RegulonDB RegulonDB 9.3:Regulon Page

DinJ-YafQ DNA-binding transcriptional repressor

Synonyms: DinJ-YafQ
The YafQ-DinJ toxin-antitoxin system was identified by its similarity to the RelE-RelB toxin-antitoxin system Gotfredsen M,1998. Expression of YafQ alone reduces protein synthesis and inhibits growth, and coexpression of DinJ alleviates that phenotype, acting as the antitoxin Motiejunaite R,2007. Szekeres S,2007. Prysak MH,2009.
YafQ and DinJ form a stable complex Motiejunaite R,2007 which can bind to the dinJ-yafQ palindrome upstream of the translation start site Prysak MH,2009.
A strain from which all five toxin-antitoxin systems have been deleted shows no deficiency in its stress response or competitiveness under nutrient-limited conditions Tsilibaris V,2007. However, biofilm formation is affected via expression of the TabA protein Kim Y,2009. A dinJ-yafQ deletion mutant is impaired in biofilm formation Kolodkin-Gal I,2009.
Deletion of any single toxin-antitoxin system encoding an RNase has no effect on persister formation, but deleting ten such systems dramatically reduces persister formation. Persister formation depends on degradation of the antitoxins by the Lon protease Maisonneuve E,2011.
A crystal structure of the DinJ-YafQ complex has been solved at 1.8 Å resolution, showing a YafQ-(DinJ)2-YafQ conformation Ruangprasert A,2014.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
DinJ-YafQ     nd nd
Connectivity class: Local Regulator
Gene name: dinJ
  Genome position: 246242-246502
  Length: 261 bp / 86 aa
Operon name: dinJ-yafQ
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) cspE, dinJ, yafQ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
cell killing (2)
transcriptional level (1)
Regulated operon(s) cspE, dinJ-yafQ
First gene in the operon(s) cspE, dinJ
Simple and complex regulons DinJ-YafQ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  DinJ-YafQ repressor cspEp1 Sigma70 -43.5 -188.5 cspE
657096 657111 [BPP], [GEA], [SM] [1]
  DinJ-YafQ repressor dinJp Sigma70 89.5 -24.5 dinJ, yafQ
246519 246534 [BPP], [HIBSCS], [SM] [2], [3]

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


 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation

 [HIBSCS] Human inference based on similarity to consensus sequences


 [1] Hu Y., Benedik MJ., Wood TK., 2012, Antitoxin DinJ influences the general stress response through transcript stabilizer CspE., Environ Microbiol. 14(3):669-79

 [2] Prysak MH., Mozdzierz CJ., Cook AM., Zhu L., Zhang Y., Inouye M., Woychik NA., 2009, Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage., Mol Microbiol. 71(5):1071-87

 [3] Ruangprasert A., Maehigashi T., Miles SJ., Giridharan N., Liu JX., Dunham CM., 2014, Mechanisms of toxin inhibition and transcriptional repression by Escherichia coli DinJ-YafQ., J Biol Chem. 289(30):20559-69