RegulonDB RegulonDB 11.2:Regulon Page
   

TreR DNA-binding transcriptional repressor

Synonyms: TreR, TreR-α,α-trehalose 6-phosphate, TreR-Trehalose, TreR-D-trehalose 6-phosphate
Summary:
"Trehalose repressor," TreR, acts as a repressor of operons involved in trehalose transport and degradation under osmotic stress [4, 5] In the presence of trehalose-6-phosphate and at low osmolarity levels, TreR derepresses an operon related to trehalose transport and catabolism [1, 2, 6, 7, 8] while trehalose is inactive [8] 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) [9, 10] 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 [10] Based on saturation transfer difference NMR, it was shown that both trehalose-6-phosphate and trehalose bind to TreR with similar affinities.
Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
TreR Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
TreR-α,α-trehalose 6-phosphate Non-Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
TreR-D-trehalose 6-phosphate Non-Functional Allosteric Holo nd nd nd
TreR-Trehalose Non-Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: GalR/LacI
TFBs length: 17
TFBs symmetry: inverted-repeat
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
treR
treRp1
treR
treRp2
treR
treRp3
treR
treRp4


Regulon       
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)
[TreR,-](1)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  TreR repressor treBp Sigma70 -81.0 -111.0 treB, treC
ccctgtcctgATCGTTTCCTGAACGATaaattgtgat
 4466283 4466299 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [2]
  TreR repressor treBp Sigma70 -48.0 -78.0 treB, treC
tgatcttcgcTGCGTTTCGGGAACGTTcccgttttta
 4466250 4466266 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3]


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


Evidence    

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [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] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [4] Strøm AR, Kaasen I, 1993, Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression., Mol Microbiol, 8(2):205 10.1111/j.1365-2958.1993.tb01564.x

 [5] 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

 [6] Boos W, Ehmann U, Forkl H, Klein W, Rimmele M, Postma P, 1990, Trehalose transport and metabolism in Escherichia coli., J Bacteriol, 172(6):3450 10.1128/jb.172.6.3450-3461.1990

 [7] Rimmele M, Boos W, 1994, Trehalose-6-phosphate hydrolase of Escherichia coli., J Bacteriol, 176(18):5654 10.1128/jb.176.18.5654-5664.1994

 [8] Pérez-Victoria I, Kemper S, Patel MK, Edwards JM, Errey JC, Primavesi LF, Paul MJ, Claridge TD, Davis BG, 2009, Saturation transfer difference NMR reveals functionally essential kinetic differences for a sugar-binding repressor protein., Chem Commun (Camb), None(39):5862 10.1039/b913489a

 [9] 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

 [10] Hars U, Horlacher R, Boos W, Welte W, Diederichs K, 1998, Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose., Protein Sci, 7(12):2511 10.1002/pro.5560071204


RegulonDB