RegulonDB RegulonDB 11.2:Regulon Page
   

IlvY DNA-binding transcriptional dual regulator

Synonyms: IlvY, IlvY-(S)-2-acetolactate, IlvY-Alfa-acetohydroxybutirate
Summary:
In the presence of α-acetolactate or α-acetohydroxybutyrate, the "isoleucine-valine" protein, IlvY, participates in activating a gene involved in isoleucine and valine biosynthesis. In the absence of the metabolites, it is autorepressed [1, 5]. IlvY binds cooperatively to two inverted repeat DNA-binding sites of 21 bp in the divergent regulatory region of the ilvY and ilvC genes for autorepression. When the inducer is bound to the IlvY-DNA complex, IlvY binding at the same DNA position activates the transcription of ilvC by inducing a conformational change in the structure of the complex that is correlated with the relief of a protein-induced bend in the DNA that enhances the recruitment of RNA polymerase [1, 5]. The transcription of the divergent genes ilvY and ilvC is coupled in a DNA supercoiling-dependent manner [7]. The protein belongs to the LysR family and contains a helix-turn-helix motif for DNA binding near its N terminus [8]. Read more >


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
IlvY Functional   Apo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [EXP-IPI] S [1]
IlvY-(S)-2-acetolactate Functional Allosteric Holo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [EXP-IPI] S [1]
IlvY-Alfa-acetohydroxybutirate Functional Allosteric Holo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [EXP-IPI] S [1]
Evolutionary Family: LysR
TFBs length: 17
TFBs symmetry: inverted-repeat
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: ilvY
  Genome position: 3956927-3957820
  Length: 894 bp / 297 aa
Operon name: ilvY
TU(s) encoding the TF:
Transcription unit        Promoter
ilvY
ilvYp1
ilvY
ilvYp2


Regulon       
Regulated gene(s) ilvC, ilvY
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
isoleucine/valine (2)
Transcription related (1)
activator (1)
repressor (1)
operon (1)
Regulated operon(s) ilvC, ilvY
First gene in the operon(s) ilvC, ilvY
Simple and complex regulons IlvY
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[IlvY,-](2)
[IlvY,+](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
  IlvY-(S)-2-acetolactate activator ilvCp Sigma70 -61.0 -119.0 ilvC
cgatgttgacGTTGCAAAAATTGCAATGtgacgttgtg
 3957843 3957860 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [2], [3], [4], [5], [5], [6]
  IlvY-(S)-2-acetolactate activator ilvCp Sigma70 -30.0 -88.0 ilvC
cgttgtgaatATATCAATTTCCGCAATAaatttcctgt
 3957874 3957891 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [5], [5], [6]
  IlvY repressor ilvYp1 Sigma70 -15.0 -62.0 ilvY
acaggaaattTATTGCGGAAATTGATATattcacaacg
 3957874 3957891 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [5], [5], [6]
  IlvY repressor ilvYp1 Sigma70 17.0 -31.0 ilvY
cacaacgtcaCATTGCAATTTTTGCAACgtcaacatcg
 3957843 3957860 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [2], [3], [4], [5], [5], [6]
  IlvY repressor ilvYp2 Sigma38 -15.0 -62.0 ilvY
acaggaaattTATTGCGGAAATTGATATattcacaacg
 3957874 3957891 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [5], [5], [6]
  IlvY repressor ilvYp2 Sigma38 17.0 -31.0 ilvY
cacaacgtcaCATTGCAATTTTTGCAACgtcaacatcg
 3957843 3957860 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [2], [3], [4], [5], [5], [6]


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


Evidence    

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IPI] Inferred from physical interaction

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

 [IC] Inferred by curator

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Rhee KY., Senear DF., Hatfield GW., 1998, Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex., J Biol Chem 273(18):11257-66

 [2] Biel AJ., Umbarger HE., 1981, Mutations in the ilvY gene of Escherichia coli K-12 that cause constitutive expression of ilvC., J Bacteriol 146(2):718-24

 [3] Pledger WJ., Umbarger HE., 1973, Isoleucine and valine metabolism in Escherichia coli. XXII. A pleiotropic mutation affecting induction of isomeroreductase activity., J Bacteriol 114(1):195-207

 [4] Watson MD., Wild J., Umbarger HE., 1979, Positive control of ilvC expression in Escherichia coli K-12; identification and mapping of regulatory gene ilvY., J Bacteriol 139(3):1014-20

 [5] Wek RC., Hatfield GW., 1988, Transcriptional activation at adjacent operators in the divergent-overlapping ilvY and ilvC promoters of Escherichia coli., J Mol Biol 203(3):643-63

 [6] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [7] Opel ML., Hatfield GW., 2001, DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths., Mol Microbiol 39(1):191-8

 [8] Henikoff S., Haughn GW., Calvo JM., Wallace JC., 1988, A large family of bacterial activator proteins., Proc Natl Acad Sci U S A 85(18):6602-6


RegulonDB