RegulonDB

RegulonDB RegulonDB 11.2: 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:	[EXP-IDA-BOUNDARIES-DEFINED] 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 -24 -12 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IMP]
Reference(s):	[3] Huerta AM., et al., 2003 [4] Janaszak A., et al., 2007 [5] Janaszak A., et al., 2009 [6] Nadratowska-Wesolowska B., et al., 2010 [2] Pallen M. 1999
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[IHF,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	IHF	activator	rpoHp6	3601133	3601145	-326.0	cgaagtttgaTATCAATGGCTTAtcattcgatg	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[4]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
IHF	activator	rpoHp6	3601133	3601145	-326.0	cgaagtttgaTATCAATGGCTTAtcattcgatg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[4]

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 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 Kallipolitis BH,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 Kallipolitis BH,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 Kallipolitis BH,1998. 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 Kallipolitis BH,1998. 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:	[EXP-IDA-BOUNDARIES-DEFINED] 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 -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[3] Huerta AM., et al., 2003 [4] Janaszak A., et al., 2007 [8] Kallipolitis BH., et al., 1998 [9] Nagai H., et al., 1990 [10] Salgado H, et al., 2012 [11] Yamamoto K., et al., 2005
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[CRP,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CRP-cyclic-AMP	activator	rpoHp5	3600880	3600901	-41.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [12]
proximal	CRP-cyclic-AMP	activator	rpoHp5	3600887	3600908	-48.5	tcacaagcttGCATTGAACTTGTGGATAAAATcacggtctga	nd	[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	nd
remote	CRP-cyclic-AMP	activator	rpoHp5	3600933	3600954	-94.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [12]

[CRP,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CRP-cyclic-AMP	repressor	rpoHp5	3600880	3600901	-41.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [12]
remote	CRP-cyclic-AMP	repressor	rpoHp5	3600933	3600954	-94.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8], [9], [12]

[CytR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CytR	repressor	rpoHp5	3600896	3600912	-54.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]
proximal	CytR	repressor	rpoHp5	3600913	3600932	-73.5	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
CRP-cyclic-AMP	activator	rpoHp5	3600933	3600954	-94.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8], [9], [12]
CRP-cyclic-AMP	repressor	rpoHp5	3600933	3600954	-94.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8], [9], [12]
CytR	repressor	rpoHp5	3600913	3600932	-73.5	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
CytR	repressor	rpoHp5	3600896	3600912	-54.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
CRP-cyclic-AMP	activator	rpoHp5	3600887	3600908	-48.5	tcacaagcttGCATTGAACTTGTGGATAAAATcacggtctga	nd	nd
CRP-cyclic-AMP	activator	rpoHp5	3600880	3600901	-41.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8], [9], [12]
CRP-cyclic-AMP	repressor	rpoHp5	3600880	3600901	-41.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8], [9], [12]

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 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 Kallipolitis BH,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 Kallipolitis BH,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 Kallipolitis BH,1998. 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 Kallipolitis BH,1998. 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:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Erickson JW., et al., 1987 [13] Narberhaus F., et al., 1996
Promoter
Name:	rpoHp4
+1:	3600863
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	80
Sequence:	tttattcacaagcttgcattgaacttgtggataaaatcacggtctgataaaacagtgaatGataacctcgttgctcttaag -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[1] Erickson JW., et al., 1987 [14] Fujita N., et al., 1987 [3] Huerta AM., et al., 2003 [4] Janaszak A., et al., 2007 [5] Janaszak A., et al., 2009 [8] Kallipolitis BH., et al., 1998 [6] Nadratowska-Wesolowska B., et al., 2010 [10] Salgado H, et al., 2012 [11] Yamamoto K., et al., 2005
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[CRP,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CRP-cyclic-AMP	repressor	rpoHp4	3600880	3600901	-27.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[12]
proximal	CRP-cyclic-AMP	repressor	rpoHp4	3600933	3600954	-80.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[12]

[CytR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CytR	repressor	rpoHp4	3600896	3600912	-40.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]
proximal	CytR	repressor	rpoHp4	3600913	3600932	-59.0	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]

[DnaA,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	DnaA-ATP	repressor	rpoHp4	3600890	3600898	-31.0	gcattgaactTGTGGATAAaatcacggtc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	nd	nd
proximal	DnaA-ATP	repressor	rpoHp4	3600914	3600922	-55.0	tgtgcgtaatTTATTCACAagcttgcatt	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	nd

