Curation Information

Publication
Genes regulated by TorR, the trimethylamine oxide response regulator of Shewanella oneidensis.;Bordi C, Ansaldi M, Gon S, Jourlin-Castelli C, Iobbi-Nivol C, Méjean V;Journal of bacteriology 2004 Jul; 186(14):4502-9 [15231782]
TF
TorR [Q8EHJ3, view regulon]
Reported TF sp.
Shewanella oneidensis MR-1
Reported site sp.
Shewanella oneidensis MR-1
Created by
Catherine Bane
Curation notes
-

Experimental Process

Visual sequence inspection of the promoter region of torECAD revealed the presence of a direct repeat of a hexameric sequence predicted to be the binding site of TorR. Site directed mutagenesis and EMSA verified the binding of TorR to the promoter region. A consensus search using bioMotif utility software located additional TorR binding sites in S. oneidensis genome. EMSA verified the binding of TorR to torR and torF promoters containing predicted binding sites. DNAse footprinting confirmed the binding of TorR to the consensus sequences in the torR and torF promoters. Real-time PCR established that TorR negatively regulates it own expression and activates the expression of torF and torC.

Transcription Factor Binding Sites


TTCATAATTTTTCATA
TTCATACTTTTTCATA
TTCATATTCATTCATA
TTCATAATTTTTCATA
TTCATACTTTTTCATA
TTCATATTCATTCATA

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
TTCATAATTTTTCATA torE, torC, torA, torD,
... ... torE torC torA torD SO_1236
Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) - activator dimer
TTCATACTTTTTCATA torR,
... ... torR SO_1227
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - repressor dimer
TTCATATTCATTCATA torF,
... ... torF vmeA vmeB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - activator dimer