title: Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators.
abstract: The understanding of how the architecture of cis-regulatory elements at bacterial promoters determines their final output is of central interest in modern biology. In this work, we attempt to gain insight into this process by analyzing complex promoter architectures in the model organism Escherichia coli. By focusing on the relationship between different TFs at the genomic scale in terms of their binding site arrangement and their effect on the target promoters, we found no strong constraint limiting the combinatorial assembly of TF pairs in E. coli. More strikingly, overlapping binding sites were found equally associated with both equivalent (both TFs have the same effect on the promoter) and opposite (one TF activates while the other repress the promoter) effects on gene expression. With this information on hand, we set an in silico approach to design overlapping sites for three global regulators (GRs) of E. coli, specifically CRP, Fis, and IHF. Using random sequence assembly and an evolutionary algorithm, we were able to identify potential overlapping operators for all TF pairs. In order to validate our prediction, we constructed two lac promoter variants containing overlapping sites for CRP and IHF designed in silico. By assaying the synthetic promoters using a GFP reporter system, we demonstrated that these variants were functional and activated by CRP and IHF in vivo. Taken together, presented results add new information on the mechanisms of signal integration in bacterial promoters and provide new strategies for the engineering of synthetic regulatory circuits in bacteria.
authors.affiliation: FFCLRP and ‡FMRP, University of São Paulo , Ribeirão Preto, SP Brazil.
authors.forename: María-Eugenia
authors.initials: ME
authors.lastname: Guazzaroni
authors.forename: Rafael
authors.initials: R
authors.lastname: Silva-Rocha
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002373:Cyclic AMP Receptor Protein / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D035021:Factor For Inversion Stimulation Protein / Q000235:genetics* / Q000378:metabolism; D017930:Genes, Reporter; D005813:Genes, Synthetic; D005818:Genetic Engineering; D016680:Genome, Bacterial; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D034982:Integration Host Factors / Q000235:genetics* / Q000378:metabolism; D056968:Lac Repressors / Q000235:genetics; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional
chemical_list: D002373:Cyclic AMP Receptor Protein; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D034982:Integration Host Factors; D056968:Lac Repressors; C539064:LacI protein, E coli; C481662:crp protein, E coli; C440502:integration host factor, E coli; D049452:Green Fluorescent Proteins
keywords: cis-regulatory elements; regulatory networks; synthetic biology