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TorR DNA-binding transcriptional dual regulator

Synonyms: TorR-TorI, TorR, TorR-phosphorylated


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
TorR Functional   Apo nd nd nd
TorR-TorI Non-Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
TorR-phosphorylated Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: OmpR
TFBs length: 10
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, torC, torR
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
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
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[TorR,+](4)
[TorR,-](3)


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
  TorR-phosphorylated repressor gadAp Sigma70 -122.5 -149.5 gadA, gadX
ataataaagtCTGTTTTTAAtattatcatg
 3667725 3667734 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  TorR-phosphorylated repressor gadAp Sigma70 73.5 46.5 gadA, gadX
cagaactactCGATTCACGTtttggcgcaa
 3667530 3667539 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
  TorR-phosphorylated repressor gadAp2 Sigma38 -122.5 -149.5 gadA, gadX
ataataaagtCTGTTTTTAAtattatcatg
 3667725 3667734 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  TorR-phosphorylated repressor gadAp2 Sigma38 73.5 46.5 gadA, gadX
cagaactactCGATTCACGTtttggcgcaa
 3667530 3667539 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
  TorR-phosphorylated activator hdeAp Sigma70 -51.5 -102.5 hdeA, hdeB, yhiD
aaaatatctgATTTTGATATtttccatcaa
 3656838 3656847 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [3]
  TorR-phosphorylated activator hdeAp Sigma70 -27.5 -78.5 hdeA, hdeB, yhiD
catcaacatgACATATACAGaaaaccaggt
 3656814 3656823 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3], [3]
  TorR-phosphorylated activator hdeAp2 Sigma38 -51.5 -102.5 hdeA, hdeB, yhiD
aaaatatctgATTTTGATATtttccatcaa
 3656838 3656847 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [3]
  TorR-phosphorylated activator hdeAp2 Sigma38 -27.5 -78.5 hdeA, hdeB, yhiD
catcaacatgACATATACAGaaaaccaggt
 3656814 3656823 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3], [3]
  TorR-phosphorylated activator tnaCp Sigma70 -102.5 -126.5 tnaC, tnaA, tnaB
cgtaatttatAATCTTTAAAaaaagcattt
 3888304 3888313 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  TorR-phosphorylated activator tnaCp Sigma70 -55.5 -79.5 tnaC, tnaA, tnaB
gattgtgattCGATTCACATttaaacaatt
 3888351 3888360 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  TorR-phosphorylated activator torCp Sigma70 -78.5 -106.5 torC, torA, torD
tttactcattCTGTTCATATctgttcatat
 1057973 1057982 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [4], [5], [6], [7]
  TorR-phosphorylated activator torCp Sigma70 -68.5 -96.5 torC, torA, torD
ctgttcatatCTGTTCATATtctgccgtaa
 1057983 1057992 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [4], [5], [6], [6], [7], [7]
  TorR-phosphorylated activator torCp Sigma70 -49.5 -77.5 torC, torA, torD
ttctgccgtaAGCCGTTCATcctgaccagt
 1058002 1058011 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [5], [7]
  TorR-phosphorylated activator torCp Sigma70 -25.5 -53.5 torC, torA, torD
accagtgccgCTGTTCATATttgctcatta
 1058026 1058035 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [5], [7]
  TorR repressor torRp Sigma70 -3.5 -33.5 torR
ttacggcagaATATGAACAGatatgaacag
 1057983 1057992 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [4], [5], [6], [6], [7], [7]
  TorR repressor torRp Sigma70 7.5 -23.5 torR
atatgaacagATATGAACAGaatgagtaaa
 1057973 1057982 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [4], [5], [6], [6], [7], [7]


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    

 [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-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [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

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] 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] 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

 [5] 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

 [6] 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

 [7] 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


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