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KdgR DNA-binding transcriptional repressor

Synonyms: KdgR
Summary:
The "2-Keto-3-deoxygluconate repressor," KdgR, is a DNA-binding transcription factor that represses transcription of the operons involved in transport and catabolism of 2-keto-3-deoxy gluconate (KDG) [1, 3, 4, 5]. Synthesis of these genes is induced when E. coli is grown in the presence of KDG and under high-temperature conditions, between 32 and 35°C. Although little is known about the regulating mechanism of KdgR, it has been shown to act as a repressor that binds to a putative inverted repeat sequence [6, 7]. Comparative analysis of intergenic DNA sequences showed the consistent occurrence of KdgR possible binding sites upstream of the genes not related to the transport and catabolism of KDG [6, 8].


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
KdgR Functional   nd nd nd
Evolutionary Family: IclR
TFBs length: 21
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: kdgR
  Genome position: 1909308-1910099
  Length: 792 bp / 263 aa
Operon name: kdgR
TU(s) encoding the TF:
Transcription unit        Promoter
kdgR
 


Regulon       
Regulated gene(s) eda, edd
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Entner-Doudoroff (2)
carbon compounds (1)
glyoxylate degradation (1)
Regulated operon(s) edd-eda
First gene in the operon(s) eda, edd
Simple and complex regulons Cra,GntR,KdgR
KdgR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[KdgR,-](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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  KdgR repressor edap1 nd 5.0 -349.0 eda
cttggtgtatTATTGGACCGGTGTTTCAAAAttgcgttagt
 1933095 1933115 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  KdgR repressor eddp Sigma70 -76.0 -185.0 edd, eda
accggtaacaTGATCTTGCGCAGATTGTAGAacaattttta
 1934779 1934799 [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2], [2]


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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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


Reference(s)    

 [1] Murray EL., Conway T., 2005, Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli., J Bacteriol 187(3):991-1000

 [2] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116

 [3] Pouyssegur J., Stoeber F., 1974, Genetic control of the 2-keto-3-deoxy-d-gluconate metabolism in Escherichia coli K-12: kdg regulon., J Bacteriol 117(2):641-51

 [4] Pouysségur J, Lagarde A, 1973, [2-Keto-3-deoxy-gluconate transport system in E. coli K 12: map location of a structural gene and of its operator]., Mol Gen Genet, 121(2):163 10.1007/BF00277530

 [5] Pouysségur J, Stoeber F, 1972, [Physiologic and genetic control of metabolism of 2-keto-3-deoxy-gluconate in E. coli K 12. Regulon kdg]., C R Acad Hebd Seances Acad Sci D, 274(15):2249 None

 [6] 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

 [7] Nasser W, Reverchon S, Condemine G, Robert-Baudouy J, 1994, Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis., J Mol Biol, 236(2):427 10.1006/jmbi.1994.1155

 [8] Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N, 2004, Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria., Microbiology (Reading), 150(Pt 11):3571 10.1099/mic.0.27041-0


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