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YefM DNA-binding transcriptional repressor

Synonyms: YefM
YoeB and YefM are a toxin-antitoxin pair [2].
YefM has similarity to the Axe protein of the Txe-Axe toxin-antitoxin pair, which is encoded by a multidrug resistance
episome isolated from Enterococcus faecium [2].
The YefM protein appears to lack secondary structure, and its native conformation is proposed to be unfolded. A
linear recognition element which can be recognized by YoeB was identified using peptide array technology [3].
Regulation has been described [4]. Transcription is induced upon biofilm formation [4].
Review: [5]

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YefM     nd nd
Evolutionary Family: YefM
Connectivity class: Local Regulator
Gene name: yefM
  Genome position: 2089462-2089713
  Length: 252 bp / 83 aa
Operon name: yefM-yoeB
TU(s) encoding the TF:
Transcription unit        Promoter

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 regulons YefM,YefM-YoeB
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 repressor yefMp Sigma70 -10.5 -30.5 yefM, yoeB
2089737 2089750 [BPP], [GEA], [HIBSCS] [1]
  YefM 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

 [2] Grady R., Hayes F., 2003, Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium., Mol Microbiol. 47(5):1419-32

 [3] Cherny I., Gazit E., 2004, The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target., J Biol Chem. 279(9):8252-61

 [4] Ren D., Bedzyk LA., Thomas SM., Ye RW., Wood TK., 2004, Gene expression in Escherichia coli biofilms., Appl Microbiol Biotechnol. 64(4):515-24

 [5] Yamaguchi Y., Park JH., Inouye M., 2011, Toxin-antitoxin systems in bacteria and archaea., Annu Rev Genet. 45:61-79