Engineering regulatory networks for complex phenotypes in E. coli

Rongming Liu, Liya Liang, Emily F. Freed, Alaksh Choudhury, Carrie A. Eckert and Ryan T. Gill ()
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Rongming Liu: University of Colorado Boulder
Liya Liang: University of Colorado Boulder
Emily F. Freed: University of Colorado Boulder
Alaksh Choudhury: University of Colorado Boulder
Carrie A. Eckert: University of Colorado Boulder
Ryan T. Gill: University of Colorado Boulder

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17721-4

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