Open AccessDesign of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
Author(s) -
Rhodius Virgil A,
SegallShapiro Thomas H,
Sharon Brian D,
Ghodasara Amar,
Orlova Ekaterina,
Tabakh Hannah,
Burkhardt David H,
Clancy Kevin,
Peterson Todd C,
Gross Carol A,
Voigt Christopher A
Publication year - 2013
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2013.58
Subject(s) - promoter , synthetic biology , biology , crosstalk , computational biology , genome , genetics , gene , gene regulatory network , gene expression , physics , optics
Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σ s as well as the specificity of their interaction with anti‐ σ s. DNA synthesis was used to build 86 ECF σ s (two from every subgroup), their promoters, and 62 anti‐ σ s identified from the genomes of diverse bacteria. A subset of 20 σ s and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σ s, anti‐ σ s, and promoters were used to build synthetic genetic switches in Escherichia coli . This represents a genome‐scale resource of the properties of ECF σ s and a resource for synthetic biology, where this set of well‐characterized regulatory parts will enable the construction of sophisticated gene expression programs.