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AppY DNA-binding transcriptional activator

Synonyms: AppY
The AppY, acid phosphatase, transcriptional regulator induces the expression of energy metabolism genes under anaerobiosis, stationary phase, and phosphate starvation. Under these same conditions, the expression of the appY gene is induced [2, 5]. The genes regulated by AppY have promoters that are recognized by both σ70 and σ38; AppY activates their transcription when any of these σ factors is bound to the RNA polymerase [5]. The specific AppY binding site has not yet been identified.
When AppY is overproduced, the expression of 30 proteins is induced or repressed in a growth phase-dependent fashion. Overproduction of AppY also causes an elevated spontaneous mutation rate. Therefore, it is possible that this protein regulates genes involved in DNA replication, recombination, or repair [6].
AppY, which belongs to the AraC/XylS family, has a C-terminal DNA-binding domain that shows a helix-turn-helix motif [7, 8].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AppY     nd nd
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: appY
  Genome position: 583681-584430
  Length: 750 bp / 249 aa
Operon name: appY
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) appA, appB, appC, appX, hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
aerobic respiration (6)
anaerobic respiration (6)
membrane (3)
electron donors (3)
electron acceptors (2)
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Regulated operon(s) appCBXA, hyaABCDEF
First gene in the operon(s) appC, hyaA
Simple and complex regulons AppY,ArcA,Fis,IscR,NarL,NarP,YdeO
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
  AppY activator appCp Sigma70 nd nd appC, appB, appX, appA nd nd [GEA] [1], [2]
  AppY activator hyaAp Sigma70 nd nd hyaA, hyaB, hyaC, hyaD, hyaE, hyaF nd nd [GEA] [3], [4]

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


 [GEA] Gene expression analysis


 [1] Atlung T., Brondsted L., 1994, Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase., J Bacteriol. 176(17):5414-22

 [2] Brondsted L., Atlung T., 1996, Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli., J Bacteriol. 178(6):1556-64

 [3] Brondsted L., Atlung T., 1994, Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli., J Bacteriol. 176(17):5423-8

 [4] King PW., Przybyla AE., 1999, Response of hya expression to external pH in Escherichia coli., J Bacteriol. 181(17):5250-6

 [5] Atlung T., Knudsen K., Heerfordt L., Brondsted L., 1997, Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation., J Bacteriol. 179(7):2141-6

 [6] Yang H., Wolff E., Kim M., Diep A., Miller JH., 2004, Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach., Mol Microbiol. 53(1):283-95

 [7] Atlung T., Nielsen A., Hansen FG., 1989, Isolation, characterization, and nucleotide sequence of appY, a regulatory gene for growth-phase-dependent gene expression in Escherichia coli., J Bacteriol. 171(3):1683-91

 [8] Gallegos MT., Michan C., Ramos JL., 1993, The XylS/AraC family of regulators., Nucleic Acids Res. 21(4):807-10