RegulonDB RegulonDB 10.8: 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 20470880 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system 20470880
Reference(s): [1] Hommais F., et al., 2004
[2] Yoshida T., et al., 1993
Promoter
Name: hdeDp
+1: 3656960
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 35
Sequence: taggaaatttttattaaatcgactgcattcttagacgcgtttttggcatagattgatagcAggggattttcttcttaattt
                            -35                  -10        +1                   
Note(s):

Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[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 GadE1 activator hdeDp 3656899 3656918 -51.5 gatactgcaaTTAGGAAATTTTTATTAAATcgactgcatt nd [AIBSCS], [APIORCISFBSCS], [BPP], , [CV(GEA)], [CV(GEA)], [GEA], [IHBCE], [1], [3], [5], [7], [9]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadX1 activator hdeDp 3656835 3656854 -115.5 atgttgatggAAAATATCAAAATCAGATATttttatttca nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [8], [9]
remote GadX2 activator hdeDp 3656856 3656875 -94.5 atcagatattTTTATTTCAATACAATGAGTtacagatgca nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [7], [8], [9]
[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-NS1 repressor hdeDp nd nd nd nd nd [BPP], [GEA] [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], [CV(GEA)], [CV(GEA)], [GEA] [6]
[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-Pasp56 activator hdeDp nd nd nd nd nd [GEA] [10]
Note(s): 1GadE is the main activator of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008.1Microarray analyses have shown that the hdeD gene is activated by the transcriptional regulator GadX, but it is not known if the effect of the regulator on the gene is direct or indirect. The positive regulation of hdeD by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
2Microarray analyses have shown that the hdeD gene is activated by the transcriptional regulator GadX, but it is not known if the effect of the regulator on the gene is direct or indirect. The positive regulation of hdeD by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.1The H-NS site for the hdeD regulatory region hasn't been determined, but Yoshida93 suggested that H-NS has two sites: one site near hdeD and the other one close to hdeA (the upstream operon in the opposite direction) and that H-NS represses transcription through the DNA binding to supercoil it or DNA already supercoiled. Futrher experiments are requiered to test this proposal.2Microarray analyses have shown that the hdeD gene is activated by the transcriptional regulator GadX, but it is not known if the effect of the regulator on the gene is direct or indirect. The positive regulation of hdeD by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
3Microarray analyses have shown that the hdeD gene is activated by the transcriptional regulator GadX, but it is not known if the effect of the regulator on the gene is direct or indirect. The positive regulation of hdeD by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
4GadE is the main activator of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008.
6The H-NS site for the hdeD regulatory region hasn't been determined, but Yoshida93 suggested that H-NS has two sites: one site near hdeD and the other one close to hdeA (the upstream operon in the opposite direction) and that H-NS represses transcription through the DNA binding to supercoil it or DNA already supercoiled. Futrher experiments are requiered to test this proposal.


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [HIPP] Human inference of promoter position

 [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

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

 [BPP] Binding of purified proteins

 [CEUMA] ChIP-exo evidence used in manual assertion

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


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] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

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