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AdiY DNA-binding transcriptional activator

Synonyms: AdiY
Summary:
AdiY is a positive DNA-binding transcriptional regulator that controls the arginine decarboxylase (adi) system, which is strongly induced in rich medium, under anaerobic conditions, and at low pH [2, 3].
Several proteins are involved in the induction of the adi system. Changes in the external pH activate the adiA gene. AdiY may function directly or indirectly with CysB to increase expression of adiA. IHF and H-NS might modulate the bending and necessary access of the adiAp promoter for activation [2]. It has also been proposed that AdiY is not the only regulator of the adi system, but the conditions under which AdiY functions remain unknown [4].
The amino acid sequence of AdiY shows homology to members of the XylS/AraC family of transcriptional regulators [2, 3]. The C-terminal region of proteins from this family features a helix-turn-helix motif. AdiY has a putative transmembrane region, suggesting that it may be a membrane-associated protein [2].
The gene adiY is located downstream of adiA and in the same orientation [2].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AdiY     nd nd
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: adiY
  Genome position: 4337168-4337929
  Length: 762 bp / 253 aa
Operon name: adiY
TU(s) encoding the TF:
Transcription unit        Promoter
adiY
adiYp


Regulon       
Regulated gene(s) adiA, gadA, gadB, gadC, gadX, gltB, gltD, gltF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (3)
glutamate (2)
nitrogen metabolism (2)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
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Regulated operon(s) adiA, gadAXW, gadBC, gltBDF
First gene in the operon(s) adiA, gadA, gadB, gltB
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac
AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB
AdiY,H-NS,IHF
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  AdiY activator adiAp Sigma70 nd nd adiA nd nd [BPP], [GEA] [1], [2]
  AdiY activator gadAp Sigma38 nd nd gadA, gadX nd nd [BPP] [1]
  AdiY activator gadBp Sigma38 nd nd gadB, gadC nd nd [BPP] [1]
  AdiY activator gltBp Sigma70 nd nd gltB, gltD, gltF nd nd [BPP] [1]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol. 10:273

 [2] Stim-Herndon KP., Flores TM., Bennett GN., 1996, Molecular characterization of adiY, a regulatory gene which affects expression of the biodegradative acid-induced arginine decarboxylase gene (adiA) of Escherichia coli., Microbiology. 142 ( Pt 5):1311-20

 [3] Stim-Herndon KP., 1995, Effect of the local anesthetics phenethyl alcohol and procaine on hns mutants of the acid-induced biodegradative arginine (adi) and lysine (cad) decarboxylases of Escherichia coli., Curr Microbiol. 30(5):281-5

 [4] Gong S., Richard H., Foster JW., 2003, YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli., J Bacteriol. 185(15):4402-9

 [5] Bobrovskyy M., Vanderpool CK., 2016, Diverse mechanisms of post-transcriptional repression by the small RNA regulator of glucose-phosphate stress., Mol Microbiol. 99(2):254-73



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