RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: rpoH
Gene(s): rpoH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Erickson JW., et al., 1987
[2] Pallen M. 1999
Promoter
Name: rpoHp6
+1: 3600813
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 30
Sequence: aacagtgaatgataacctcgttgctcttaagctctggcacagttgttgctaccactgaagCgccagaagatatcgattgag
                                   -12         -24          +1                   
Evidence: [CV(FP/TIM)]
[FP]
[HIPP]
[TIM]
Reference(s): [3] Janaszak A., et al., 2007
[2] Pallen M. 1999
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s): [4] Yura T., et al., 1984
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 IHF activator rpoHp6 3601133 3601145 -326.0 cgaagtttgaTATCAATGGCTTAtcattcgatg nd [BPP], [GEA] [3]


Transcription unit          
Name: rpoH
Synonym(s): OP00113
Gene(s): rpoH   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 |CITS:[10347150] [8969182]|. 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 |CITS: [9155036][9466254]|. 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 |CITS:[9767576]|. 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 |CITS:[ 9767576][1327747][20000490][9155036][2170326][12391883]|.
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 |CITS:[ 9767576][8736525][10766824]|. The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP |CITS:[9767576][1962841][2170326][1649947]|. At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation |CITS:[ 8736525]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Erickson JW., et al., 1987
Promoter
Name: rpoHp5
+1: 3600849
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 66
Sequence: tgcattgaacttgtggataaaatcacggtctgataaaacagtgaatgataacctcgttgcTcttaagctctggcacagttg
                      -10                        -35        +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Janaszak A., et al., 2007
[5] Kallipolitis BH., et al., 1998
[6] Nagai H., et al., 1990
[7] Salgado H, et al., 2012
[8] Yamamoto K., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s): [4] Yura T., et al., 1984
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 dual rpoHp5 3600880 3600901 -41.5 cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
proximal CRP-cAMP2 dual rpoHp5 3600880 3600901 -41.5 cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
remote CRP-cAMP dual rpoHp5 3600933 3600954 -94.5 tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
remote CRP-cAMP4 dual rpoHp5 3600933 3600954 -94.5 tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
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 rpoHp5 3600887 3600908 -48.5 tcacaagcttGCATTGAACTTGTGGATAAAATcacggtctga nd [BCE] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR1 repressor rpoHp5 3600896 3600912 -54.5 ttattcacaaGCTTGCATTGAACTTGTggataaaatc nd [BPP], [GEA], [HIBSCS] [5]
proximal CytR repressor rpoHp5 3600913 3600932 -73.5 tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg nd [BPP], [GEA], [HIBSCS] [5]
Note(s): 2CRP alone activates rpoH transcription, but CytR and CRP act in concert to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules, CRP-CytR-CRP.
4CRP alone activates rpoH transcription, but CytR and CRP act together to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.1CytR and CRP act together to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.
2CRP alone activates rpoH transcription, but CytR and CRP act together to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.
4CytR and CRP act together to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.
7CRP alone activates rpoH transcription, but CytR and CRP act in concert to repress transcription from the rpoHp5 promoter. A single CytR molecule binds between two CRP molecules, CRP-CytR-CRP.


