RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: cdd
Gene(s): cdd   Genome Browser M3D Gene expression COLOMBOS
Note(s): Gavigan et al. (1999) and Perini et al. (1996) showed that CytR binds in tandem in the regulated intergenic region Gavigan SA,1999. Perini LT,1996 On the other hand, in 1997, Pedersen and Valentin-Hanses showed that CytR binds to octamer repeats, GTTGCATT in either the direct or inverted orientation and preferably separated by 2 or 3 bp Pedersen H,1997. Jorgensen CI,1998. For this reason the length of the CytR DNA-binding site is variable.
However, footprinting analyses showed that the dimers of CytR are flanked or sandwiched by two dimers of CRP Holt AK,2010. Holst B,1992. Jorgensen CI,1998 Thus, the binding sites of CytR located in this region were assigned by the curator in agreement based on similarity to the consensus sequence and on the data from the footprinting assays and mutational evidence Jorgensen CI,1998. Holst B,1992. Holt AK,2010. Pedersen H,1997. Sogaard-Andersen L,1990. Zolotukhina MA,2002
The repressor CytR and the activator CRP, two dimeric proteins, interact to form a complex repressor nucleoprotein in the intergenic region. When only CRP is bound to this promoter, it functions as an activator, and then, when CytR binds to DNA and to CRP, the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription Holst B,1992. 8736525. 10766824 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Holst B,1992. Sogaard-Andersen L,1990. Sogaard-Andersen L,1990. Sogaard-Andersen L,1991 At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation 8736525. Holst B,1992
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: cddp
+1: 2231819
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: gcataattaatgagattcagatcacatataaagccacaacgggttcgtaaactgttatccCattacatgattatgaggcaa
                     -35                        -10         +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Holst B., et al., 1992
[2] Valentin-Hansen P., et al., 1989
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 CRP-cAMP activator cddp 2231716 2231737 -92.5 atgggctaaaATTTGCGATGCGTCGCGCATTTttgatgtatg nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [2]
proximal CRP-cAMP2 activator cddp 2231766 2231787 -42.5 gttgcataatTAATGAGATTCAGATCACATATaaagccacaa nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 repressor cddp 2231714 2231735 -94.5 taatgggctaAAATTTGCGATGCGTCGCGCATttttgatgta nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [2]
proximal CRP-cAMP2 repressor cddp 2231766 2231787 -42.5 gttgcataatTAATGAGATTCAGATCACATATaaagccacaa nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor cddp 2231729 2231745 -82.5 tgcgatgcgtCGCGCATTTTTGATGTAtgtttcacgc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1], [3], [4]
proximal CytR2 repressor cddp 2231747 2231764 -64.0 tttgatgtatGTTTCACGCGTTGCATAAttaatgagat nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1], [2], [3], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NsrR repressor cddp 2231822 2231833 9.0 gttatcccatTACATGATTATGaggcaacgcc nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [5]
Note(s): 2CRP and CytR bind cooperatively to cddp.1CRP and CytR bind cooperatively to cddp.
2CRP and CytR bind cooperatively to cddp.2CRP and CytR bind cooperatively to cddp.1CRP and CytR bind cooperatively to cddp.
4CRP and CytR bind cooperatively to cddp.
5CRP and CytR bind cooperatively to cddp.
6CRP and CytR bind cooperatively to cddp.





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