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YebK DNA-binding transcriptional dual regulator

Synonyms: YebK, YebK-2-dehydro-3-deoxy-D-gluconate 6-phosphate
Summary:
YebK is a transcriptional regulator implicated in the adaptation to the transition from rich medium to cellobiose minimal medium, reducing the length of the lag phase [1] Expression of YebK is higher in cellobiose minimal medium than in glucose minimal medium. DNA binding of YebK is reversed by 2-keto-3-deoxygluconate-6-phosphate (KDPG) [1] Genome-wide YebK binding sites were determined in vivo by chromatin immunoprecipitation method combined with lambda exonuclease digestion (ChIP-exo) in glucose M9 minimal medium [2].


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
YebK Functional   Apo nd nd nd
YebK-2-dehydro-3-deoxy-D-gluconate 6-phosphate Non-Functional   Holo nd nd nd
Evolutionary Family: RpiR
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yebK
  Genome position: 1936652-1937521
  Length: 870 bp / 289 aa
Operon name: yebK
TU(s) encoding the TF:
Transcription unit        Promoter
yebK
 


Regulon       
Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


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



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  YebK repressor yebK Transcription-Unit nd
nd
nd nd nd nd [COMP-IBA], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-IBA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


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


Evidence    


Reference(s)    

 [1] Parisutham V., Lee SK., 2015, Novel Functions and Regulation of Cryptic Cellobiose Operons in Escherichia coli., PLoS One 10(6):e0131928

 [2] Gao Y., Lim HG., Verkler H., Szubin R., Quach D., Rodionova I., Chen K., Yurkovich JT., Cho BK., Palsson BO., 2021, Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo., Nucleic Acids Res 49(17):9696-9710


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