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HicB DNA-binding transcriptional repressor

Synonyms: HicB
Summary:
HicB acts as the antitoxin of the HicA-HicB toxin-antitoxin system, and it also regulates the transcription of the operon that encodes the toxin-antitoxin system. HicB recognizes and binds an inverted repeat DNA sequence to regulate transcription, suggesting that HicB binds to DNA as a dimer [1]. An HTH motif has been identified in the C terminus of HicB [1]. Overexpression of HicA induces mRNA cleavage and growth inhibition, but not cell death. Expression of HicB neutralizes the effect of HicA [2]. The loss of HicB downregulates the extracytoplasmic stress response mediated by σE and the production of outer membrane vesicles. It reduces the cellular levels of DegP and Spy and downregulates the Cpx response independently of CpxR [3]. hicB insertion mutants suppress the essential nature of |FRAME: RPOE-MONOMER σE| [3].
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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
HicB Functional   nd nd nd
Evolutionary Family: HTH_3
TFBs length: 22
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: hicB
  Genome position: 1509508-1509924
  Length: 417 bp / 138 aa
Operon name: hicAB
TU(s) encoding the TF:
Transcription unit        Promoter
hicAB
hicAp1
hicAB
hicAp2


Regulon       
Regulated gene(s) hicA, hicB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
RNA degradation (1)
unknown (1)
adaptations (1)
Regulated operon(s) hicAB
First gene in the operon(s) hicA
Simple and complex regulons HicB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[HicB,-](1)


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
  HicB repressor hicAp2 Sigma70 -30.5 -41.5 hicA, hicB
ttacacacggAGGTAAACACTAATGTTTACTTtgttgatata
 1509234 1509255 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1]


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] Turnbull KJ., Gerdes K., 2017, HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin., Mol Microbiol 104(5):781-792

 [2] Jorgensen MG., Pandey DP., Jaskolska M., Gerdes K., 2009, HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea., J Bacteriol 191(4):1191-9

 [3] Button JE., Silhavy TJ., Ruiz N., 2007, A suppressor of cell death caused by the loss of sigmaE downregulates extracytoplasmic stress responses and outer membrane vesicle production in Escherichia coli., J Bacteriol 189(5):1523-30

 [4] Daimon Y, Narita S, Akiyama Y, 2015, Activation of Toxin-Antitoxin System Toxins Suppresses Lethality Caused by the Loss of ?E in Escherichia coli., J Bacteriol, 197(14):2316 10.1128/JB.00079-15

 [5] Manav MC, Turnbull KJ, Jur?nas D, Garcia-Pino A, Gerdes K, Brodersen DE, 2019, The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain., Structure, 27(11):1675 10.1016/j.str.2019.08.008

 [6] Yamaguchi Y, Park JH, Inouye M, 2011, Toxin-antitoxin systems in bacteria and archaea., Annu Rev Genet, 45(None):61 10.1146/annurev-genet-110410-132412


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