RegulonDB RegulonDB 10.7:Regulon Page

YiaJ DNA-binding transcriptional repressor

Synonyms: YiaJ
YiaJ is a transcriptional repressor that negatively controls the expression of genes involved in the catabolism of the rare pentose l-lyxose [1, 3, 4] 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]. YiaJ is negatively autoregulated, and coordinately represses transcription of the divergent yiaK-S operon, related to degradation of l-lyxose [3] Additionally, its operon is activated by insertion of IS1 into the yiaJ gene [1] Although little is known about the mechanism of regulation of the YiaJ regulator, recently it has been demonstrated to act as a repressor by binding to cis-acting elements that overlap yiaKp [3] YiaJ shows high homology to the IclR family of regulators; it is composed of two domains, an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal region featuring a second motif of unknown function [1] Compared to known global TFs, YiaJ exhibits some interesting regulatory features.
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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: yiaJ
  Genome position: 3741684-3742532
  Length: 849 bp / 282 aa
Operon name: yiaJ
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) lyxK, sgbE, sgbH, sgbU, yiaJ, 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)
unassigned reversible reactions (1)
Transcription related (1)
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Regulated operon(s) yiaJ, yiaKLMNO-lyxK-sgbHUE
First gene in the operon(s) yiaJ, yiaK
Simple and complex regulons CRP,IHF,YiaJ
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 (Confirmed, Strong, Weak) References
  YiaJ repressor yiaJp Sigma70 -55.0 -141.0 yiaJ
3742663 3742683 [BCE], [GEA] [3]
  YiaJ repressor yiaKp Sigma70 -1.0 -60.0 yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE
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


 [APPH] Assay of protein purified to homogeneity

 [GEA] Gene expression analysis

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction

 [BCE] Binding of cellular extracts


 [1] Badia J., Ibanez E., Sabate M., Baldoma L., Aguilar J., 1998, A rare 920-kilobase chromosomal inversion mediated by IS1 transposition causes constitutive expression of the yiaK-S operon for carbohydrate utilization in Escherichia coli., J Biol Chem 273(14):8376-81

 [2] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [3] Ibanez E., Campos E., Baldoma L., Aguilar J., Badia J., 2000, Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors., J Bacteriol 182(16):4617-24

 [4] Plantinga TH, van der Does C, Tomkiewicz D, van Keulen G, Konings WN, Driessen AJ, 2005, Deletion of the yiaMNO transporter genes affects the growth characteristics of Escherichia coli K-12., Microbiology, 2005 May