RegulonDB RegulonDB 10.7: 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
REGULONDB:
b3512
STRING:
511145.b3512
M3D: gadE
COLOMBOS: gadE
PortEco: b3512


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
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] Hommais F., et al., 2004
[4] Ma Z., et al., 2003
[5] Masuda N., et al., 2002
[6] Masuda N., et al., 2003
[7] Tatsuno I., et al., 2003
[8] Tucker DL., et al., 2002
External database links:  
DIP:
DIP-48091N
ECOCYC:
EG11544-MONOMER
ECOLIWIKI:
b3512
INTERPRO:
IPR000792
INTERPRO:
IPR016032
INTERPRO:
IPR036388
PFAM:
PF00196
PRIDE:
P63204
PRODB:
PRO_000022743
PROSITE:
PS50043
PROTEINMODELPORTAL:
P63204
REFSEQ:
NP_417969
SMR:
P63204
UNIPROT:
P63204


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


Transcriptional Regulation      
Display Regulation             
Activated by: EvgA, GadX, PhoP, ArcA, GadW, 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] [9]
  promoter TSS_4127 3658889 forward nd [RS-EPT-CBR] [9]


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] 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

 [4] 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

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

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

 [7] 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

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

 [9] 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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