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QseB DNA-binding transcriptional dual regulator

Synonyms: QseB-Phosphorylated, QseB
Summary:
QseB, "quorum-sensing E. coli regulator B", is the response regulator component of the QseB-QseC two-component system, which is one component of the quorum-sensing regulatory cascade involved in the regulation of biofilm formation[2], motility and flagella genes by activating transcription of flhDC, an operon that encodes the master regulator of these genes [3].QseB also regulates replication initiation by regulating DnaA expression [6]. This protein also may have an undetermined role in metal metabolism, because qseBC deletion mutants show hypersensitivity to several toxic cations [7]. QseB forms complexes with the chaperone DnaK and with the cell division protein FtsZ [6]. QseB and QseC of enterohemorrhagic E. coli (EHEC) and of E.
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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
QseB Non-Functional   Apo nd nd nd
QseB-Phosphorylated Functional Covalent Holo nd nd nd
Evolutionary Family: OmpR
TFBs length: 13
TFBs symmetry: inverted-repeat
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: qseB
  Genome position: 3169828-3170487
  Length: 660 bp / 219 aa
Operon name: qseBC
TU(s) encoding the TF:
Transcription unit        Promoter
qseBC
qseBp1
qseBC
qseBp2


Regulon       
Regulated gene(s) feaR, fimA, fimC, fimD, fimF, fimG, fimH, fimI, flhC, flhD, qseB, qseC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pilus (7)
Transcription related (4)
activator (4)
operon (3)
flagellum (2)
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Regulated operon(s) feaR, fimAICDFGH, flhDC, qseBC
First gene in the operon(s) feaR, fimA, flhD, qseB
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
BasR,QseB
CRP,Nac,NsrR,PhoB,QseB
H-NS,IHF,Lrp,QseB
QseB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[QseB,-](1)
[QseB,+](4)


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
  QseB-Phosphorylated activator feaRp1 Sigma70 -49.0 -115.0 feaR
caaatcgtgaCAATAACCGCTTAtgtctctatg
 1447392 1447404 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  QseB-Phosphorylated repressor feaRp2 Sigma70 -3.0 -29.0 feaR
acaaatgcaaCAATAAAAATACAtttcacagag
 1447306 1447318 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  QseB-Phosphorylated activator fimAp Sigma70 nd nd fimA, fimI, fimC, fimD, fimF, fimG, fimH
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
  QseB-Phosphorylated activator flhDp Sigma70 nd nd flhD, flhC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [3]
  QseB-Phosphorylated activator qseBp2 Sigma70 -462.0 -541.0 qseB, qseC
ggagcggtaaCAATTACGGATTTactttgcgga
 3169281 3169293 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4], [5]
  QseB-Phosphorylated activator qseBp2 Sigma70 6.0 -74.0 qseB, qseC
ttaagggaaaAAAATAAAATTTAgtgctgtaca
 3169748 3169760 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4], [5]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  QseB-Phosphorylated repressor dnaA Gene nd
tgactccggaGTGTACAATTATTACaatccggcct
3884216 3884230 3884222.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]
  QseB-Phosphorylated repressor dnaA Gene nd
ccaataaagcCATTGAATTTATTCAagtttaggta
3884302 3884316 3884308.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]
  QseB-Phosphorylated repressor dnaA Gene nd
tcggtgtccaTCGTTTCATTTTTCGGcggatatcca
3884269 3884284 3884276.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]


Alignment and PSSM for QseB TFBSs    

Aligned TFBS of QseB   
  Sequence
  GTAACAATTACGGATT
  GTGACAATAACCGCTT
  GCAACAATAAAAATAC
  GAAAAAAATAAAATTT

Position weight matrix (PWM). QseB matrix-quality result    
A	0	1	3	4	1	4	4	1	2	4	2	2	2	1	1	0
C	0	1	0	0	3	0	0	0	0	0	2	1	0	1	0	1
G	4	0	1	0	0	0	0	0	0	0	0	1	2	0	0	0
T	0	2	0	0	0	0	0	3	2	0	0	0	0	2	3	3

Consensus    
;	consensus.strict             	GtaACAAtaAcagttt
;	consensus.strict.rc          	AAACTGTTATTGTTAC
;	consensus.IUPAC              	GyrACAAtwAmvryty
;	consensus.IUPAC.rc           	RARYBKTWATTGTYRC
;	consensus.regexp             	G[ct][ag]ACAAt[at]A[ac][acg][ag][ct]t[ct]
;	consensus.regexp.rc          	[AG]A[AG][CT][CGT][GT]T[AT]ATTGT[CT][AG]C

PWM logo   


 


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


Evidence    

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Pasupuleti S., Sule N., Manson MD., Jayaraman A., 2018, Conversion of Norepinephrine to 3,4-Dihdroxymandelic Acid in Escherichia coli Requires the QseBC Quorum-Sensing System and the FeaR Transcription Factor., J Bacteriol 200(1)

 [2] Gou Y., Liu W., Wang JJ., Tan L., Hong B., Guo L., Liu H., Pan Y., Zhao Y., 2019, CRISPR-Cas9 knockout of qseB induced asynchrony between motility and biofilm formation in Escherichia coli., Can J Microbiol 65(9):691-702

 [3] Sperandio V., Torres AG., Kaper JB., 2002, Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli., Mol Microbiol 43(3):809-21

 [4] Clarke MB., Sperandio V., 2005, Transcriptional autoregulation by quorum sensing Escherichia coli regulators B and C (QseBC) in enterohaemorrhagic E. coli (EHEC)., Mol Microbiol 58(2):441-55

 [5] Clarke MB., Sperandio V., 2005, Transcriptional regulation of flhDC by QseBC and sigma (FliA) in enterohaemorrhagic Escherichia coli., Mol Microbiol 57(6):1734-49

 [6] Wu D., Baigalmaa L., Yao Y., Li G., Su M., Fan L., Morigen., 2021, The Escherichia coli QseB/QseC signaling is required for correct timing of replication initiation and cell motility., Gene 773:145374

 [7] Zhou L., Lei XH., Bochner BR., Wanner BL., 2003, Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems., J Bacteriol 185(16):4956-72

 [8] Clarke MB, Hughes DT, Zhu C, Boedeker EC, Sperandio V, 2006, The QseC sensor kinase: a bacterial adrenergic receptor., Proc Natl Acad Sci U S A, 103(27):10420 10.1073/pnas.0604343103

 [9] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661


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