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YefM-YoeB DNA-binding transcriptional repressor

Synonyms: YefM-YoeB
YefM is a transcriptional DNA-binding autorepressor for the yefM-yoeB operon. In addition, YefM also functions as an antitoxin to form a complex with YoeB, which is a toxin that is counteracted by YefM antitoxin Kedzierska B,2007 YefM can bind alone with low affinity to the yefM-yoeB operator, but together with YoeB it has an enhanced DNA-binding affinity compared to free YefM Kedzierska B,2007 YoeB enhances the interaction with YefM by affecting the YefM conformation to one that is more favorable for DNA binding and/or by stabilizing the nucleoprotein complex at the operator site and reducing basal expression of the yefM-yoeB operon Kedzierska B,2007. Bailey SE,2009
The yefM gene is upregulated during growth in biofilms Ren D,2004and yefM-yoeB is upregulated in persister cells Shah D,2006 it is probable that derepression of yefM-yoeB autoregulation occurs in these circumstances in response to an as-yet-unknown environmental or cell cycle signal(s) that interferes with the YefM-YoeB-operator interaction Bailey SE,2009
The operator site 5' of yefM-yoeB comprises adjacent long (L) and short (S) palindromes with core 5'-TGTACA-3' motifs with a center-to-center distance of 12 bp Kedzierska B,2007 which was suggested to be crucial for the correct stable positioning of YefM-YoeB at the two repeats Bailey SE,2009 This sequence organization is common in yefM-yoeB regulatory regions in diverse genomes, suggesting that interaction of YefM-YoeB with these motifs is a conserved mechanism of operon autoregulation Kedzierska B,2007
Nevertheless, YefM originally was described as a native unstructured protein Cherny I,2004 later it was reevaluated as experimental, and modeling data have demonstrated that the protein is at least partially folded Kedzierska B,2007.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YefM-YoeB     nd nd
Evolutionary Family: YefM, YoeB/Txe_like
Connectivity class: Local Regulator

No gene found!

Regulated gene(s) yefM, yoeB
Multifun term(s) of regulated gene(s)
defense/survival (2)
Regulated operon(s) yefM-yoeB
First gene in the operon(s) yefM
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
  YefM-YoeB repressor yefMp Sigma70 -10.5 -30.5 yefM, yoeB
2089737 2089750 [BPP], [GEA], [HIBSCS] [1]
  YefM-YoeB repressor yefMp Sigma70 2.5 -18.5 yefM, yoeB
2089725 2089738 [BPP], [GEA], [HIBSCS] [1]

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

 [HIBSCS] Human inference based on similarity to consensus sequences


 [1] Kedzierska B., Lian LY., Hayes F., 2007, Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression., Nucleic Acids Res. 35(1):325-39