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FliZ DNA-binding transcriptional repressor

Synonyms: FliZ
Summary:
The transcriptional repressor FliZ controls the transcription of genes involved in the regulation of curli expression and the motility system [1, 2]. During the post-exponential growth phase, this regulator is an abundant protein in the genome, with about 21,500 molecules per cell. Transcriptome expression analysis showed a global antagonistic effect between FliZ and σS that resulted in physiological traits, including flagellum-mediated motility and curli fimbria-mediated adhesion [1, 2]. FliZ interferes with binding within σS-dependent promoters, can also discriminate vegetative promoters, and can recognize alternative σS promoter-like sequences [2]. The C-terminal domain of FliZ contains an α-helix that is similar to helix 3.0 of σS, and this structure promotes DNA binding [2]. In FliZ, this α-helix contains a positively charged amino acid (R108) that is involved in recognition of the extended -10 promoter.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
FliZ Functional   [IMP] [1]
Connectivity class: Local Regulator
Gene name: fliZ
  Genome position: 2000473-2001024
  Length: 552 bp / 183 aa
Operon name: fliAZ-tcyJ
TU(s) encoding the TF:
Transcription unit        Promoter
fliAZ-tcyJ
fliAp1
fliAZ-tcyJ
fliAp2


Regulon       
Regulated gene(s) csgA, csgB, csgC, csgD, csgE, csgF, csgG, flhC, flhD, gadB, gadC, gadE, gadF, hdeA, hdeB, mdtE, mdtF, mlrA, osmY, pdeR, yhiD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transcription related (6)
activator (4)
pH (4)
defense/survival (3)
repressor (3)
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Regulated operon(s) csgBAC, csgDEFG, flhDC, gadBC, gadEF-mdtEF, hdeAB-yhiD, mlrA, osmY, pdeR
First gene in the operon(s) csgB, csgD, csgD, flhD, gadB, gadE, hdeA, mlrA, osmY, pdeR
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB
BasR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO
CRP,Fis,FliZ,IHF,Lrp
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[FliZ,-](5)


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
  FliZ repressor csgBp Sigma38, Sigma70, Sigma38 nd -1103951.0 csgB, csgA, csgC nd nd [GEA] [1]
  FliZ repressor csgDp1 Sigma38, Sigma70 nd 1103196.0 csgD, csgE, csgF, csgG nd nd [BPP], [GEA] [1], [2]
  FliZ repressor csgDp2 Sigma38, Sigma38, Sigma70 nd 1103196.0 csgD, csgE, csgF, csgG nd nd [BPP], [GEA] [1], [2]
  FliZ repressor flhDp Sigma70 12.0 -187.5 flhD, flhC
tgggtctttaCACTTATCTAAGATTTTTCCTAAATCGACgcaactgtac
1978370 1978399 [BPP], [GEA] [2]
  FliZ repressor gadBp Sigma38, Sigma70, Sigma38, Sigma70 nd 1572045.0 gadB, gadC nd nd [BPP], [GEA] [1], [2]
  FliZ repressor gadEp Sigma38 9.5 -12.0 gadE, gadF, mdtE, mdtF
aataatgaaaAGGATGACATATTCGAAACGATAACGGCTAAGGAGCAAGTTATGATTTTTCTCATGACgaaagattct
3658325 3658383 [BPP], [GEA], [SM] [2]
  FliZ repressor hdeAp Sigma38, Sigma70, Sigma70, Sigma38 8.0 -44.5 hdeA, hdeB, yhiD
atcctcaactATAAAGTGAAAGAGCCGTCACGAATCAATTTCGACACTGAGGTTATAACCTGGTTttctgtatat
3656757 3656812 [BPP], [GEA] [2]
  FliZ repressor mlrAp Sigma70, Sigma38 -10.0 -35.5 mlrA
acctggttcgCAAAACTGCGTCTAAAGTTAAACCGGGACctcgcgagca
2214816 2214845 [BPP], [GEA], [SM] [1], [2]
  FliZ repressor osmYp Sigma70, Sigma38 nd -4611396.0 osmY nd nd [BPP], [GEA] [1], [2]
  FliZ repressor pdeRp Sigma38 -37.5 -139.0 pdeR
ttatttgtaaTCCAGTTTTGGAAAAACGCCAGTTTTCAAACGAAAGTCAGTTAAAAAAtctgcctgga
1346857 1346905 [BPP], [GEA], [SM] [1], [2]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  FliZ repressor yjbJ nd nd nd nd [ICWHO] nd


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


Evidence    

 [IMP] Inferred from mutant phenotype

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [2] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [3] Mytelka DS., Chamberlin MJ., 1996, Escherichia coli fliAZY operon., J Bacteriol 178(1):24-34



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