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IdnR DNA-binding transcriptional dual regulator

Synonyms: IdnR-Idonate, IdnR, IdnR-5-dehydro-D-gluconate
Summary:
"L-idonate regulator," IdnR, is a transcription factor that regulates genes involved in L-idonate metabolism, which are organized in two coordinately regulated transcription units [1, 3]. This regulator is positively autoregulated and co-regulates with CRP, a global transcriptional regulator; these regulators bind cooperatively to activate transcription of an operon related to transport and catabolism of L-idonate [1]. Synthesis of this operon is induced when Escherichia coli is grown on L-idonate/5KG in the absence of glucose and gluconate. In addition, this regulator represses transcription of genes related to gluconate metabolism [3]. In the presence of L-idonate, IdnR binds to 16-nucleotide-long DNA-target sites in the idnK/idnDOTR intergenic region to coordinately activate transcription of idnKp and idnDp [1]. IdnR exhibits a high similarity to GntR (53%) and belongs to the LacI/GalR family of transcriptional regulators [5].
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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
IdnR Non-Functional   Apo [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP] W [1]
IdnR-5-dehydro-D-gluconate Functional Allosteric Holo [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP] W [1]
IdnR-Idonate Functional Allosteric Holo [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP] W [1]
Evolutionary Family: GalR/LacI
TFBs length: 16
TFBs symmetry: inverted-repeat
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: idnR
  Genome position: 4490141-4491139
  Length: 999 bp / 332 aa
Operon name: idnDOTR
TU(s) encoding the TF:
Transcription unit        Promoter
idnDOTR
idnDp
idnR
idnRp


Regulon       
Regulated gene(s) gntK, gntU, idnD, idnK, idnO, idnR, idnT
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) (2)
membrane (2)
misc. glucose metabolism (1)
Transcription related (1)
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Regulated operon(s) gntRKU, idnDOTR, idnK
First gene in the operon(s) gntK, idnD, idnK
Simple and complex regulons CRP,GntR,IdnR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[IdnR,+](2)
[IdnR,-](1)


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
  IdnR-5-dehydro-D-gluconate repressor gntKp Sigma70 2.5 -51.5 gntK, gntU
cggctggacaATGTTACCGATAACAGttacccgtaa
 3577636 3577651 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2], [2]
  IdnR-5-dehydro-D-gluconate repressor gntKp Sigma70 15.5 -38.5 gntK, gntU
ttaccgataaCAGTTACCCGTAACATttttaattct
 3577623 3577638 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2], [2]
  IdnR-5-dehydro-D-gluconate activator idnDp nd -78.5 -107.5 idnD, idnO, idnT, idnR
aaggcacatcACGTTATGCGTAACATagtaatgtaa
 4494506 4494521 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [3], [4], [4]
  IdnR activator idnKp Sigma70 -83.5 -109.5 idnK
ttacattactATGTTACGCATAACGTgatgtgcctt
 4494506 4494521 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [3], [4], [4]


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


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IMP] Inferred from mutant phenotype

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Bausch C., Ramsey M., Conway T., 2004, Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli., J Bacteriol 186(5):1388-97

 [2] Tsunedomi R., Izu H., Kawai T., Matsushita K., Ferenci T., Yamada M., 2003, The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli., J Bacteriol 185(6):1783-95

 [3] Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T., 1998, Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli., J Bacteriol 180(14):3704-10

 [4] Tsunedomi R., Izu H., Kawai T., Yamada M., 2003, Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli., J Mol Microbiol Biotechnol 6(1):41-56

 [5] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol 38(4):673-83


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