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YiaJ DNA-binding transcriptional repressor

Synonyms: YiaJ
Summary:
YiaJ is a transcriptional repressor that negatively controls the expression of genes involved in the catabolism of the rare pentose L-lyxose [1, 3] YiaJ was confirmed as a TF through an integrated workflow comprised of computational prediction, knowledge-based classification, and experimental validation of candidate TFs at the genome scale [2]. YiaJ regulates genes that are responsible for utilization of L-ascorbate [2].Accordingly, YiaJ is involved in utilization control of other plant-derived nutrients, such as galacturonate from plant pectin, sorbitol (sugar alcohol) in many edible fruits, and fructose and its Maillard reaction product (fructose-lysine) in many vegetables. YiaJ also controls the expression of a number of genes for survival of E. coli K-12 under stressful conditions in nature. Based on these roles, it was proposed to rename YiaJ as PlaR (regulator of plant utilization) []. When wild-type E.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YiaJ Functional   [APPH], [GEA], [IMP], [IPI] [1], [2], [3]
Evolutionary Family: IclR
Connectivity class: Local Regulator
Gene name: plaR
  Genome position: 3741684-3742532
  Length: 849 bp / 282 aa
Operon name: plaR
TU(s) encoding the TF:
Transcription unit        Promoter
plaR
plaRp


Regulon       
Regulated gene(s) lyxK, plaR, sgbE, sgbH, sgbU, yiaK, yiaL, yiaM, yiaN, yiaO
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (4)
Porters (Uni-, Sym- and Antiporters) (3)
membrane (2)
Transcription related (1)
repressor (1)
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Regulated operon(s) plaR, yiaKLMNO-lyxK-sgbHUE
First gene in the operon(s) plaR, yiaK
Simple and complex regulons CRP,IHF,YiaJ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YiaJ,-](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 (Confirmed, Strong, Weak) References
  YiaJ repressor plaRp Sigma70 -55.0 -141.0 plaR
aaaatttcaaTATGCGAAACTTGATTTCAAATatatcgatca
3742663 3742683 [BCE], [GEA] [3]
  YiaJ repressor yiaKp Sigma70 -1.0 -60.0 yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE
tgatcgatatATTTGAAATCAAGTTTCGCATAttgaaatttt
3742663 3742683 [BCE], [GEA] [3]


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






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