Engineering regulatory networks for complex phenotypes in E. coli
Abstract
Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli, with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.
- Authors:
-
[1];
[2];
- Univ. of Colorado, Boulder, CO (United States)
- Univ. of Colorado, Boulder, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Univ. of Colorado, Boulder, CO (United States); Technical Univ. of Denmark, Lyngby (Denmark)
- Publication Date:
- Research Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
- OSTI Identifier:
- 1660231
- Report Number(s):
- NREL/JA-2700-77377
Journal ID: ISSN 2041-1723; MainId:26323;UUID:3d00df03-740b-4ba3-be71-5385776edcce;MainAdminID:17319
- Grant/Contract Number:
- AC36-08GO28308; SC0018368
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; CRISPR; isobutanol; isopropanol; large scale saturation; mutagenesis library; regulatory networks
Citation Formats
Liu, Rongming, Liang, Liya, Freed, Emily F., Choudhury, Alaksh, Eckert, Carrie A., and Gill, Ryan T. Engineering regulatory networks for complex phenotypes in E. coli. United States: N. p., 2020.
Web. doi:10.1038/s41467-020-17721-4.
Liu, Rongming, Liang, Liya, Freed, Emily F., Choudhury, Alaksh, Eckert, Carrie A., & Gill, Ryan T. Engineering regulatory networks for complex phenotypes in E. coli. United States. https://doi.org/10.1038/s41467-020-17721-4
Liu, Rongming, Liang, Liya, Freed, Emily F., Choudhury, Alaksh, Eckert, Carrie A., and Gill, Ryan T. Thu .
"Engineering regulatory networks for complex phenotypes in E. coli". United States. https://doi.org/10.1038/s41467-020-17721-4. https://www.osti.gov/servlets/purl/1660231.
@article{osti_1660231,
title = {Engineering regulatory networks for complex phenotypes in E. coli},
author = {Liu, Rongming and Liang, Liya and Freed, Emily F. and Choudhury, Alaksh and Eckert, Carrie A. and Gill, Ryan T.},
abstractNote = {Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli, with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.},
doi = {10.1038/s41467-020-17721-4},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United States},
year = {Thu Aug 13 00:00:00 EDT 2020},
month = {Thu Aug 13 00:00:00 EDT 2020}
}
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