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DinJ-YafQ DNA-binding transcriptional repressor

Synonyms: DinJ-YafQ
Summary:
The YafQ-DinJ toxin-antitoxin system was identified by its similarity to the RelE-RelB toxin-antitoxin system [4]. Expression of YafQ alone reduces protein synthesis and inhibits growth, and coexpression of DinJ alleviates that phenotype, acting as the antitoxin [2, 5, 6].
YafQ and DinJ form a stable complex [5] which can bind to the dinJ-yafQ palindrome upstream of the translation start site [2].
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 [7]. However, biofilm formation is affected via expression of the TabA protein [8].
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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
dinJ-yafQ
dinJp
Gene name: yafQ
  Genome position: 245961-246239
  Length: 279 bp / 92 aa
Operon name: dinJ-yafQ
TU(s) encoding the TF:
Transcription unit        Promoter
dinJ-yafQ
dinJp


Regulon       
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
DinJ-YafQ,LexA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DinJ-YafQ,-](2)


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
tgtactttgcCTGGATGCGCTTTCAGttttgagaca
657096 657111 [BPP], [GEA], [SM] [1]
  DinJ-YafQ repressor dinJp Sigma70 89.5 -24.5 dinJ, yafQ
acaattcaagCTGAATAAATATACAGcacaggagat
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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation

 [HIBSCS] Human inference based on similarity to consensus sequences



Reference(s)    

 [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

 [4] Gotfredsen M., Gerdes K., 1998, The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family., Mol Microbiol. 29(4):1065-76

 [5] Motiejunaite R., Armalyte J., Markuckas A., Suziedeliene E., 2007, Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module., FEMS Microbiol Lett. 268(1):112-9

 [6] Szekeres S., Dauti M., Wilde C., Mazel D., Rowe-Magnus DA., 2007, Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection., Mol Microbiol. 63(6):1588-605

 [7] Tsilibaris V., Maenhaut-Michel G., Mine N., Van Melderen L., 2007, What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome?, J Bacteriol. 189(17):6101-8

 [8] Kim Y., Wang X., Ma Q., Zhang XS., Wood TK., 2009, Toxin-Antitoxin Systems in Escherichia coli Influence Biofilm Formation Through YjgK (TabA) and Fimbriae., J Bacteriol. 191(4):1258-67

 [9] Kolodkin-Gal I., Verdiger R., Shlosberg-Fedida A., Engelberg-Kulka H., 2009, A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation., PLoS One. 4(8):e6785

 [10] Maisonneuve E., Shakespeare LJ., Jorgensen MG., Gerdes K., 2011, Bacterial persistence by RNA endonucleases., Proc Natl Acad Sci U S A. 108(32):13206-11

 [11] Liang Y., Gao Z., Wang F., Zhang Y., Dong Y., Liu Q., 2014, Structural and functional characterization of Escherichia coli toxin-antitoxin complex DinJ-YafQ., J Biol Chem. 289(30):21191-202

 [12] Gerdes K., 2000, Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress., J Bacteriol. 182(3):561-72

 [13] Buts L., Lah J., Dao-Thi MH., Wyns L., Loris R., 2005, Toxin-antitoxin modules as bacterial metabolic stress managers., Trends Biochem Sci. 30(12):672-9

 [14] Gerdes K., Christensen SK., Lobner-Olesen A., 2005, Prokaryotic toxin-antitoxin stress response loci., Nat Rev Microbiol. 3(5):371-82

 [15] Condon C., 2006, Shutdown decay of mRNA., Mol Microbiol. 61(3):573-83

 [16] Inouye M., 2006, The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology., J Cell Physiol. 209(3):670-6

 [17] Magnuson RD., 2007, Hypothetical functions of toxin-antitoxin systems., J Bacteriol. 189(17):6089-92



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