Engineering Regulatory Networks for Complex Phenotypes in E. coli: Article No. 4050

Rongming Liu, Liya Liang, Emily Freed, Alaksh Choudhury, Carrie Eckert, Ryan Gill

Research output: Contribution to journalArticlepeer-review

19 Scopus Citations


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.
Original languageAmerican English
Number of pages13
JournalNature Communications
StatePublished - 2020

NREL Publication Number

  • NREL/JA-2700-77377


  • isobutanol
  • isopropanol
  • large scale saturation
  • mutagenesis library
  • regulatory networks


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