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TorR DNA-binding transcriptional dual regulator

Synonyms: TorR, TorR-Pasp, TorR-TorI
Summary:
TorR is located at the old cell pole in a cell cycle-dependent fashion, and interaction with MreB and DnaK proteins is required for the formation of the TorR focus [12]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
TorR Non-Functional   Apo nd nd
TorR-Pasp Functional Covalent Holo [APPH], [BPP], [IEP], [IPI] [1], [2]
TorR-TorI Non-Functional Covalent Holo [BPP], [IE], [IPI] [2], [3], [4], [5], [6], [7], [8]
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,ppGpp
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,+](3)
[TorR,-](2)


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
  TorR-Pasp repressor gadAp Sigma38, Sigma70, Sigma38, Sigma70 -122.5 -149.5 gadA, gadX
ataataaagtCTGTTTTTAAtattatcatg
3667725 3667734 [AIBSCS], [GEA] [1]
  TorR-Pasp repressor gadAp Sigma38, Sigma70, Sigma38, Sigma70 73.5 46.5 gadA, gadX
cagaactactCGATTCACGTtttggcgcaa
3667530 3667539 [AIBSCS], [GEA] [1]
  TorR-Pasp activator hdeAp Sigma38, Sigma70, Sigma70, Sigma38 -51.5 -102.5 hdeA, hdeB, yhiD
aaaatatctgATTTTGATATtttccatcaa
3656838 3656847 [AIBSCS], [GEA] [9]
  TorR-Pasp activator hdeAp Sigma38, Sigma70, Sigma70, Sigma38 -27.5 -78.5 hdeA, hdeB, yhiD
catcaacatgACATATACAGaaaaccaggt
3656814 3656823 [AIBSCS], [GEA] [1], [9]
  TorR-Pasp activator tnaCp Sigma70 -102.5 -126.5 tnaC, tnaA, tnaB
cgtaatttatAATCTTTAAAaaaagcattt
3888304 3888313 [BPP], [GEA] [1]
  TorR-Pasp activator tnaCp Sigma70 -55.5 -79.5 tnaC, tnaA, tnaB
gattgtgattCGATTCACATttaaacaatt
3888351 3888360 [BPP], [GEA] [1]
  TorR-Pasp activator torCp Sigma70 -78.5 -106.5 torC, torA, torD
tttactcattCTGTTCATATctgttcatat
1057973 1057982 [APIORCISFBSCS], [BCE], [BPP], [CV(GEA/GS)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [6], [10], [11]
  TorR-Pasp activator torCp Sigma70 -68.5 -96.5 torC, torA, torD
ctgttcatatCTGTTCATATtctgccgtaa
1057983 1057992 [APIORCISFBSCS], [BCE], [BPP], [CV(GEA/GS)], [GEA], [GS] [6], [10], [11]
  TorR-Pasp activator torCp Sigma70 -49.5 -77.5 torC, torA, torD
ttctgccgtaAGCCGTTCATcctgaccagt
1058002 1058011 [APIORCISFBSCS], [BCE] [6]
  TorR-Pasp activator torCp Sigma70 -25.5 -53.5 torC, torA, torD
accagtgccgCTGTTCATATttgctcatta
1058026 1058035 [APIORCISFBSCS], [BCE] [6]
  TorR repressor torRp Sigma70 -3.5 -33.5 torR
ttacggcagaATATGAACAGatatgaacag
1057983 1057992 [APIORCISFBSCS], [BCE], [BPP], [CV(GEA/GS)], [GEA], [GS] [6], [10], [11]
  TorR repressor torRp Sigma70 7.5 -23.5 torR
atatgaacagATATGAACAGaatgagtaaa
1057973 1057982 [APIORCISFBSCS], [BCE], [BPP], [CV(GEA/GS)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [6], [10], [11]


Alignment and PSSM for TorR TFBSs    

Aligned TFBS of TorR   
  Sequence
  AAATATGAACAGC
  GAATATGAACAGA
  AGATATGAACAGA
  AAATGTGAATCGA
  TATTAAAAACAGA
  AAACGTGAATCGA
  TGACATATACAGA
  TATCAAAATCAGA
  CAGGATGAACGGC
  TAATCTTTAAAAA

Position weight matrix (PWM). TorR matrix-quality result   
A	4	8	7	0	7	2	3	8	9	1	7	1	8
C	1	0	0	3	1	0	0	0	0	7	2	0	2
G	1	2	1	1	2	0	6	0	0	0	1	9	0
T	4	0	2	6	0	8	1	2	1	2	0	0	0

Consensus   
;	consensus.strict             	aaatatGaACaGa
;	consensus.strict.rc          	TCTGTTCATATTT
;	consensus.IUPAC              	waayatRaACaGa
;	consensus.IUPAC.rc           	TCTGTTYATRTTW
;	consensus.regexp             	[at]aa[ct]at[AG]aACaGa
;	consensus.regexp.rc          	TCTGTT[CT]AT[AG]TT[AT]

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    

 [APPH] Assay of protein purified to homogeneity

 [BPP] Binding of purified proteins

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [IE] Inferred from experiment

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

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

 [BCE] Binding of cellular extracts

 [CV(GEA/GS)] cross validation(GEA/GS)

 [CV(GEA/SM/GS)] cross validation(GEA/SM/GS)

 [GS] genomic SELEX

 [SM] Site mutation



Reference(s)    

 [1] 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

 [2] 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

 [3] Pao GM., Saier MH., 1995, Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution., J Mol Evol 40(2):136-54

 [4] Parkinson JS., 1993, Signal transduction schemes of bacteria., Cell 73(5):857-71

 [5] Parkinson JS., Kofoid EC., 1992, Communication modules in bacterial signaling proteins., Annu Rev Genet 26:71-112

 [6] 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

 [7] Simon G., Mejean V., Jourlin C., Chippaux M., Pascal MC., 1994, The torR gene of Escherichia coli encodes a response regulator protein involved in the expression of the trimethylamine N-oxide reductase genes., J Bacteriol 176(18):5601-6

 [8] Stock JB., Stock AM., Mottonen JM., 1990, Signal transduction in bacteria., Nature 344(6265):395-400

 [9] 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

 [10] 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

 [11] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [12] Yao Y, Fan L, Shi Y, Odsbu I, Morigen, 2016, A Spatial Control for Correct Timing of Gene Expression during the Escherichia coli Cell Cycle., Genes (Basel), 2016 Dec 23



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