RegulonDB RegulonDB 10.7:Regulon Page

HdfR DNA-binding transcriptional dual regulator

Synonyms: HdfR
"Hns-dependent flhDCregulator," HdfR, negatively regulates the expression of the flagellar master operon, flhDC [2]and positively regulates the expression of the gltBD operon [3] H-NS is a direct activator of the flhDC operon and represses transcription of hdfR. HdfR is a transcriptional regulator that belongs to the LysR family. It consist of two domains, an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in co-inducer recognition [2, 4] Little is known about the regulatory role of HdfR, and the binding sites for this transcription factor have not yet been determined. In systematic studies of oligomerization, it was shown that some members of the LysR family, like HdfR, interact with other members of the family to form heterodimers, but the physiological significance of this is unknown [5] The hdfR gene loss of function caused by an amino acid change of glutamate to lysine favored NADPH availability in E.
Read more >

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
HdfR Functional   [APPH], [APPINH], [GEA] [1], [2], [3]
Evolutionary Family: LysR
Connectivity class: Local Regulator
Gene name: hdfR
  Genome position: 3947128-3947967
  Length: 840 bp / 279 aa
Operon name: hdfR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) flhC, flhD, gltB, gltD, gltF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
operon (3)
flagellum (2)
Transcription related (2)
activator (2)
repressor (2)
Read more >
Regulated operon(s) flhDC, gltBDF
First gene in the operon(s) flhD, gltB
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

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
  HdfR repressor flhDp Sigma70 nd nd flhD, flhC nd nd [BPP], [GEA] [2]
  HdfR activator gltBp Sigma38, Sigma70 nd nd gltB, gltD, gltF nd nd [BPP] [3]

High-throughput Transcription factor binding sites (TFBSs)

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  HdfR activator yifE nd nd nd nd nd [GEA] [1]

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


 [APPH] Assay of protein purified to homogeneity

 [APPINH] Assay of protein partially-purified from its native host

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins


 [1] Bartoli J., My L., Belmudes L., Coute Y., Viala JP., Bouveret E., 2017, The Long Hunt for pssR -Looking for a Phospholipid Synthesis Transcriptional Regulator, Finding the Ribosome., J Bacteriol 199(14)

 [2] Ko M., Park C., 2000, H-NS-Dependent regulation of flagellar synthesis is mediated by a LysR family protein., J Bacteriol 182(16):4670-2

 [3] 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

 [4] Schell MA., 1993, Molecular biology of the LysR family of transcriptional regulators., Annu Rev Microbiol 47:597-626

 [5] Knapp GS, Hu JC, 2010, Specificity of the E. coli LysR-type transcriptional regulators., PLoS One, 2010 Dec 20

 [6] Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT, 2017, ROS mediated selection for increased NADPH availability in Escherichia coli., Biotechnol Bioeng, 2017 Nov