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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]. Overexpression of FliZ slightly increased polyP accumulation [3]. Moreover, 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].
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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
FliZ Functional   nd nd nd
TFBs symmetry: inverted-repeat
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
fliAZY
fliAp1
fliAZY
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)
fimbri, pili (3)
defense/survival (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, 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,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
BtsR,CpxR,CsgD,FliZ
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[FliZ,-](17)


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
  FliZ repressor csgBp Sigma70 nd nd csgB, csgA, csgC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
  FliZ repressor csgBp2 Sigma38 nd nd csgB, csgA, csgC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
  FliZ repressor csgDp Sigma38 nd nd csgD, csgE, csgF, csgG
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor csgDp1 Sigma70 nd nd csgD, csgE, csgF, csgG
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor csgDp2 Sigma70 nd nd csgD, csgE, csgF, csgG
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor csgDp3 Sigma38 nd nd csgD, csgE, csgF, csgG
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor flhDp Sigma70 12.0 -187.0 flhD, flhC
agtacagttgCGTCGATTTAGGAAAAATCTTAGATAAGTGtaaagaccca
 1978370 1978399 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  FliZ repressor gadBp Sigma70 nd nd gadB, gadC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor gadBp2 Sigma38 nd nd gadB, gadC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor gadEp2 Sigma38 9.5 -12.5 gadE, gadF, mdtE, mdtF
aataatgaaaAGGATGACATATTCGAAACGATAACGGCTAAGGAGCAAGTTATGATTTTTCTCATGACGaaagattctt
 3658325 3658383 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2]
  FliZ repressor hdeAp Sigma70 8.0 -44.0 hdeA, hdeB, yhiD
catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat
 3656757 3656812 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  FliZ repressor hdeAp2 Sigma38 8.0 -44.0 hdeA, hdeB, yhiD
catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat
 3656757 3656812 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  FliZ repressor mlrAp Sigma70 -10.0 -36.0 mlrA
acctggttcgCAAAACTGCGTCTAAAGTTAAACCGGGACCtcgcgagcaa
 2214816 2214845 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [2]
  FliZ repressor mlrAp2 Sigma38 -10.0 -36.0 mlrA
acctggttcgCAAAACTGCGTCTAAAGTTAAACCGGGACCtcgcgagcaa
 2214816 2214845 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [2]
  FliZ repressor osmYp Sigma70 nd nd osmY
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor osmYp2 Sigma38 nd nd osmY
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  FliZ repressor pdeRp Sigma38 -37.5 -138.5 pdeR
atccaggcagATTTTTTAACTGACTTTCGTTTGAAAACTGGCGTTTTTCCAAAACTGGAttacaaataa
 1346857 1346905 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [2]



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
  FliZ repressor yjbJ Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2]


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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


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] Gray MJ, 2020, Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli., J Bacteriol, 202(14):None 10.1128/JB.00133-20

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


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