Transcription unit          
Name: rpoH
Synonym(s): OP00113
Gene(s): rpoH   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 |CITS:[10347150] [8969182]|. 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 |CITS: [9155036][9466254]|. 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 |CITS:[9767576]|. 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 |CITS:[ 9767576][1327747][20000490][9155036][2170326][12391883]|.
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 |CITS:[ 9767576][8736525][10766824]|. The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP |CITS:[9767576][1962841][2170326][1649947]|. At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation |CITS:[ 8736525]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Erickson JW., et al., 1987
[10] Narberhaus F., et al., 1996
Promoter
Name: rpoHp4
+1: 3600863
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 80
Sequence: tttattcacaagcttgcattgaacttgtggataaaatcacggtctgataaaacagtgaatGataacctcgttgctcttaag
                         -10                    -35         +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Erickson JW., et al., 1987
[11] Fujita N., et al., 1987
[3] Janaszak A., et al., 2007
[5] Kallipolitis BH., et al., 1998
[7] Salgado H, et al., 2012
[8] Yamamoto K., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s): [4] Yura T., et al., 1984
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 rpoHp4 3600880 3600901 -27.5 cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
proximal CRP-cAMP repressor rpoHp4 3600933 3600954 -80.5 tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor rpoHp4 3600896 3600912 -40.5 ttattcacaaGCTTGCATTGAACTTGTggataaaatc nd [BPP], [GEA], [HIBSCS] [5]
proximal CytR repressor rpoHp4 3600913 3600932 -59.0 tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg nd [BPP], [GEA], [HIBSCS] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal DnaA-ATP repressor rpoHp4 3600890 3600898 -31.0 gcattgaactTGTGGATAAaatcacggtc nd [HIBSCS] [12]
proximal DnaA-ATP repressor rpoHp4 3600914 3600922 -55.0 tgtgcgtaatTTATTCACAagcttgcatt nd [BCE], [HIBSCS] [12]


Transcription unit          
Name: rpoH
Gene(s): rpoH   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 |CITS:[10347150] [8969182]|. 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 |CITS: [9155036][9466254]|. 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 |CITS:[9767576]|. 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 |CITS:[ 9767576][1327747][20000490][9155036][2170326][12391883]|.
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 |CITS:[ 9767576][8736525][10766824]|. The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP |CITS:[9767576][1962841][2170326][1649947]|. At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation |CITS:[ 8736525]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Erickson JW., et al., 1987
Promoter
Name: rpoHp3
+1: 3600870
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 87
Sequence: tgcgtaatttattcacaagcttgcattgaacttgtggataaaatcacggtctgataaaacAgtgaatgataacctcgttgc
                            -10                   -35       +1                   
Note(s): Heat shock seems to induce transcription from this promoter.
The rpoHp3 promoter was induced by zinc in a microarray analysis Yamamoto K,2005
Evidence: [AIPP]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Erickson JW., et al., 1987
[11] Fujita N., et al., 1987
[3] Janaszak A., et al., 2007
[5] Kallipolitis BH., et al., 1998
[6] Nagai H., et al., 1990
[13] Rhodius VA., et al., 2005
[7] Salgado H, et al., 2012
[8] Yamamoto K., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s): [4] Yura T., et al., 1984
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-cAMP1 repressor rpoHp3 3600880 3600901 -20.5 cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
proximal CRP-cAMP2 repressor rpoHp3 3600933 3600954 -73.5 tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat nd [AIBSCS], [BPP], [GEA] [5], [6], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR1 repressor rpoHp3 3600896 3600912 -33.5 ttattcacaaGCTTGCATTGAACTTGTggataaaatc nd [BPP], [GEA], [HIBSCS] [5]
proximal CytR repressor rpoHp3 3600913 3600932 -52.0 tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg nd [BPP], [GEA], [HIBSCS] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal DnaA-ATP repressor rpoHp3 3600914 3600922 -48.0 tgtgcgtaatTTATTCACAagcttgcatt nd [BCE], [HIBSCS] [12]
Note(s): 1CytR and CRP act together to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.
2CytR and CRP act together to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.1CytR and CRP act in concert to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP
1CytR and CRP act together to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.
4CytR and CRP act in concert to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP
5CytR and CRP act together to repress transcription from the rpoHp3 promoter. A single CytR molecule binds between two CRP molecules. CRP-CytR-CRP.


