RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: udp
Synonym(s): OP00178
Gene(s): udp   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 Gavigan SA,1999. Brikun I,1996 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 Gavigan SA,1999. Brikun I,1996. 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 Gavigan SA,1999. Brikun I,1996. 8736525. 10766824 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Gavigan SA,1999. Brikun I,1996. 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
Reference(s): [1] Brikun I., et al., 1996
Promoter
Name: udpP
+1: 4016391
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: atttgcgtcatggtgatgagtatcacgaaaaaatgttaaacccttcggtaaagtgtctttTtgcttcttctgactaaaccg
                      -35                        -10        +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [1] Brikun I., et al., 1996
[2] Huerta AM., et al., 2003
[3] Ovcharova IV., et al., 2004
[4] Zolotukhina M., et al., 2003
[5] Zolotukhina MA., et al., 2002
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
remote CRP-cAMP activator udpP 4016287 4016308 -93.5 gaagggtgatTTATGTGATTTGCATCACTTTTGgtgggtaaat nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [3], [4], [6]
proximal CRP-cAMP activator udpP 4016339 4016360 -41.5 gcatttgcgtCATGGTGATGAGTATCACGAAAAaatgttaaac nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [3], [4], [5], [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP repressor udpP 4016287 4016308 -93.5 gaagggtgatTTATGTGATTTGCATCACTTTTGgtgggtaaat nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [3], [4], [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor udpP 4016295 4016314 -87.0 atttatgtgaTTTGCATCACTTTTGGTGGGtaaatttatg nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [4], [6]
proximal CytR repressor udpP 4016313 4016329 -70.5 acttttggtgGGTAAATTTATGCAACGcatttgcgtc nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [4], [5], [6]
proximal CytR repressor udpP 4016321 4016340 -61.0 tgggtaaattTATGCAACGCATTTGCGTCAtggtgatgag nd [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [4], [5], [6]





RegulonDB