RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: cytR
Gene(s): cytR   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.
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 Gerlach P,1990. Pedersen H,1992. Gerlach P,1991. 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 Gerlach P,1990. Pedersen H,1992. Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996. Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P,2000 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Gerlach P,1990. Pedersen H,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 Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: cytRp
+1: 4124509
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 53
Sequence: cacacttttcatgaaaattctgtaaccgttttcacgcgctatctgctaaaaatgttgccgAtgtgaagtaaacatggatgt
                      -35                      -10          +1                   
Evidence: [AH]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Gerlach P., et al., 1990
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
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-cyclic-AMP activator cytRp 4124563 4124584 -64.5 gcggatcgaaAAATTCAATATTCATCACACTTttcatgaaaa nd [GEA], [APIORCISFBSCS], [BPP] [1], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP repressor cytRp 4124563 4124584 -64.5 gcggatcgaaAAATTCAATATTCATCACACTTttcatgaaaa nd [GEA], [APIORCISFBSCS], [BPP] [1], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor cytRp 4124521 4124542 -22.0 ttctgtaaccGTTTTCACGCGCTATCTGCTAAaaatgttgcc nd [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] [1], [4]
proximal CytR repressor cytRp 4124544 4124561 -43.0 atcacactttTCATGAAAATTCTGTAACcgttttcacg nd [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] [1], [4], [5]
proximal CytR repressor cytRp 4124557 4124580 -59.0 atcgaaaaatTCAATATTCATCACACTTTTCATGaaaattctgt nd [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] [1], [4]




Reference(s)    

 [1] Gerlach P., Valentin-Hansen P., Bremer E., 1990, Transcriptional regulation of the cytR repressor gene of Escherichia coli: autoregulation and positive control by the cAMP/CAP complex., Mol Microbiol 4(3):479-88

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Pedersen H., Sogaard-Andersen L., Holst B., Gerlach P., Bremer E., Valentin-Hansen P., 1992, cAMP-CRP activator complex and the CytR repressor protein bind co-operatively to the cytRP promoter in Escherichia coli and CytR antagonizes the cAMP-CRP-induced DNA bend., J Mol Biol 227(2):396-406

 [5] Pedersen H., Valentin-Hansen P., 1997, Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member., EMBO J 16(8):2108-18


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