RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: hdeD
Gene(s): hdeD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The positive regulation of the hdeD gene by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
The transcription of hdeD appears to be increased under acidic growth conditions during stationary and exponential phases in a RcsB-dependent manner Johnson MD,2011
Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010
Reference(s): [1] Hommais F., et al., 2004
[2] Yoshida T., et al., 1993
Promoter
Name: hdeDp2
+1: 3656960
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 35
Sequence: taggaaatttttattaaatcgactgcattcttagacgcgtttttggcatagattgatagcAggggattttcttcttaattt
Evidence: [HIPP]
[IEP]
[IPI]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Hommais F., et al., 2004
[3] Itou J., et al., 2009
[4] Salgado H, et al., 2012
[5] Seo SW., et al., 2015
TF binding sites (TFBSs)
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadE activator hdeDp2 3656899 3656918 -51.5 gatactgcaaTTAGGAAATTTTTATTAAATcgactgcatt nd [AIBSCS], [BPP], [GEA], [RSE], [AIBSCS], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] [1], [5], [8]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadX activator hdeDp2 3656835 3656854 -115.5 atgttgatggAAAATATCAAAATCAGATATttttatttca nd [APIORCISFBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [1], [8], [9], [10]
remote GadX activator hdeDp2 3656856 3656875 -94.5 atcagatattTTTATTTCAATACAATGAGTtacagatgca nd [AIBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [1], [8], [9], [10]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor hdeDp2 nd nd nd nd nd [GEA], [BPP] [2]
[PhoP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-phosphorylated activator hdeDp2 3656815 3656831 -137.0 cctggttttcTGTATATGTCATGTTGAtggaaaatat nd [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] [7]
[RcsB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsB-phosphorylated activator hdeDp2 nd nd nd nd nd [GEA], [BPP] [11]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA CyaR hdeD repressor 3656985 3656994 GGGUGGUUCU TRANSLATION-BLOCKING, MRNA-DEGRADATION [IEP], [IPI], [SM] [6]
small regulatory RNA RprA hdeD repressor 3656960 3656970 AGGGGAUUUUC TRANSLATION-BLOCKING [GEA], [SM] [6]
small regulatory RNA RprA hdeD repressor 3656985 3656997 GGGUGGUUCUAUG TRANSLATION-BLOCKING [IEP], [IMP] [6]


Transcription unit          
Name: hdeD
Gene(s): hdeD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The positive regulation of the hdeD gene by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
The transcription of hdeD appears to be increased under acidic growth conditions during stationary and exponential phases in a RcsB-dependent manner Johnson MD,2011
Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010
Reference(s): [1] Hommais F., et al., 2004
[2] Yoshida T., et al., 1993
Promoter
Name: hdeDp
+1: 3656960
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: taggaaatttttattaaatcgactgcattcttagacgcgtttttggcatagattgatagcAggggattttcttcttaattt
                            -35                  -10        +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Hommais F., et al., 2004
[12] Huerta AM., et al., 2003
[3] Itou J., et al., 2009
[4] Salgado H, et al., 2012
[5] Seo SW., et al., 2015
TF binding sites (TFBSs)
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadE activator hdeDp 3656899 3656918 -51.5 gatactgcaaTTAGGAAATTTTTATTAAATcgactgcatt nd [AIBSCS], [BPP], [GEA], [RSE], [AIBSCS], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] [1], [5], [8]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadX activator hdeDp 3656835 3656854 -115.5 atgttgatggAAAATATCAAAATCAGATATttttatttca nd [APIORCISFBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [1], [8], [9], [10]
remote GadX activator hdeDp 3656856 3656875 -94.5 atcagatattTTTATTTCAATACAATGAGTtacagatgca nd [AIBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [1], [8], [9], [10]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor hdeDp nd nd nd nd nd [GEA], [BPP] [2]
[PhoP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-phosphorylated activator hdeDp 3656815 3656831 -137.0 cctggttttcTGTATATGTCATGTTGAtggaaaatat nd [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] [7]
[RcsB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsB-phosphorylated activator hdeDp nd nd nd nd nd [GEA], [BPP] [11]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA CyaR hdeD repressor 3656985 3656994 GGGUGGUUCU TRANSLATION-BLOCKING, MRNA-DEGRADATION [IEP], [IPI], [SM] [6]
small regulatory RNA RprA hdeD repressor 3656960 3656970 AGGGGAUUUUC TRANSLATION-BLOCKING [GEA], [SM] [6]
small regulatory RNA RprA hdeD repressor 3656985 3656997 GGGUGGUUCUAUG TRANSLATION-BLOCKING [IEP], [IMP] [6]


Evidence    

 [HIPP] Human inference of promoter position

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [RSE] RNA-seq evidence

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [SM] Site mutation

 [IMP] Inferred from mutant phenotype

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [2] Yoshida T., Ueguchi C., Yamada H., Mizuno T., 1993, Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant., Mol Gen Genet 237(1-2):113-22

 [3] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [4] 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.

 [5] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [6] Lalaouna D., Prevost K., Laliberte G., Houe V., Masse E., 2018, Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli., Nucleic Acids Res 46(5):2600-2612

 [7] Zwir I., Shin D., Kato A., Nishino K., Latifi T., Solomon F., Hare JM., Huang H., Groisman EA., 2005, Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica., Proc Natl Acad Sci U S A 102(8):2862-7

 [8] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol 190(4):1290-7

 [9] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82

 [10] Tucker DL., Tucker N., Ma Z., Foster JW., Miranda RL., Cohen PS., Conway T., 2003, Genes of the GadX-GadW regulon in Escherichia coli., J Bacteriol 185(10):3190-201

 [11] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [12] 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

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