RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

rseD-rpoE-rseABC operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	rseD-rpoE-rseABC
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	rseABC
Gene(s):	rseC, rseB, rseA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997 [2] Rhodius VA., et al., 2005
Promoter
Name:	rseAp3
+1:	2709632
Sigma Factor:	Sigma24 Sigmulon
Distance from start of the gene:	228
Sequence:	aagtggcggcgcgttgaaagaaatttcgaaccctgagaacttaatgttgtcagaagaactGagacagatagttttccgaac -35 -10 +1
Note(s):	Presumably there is an internal promoter at the 3' end of the rpoE gene that directs constitutive expression of rseA, thus leading to inhibition of σ^E activity. However, Rhodius VA,2005 determined that the rseABC genes were transcribed from a σ^E-type promoter. This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence:	[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-AINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[3] Huerta AM., et al., 2003 [1] Missiakas D., et al., 1997 [2] Rhodius VA., et al., 2005

Allosteric regulation of RNA-polymerase

Regulator	Function	Promoter target of RNApol	Growth Conditions	Evidence	Reference
DksA	activation	rseAp3	nd	[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] [EXP-IEP]	[4]
DksA-ppGpp	activation	rseAp3	nd	[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] [EXP-IEP]	[4]
ppGpp	activation	rseAp3	nd	[EXP-IEP]	[4]

Evidence:	[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins [EXP-IEP] Inferred from expression pattern
Reference(s):	[4] Costanzo A., et al., 2008

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE Genome Browser M3D Gene expression COLOMBOS
Note(s):	Further genetic characterization and sequence analysis showed that rpoE is part of a four-gene operon (rpoE-rseA-rseB-rseC). An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-More et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σ^E pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-More et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP] Inferred from expression pattern [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp2a
+1:	2710087
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	75
Sequence:	tgacaaacaaaaacagatgcgttacggaactttacaaaaacgagacactctaaccctttgCttgctcaaattgcagctaat -35 -10 +1
Note(s):	The transcription initiation of rpoEp2 was determined by S1 mapping, and it was 4 nucleotides upstream from the site previously identified. This promoter was induced by zinc in a microarray analysis Yamamoto K,2005 The NsrR transcriptional repressor inhibits the activity of the rpoEp2 promoter, but it is not known if this effect is direct or indirect Thompson KM,2007 This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[3] Huerta AM., et al., 2003 [5] Klein G., et al., 2016 [1] Missiakas D., et al., 1997 [6] Raina S., et al., 1995 [7] Rouviere PE., et al., 1995 [8] Yamamoto K., et al., 2005

Allosteric regulation of RNA-polymerase

Regulator	Function	Promoter target of RNApol	Growth Conditions	Evidence	Reference
DksA	activation	rpoEp2a	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]
DksA-ppGpp	activation	rpoEp2a	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]
ppGpp	activation	rpoEp2a	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[9] Gopalkrishnan S., et al., 2014

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE Genome Browser M3D Gene expression COLOMBOS
Note(s):	Further genetic characterization and sequence analysis showed that rpoE is part of a four-gene operon (rpoE-rseA-rseB-rseC). An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-More et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σ^E pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-More et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP] Inferred from expression pattern [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp
+1:	2710087
Sigma Factor:	Sigma24 Sigmulon
Distance from start of the gene:	75
Sequence:	tgacaaacaaaaacagatgcgttacggaactttacaaaaacgagacactctaaccctttgCttgctcaaattgcagctaat -35 -10 +1
Note(s):	The transcription initiation of rpoEp2 was determined by S1 mapping, and it was 4 nucleotides upstream from the site previously identified. This promoter was induced by zinc in a microarray analysis Yamamoto K,2005 The NsrR transcriptional repressor inhibits the activity of the rpoEp2 promoter, but it is not known if this effect is direct or indirect Thompson KM,2007 This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[3] Huerta AM., et al., 2003 [5] Klein G., et al., 2016 [1] Missiakas D., et al., 1997 [6] Raina S., et al., 1995 [7] Rouviere PE., et al., 1995 [8] Yamamoto K., et al., 2005

Allosteric regulation of RNA-polymerase

Regulator	Function	Promoter target of RNApol	Growth Conditions	Evidence	Reference
DksA	activation	rpoEp	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]
DksA-ppGpp	activation	rpoEp	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]
ppGpp	activation	rpoEp	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[9] Gopalkrishnan S., et al., 2014

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp5
+1:	2710165
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	153
Sequence:	aatgggcatttctacacagataatgcgatgttcagattctgtagacttataatgatagatAatgatccgtctacagcatga -35 -10 +1
Note(s):	With the rpoEp1b and rpoEp5 promoters, no specific growth conditions or regulatory factors could be identified that altered their activity Klein G,2016
Evidence:	[COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Klein G., et al., 2016

