RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: ppiA
Synonym(s): rot, rotA
Gene(s): ppiA   Genome Browser M3D Gene expression COLOMBOS
Note(s): This operon is expressed in a complex manner from four overlapping promoters.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Norregaard-Madsen M., et al., 1994
Promoter
Name: ppiAp1
+1: 3492335
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 38
Sequence: agatacgtaaaattaggtaaagggatggccttgttcttgaaggctatttagaatctcttcActtgctttttttctgctctg
                         -35                     -10        +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Norregaard-Madsen M., et al., 1994
[3] Salgado H, et al., 2012
[4] Yamamoto K., et al., 2006
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 CpxR-phosphorylated activator ppiAp1 3492375 3492389 -47.0 atttcagataCGTAAAATTAGGTAAAgggatggcct nd [APIORCISFBSCS], [BPP], [GEA] [4], [5], [6]


Transcription unit          
Name: ppiA
Synonym(s): rot, rotA
Gene(s): ppiA   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 Norregaard-Madsen M,1994 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 Norregaard-Madsen M,1994. 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 Norregaard-Madsen M,1994. 8736525. 10766824 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Norregaard-Madsen M,1994. 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
This operon is expresed in a complex manner from four overlapping promoters.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Norregaard-Madsen M., et al., 1994
Promoter
Name: ppiAp2
+1: 3492395
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 98
Sequence: cattttaagaggtgattttgatcacggaataaaaagtgatcgtcaggttacatatatttcAgatacgtaaaattaggtaaa
                             -35                     -10    +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Norregaard-Madsen M., et al., 1994
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 ppiAp2 3492427 3492448 -42.5 attgcattttAAGAGGTGATTTTGATCACGGAAtaaaaagtga nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor ppiAp2 3492427 3492448 -42.5 attgcattttAAGAGGTGATTTTGATCACGGAAtaaaaagtga nd [APIORCISFBSCS], [BPP], [GEA] [1]
remote CRP-cAMP repressor ppiAp2 3492480 3492501 -95.5 attttaggtgATTTTGTGATCTGTTTAAATGTTttattgcaat nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor ppiAp2 3492452 3492468 -64.5 tattgcaatcGGTTGCTAAATTGCATTttaagaggtg nd [APIORCISFBSCS], [BPP], [GEA] [1]
proximal CytR repressor ppiAp2 3492470 3492487 -83.0 gtgatctgttTAAATGTTTTATTGCAATcggttgctaa nd [APIORCISFBSCS], [BPP], [GEA], [IC] [1]


Transcription unit          
Name: ppiA
Synonym(s): rot, rotA
Gene(s): ppiA   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 Norregaard-Madsen M,1994 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 Norregaard-Madsen M,1994. 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 Norregaard-Madsen M,1994. 8736525. 10766824 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Norregaard-Madsen M,1994. 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

This operon is expresed in a complex manner from four overlapping promoters.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Norregaard-Madsen M., et al., 1994
Promoter
Name: ppiAp3
+1: 3492430
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 133
Sequence: gtttaaatgttttattgcaatcggttgctaaattgcattttaagaggtgattttgatcacGgaataaaaagtgatcgtcag
                         -35                     -10        +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Norregaard-Madsen M., et al., 1994
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 ppiAp3 3492480 3492501 -60.5 attttaggtgATTTTGTGATCTGTTTAAATGTTttattgcaat nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor ppiAp3 3492427 3492448 -7.5 attgcattttAAGAGGTGATTTTGATCACGGAAtaaaaagtga nd [APIORCISFBSCS], [BPP], [GEA] [1]
proximal CRP-cAMP repressor ppiAp3 3492480 3492501 -60.5 attttaggtgATTTTGTGATCTGTTTAAATGTTttattgcaat nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor ppiAp3 3492452 3492468 -29.5 tattgcaatcGGTTGCTAAATTGCATTttaagaggtg nd [APIORCISFBSCS], [BPP], [GEA] [1]
proximal CytR repressor ppiAp3 3492470 3492487 -48.0 gtgatctgttTAAATGTTTTATTGCAATcggttgctaa nd [BPP], [IC], [APIORCISFBSCS], [BPP], [GEA], [IC] [1]


Transcription unit          
Name: ppiA
Synonym(s): rot, rotA
Gene(s): ppiA   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 Norregaard-Madsen M,1994 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 Norregaard-Madsen M,1994. 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 Norregaard-Madsen M,1994. 8736525. 10766824 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Norregaard-Madsen M,1994. 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

This operon is expresed in a complex manner from four overlapping promoters.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Norregaard-Madsen M., et al., 1994
Promoter
Name: ppiAp4
+1: 3492449
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 152
Sequence: ttaggtgattttgtgatctgtttaaatgttttattgcaatcggttgctaaattgcattttAagaggtgattttgatcacgg
                     -35                        -10         +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Norregaard-Madsen M., et al., 1994
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 repressor ppiAp4 3492427 3492448 12.5 attgcattttAAGAGGTGATTTTGATCACGGAAtaaaaagtga nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor ppiAp4 3492452 3492468 -10.5 tattgcaatcGGTTGCTAAATTGCATTttaagaggtg nd [APIORCISFBSCS], [BPP], [GEA] [1]
proximal CytR repressor ppiAp4 3492470 3492487 -29.0 gtgatctgttTAAATGTTTTATTGCAATcggttgctaa nd [APIORCISFBSCS], [BPP], [GEA], [IC] [1]




Reference(s)    

 [1] Norregaard-Madsen M., Mygind B., Pedersen R., Valentin-Hansen P., Sogaard-Andersen L., 1994, The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor., Mol Microbiol 14(5):989-97

 [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] Yamamoto K., Ishihama A., 2006, Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli., Biosci Biotechnol Biochem 70(7):1688-95

 [5] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [6] Pogliano J., Lynch AS., Belin D., Lin EC., Beckwith J., 1997, Regulation of Escherichia coli cell envelope proteins involved in protein folding and degradation by the Cpx two-component system., Genes Dev 11(9):1169-82


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