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TreR DNA-binding transcriptional repressor

Synonyms: TreR-Trehalose, TreR, TreR-α,α-trehalose 6-phosphate
"Trehalose repressor," TreR, acts as a repressor of operons involved in trehalose transport and degradation under osmotic stress [3, 4] In the presence of trehalose-6-phosphate and at low osmolarity levels, TreR derepresses an operon related to trehalose transport and catabolism [1, 2] while trehalose is inactive [] TreR occurs as a homodimer and is composed of two domains: an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif, and a carboxy-terminal domain involved in effector recognition [1] This transcription factor is a regulator that belongs to the LacI/GalR family (specifically, to the HutC subfamily) [5] This regulator binds to a 14-bp-long palindromic sequence [1, 2] The crystal structure of the trehalose repressor (TreR) in a complex with its inducer trehalose-6-phosphate has been published [] Based on saturation transfer difference NMR, it was shown that both trehalose-6-phosphate and trehalose bind to TreR with similar affinities.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
TreR Functional   Apo [AIFS], [APPH], [BPP], [GEA], [IEP], [IPI] [1], [2]
TreR-α,α-trehalose 6-phosphate Non-Functional Allosteric Holo nd [1]
TreR-Trehalose Non-Functional Allosteric Holo [BPP], [IPI] [1]
Evolutionary Family: GalR/LacI
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: treR
  Genome position: 4466299-4467246
  Length: 948 bp / 315 aa
Operon name: treR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) treB, treC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
misc. glucose metabolism (1)
Phosphotransferase Systems (PEP-dependent PTS) (1)
membrane (1)
carbon compounds (1)
Regulated operon(s) treBC
First gene in the operon(s) treB
Simple and complex regulons ArcA,CRP,TreR
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
  TreR repressor treBp Sigma70 -81.0 -111.0 treB, treC
4466283 4466299 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [2]
  TreR repressor treBp Sigma70 -48.0 -78.0 treB, treC
4466250 4466266 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [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


 [AIFS] Automated inference of function from sequence

 [APPH] Assay of protein purified to homogeneity

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)


 [1] Horlacher R., Boos W., 1997, Characterization of TreR, the major regulator of the Escherichia coli trehalose system., J Biol Chem 272(20):13026-32

 [2] Klein W., Horlacher R., Boos W., 1995, Molecular analysis of treB encoding the Escherichia coli enzyme II specific for trehalose., J Bacteriol 177(14):4043-52

 [3] Strøm AR, Kaasen I, 1993, Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression., Mol Microbiol, 1993 Apr

 [4] Klein W., Ehmann U., Boos W., 1991, The repression of trehalose transport and metabolism in Escherichia coli by high osmolarity is mediated by trehalose-6-phosphate phosphatase., Res Microbiol 142(4):359-71

 [5] Fukami-Kobayashi K., Tateno Y., Nishikawa K., 2003, Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins., Mol Biol Evol 20(2):267-77