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RhaR DNA-binding transcriptional activator

Synonyms: RhaR-α-L-rhamnopyranose, RhaR, RhaR-L-rhamnose
The "Rhamnose regulator," RhaR, is a transcription factor that regulates genes involved in L-rhamnose degradation and coregulates with the global transcriptional regulator CRP. These regulators bind cooperatively to activate transcription of the unusual operon rhaSR, which encodes two transcriptional regulators, RhaS and RhaR (30% identical), both members of the AraC/XylS family of transcriptional regulators and involved in L-rhamnose transport and degradation [9, 10]. In vitro transcription assays indicate that the α-CTD of the RNA polymerase is partially dispensable for RhaR activation and is required for CRP activation of the rhaSR operon [9, 10]. Apparently, expression of the operons involved in transport and degradation of L-rhamnose first requires expression of RhaR, which induces transcription of the rhaSR operon. In this way, RhaS activates transcription of L-rhamnose gene clusters. Transcription of the rhaSR operon is induced when E. coli is grown on L-rhamnose in the absence of glucose. Gene induction occurs when the physiological inducer, L-rhamnose, binds to RhaR and when cellular cyclic AMP levels are high [9, 10]. This transcription factor is composed of two domains, a C-terminal domain that contains two potential helix-turn-helix DNA-binding motifs and an N-terminal domain involved in l-rhamnose binding and dimerization of the protein [2, 5, 11].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RhaR Non-Functional   Apo nd nd
RhaR-α-L-rhamnopyranose Functional Allosteric Holo nd nd
RhaR-L-rhamnose Functional   Holo [APPH], [HIFS], [IEP] [1], [2]
Evolutionary Family: AraC/XylS
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: rhaR
  Genome position: 4098646-4099494
  Length: 849 bp / 282 aa
Operon name: rhaSR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) rhaR, rhaS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (2)
Transcription related (2)
activator (2)
operon (2)
Regulated operon(s) rhaSR
First gene in the operon(s) rhaS
Simple and complex regulons CRP,RhaR,RhaS
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
  RhaR-L-rhamnose activator rhaSp Sigma70, Sigma38 -74.0 -99.0 rhaS, rhaR
4097629 4097645 [APIORCISFBSCS], [BCE], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [2], [3], [4], [5]
  RhaR-L-rhamnose activator rhaSp Sigma70, Sigma38 -40.0 -65.0 rhaS, rhaR
4097663 4097679 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [2], [4], [5], [6], [7], [8]

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


 [1] Bhende PM., Egan SM., 1999, Amino acid-DNA contacts by RhaS: an AraC family transcription activator., J Bacteriol 181(17):5185-92

 [2] Wickstrum JR., Skredenske JM., Kolin A., Jin DJ., Fang J., Egan SM., 2007, Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain., J Bacteriol 189(14):4984-93

 [3] Egan SM., Schleif RF., 1993, A regulatory cascade in the induction of rhaBAD., J Mol Biol 234(1):87-98

 [4] Holcroft CC., Egan SM., 2000, Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR., J Bacteriol 182(23):6774-82

 [5] Wickstrum JR., Egan SM., 2004, Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR., J Bacteriol 186(18):6277-85

 [6] Tobin JF., Schleif RF., 1990, Transcription from the rha operon psr promoter., J Mol Biol 211(1):1-4

 [7] Tobin JF., Schleif RF., 1990, Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of Escherichia coli., J Mol Biol 211(1):75-89

 [8] Tobin JF., Schleif RF., 1987, Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes., J Mol Biol 196(4):789-99

 [9] Wickstrum JR., Santangelo TJ., Egan SM., 2005, Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli., J Bacteriol 187(19):6708-18

 [10] Holcroft CC, Egan SM., 2000, Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR., J Bacteriol. 2000 Dec;182(23):6774-82.

 [11] Kolin A., Balasubramaniam V., Skredenske JM., Wickstrum JR., Egan SM., 2008, Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR., Mol Microbiol 68(2):448-61