Curation Information

Publication
Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli.;Gosset G, Zhang Z, Nayyar S, Cuevas WA, Saier MH Jr;Journal of bacteriology 2004 Jun; 186(11):3516-24 [15150239]
TF
CRP [P0ACJ8, view regulon]
Reported TF sp.
Escherichia coli BW25113
Reported site sp.
Escherichia coli BW25113
Created by
Patrick O'Neill
Curation notes
E. coli k12 MG1655 used as surrogate genome since BW25113 was not available. Several reported sites omitted for search failure against MG1655 genome.

Experimental Process

Determination of binding by GRASP-DNA search. Determination of regulation by real-time pcr and beta-gal assay.

Transcription Factor Binding Sites


GGTGGAGGAGGTCACG
TTTGATCTCGCTCACA
TTTGACGGCTATCACG
CGTGATAGCCGTCAAA
TTTTATAGGTGTCACA
GGTGAAGGAGGTCACG
TTTGATCTCGCTCACA
TTTGACGGCTATCACG
CGTGATAGCCGTCAAA
TTTTATAGGTGTCACA

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
GGTGAAGGAGGTCACG aceE,
... ... aceE pdhR aceF
Experimental technique details Beta-gal reporter assay - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TTTGATCTCGCTCACA
... ... xseA guaB yfgJ
Experimental technique details Beta-gal reporter assay - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TTTGACGGCTATCACG ptsG,
... ... ptsG ycfH holB tmk yceG pabC
Experimental technique details Beta-gal reporter assay - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
CGTGATAGCCGTCAAA ptsG,
... ... ptsG ycfH holB tmk yceG pabC
Experimental technique details Beta-gal reporter assay - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TTTTATAGGTGTCACA fis,
... ... fis dusB yhdJ
Experimental technique details Beta-gal reporter assay - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer