Curation Information

The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility.;White CE, Winans SC;Molecular microbiology 2007 Apr; 64(1):245-56 [17376086]
TraR [P54294, view regulon]
Reported TF sp.
Agrobacterium fabrum str. C58
Reported site sp.
Agrobacterium fabrum str. C58
Created by
Dinara Sagitova
Curation notes
b) less than 90% of the sites were located as exact matches

Experimental Process

The objective of the authors was to systematically alter a TraR binding site (tra box) to all possible bases and determine the resulting affinity of the TraR to the altered sites. Site-directed mutagenesis was used to 27 tra box sequence variants. EMSA confirmed that TraR binds to the wild type tra box and determined the affinity of TraR to each mutant tra box. traI-lacZ fusion was used to test the effect of the tra box defects on transcription activation in vivo.

Transcription Factor Binding Sites


Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
... ... traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030 repA repB
Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator dimer