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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 [3]. Expression of YafQ alone reduces protein synthesis and inhibits growth, and coexpression of DinJ alleviates that phenotype, acting as the antitoxin [2, 4, 5]. YafQ and DinJ form a stable complex [4] 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 [6]. However, biofilm formation is affected via expression of the TabA protein [7].
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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
DinJ-YafQ Functional   nd nd nd
TFBs length: 16
TFBs symmetry: inverted-repeat
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 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
  DinJ-YafQ repressor cspEp1 Sigma70 -43.5 -188.5 cspE
tgtactttgcCTGGATGCGCTTTCAGTtttgagacaa
 657096 657112 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
  DinJ-YafQ repressor dinJp Sigma70 89.5 -24.5 dinJ, yafQ
tacaattcaaGCTGAATAAATATACAGcacaggagat
 246519 246535 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


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] Gotfredsen M, Gerdes K, 1998, The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family., Mol Microbiol, 29(4):1065 10.1046/j.1365-2958.1998.00993.x

 [4] 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

 [5] 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 10.1111/j.1365-2958.2007.05613.x

 [6] 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 10.1128/JB.00527-07

 [7] 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 10.1128/JB.01465-08

 [8] 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 10.1371/journal.pone.0006785

 [9] 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

 [10] 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

 [11] Gerdes K, 2000, Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress., J Bacteriol, 182(3):561 10.1128/JB.182.3.561-572.2000

 [12] 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 10.1016/j.tibs.2005.10.004

 [13] Gerdes K, Christensen SK, Løbner-Olesen A, 2005, Prokaryotic toxin-antitoxin stress response loci., Nat Rev Microbiol, 3(5):371 10.1038/nrmicro1147

 [14] Condon C, 2006, Shutdown decay of mRNA., Mol Microbiol, 61(3):573 10.1111/j.1365-2958.2006.05270.x

 [15] Inouye M, 2006, The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology., J Cell Physiol, 209(3):670 10.1002/jcp.20801

 [16] Magnuson RD, 2007, Hypothetical functions of toxin-antitoxin systems., J Bacteriol, 189(17):6089 10.1128/JB.00958-07

 [17] Maisonneuve E, Shakespeare LJ, Jørgensen MG, Gerdes K, 2011, Bacterial persistence by RNA endonucleases., Proc Natl Acad Sci U S A, 108(32):13206 10.1073/pnas.1100186108

 [18] null, 2018, Retraction for Maisonneuve et al., Bacterial persistence by RNA endonucleases., Proc Natl Acad Sci U S A, 115(12):E2901 10.1073/pnas.1803278115


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