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 K12 BW25113
Reported site sp.
Escherichia coli K12 BW25113
Created by
Patrick O'Neill
Curation notes
Unclear if evidence for determination of binding meets our criteria.

Experimental Process

Candidate genes were identified by microarray analysis. Regulation of enzymes and transport genes verified by phenotypic analysis of oxidation rates for various carbon, nitrogen sources. Several genes selected for confirmation by RT-PCR. Binding sites identified by computational search with GRASP-DNA, a PWM-based search tool. No experimental evidence of binding.

Transcription Factor Binding Sites


GGTGGAGGAGGTCACG
TGTGAGCGAGATCAAA
TTTGATCTCGCTCACA
CGTGATAGCCGTCAAA
TTTGACGGCTATCACG
TTTTATAGGTGTCACA
TGTAATGGATGTCACG
CGTGAGCAATATCACG
AGTGATCCAGGTCACG
TGTGACAAATATCACA
TGTGATATTTGTCACA
CGAGATAACGATCACA
TGTTTTCGATTTCAAA
TGTGCGGCAATTCACA
TGTTATACATATCACT
GGTAATTGATTTCACT
CGCGATAGATTTCACG
TGTGCGGCAATTCACA
TGTAACAGAGATCACA
TGTGATCTCTGTTACA
TGTAACAGAGATCACA
TGTGATCTCTGTTACA
TGTGAGTGATTTCACA
TGTGAAATCACTCACA
GGTGATCTATTTCACA
CGTAATCTGGATCACT
TGCTACGCATGTCACA
TGTGATTCGATTCACA
TGTGAATCGAATCACA
TGTATTCTGCTTCACG
TGTGATTCGATTCACA
TGTGAATCGAATCACA
GGTGAAGGAGGTCACG
TGTGAGCGAGATCAAA
TTTGATCTCGCTCACA
CGTGATAGCCGTCAAA
TTTGACGGCTATCACG
TTTTATAGGTGTCACA
TGTAATGGATGTCACG
CGTGAGCAATATCACG
AGTGATCCAGGTCACG
TGTGACAAATATCACA
TGTGATATTTGTCACA
CGAGATAACGATCACA
TGTTTTCGATTTCAAA
TGTGCGGCAATTCACA
TGTTATACATATCACT
GGTAATTGATTTCACT
CGCGATAGATTTCACG
TGTGCGGCAATTCACA
TGTAACAGAGATCACA
TGTGATCTCTGTTACA
TGTAACAGAGATCACA
TGTGATCTCTGTTACA
TGTGAGTGATTTCACA
TGTGAAATCACTCACA
GGTGATCTATTTCACA
CGTAATCTGGATCACT
TGCTACGCATGTCACA
TGTGATTCGATTCACA
TGTGAATCGAATCACA
TGTATTCTGCTTCACG
TGTGATTCGATTCACA
TGTGAATCGAATCACA

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
... ... aceF aceE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTGAGCGAGATCAAA
... ... xseA guaB guaA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTTGATCTCGCTCACA
... ... xseA guaB guaA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
CGTGATAGCCGTCAAA
... ... ptsG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - repressor not specified
TTTGACGGCTATCACG
... ... ptsG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - repressor not specified
TTTTATAGGTGTCACA
... ... yhdJ yhdU
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - repressor not specified
TGTAATGGATGTCACG
... ... aceK
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
CGTGAGCAATATCACG
... ... fumA fumC manA ydgA
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - activator not specified
AGTGATCCAGGTCACG
... ... gltA sdhC sdhD sdhA sdhB
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - activator not specified
TGTGACAAATATCACA
... ... fdhD fdoG fdoH fdoI fdhE yiiG
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGTGATATTTGTCACA
... ... fdhD fdoG fdoH fdoI fdhE yiiG
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
CGAGATAACGATCACA
... ... gatY gatZ gatA gatB gatC gatD
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGTTTTCGATTTCAAA
... ... gatY gatZ gatA gatB gatC gatD
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGTGCGGCAATTCACA
... ... glpT glpQ glpA glpB glpC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGTTATACATATCACT
... ... glpE glpG glpR glpD
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
GGTAATTGATTTCACT
... ... glpD glpE glpG glpR
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
CGCGATAGATTTCACG
... ... glpQ
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGCGGCAATTCACA
... ... glpT glpQ glpA glpB glpC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTAACAGAGATCACA
... ... malE malK lamB
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGATCTCTGTTACA
... ... malE malK lamB
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTAACAGAGATCACA
... ... malE malK lamB
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGATCTCTGTTACA
... ... malE malK lamB
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGAGTGATTTCACA
... ... mglB mglA mglC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGAAATCACTCACA
... ... mglB mglA mglC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
GGTGATCTATTTCACA
... ... aspA dcuA cutA dsbD yjdC pheU fxsA
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
CGTAATCTGGATCACT
... ... aspA dcuA cutA dsbD yjdC pheU fxsA
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGCTACGCATGTCACA
... ... putA putP
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGATTCGATTCACA
... ... tnaC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGAATCGAATCACA
... ... tnaC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTATTCTGCTTCACG
... ... tnaA tnaB mdtL yidZ
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - activator monomer
TGTGATTCGATTCACA
... ... tnaC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer
TGTGAATCGAATCACA
... ... tnaC
Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator monomer