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE, rseD Genome Browser M3D Gene expression COLOMBOS
Note(s):	Further genetic characterization and sequence analysis showed that rpoE is part of a four-gene operon (rpoE-rseA-rseB-rseC). An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σ^E pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Missiakas D., et al., 1997 [6] Raina S., et al., 1995
Promoter
Name:	rpoEp1a
+1:	2710186
Distance from start of the gene:	22
Sequence:	gggttactcttcaggcagttaaatgggcatttctacacagataatgcgatgttcagattcTgtagacttataatgatagat
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Raina S., et al., 1995 [8] Yamamoto K., et al., 2005

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)
remote	CpxR-phosphorylated	repressor	rpoEp1a	2710119	2710120	67.0	tgcgttacggAactttacaaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[10]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
CpxR-phosphorylated	repressor	rpoEp1a	2710119	2710120	67.0	tgcgttacggAactttacaaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[10]

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE, rseD Genome Browser M3D Gene expression COLOMBOS
Note(s):	rpoEp4 is regulated by RpoS and it is induced upon a shift to high osmolarity. On the other hand, factors that control RpoS transcription/stability, such as ArcAB, RssB, RprA, and PcnB, were identified that affect rpoEp4 activity Klein G,2016 Overexpresion of the fliZ gene repressed rpoEp4 promoter activity by 40% Klein G,2016
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp4
+1:	2710230
Sigma Factor:	Sigma38 Sigmulon
Distance from start of the gene:	66
Sequence:	ttactggctggtggaggattaggtggtgaaataaaaaggccgttgggttactcttcaggcAgttaaatgggcatttctaca -35 -10 +1
Evidence:	[COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IPI] [RS-EPT-CBR]
Reference(s):	[5] Klein G., et al., 2016 [11] Salgado H, et al., 2012

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE, rseD Genome Browser M3D Gene expression COLOMBOS
Note(s):	The rpoEp2b promoter controlled by RpoN is positively regulated by GlrR and NtrC transcriptional activators. GlrR is the main activator/enhancer of the rpoEp2b promoter controlled by RpoN and it provides a link between RpoN and RpoE via the GlrR/GlrK two-component system Klein G,2016 The rpoEp2b promoter controlled by RpoN senses lipopolysaccharide (LPS) defects Klein G,2016 The rpoEp2b promoter controlled by RpoD is positively regulated by the Rcs system in response to defects in lipopolysaccharide (LPS) in an RcsB-dependent manner and by the CRP transcriptional dual regulator Klein G,2016 Mutations in the yqjA-mzrA operon influence rpoE transcription through the rpoEp2b promoter controlled by RpoD Klein G,2016 Based on gene expression analysis, it was determined that Fis represses rpoE expression Amores GR,2017
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rseDp
+1:	2710339
Sigma Factor:	Sigma54 Sigmulon
Distance from start of the gene:	175
Sequence:	aacatggtttggtcagcatagcatcatgttgtgcggataaacacctgctattttaatattTgttacagttgctaaacacgc -24 -12 +1
Evidence:	[COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IPI]
Reference(s):	[5] Klein G., et al., 2016

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	rseDp	2710354	2710371	-23.0	tagcatcatgTTGTGCGGATAAACACCTgctattttaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]

[GlrR,+] 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	GlrR-phosphorylated	activator	rseDp	2710357	2710374	-26.5	gcatagcatcATGTTGTGCGGATAAACAcctgctattt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]
proximal	GlrR-phosphorylated	activator	rseDp	2710396	2710413	-65.5	tcattttcttTGTTTAATTTACTAAACAtggtttggtc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]
proximal	GlrR-phosphorylated	activator	rseDp	2710420	2710440	-90.5	cgtcacatgaATGTTCAGGGAGAGTATTCATtttctttgtt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]

[NtrC,+] 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	NtrC-phosphorylated	activator	rseDp	2710364	2710382	-33.5	tttggtcagcATAGCATCATGTTGTGCGGataaacacct	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[5]

[RcsB,+] 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	RcsB-phosphorylated	activator	rseDp	2710385	2710398	-52.5	aatttactaaACATGGTTTGGTCAgcatagcatc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[5]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
GlrR-phosphorylated	activator	rseDp	2710420	2710440	-90.5	cgtcacatgaATGTTCAGGGAGAGTATTCATtttctttgtt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
GlrR-phosphorylated	activator	rseDp	2710396	2710413	-65.5	tcattttcttTGTTTAATTTACTAAACAtggtttggtc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
RcsB-phosphorylated	activator	rseDp	2710385	2710398	-52.5	aatttactaaACATGGTTTGGTCAgcatagcatc	nd	[5]
NtrC-phosphorylated	activator	rseDp	2710364	2710382	-33.5	tttggtcagcATAGCATCATGTTGTGCGGataaacacct	nd	[5]
GlrR-phosphorylated	activator	rseDp	2710357	2710374	-26.5	gcatagcatcATGTTGTGCGGATAAACAcctgctattt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
CRP-cyclic-AMP	activator	rseDp	2710354	2710371	-23.0	tagcatcatgTTGTGCGGATAAACACCTgctattttaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE, rseD Genome Browser M3D Gene expression COLOMBOS
Note(s):	The rpoEp2b promoter controlled by RpoN is positively regulated by GlrR and NtrC transcriptional activators. GlrR is the main activator/enhancer of the rpoEp2b promoter controlled by RpoN and it provides a link between RpoN and RpoE via the GlrR/GlrK two-component system Klein G,2016 The rpoEp2b promoter controlled by RpoN senses lipopolysaccharide (LPS) defects Klein G,2016 The rpoEp2b promoter controlled by RpoD is positively regulated by the Rcs system in response to defects in lipopolysaccharide (LPS) in an RcsB-dependent manner and by the CRP transcriptional dual regulator Klein G,2016 Mutations in the yqjA-mzrA operon influence rpoE transcription through the rpoEp2b promoter controlled by RpoD Klein G,2016 Based on gene expression analysis, it was determined that Fis represses rpoE expression Amores GR,2017
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp2b
+1:	2710339
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	175
Sequence:	aacatggtttggtcagcatagcatcatgttgtgcggataaacacctgctattttaatattTgttacagttgctaaacacgc -35 -10 +1
Evidence:	[COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IPI]
Reference(s):	[5] Klein G., et al., 2016

