RegulonDB RegulonDB 10.8: Gene Form
   

gadE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gadE gadF arrS FliZ CRP GadE GadE PhoP GadE TSS_4127 TSS_4127 TSS_4126 TSS_4126 gadEp gadEp gadEp1 gadEp1 gadEp4 gadEp4 arrSp arrSp

Gene      
Name: gadE    Texpresso search in the literature
Synonym(s): ECK3496, EG11544, b3512, yhiE, yhiT
Genome position(nucleotides): 3658366 --> 3658893 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
32.95
Note(s): The gadE gene expression could be repressed in a direct or indirect way by the OmpR protein. Since, using a gene array system, a repression of this gene was observed as a result of an up mutation in the ompR gene Brombacher E,2003.
External database links:  
ASAP:
ABE-0011475
ECHOBASE:
EB1506
OU-MICROARRAY:
b3512
PortEco:
gadE
STRING:
511145.b3512
COLOMBOS: gadE


Product      
Name: DNA-binding transcriptional activator GadE
Synonym(s): GadE, YhiE, YhiT, acid-responsive regulator of gadA and gadBC
Sequence: Get amino acid sequence Fasta Format
Regulator Family: LuxR/UhpA
Cellular location: cytosol
Molecular weight: 20.599
Isoelectric point: 10.365
Motif(s):
 
Type Positions Sequence
133 -> 152 ESNITSTLNISQQTLKIQKF
109 -> 174 HKNSQLCFSHNQFKIMQLILKNKNESNITSTLNISQQTLKIQKFNIMYKLKLRRMSDIVTLGITSY
117 -> 167 SHNQFKIMQLILKNKNESNITSTLNISQQTLKIQKFNIMYKLKLRRMSDIV

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [IE] Inferred from experiment
Reference(s): [1] Bordi C., et al., 2003
[2] Griffith JM., et al., 2019
[3] Hersch SJ., et al., 2020
[4] Hommais F., et al., 2004
[5] Ma Z., et al., 2003
[6] Masuda N., et al., 2002
[7] Masuda N., et al., 2003
[8] Tatsuno I., et al., 2003
[9] Tucker DL., et al., 2002
External database links:  
DIP:
DIP-48091N
ECOCYC:
EG11544-MONOMER
ECOLIWIKI:
b3512
INTERPRO:
IPR016032
INTERPRO:
IPR000792
INTERPRO:
IPR036388
PFAM:
PF00196
PRIDE:
P63204
PRODB:
PRO_000022743
PROSITE:
PS50043
REFSEQ:
NP_417969
SMR:
P63204
UNIPROT:
P63204


Operon      
Name: gadEF-mdtEF         
Operon arrangement:
Transcription unit        Promoter
gadE
gadE-mdtEF
gadE
gadEF-mdtEF
mdtEF
mdtEF
mdtEF


Transcriptional Regulation      
Display Regulation             
Activated by: EvgA, GadX, PhoP, GadW, ArcA, YdeO, GadE
Repressed by: CRP, FliZ, H-NS


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4126 3658886 forward nd [RS-EPT-CBR] [10]
  promoter TSS_4127 3658889 forward nd [RS-EPT-CBR] [10]


Evidence    

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



Reference(s)    

 [1] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23

 [2] Griffith JM., Basting PJ., Bischof KM., Wrona EP., Kunka KS., Tancredi AC., Moore JP., Hyman MRL., Slonczewski JL., 2019, Experimental Evolution of Escherichia coli K-12 in the Presence of Proton Motive Force (PMF) Uncoupler Carbonyl Cyanide m -Chlorophenylhydrazone Selects for Mutations Affecting PMF-Driven Drug Efflux Pumps., Appl Environ Microbiol 85(5)

 [3] Hersch SJ., Watanabe N., Stietz MS., Manera K., Kamal F., Burkinshaw B., Lam L., Pun A., Li M., Savchenko A., Dong TG., 2020, Envelope stress responses defend against type six secretion system attacks independently of immunity proteins., Nat Microbiol

 [4] 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

 [5] Ma Z., Gong S., Richard H., Tucker DL., Conway T., Foster JW., 2003, GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12., Mol Microbiol 49(5):1309-20

 [6] Masuda N., Church GM., 2002, Escherichia coli gene expression responsive to levels of the response regulator EvgA., J Bacteriol 184(22):6225-34

 [7] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [8] Tatsuno I., Nagano K., Taguchi K., Rong L., Mori H., Sasakawa C., 2003, Increased adherence to Caco-2 cells caused by disruption of the yhiE and yhiF genes in enterohemorrhagic Escherichia coli O157:H7., Infect Immun 71(5):2598-606

 [9] Tucker DL., Tucker N., Conway T., 2002, Gene expression profiling of the pH response in Escherichia coli., J Bacteriol 184(23):6551-8

 [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.


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