Curation Information

The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein.;Yamamoto K, Ishihama A, Busby SJ, Grainger DC;Journal of bacteriology 2011 Mar; 193(6):1477-80 [21239586]
MntR [P0A9F1, view regulon]
Reported TF sp.
Escherichia coli strain BW25113
Reported site sp.
Escherichia coli strain BW25113
Created by
Erill Lab
Curation notes

Experimental Process

Beta-gal assays used to confirm induction on ChIP-chip binding data for a single gene (dps).

The paper reports that TF forms complex with other proteins for binding with reported sites.

Interaction with Fis and OxyR using expression analysis.

ChIP assay conditions
MntR: Strain BW25113 (6) was grown aerobically in LB medium supplemented with either 0.2 mM MnCl2 (to stimulate DNA binding by MntR) or 0.1 mM EDTA (as a negative control).
ChIP notes
At an optical density at 650 nm (OD650) of 0.3 to 0.4, cells were treated with formaldehyde, and cellular DNA was extracted and sonicated, yielding DNA fragments of 500 to 1,000 bp. After immunoprecipitation with anti-MntR antibodies, DNA fragments from MnCl2 or control EDTA-treated cells were purified and labeled with Cy5 and Cy3, respectively. The two DNA samples were then mixed and hybridized to the 43,450-feature DNA microarray (Oxford Gene Technology, Oxford, United Kingdom). After washing and scanning, the Cy5/Cy3 signal intensity ratio was calculated for each probe. The experiment was done in duplicate, and an average of the two Cy5/Cy3 ratios was used for further analysis.

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
... ... dps rhtA
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-chip (ECO:0006007) - repressor dimer