Transcription unit          
Name: rpoH
Gene(s): rpoH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Erickson JW., et al., 1987
Promoter
Name: rpoHp1
+1: 3601003
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 220
Sequence: acggtacaacatttacgccactttacgcctgaataataaaagcgtgttatactctttcccTgcaatgggttccgtagcagg
                      -10                       -35         +1                   
Note(s): The σ70 and σS RNA polymerase subunits direct transcription from the rpoHp1 promoter in the exponential and stationary growth phases, respectively, and transcriptional start sites for the two holoenzymes differ by 1 nt Janaszak A,2009
Under nonstress conditions, the distal P1 promoter contributes to the majority of rpoH transcription Erickson JW,1987. Yura T, Nagai H, Mori H,1993.
There are four sigma factors (σ70, σS, σ54, and σ24) cooperatively controlling rpoH32) gene expression, which provides high flexibility of the stress response Janaszak A,2009

Evidence: [HIPP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] Erickson JW., et al., 1987
[11] Fujita N., et al., 1987
[14] Janaszak A., et al., 2009
[5] Kallipolitis BH., et al., 1998
[8] Yamamoto K., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s): [4] Yura T., et al., 1984
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
nd CpxR-Phosphorylated1 activator rpoHp1 nd nd nd nd nd [GEA] [15]
Note(s): 1The regulation of CpxR on the rpoHp1 promoter was observed under the stress condition caused by the introduction of the R1-16 plasmid that encodes the type V secretion system (T4S machinery) in the cell Zahrl D,20061The regulation of CpxR on the rpoHp1 promoter was observed under the stress condition caused by the introduction of the R1-16 plasmid that encodes the type V secretion system (T4S machinery) in the cell Zahrl D,2006




Reference(s)    

 [1] Erickson JW., Vaughn V., Walter WA., Neidhardt FC., Gross CA., 1987, Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene., Genes Dev 1(5):419-32

 [2] Pallen M., 1999, RpoN-dependent transcription of rpoH?, Mol Microbiol 31(1):393

 [3] Janaszak A., Majczak W., Nadratowska B., Szalewska-Palasz A., Konopa G., Taylor A., 2007, A {sigma}54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene., Microbiology 153(Pt 1):111-23

 [4] Yura T., Tobe T., Ito K., Osawa T., 1984, Heat shock regulatory gene (htpR) of Escherichia coli is required for growth at high temperature but is dispensable at low temperature., Proc Natl Acad Sci U S A 81(21):6803-7

 [5] Kallipolitis BH., Valentin-Hansen P., 1998, Transcription of rpoH, encoding the Escherichia coli heat-shock regulator sigma32, is negatively controlled by the cAMP-CRP/CytR nucleoprotein complex., Mol Microbiol 29(4):1091-9

 [6] Nagai H., Yano R., Erickson JW., Yura T., 1990, Transcriptional regulation of the heat shock regulatory gene rpoH in Escherichia coli: involvement of a novel catabolite-sensitive promoter., J Bacteriol 172(5):2710-5

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.

 [8] Yamamoto K., Ishihama A., 2005, Transcriptional response of Escherichia coli to external zinc., J Bacteriol 187(18):6333-40

 [9] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [10] Narberhaus F., Weiglhofer W., Fischer HM., Hennecke H., 1996, The Bradyrhizobium japonicum rpoH1 gene encoding a sigma 32-like protein is part of a unique heat shock gene cluster together with groESL1 and three small heat shock genes., J Bacteriol 178(18):5337-46

 [11] Fujita N., Ishihama A., 1987, Heat-shock induction of RNA polymerase sigma-32 synthesis in Escherichia coli: transcriptional control and a multiple promoter system., Mol Gen Genet 210(1):10-5

 [12] Wang QP., Kaguni JM., 1989, dnaA protein regulates transcriptions of the rpoH gene of Escherichia coli., J Biol Chem 264(13):7338-44

 [13] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [14] Janaszak A., Nadratowska-Wesolowska B., Konopa G., Taylor A., 2009, The P1 promoter of the Escherichia coli rpoH gene is utilized by sigma 70 -RNAP or sigma s -RNAP depending on growth phase., FEMS Microbiol Lett 291(1):65-72

 [15] Zahrl D., Wagner M., Bischof K., Koraimann G., 2006, Expression and assembly of a functional type IV secretion system elicit extracytoplasmic and cytoplasmic stress responses in Escherichia coli., J Bacteriol 188(18):6611-21


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