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	rpoEp2b	2710354	2710371	-23.0	tagcatcatgTTGTGCGGATAAACACCTgctattttaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]

[GlrR,+] 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	GlrR-phosphorylated	activator	rpoEp2b	2710357	2710374	-26.5	gcatagcatcATGTTGTGCGGATAAACAcctgctattt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]
proximal	GlrR-phosphorylated	activator	rpoEp2b	2710396	2710413	-65.5	tcattttcttTGTTTAATTTACTAAACAtggtttggtc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]
proximal	GlrR-phosphorylated	activator	rpoEp2b	2710420	2710440	-90.5	cgtcacatgaATGTTCAGGGAGAGTATTCATtttctttgtt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[5]

[NtrC,+] 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	NtrC-phosphorylated	activator	rpoEp2b	2710364	2710382	-33.5	tttggtcagcATAGCATCATGTTGTGCGGataaacacct	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[5]

[RcsB,+] 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	RcsB-phosphorylated	activator	rpoEp2b	2710385	2710398	-52.5	aatttactaaACATGGTTTGGTCAgcatagcatc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[5]

Transcription unit

Name:	rpoE-rseABC
Gene(s):	rseC, rseB, rseA, rpoE, rseD Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Missiakas D., et al., 1997
Promoter
Name:	rpoEp1b
+1:	2710393
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	229
Sequence:	acacgtcacatgaatgttcagggagagtattcattttctttgtttaatttactaaacatgGtttggtcagcatagcatcat -35 -10 +1
Note(s):	With the rpoEp1b and rpoEp5 promoters, no specific growth conditions or regulatory factors could be identified that altered their activity Klein G,2016
Evidence:	[COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Klein G., et al., 2016

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)
proximal	IHF	repressor	rpoEp1b	2710447	2710459	-59.5	ccgctaccgaTAATCAACACGTCacatgaatgt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [IC]	W	[5], [12]

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Translational
Strand:	reverse

	Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
	terminator	-6.5	2710011	2710034	tggaaatttgGTTTGGGGAGACTTTACCTCGGAtgagcgagca

Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[EXP-IDA] Inferred from direct assay
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IEP] Inferred from expression pattern
[EXP-IPI] Inferred from physical interaction
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[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-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IMP-SITE-MUTATION] Site mutation
[IC] Inferred by curator

Reference(s)
[1] Missiakas D., Mayer MP., Lemaire M., Georgopoulos C., Raina S., 1997, Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins., Mol Microbiol 24(2):355-71
[2] 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
[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] Costanzo A., Nicoloff H., Barchinger SE., Banta AB., Gourse RL., Ades SE., 2008, ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms., Mol Microbiol 67(3):619-32
[5] Klein G., Stupak A., Biernacka D., Wojtkiewicz P., Lindner B., Raina S., 2016, Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective., J Biol Chem 291(44):22999-23019
[6] Raina S., Missiakas D., Georgopoulos C., 1995, The rpoE gene encoding the sigma E (sigma 24) heat shock sigma factor of Escherichia coli., EMBO J 14(5):1043-55
[7] Rouviere PE., De Las Penas A., Mecsas J., Lu CZ., Rudd KE., Gross CA., 1995, rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli., EMBO J 14(5):1032-42
[8] Yamamoto K., Ishihama A., 2005, Transcriptional response of Escherichia coli to external zinc., J Bacteriol 187(18):6333-40
[9] Gopalkrishnan S., Nicoloff H., Ades SE., 2014, Co-ordinated regulation of the extracytoplasmic stress factor, sigmaE, with other Escherichia coli sigma factors by (p)ppGpp and DksA may be achieved by specific regulation of individual holoenzymes., Mol Microbiol 93(3):479-93
[10] De Wulf P., McGuire AM., Liu X., Lin EC., 2002, Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli., J Biol Chem 277(29):26652-61
[11] 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.
[12] Amores GR., de Las Heras A., Sanches-Medeiros A., Elfick A., Silva-Rocha R., 2017, Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli., Sci Rep 7(1):16768

RegulonDB