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IclR Genetic Sensory Response Unit in Escherichia coli K-12 genome


Gensor Unit Map          
L-malate AceA AceB AceK I-CIT IclR pyruvate a phosphorylated isocitrate dehydrogenase aceBAK aceBAK_mRNA ac-CoA an isocitrate dehydrogenase CoA glyoxylate iclR iclR_mRNA phosphate succinate IclR pyruvate IclR glyoxylate


Gensor Unit       
Name: IclR
Description: Molecular biology level
Detailed: In the presence of pyruvate, IclR negatively regulates the expression of genes required for tricarboxylic acid cycle and glyoxylate cycle and for regulation of them. Under these conditions, IclR is modified to IclR-pyruvate, binds its target sites preventing the expression of its regulated genes. In the absence of pyruvate, Iclr unbinds its target sites enabling the expression of its regulated genes.
Less detailed: In the presence of pyruvate IclR negatively regulates the expression of genes needed for tricarboxylic acid cycle and glyoxylate cycle and for regulation of them.

Physiology level
Detailed: The presence of pyruvate inhibits the expression of genes involved with tricarboxylic acid cycle and glyoxylate cycle and for regulation of these processes. Under these conditions, the genes necessary for conversion of D-threo-isocitrate to glyoxylate, conversion of glyoxalate and acetyl CoA to L-malate and control of isocitrate dehydrogenase phosporylation, are not expressed.
Less detailed: The presence of pyruvate inhibits the expression of genes needful for conversion of D-threo-isocitrate to glyoxylate, conversion of glyoxalate and acetyl CoA to L-malate and control of isocitrate dehydrogenase phosporylation.
Classification:
Groups: Unclassified Gensor Units
Gene Ontology Terms (GO): biological_process GO:0016311 - dephosphorylation
GO:0006097 - glyoxylate cycle
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0018105 - peptidyl-serine phosphorylation
GO:0006470 - protein dephosphorylation
GO:0050790 - regulation of catalytic activity
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cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016208 - AMP binding
GO:0005524 - ATP binding
GO:0003677 - DNA binding
GO:0003700 - DNA binding transcription factor activity
GO:0008772 - [isocitrate dehydrogenase (NADP+)] kinase activity
GO:0101014 - [isocitrate dehydrogenase (NADP+)] phosphatase activity
GO:0043169 - cation binding
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Components: Show/Hide Components Table (20 more...)
Function Name Type
protein AceA protein
protein AceB protein
protein AceK protein
simple_molecule I-CIT simple_molecule
protein IclR protein
complex IclR-glyoxylate complex
complex IclR-pyruvate complex
gene aceBAK gene
RNA aceBAK_mRNA RNA
simple_molecule acetyl-CoA simple_molecule
simple_molecule coenzyme A simple_molecule
simple_molecule glyoxylate simple_molecule
gene iclR gene
RNA iclR_mRNA RNA
simple_molecule isocitrate dehydrogenase-P simple_molecule
simple_molecule isocitrate-dehydrogenase simple_molecule
simple_molecule malate simple_molecule
simple_molecule phosphate simple_molecule
simple_molecule pyruvate simple_molecule
simple_molecule succinate simple_molecule


