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HyfR DNA-binding transcriptional activator

Synonyms: HyfR
Summary:
HyfR , hydrogenase four regulator, controls the expression of genes responsible for the proton-translocating formate hydrogenase system and for formate transport under anaerobiosis, low pH, and post-exponential growth conditions |CITS:[ 9387241]|.
As a member of the group of σ54-dependent transcriptional regulators, HyfR contains three domains: the sensory domain, located in the N terminus; the central domain, involved in open complex formation, ATP hydrolysis, and interaction with σ54, and the C-terminal domain, which contains a helix-turn-helix motif for DNA binding |CITS:[ 9387241]|. An iron-sulfur cluster and a metal cofactor (possibly a similar metal or formate) have been proposed as the signals sensed by HyfR |CITS:[12426353]|.
HyfR shows 46% identity to FhlA, a member of the same group. These proteins are dissimilar in their N-terminal regions, which in FhlA recognizes formate. However, they show only one different residue in their helix-turn-helix motif, suggesting that they recognize similar DNA-binding sites |CITS:[9387241]|.
The HyfR protein is autoregulated. The gene that codes for it is the 11th in the hyf operon, which contains 12 genes that are not expressed at significant levels. This operon is induced under anaerobiosis, at low pH, and under fermentative conditions by formate, and it is subject to catabolite repression |CITS:[14702328][ 12426353]|.


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
HyfR     nd nd
Evolutionary Family: EBP
Connectivity class: Local Regulator
Gene name: hyfR
  Genome position: 2611900-2613912
  Length: 2013 bp / 670 aa
Operon name: hyfABCDEFGHIJR-focB
TU(s) encoding the TF:
Transcription unit        Promoter
hyfABCDEFGHIJR-focB
hyfAp


Regulon       
Regulated gene(s) focB, hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
anaerobic respiration (10)
membrane (6)
Porters (Uni-, Sym- and Antiporters) (1)
protein related (1)
Transcription related (1)
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Regulated operon(s) hyfABCDEFGHIJR-focB
First gene in the operon(s) hyfA
Simple and complex regulons CRP,FNR,FhlA,HyfR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[HyfR,+](1)


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
  HyfR activator hyfAp Sigma54 -129.5 -159.5 hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB
cgctttccccTGCGACACGGGTGTCGAAtccatttttt
2601033 2601050 [AIBSCS], [GEA] [1], [2]


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


Evidence    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis



Reference(s)    

 [1] Self WT., Hasona A., Shanmugam KT., 2004, Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli., J Bacteriol. 186(2):580-7

 [2] Skibinski DA., Golby P., Chang YS., Sargent F., Hoffman R., Harper R., Guest JR., Attwood MM., Berks BC., Andrews SC., 2002, Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR., J Bacteriol. 184(23):6642-53



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