Curation Information

Publication

Optimization of the palindromic order of the TtgR operator enhances binding cooperativity.;Krell T, Terán W, Mayorga OL, Rivas G, Jiménez M, Daniels C, Molina-Henares AJ, Martínez-Bueno M, Gallegos MT, Ramos JL;Journal of molecular biology 2007 Jun 22; 369(5):1188-99 [17498746]

TF

TtgR [Q9AIU0, view regulon]

Reported TF sp.

Pseudomonas putida DOT-T1E

Reported site sp.

Pseudomonas putida DOT-T1E

Created by

Joe Sparenberg

Curation notes

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Experimental Process

DMS footprinting protected a 36-bp sequence in the ttgABC-ttgR intergenic region. EMSA showed that TtgR binds to a 40-bp sequence that includes the 36-bp sequence protected by DMS footprinting. Site directed mutagenesis and EMSA identified the minimum length of the sequence that binds TtgR. Isothermal titration calorimetry confirmed these results.

Transcription Factor Binding Sites

• Sites reported in the paper
• Sites matched in the genome

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.