RegulonDB RegulonDB 10.8:Regulon Page

HipB DNA-binding transcriptional repressor

Synonyms: HipB
HipB is a transcriptional repressor that functions as the antagonist of HipA, which was the first protein found to mediate the phenomenon of persistence in E. coli. A small fraction of cells within a population are dormant persister cells; these cells are phenotypic variants that are not killed by antibiotics, leading to multidrug tolerance (MDT). Persistence may be ultimately due to global remodeling of the persister cell's ribosomes []. The HipAB system can be categorized as a type II toxin/antitoxin module. In the absence of its binding partner HipB, HipA is toxic to the cell [4, 5]. Above a certain threshold, the level of HipA in the cell determines the typical duration of growth arrest. The threshold level is determined by the level of HipB []. The HipAB system appears to be regulated at the level of HipB stability. Degradation of HipB is mainly dependent on the Lon protease, and is dependent on an unstructured 16 amino acid domain at the C terminus of the protein []. A variety of crystal structures of HipB in complexes with DNA and HipA have been solved [].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
HipB Functional   nd [1], [2]
Evolutionary Family: HTH_3
Connectivity class: Local Regulator
Gene name: hipB
  Genome position: 1592176-1592442
  Length: 267 bp / 88 aa
Operon name: hipBA
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) fadH, hipA, hipB, mazE, mazF, relA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
translation (2)
defense/survival (2)
starvation (2)
other (mechanical, nutritional, oxidative stress) (2)
cell killing (2)
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Regulated operon(s) fadH, hipBA, relA-mazEFG
First gene in the operon(s) fadH, hipB, relA
Simple and complex regulons ArcA,CRP,FadR,HipB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  HipB repressor fadHp nd -132.5 -173.5 fadH
3231474 3231510 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [3]
  HipB repressor hipBp Sigma70 -85.5 -125.5 hipB, hipA
1592558 1592577 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [4]
  HipB repressor hipBp Sigma70 -57.5 -97.5 hipB, hipA
1592530 1592549 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [4]
  HipB repressor hipBp Sigma70 -18.5 -58.5 hipB, hipA
1592491 1592511 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [4]
  HipB repressor hipBp Sigma70 10.5 -30.5 hipB, hipA
1592463 1592482 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [4]
  HipB repressor relAp1 Sigma70 5.0 -174.0 relA, mazE, mazF
2913809 2913842 [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [3]

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 (Confirmed, Strong, Weak) References
  HipB repressor nd tu nd
2568161 2568197 2568178.5 nd [AIBSCS], [BPP], [GEA] [3]
  HipB repressor nd tu nd
2568261 2568297 2568278.5 nd [APIORCISFBSCS], [BPP], [GEA] [3]

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