing; Nathan M Belliveau, Conceptualization, Methodology, Writing - review and editing; Michael J Sweredoski, Formal analysis, Methodology, Writing - review and editing; Annie Moradian, Methodology, Writing - review and editing; Justin B Kinney, Software, Methodology, Writing - review and editing; Rob Phillips, Conceptualization, Resources, Supervision, Funding acquisition, Validation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing. Data availability: Sequencing data has been deposited in the SRA under accession no.PRJNA599253 and PRJNA603368. Mass spectrometry data is deposited in the CalTech data repository at doi:10.22002/d1.1336. Model files and inferred information footprints are deposited in the CalTech data repository at doi:10.22002/D1.1331. Processed sequencing data sets and analysis software are available in the GitHub repository available at https://doi.org/10.5281/zenodo.3953312.
Funders:
Funding AgencyGrant Number
NIHDP1 OD000217
NIH1R35 GM118043-01
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIH Predoctoral Fellowship5T32GM007616-38
Caltech Beckman InstituteUNSPECIFIED
NIH1S10OD02001301
Issue or Number:9
PubMed Central ID:PMC7567609
Record Number:CaltechAUTHORS:20200121-102719123
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200121-102719123
Official Citation:Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife 2020;9: e5530; DOI: 10.7554/eLife.55308.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:100811
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Jan 2020 19:18
Last Modified:20 Oct 2020 20:36

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