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
CRP-cyclic-AMP	repressor	rpoHp4	3600933	3600954	-80.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12]
CytR	repressor	rpoHp4	3600913	3600932	-59.0	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
DnaA-ATP	repressor	rpoHp4	3600914	3600922	-55.0	tgtgcgtaatTTATTCACAagcttgcatt	nd	nd
CytR	repressor	rpoHp4	3600896	3600912	-40.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
DnaA-ATP	repressor	rpoHp4	3600890	3600898	-31.0	gcattgaactTGTGGATAAaatcacggtc	nd	nd
CRP-cyclic-AMP	repressor	rpoHp4	3600880	3600901	-27.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[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 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 Kallipolitis BH,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 Kallipolitis BH,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 Kallipolitis BH,1998. 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 Kallipolitis BH,1998. 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:	[EXP-IDA-BOUNDARIES-DEFINED] 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 -35 -10 +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 It was suggested, from high-throughput screening of maps of transcriptional start sites (TSSs), that the TSS (3600870) assigned for this promoter is an RNA processing site Lacoux C,2020.
Evidence:	[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-AINF-SIMILAR-TO-CONSENSUS] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[1] Erickson JW., et al., 1987 [14] Fujita N., et al., 1987 [3] Huerta AM., et al., 2003 [4] Janaszak A., et al., 2007 [8] Kallipolitis BH., et al., 1998 [6] Nadratowska-Wesolowska B., et al., 2010 [9] Nagai H., et al., 1990 [15] Rhodius VA., et al., 2005 [10] Salgado H, et al., 2012 [11] Yamamoto K., et al., 2005
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[CRP,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CRP-cyclic-AMP	repressor	rpoHp3	3600880	3600901	-20.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[12]
proximal	CRP-cyclic-AMP	repressor	rpoHp3	3600933	3600954	-73.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[12]

[CytR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	CytR	repressor	rpoHp3	3600896	3600912	-33.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]
proximal	CytR	repressor	rpoHp3	3600913	3600932	-52.0	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[8]

[DnaA,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	DnaA-ATP	repressor	rpoHp3	3600914	3600922	-48.0	tgtgcgtaatTTATTCACAagcttgcatt	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	nd

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
CRP-cyclic-AMP	repressor	rpoHp3	3600933	3600954	-73.5	tcttcccggtATTTCATCTCTATGTCACATTTtgtgcgtaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12]
CytR	repressor	rpoHp3	3600913	3600932	-52.0	tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
DnaA-ATP	repressor	rpoHp3	3600914	3600922	-48.0	tgtgcgtaatTTATTCACAagcttgcatt	nd	nd
CytR	repressor	rpoHp3	3600896	3600912	-33.5	ttattcacaaGCTTGCATTGAACTTGTggataaaatc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
CRP-cyclic-AMP	repressor	rpoHp3	3600880	3600901	-20.5	cttgcattgaACTTGTGGATAAAATCACGGTCtgataaaaca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12]

Transcription unit

Name:	rpoH
Gene(s):	rpoH Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Erickson JW., et al., 1987
Promoter
Name:	rpoHp1
+1:	3601003
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	220
Sequence:	acggtacaacatttacgccactttacgcctgaataataaaagcgtgttatactctttcccTgcaatgggttccgtagcagg -35 -10 +1
Note(s):	The σ⁷⁰ and σ^S 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, σ^S, σ⁵⁴, and σ²⁴) cooperatively controlling rpoH (σ³²) gene expression, which provides high flexibility of the stress response Janaszak A,2009
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IPI]
Reference(s):	[1] Erickson JW., et al., 1987 [14] Fujita N., et al., 1987 [3] Huerta AM., et al., 2003 [5] Janaszak A., et al., 2009 [8] Kallipolitis BH., et al., 1998 [6] Nadratowska-Wesolowska B., et al., 2010 [11] Yamamoto K., et al., 2005
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[CpxR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	CpxR-phosphorylated	activator	rpoHp1	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[16]

Transcription unit

Name:	rpoH
Gene(s):	rpoH Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Erickson JW., et al., 1987
Promoter
Name:	rpoHp2
+1:	3601003
Sigma Factor:	Sigma38 Sigmulon
Distance from start of the gene:	220
Sequence:	acggtacaacatttacgccactttacgcctgaataataaaagcgtgttatactctttcccTgcaatgggttccgtagcagg -35 -10 +1
Note(s):	The σ⁷⁰ and σ^S 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, σ^S, σ⁵⁴, and σ²⁴) cooperatively controlling rpoH (σ³²) gene expression, which provides high flexibility of the stress response Janaszak A,2009
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IPI]
Reference(s):	[1] Erickson JW., et al., 1987 [14] Fujita N., et al., 1987 [3] Huerta AM., et al., 2003 [5] Janaszak A., et al., 2009 [8] Kallipolitis BH., et al., 1998 [6] Nadratowska-Wesolowska B., et al., 2010 [11] Yamamoto K., et al., 2005
Terminator(s)
Type:	rho-independent
Sequence:	aaaaacaaaaACCCCGGACTCTCATCCAGGGttctctgctt
Reference(s):	[7] Yura T., et al., 1984

TF binding sites (TFBSs)

[CpxR,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	CpxR-phosphorylated	activator	rpoHp2	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[16]

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IDA] Inferred from direct assay
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[EXP-IMP] Inferred from mutant phenotype
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing
[COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-IPI] Inferred from physical interaction

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] 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
[4] 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
[5] 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
[6] Nadratowska-Wesolowska B., Slominska-Wojewodzka M., Lyzen R., Wegrzyn A., Szalewska-Palasz A., Wegrzyn G., 2010, Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors., Mol Genet Genomics 284(4):289-305
[7] 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
[8] 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
[9] 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
[10] 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.
[11] Yamamoto K., Ishihama A., 2005, Transcriptional response of Escherichia coli to external zinc., J Bacteriol 187(18):6333-40
[12] 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
[13] 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
[14] 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
[15] 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
[16] 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

RegulonDB