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TorR DNA-binding transcriptional dual regulator

Synonyms: TorR-Phosphorylated, TorR-TorI


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
TorR-Phosphorylated Functional Covalent Holo [BPP], [IPI] [1]
TorR-TorI Non-Functional Covalent Holo [BPP], [IPI] [1]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: torR
  Genome position: 1057262-1057954
  Length: 693 bp / 230 aa
Operon name: torR
TU(s) encoding the TF:
Transcription unit        Promoter
torR
torRp


Regulon       
Regulated gene(s) gadA, gadX, hdeA, hdeB, tnaA, tnaB, tnaC, torA, torC, torD, torR, yhiD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (3)
anaerobic respiration (3)
Transcription related (2)
activator (2)
amino acids (2)
Read more >
Regulated operon(s) gadAXW, hdeAB-yhiD, tnaCAB, torCAD, torR
First gene in the operon(s) gadA, hdeA, tnaC, tnaC, torC, torR
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
CRP,TorR
FliZ,GadE,GadW,GadX,H-NS,Lrp,MarA,PhoP,RcsB,TorR
NarL,TorR
TorR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[TorR,-](2)
[TorR,+](3)


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
  TorR-TorI repressor gadAp Sigma38 -122.5 -149.5 gadA, gadX
ataataaagtCTGTTTTTAAtattatcatg
3667725 3667734 [AIBSCS], [GEA] [2]
  TorR-TorI repressor gadAp Sigma38 73.5 45.5 gadA, gadX
cagaactactCGATTCACGTtttggcgcaa
3667530 3667539 [AIBSCS], [GEA] [2]
  TorR-TorI activator hdeAp Sigma38 -51.5 -102.5 hdeA, hdeB, yhiD
aaaatatctgATTTTGATATtttccatcaa
3656838 3656847 [AIBSCS], [GEA] [3]
  TorR-TorI activator hdeAp Sigma38 -27.5 -78.5 hdeA, hdeB, yhiD
catcaacatgACATATACAGaaaaccaggt
3656814 3656823 [AIBSCS], [GEA] [2], [3]
  TorR-Phosphorylated activator tnaCp Sigma70 -102.5 -126.5 tnaC, tnaA, tnaB
cgtaatttatAATCTTTAAAaaaagcattt
3888304 3888313 [BPP], [GEA] [2]
  TorR-Phosphorylated activator tnaCp Sigma70 -55.5 -79.5 tnaC, tnaA, tnaB
gattgtgattCGATTCACATttaaacaatt
3888351 3888360 [BPP], [GEA] [2]
  TorR-Phosphorylated activator torCp Sigma70 -78.5 -106.5 torC, torA, torD
tttactcattCTGTTCATATctgttcatat
1057973 1057982 [BCE], [BPP], [GEA], [HIBSCS], [SM] [4]
  TorR-Phosphorylated activator torCp Sigma70 -68.5 -96.5 torC, torA, torD
ctgttcatatCTGTTCATATtctgccgtaa
1057983 1057992 [BCE], [BPP], [GEA], [HIBSCS] [4]
  TorR-Phosphorylated activator torCp Sigma70 -49.5 -77.5 torC, torA, torD
ttctgccgtaAGCCGTTCATcctgaccagt
1058002 1058011 [BCE], [HIBSCS] [4]
  TorR-Phosphorylated activator torCp Sigma70 -25.5 -53.5 torC, torA, torD
accagtgccgCTGTTCATATttgctcatta
1058026 1058035 [BCE], [HIBSCS] [4]
  TorR-Phosphorylated repressor torRp Sigma70 -3.5 -33.5 torR
ttacggcagaATATGAACAGatatgaacag
1057983 1057992 [BCE], [BPP], [GEA], [HIBSCS] [4], [5]
  TorR-Phosphorylated repressor torRp Sigma70 7.5 -23.5 torR
atatgaacagATATGAACAGaatgagtaaa
1057973 1057982 [BCE], [BPP], [GEA], [HIBSCS], [SM] [4], [5]


Alignment and PSSM for TorR TFBSs    

Aligned TFBS of TorR   
  Sequence
  TCTGTTCAT
  TCTGTTCAT
  GCCGTTCAT
  GCTGTTCAT
  TCTGTATAT
  TCTGATTTT
  TCGATTCAC
  TCTGTTTTT
  TATAATCTT
  TCGATTCAC

Position weight matrix (PWM).   
A	0	1	0	3	2	1	0	7	0
C	0	9	1	0	0	0	7	0	2
G	2	0	2	7	0	0	0	0	0
T	8	0	7	0	8	9	3	3	8

PWM logo   


 


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


Evidence    

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [BCE] Binding of cellular extracts

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem. 280(2):1448-56

 [2] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol. 48(1):211-23

 [3] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol. 190(4):1290-7

 [4] Simon G., Jourlin C., Ansaldi M., Pascal MC., Chippaux M., Mejean V., 1995, Binding of the TorR regulator to cis-acting direct repeats activates tor operon expression., Mol Microbiol. 17(5):971-80

 [5] Ansaldi M., Simon G., Lepelletier M., Mejean V., 2000, The TorR high-affinity binding site plays a key role in both torR autoregulation and torCAD operon expression in Escherichia coli., J Bacteriol. 182(4):961-6



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