RegulonDB RegulonDB 10.8: Operon Form
   

ydeP operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ydeP
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ydeP
Gene(s): ydeP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of ydeP appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011
Masuda N,2003proposed a model of the regulatory network of the acid resistance genes, including evgA, ydeP, ydeO, yhiE, gadABC, and hdeAB, using a combination of microarray analysis and gene replacement techniques. With these assays, seven operons were identified as induced when EvgA is overexpressed and YdeO is absent; on the other hand, 12 operons were identified as induced when YdeO is overexpressed. To confirm these regulatory interactions, the EvgA consensus site was searched with the ALIGNACE program, and the 18-bp site found was tested by gel shift analysis with the upstream regions of the corresponding operons. As the result, just six operons are regulated by EvgA, among which the ydeP gene is included.
Based on results of gene expression analysis, EMSA, and a LacZ reporter assay, it was determined that the ydeP promotor is activated by five transcription factors: NarL, NarP, RcsB, UhpA, and UvrY Yoshida M,2015.
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: ydePp
+1: 1586664
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 178
Sequence: gcgcacaattgaagccagagtcttattttttatattgaaaaatatgttaatttaaacactAtgagagatgatgcttaactt
                           -35                  -10         +1                   
Note(s): The ydeP promoter is considered one of the group of multifactor promoters Aseev LV,2015
Evidence: [IHBCE]
[TIM]
Reference(s): [2] Itou J., et al., 2009
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal EvgA-Phosphorylated activator ydePp 1586730 1586747 -74.5 gaaggctattAGCCTACACCTGTAAGAAaatccgcgca nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor ydePp nd nd nd nd nd [BPP] [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NagC1 repressor ydePp 1586681 1586703 -28.0 aagccagagtCTTATTTTTTATATTGAAAAATAtgttaattta nd [AIBSCS] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarL-Phosphorylated activator ydePp nd nd nd nd nd [BPP], [GEA] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarP-Phosphorylated repressor ydePp nd nd nd nd nd [BPP], [GEA] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-Phosphorylated repressor ydePp 1586622 1586640 34.5 ttaacttatcGTATTTAATCTATTGTTTAacgataatag nd [APIORCISFBSCS], [CV(GEA)], [GEA] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsB-Pasp56 activator ydePp nd nd nd nd nd [BPP], [GEA] [5], [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd UvrY-Phosphorylated activator ydePp nd nd nd nd nd [BPP], [GEA] [6]
Note(s): 1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.2This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.





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