RegulonDB RegulonDB 10.8: 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: [ITC] 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 σE activity. However, Rhodius VA,2005 determined that the rseABC genes were transcribed from a σE-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: [AIPP]
[TIM]
Reference(s): [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 Note Evidence Reference
  DksA activation rseAp3   [BPP]
[IEP]
[3]
  DksA-ppGpp activation rseAp3   [BPP]
[IEP]
[3]
  ppGpp activation rseAp3   [IEP] [3]
Evidence: [BPP] Binding of purified proteins
[IEP] Inferred from expression pattern
Reference(s): [3] 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 σE 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 19763168
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 19763168
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITC] Inferred through co-regulation
Reference(s): [1] Missiakas D., et al., 1997
Promoter
Name: rpoEp2a
+1: 2710087
Sigma Factor: Sigma70, Sigma24
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: [HIPP]
[TIM]
Reference(s): [4] Klein G., et al., 2016
[1] Missiakas D., et al., 1997
[5] Raina S., et al., 1995
[6] Rouviere PE., et al., 1995
[7] Yamamoto K., et al., 2005
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA activation rpoEp2a   [GEA] [8]
  DksA-ppGpp activation rpoEp2a   [GEA] [8]
  ppGpp activation rpoEp2a   [GEA] [8]
Evidence: [GEA] Gene expression analysis
Reference(s): [8] Gopalkrishnan S., et al., 2014


Transcription unit       
Name: rpoE-rseABC
Gene(s): rseC, rseB, rseA, rpoE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITC] 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: [TIM]
Reference(s): [4] 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 σE 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 19763168
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 19763168
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Missiakas D., et al., 1997
[5] Raina S., et al., 1995
Promoter
Name: rpoEp1a
+1: 2710186
Distance from start of the gene: 22
Sequence: gggttactcttcaggcagttaaatgggcatttctacacagataatgcgatgttcagattcTgtagacttataatgatagat
Note(s): There are no obvious σ70 consensus promoter sequences upstream of this promoter.
Evidence: [TIM]
Reference(s): [5] Raina S., et al., 1995
[7] Yamamoto K., et al., 2005
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 CpxR-Phosphorylated repressor rpoEp1a 2710113 2710127 67.0 aaacagatgcGTTACGGAACTTTACaaaaacgaga nd [AIBSCS], [CV(GEA)], [GEA] [9]


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: [BTEI] Boundaries of transcription experimentally identified
[ITC] 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: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Klein G., et al., 2016
[10] 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: [BTEI] Boundaries of transcription experimentally identified
[ITC] Inferred through co-regulation
Reference(s): [1] Missiakas D., et al., 1997
Promoter
Name: rpoEp2b
+1: 2710339
Sigma Factor: Sigma70, Sigma54
Distance from start of the gene: 175
Sequence: aacatggtttggtcagcatagcatcatgttgtgcggataaacacctgctattttaatattTgttacagttgctaaacacgc
                          -35                    -10        +1                   
Evidence: [TIM]
Reference(s): [4] Klein G., et al., 2016
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 rpoEp2b 2710354 2710371 -23.0 tagcatcatgTTGTGCGGATAAACACCTgctattttaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GlrR-Pasp56 activator rpoEp2b 2710357 2710374 -26.5 gcatagcatcATGTTGTGCGGATAAACAcctgctattt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
proximal GlrR-Pasp56 activator rpoEp2b 2710396 2710413 -65.5 tcattttcttTGTTTAATTTACTAAACAtggtttggtc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
proximal GlrR-Pasp56 activator rpoEp2b 2710420 2710440 -90.5 cgtcacatgaATGTTCAGGGAGAGTATTCATtttctttgtt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NtrC-Pasp activator rpoEp2b 2710364 2710382 -33.5 tttggtcagcATAGCATCATGTTGTGCGGataaacacct nd [APIORCISFBSCS], [BPP] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-Pasp56 activator rpoEp2b 2710385 2710398 -52.5 aatttactaaACATGGTTTGGTCAgcatagcatc nd [APIORCISFBSCS], [BPP], [CV(SM)], [SM] [4]


Transcription unit          
Name: rpoE-rseABC
Gene(s): rseC, rseB, rseA, rpoE, rseD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITC] 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: [TIM]
Reference(s): [4] Klein G., et al., 2016
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 IHF1 repressor rpoEp1b 2710447 2710459 -59.5 ccgctaccgaTAATCAACACGTCacatgaatgt nd [APIORCISFBSCS], [CV(GEA)], [GEA], [IC] [4], [11]
Note(s): 1The effect of IHF at the upstream region of rpoEp1b was determined based on that position; IHF usually functions as an activator of the transcription Klein G,2016. However, based on gene expression analysis, it was determined that IHF represses rpoE expression Amores GR,20171The effect of IHF at the upstream region of rpoEp1b was determined based on that position; IHF usually functions as an activator of the transcription Klein G,2016. However, based on gene expression analysis, it was determined that IHF represses rpoE expression Amores GR,2017


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"




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] 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

 [4] 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

 [5] 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

 [6] 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

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

 [8] 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

 [9] 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

 [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] 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


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