Reactions       
Showing 14 reactions
pyruvate + IclR IclR-pyruvate
Name: pyruvate + IclR -> IclR-pyruvate
Description: Reaction transforming pyruvate, IclR into IclR-pyruvate
Type: state transition
Pathway Components: pyruvate + IclR -> IclR-pyruvate
Components:
Function Name Type Evidence Reference(s)
reactant IclR protein nd nd
product IclR-pyruvate complex nd nd
reactant pyruvate simple_molecule nd nd
IclR-pyruvate aceBAK aceBAK_mRNA
Name: aceBAK -> aceBAK_mRNA
Description: Transcription of transcription unit aceBAK. Reaction inhibition by IclR-pyruvate.
Type: transcription
Pathway Components: aceBAK - IclR-pyruvate -> aceBAK_mRNA
Components:
Function Name Type Evidence Reference(s)
inhibitor IclR-pyruvate complex nd nd
reactant aceBAK gene nd nd
product aceBAK_mRNA RNA nd nd
IclR-pyruvate iclR iclR_mRNA
Name: iclR -> iclR_mRNA
Description: Transcription of transcription unit iclR. Reaction inhibition by IclR-pyruvate.
Type: transcription
Pathway Components: iclR - IclR-pyruvate -> iclR_mRNA
Components:
Function Name Type Evidence Reference(s)
inhibitor IclR-pyruvate complex nd nd
reactant iclR gene nd nd
product iclR_mRNA RNA nd nd
glyoxylate + IclR IclR-glyoxylate
Name: glyoxylate + IclR -> IclR-glyoxylate
Description: Reaction transforming glyoxylate, IclR into IclR-glyoxylate
Type: state transition
Pathway Components: glyoxylate + IclR -> IclR-glyoxylate
Components:
Function Name Type Evidence Reference(s)
reactant IclR protein nd nd
product IclR-glyoxylate complex nd nd
reactant glyoxylate simple_molecule nd nd
iclR_mRNA IclR
Name: iclR_mRNA -> IclR
Description: Translation of IclR
Type: translation
Pathway Components: iclR_mRNA -> IclR
Components:
Function Name Type Evidence Reference(s)
product IclR protein nd nd
reactant iclR_mRNA RNA nd nd
aceBAK_mRNA AceB
Name: aceBAK_mRNA -> AceB
Description: Translation of AceB
Type: translation
Pathway Components: aceBAK_mRNA -> AceB
Components:
Function Name Type Evidence Reference(s)
product AceB protein nd nd
reactant aceBAK_mRNA RNA nd nd
AceB acetyl-CoA + glyoxylate coenzyme A + malate
Name: acetyl-CoA + glyoxylate -> coenzyme A + malate
Description: Reaction transforming acetyl-CoA, glyoxylate into coenzyme A, malate
Type: state transition
Pathway Components: acetyl-CoA + glyoxylate - AceB -> coenzyme A + malate
Components:
Function Name Type Evidence Reference(s)
catalyzer AceB protein nd nd
reactant acetyl-CoA simple_molecule nd nd
product coenzyme A simple_molecule nd nd
reactant glyoxylate simple_molecule nd nd
product malate simple_molecule nd nd
aceBAK_mRNA AceA
Name: aceBAK_mRNA -> AceA
Description: Translation of AceA
Type: translation
Pathway Components: aceBAK_mRNA -> AceA
Components:
Function Name Type Evidence Reference(s)
product AceA protein nd nd
reactant aceBAK_mRNA RNA nd nd
AceA succinate I-CIT glyoxylate + succinate
Name: I-CIT -> glyoxylate + succinate
Description: Reaction transforming I-CIT into glyoxylate, succinate
Type: state transition
Pathway Components: I-CIT - AceA - succinate -> glyoxylate + succinate
Components:
Function Name Type Evidence Reference(s)
catalyzer AceA protein nd nd
reactant I-CIT simple_molecule nd nd
product glyoxylate simple_molecule nd nd
inhibitor succinate simple_molecule nd nd
product succinate simple_molecule nd nd
aceBAK_mRNA AceK
Name: aceBAK_mRNA -> AceK
Description: Translation of AceK
Type: translation
Pathway Components: aceBAK_mRNA -> AceK
Components:
Function Name Type Evidence Reference(s)
product AceK protein nd nd
reactant aceBAK_mRNA RNA nd nd
AceK I-CIT isocitrate dehydrogenase-P isocitrate-dehydrogenase + phosphate
Name: isocitrate dehydrogenase-P -> isocitrate-dehydrogenase + phosphate
Description: Reaction transforming isocitrate dehydrogenase-P into isocitrate-dehydrogenase, phosphate
Type: state transition
Pathway Components: isocitrate dehydrogenase-P - AceK - I-CIT -> isocitrate-dehydrogenase + phosphate
Components:
Function Name Type Evidence Reference(s)
catalyzer AceK protein nd nd
inhibitor I-CIT simple_molecule nd nd
reactant isocitrate dehydrogenase-P simple_molecule nd nd
product isocitrate-dehydrogenase simple_molecule nd nd
product phosphate simple_molecule nd nd
AceK I-CIT glyoxylate isocitrate-dehydrogenase isocitrate dehydrogenase-P
Name: isocitrate-dehydrogenase -> isocitrate dehydrogenase-P
Description: Reaction transforming isocitrate-dehydrogenase into isocitrate dehydrogenase-P
Type: state transition
Pathway Components: isocitrate-dehydrogenase - AceK - I-CIT - glyoxylate -> isocitrate dehydrogenase-P
Components:
Function Name Type Evidence Reference(s)
catalyzer AceK protein nd nd
inhibitor I-CIT simple_molecule nd nd
inhibitor glyoxylate simple_molecule nd nd
product isocitrate dehydrogenase-P simple_molecule nd nd
reactant isocitrate-dehydrogenase simple_molecule nd nd
malate I-CIT
Name: malate -> I-CIT
Description: Transformation of malate into I-CIT by one or more reactions not shown.
Type: complementary pathway reaction
Pathway Components: malate / MALATE-DEH-RXN / CITSYN-RXN / ACONITATEDEHYDR-RXN / ACONITATEHYDR-RXN / I-CIT
Components:
Function Name Type Evidence Reference(s)
product I-CIT simple_molecule nd nd
reactant malate simple_molecule nd nd
acetyl-CoA I-CIT
Name: acetyl-CoA -> I-CIT
Description: Transformation of acetyl-CoA into I-CIT by one or more reactions not shown.
Type: complementary pathway reaction
Pathway Components: acetyl-CoA / CITSYN-RXN / ACONITATEDEHYDR-RXN / ACONITATEHYDR-RXN / I-CIT
Components:
Function Name Type Evidence Reference(s)
product I-CIT simple_molecule nd nd
reactant acetyl-CoA simple_molecule nd nd



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