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


Gensor Unit Map          
inosine 5'-IMP RbsB RbsR rbsDACBKR deoxyadenosine glycine FAICAR PurD deoxyinosine adenosine phosphate beta-D-ribofuranose ribose add_mRNA RbsC RbsA purHD_mRNA PurH Add add ribose 5'-p-ribosylglycinamide RbsA ammonium purHD beta-D-ribopyranose RbsD rbsDACBKR_mRNA AICAR RbsR 10-formyl-THF mono-L-glutamate RbsC RbsK RbsB 5-phosphoribosylamine THF polyglutamate beta-D-ribopyranose_Ext alpha-D-ribose 5-phosphate alpha D-ribose


Gensor Unit       
Name: RbsR
Description: Molecular biology level
Detailed: In the presence of ribose, RbsR positively regulates the expression of genes required for adenosine catabolic process. Under these conditions, RbsR is modified to RbsR-ribose, binds its target sites enabling the expression of its regulated genes. RbsR negatively regulates its own expression and the expression of genes required for ribose catabolism and purine biosynthesis in the absence of ribose. Under these conditions, RbsR binds its target sites preventing the expression of its regulated genes.
Less detailed: In the presence of ribose RbsR positively regulates the expression of genes needed for adenosine catabolic process. RbsR negatively regulates the expression of genes involved in ribose catabolism and purine biosynthesis in the absence of ribose.

Physiology level
Detailed: The presence of ribose induces the expression of genes involved with adenosine catabolism. Under these conditions the genes necessary for degradation of adenosine to ammonium are expressed. The absence of ribose inhibits the expression of genes required for ribose catabolism and purine biosynthesis. Under this condition, the genes necessary for transport of ribose and and its conversion from furan to pyran form are not expressed; and the genes necessary for conversion of PRA (5-phosphoribosylamine) to GAR ( 5'-phosphoribosylglycinamide), and AICAR (5-amino-1-beta-D-ribofuranosyl-, 5-(dihydrogen phosphate)) to FAICAR (5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide), are not expressed.
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Classification:
Groups: Transcription
Carbohydrate transport and metabolism
Nucleotide transport and metabolism
Gene Ontology Terms (GO): biological_process GO:0006189 - 'de novo' IMP biosynthetic process
GO:0019303 - D-ribose catabolic process
GO:0006014 - D-ribose metabolic process
GO:0015752 - D-ribose transmembrane transport
GO:0006154 - adenosine catabolic process
GO:0005975 - carbohydrate metabolic process
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cellular_component GO:0043190 - ATP-binding cassette (ABC) transporter complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016021 - integral component of membrane
GO:0005887 - integral component of plasma membrane
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
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molecular_function GO:0005524 - ATP binding
GO:0016887 - ATPase activity
GO:0042623 - ATPase activity, coupled
GO:0015591 - D-ribose transmembrane transporter activity
GO:0003677 - DNA binding
GO:0001216 - DNA-binding transcription activator activity
GO:0003937 - IMP cyclohydrolase activity
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Components:
  Function Name Type
  simple_molecule α D-ribose simple_molecule
  simple_molecule α-D-ribose 5-phosphate simple_molecule
  simple_molecule 10-formyl-THF mono-L-glutamate simple_molecule
  simple_molecule 5'-IMP simple_molecule
  simple_molecule 5'-p-ribosylglycinamide simple_molecule
  simple_molecule 5-phosphoribosylamine simple_molecule
  simple_molecule AICAR simple_molecule
  protein Add protein
  simple_molecule FAICAR simple_molecule
  protein PurD protein
  protein PurH protein
  protein RbsA protein
  complex RbsA-RbsC-RbsB complex
  protein RbsB protein
  protein RbsC protein
  protein RbsD protein
  protein RbsK protein
  protein RbsR protein
  complex RbsR-ribose complex
  simple_molecule THF polyglutamate simple_molecule
  gene add gene
  RNA add_mRNA RNA
  simple_molecule adenosine simple_molecule
  simple_molecule ammonium simple_molecule
  simple_molecule beta-D-ribofuranose simple_molecule
  simple_molecule beta-D-ribopyranose simple_molecule
  simple_molecule beta-D-ribopyranose_Ext simple_molecule
  simple_molecule deoxyadenosine simple_molecule
  simple_molecule deoxyinosine simple_molecule
  simple_molecule glycine simple_molecule
  simple_molecule inosine simple_molecule
  simple_molecule phosphate simple_molecule
  gene purHD gene
  RNA purHD_mRNA RNA
  gene rbsDACBKR gene
  RNA rbsDACBKR_mRNA RNA
  simple_molecule ribose simple_molecule


Reactions       
Showing 24 reactions
RbsR purHD purHD_mRNA
Name: purHD -> purHD_mRNA
Description: Transcription of transcription unit purHD. Reaction inhibition by RbsR.
Type: transcription
Pathway Components: purHD - RbsR -> purHD_mRNA
Components:
Function Name Type
inhibitor RbsR protein
reactant purHD gene
product purHD_mRNA RNA
RbsR rbsDACBKR rbsDACBKR_mRNA
Name: rbsDACBKR -> rbsDACBKR_mRNA
Description: Transcription of transcription unit rbsDACBKR. Reaction inhibition by RbsR.
Type: transcription
Pathway Components: rbsDACBKR - RbsR -> rbsDACBKR_mRNA
Components:
Function Name Type
inhibitor RbsR protein
reactant rbsDACBKR gene
product rbsDACBKR_mRNA RNA
ribose + RbsR RbsR-ribose
Name: ribose + RbsR -> RbsR-ribose
Description: Reaction transforming ribose, RbsR into RbsR-ribose
Type: state transition
Pathway Components: ribose + RbsR -> RbsR-ribose
Components:
Function Name Type
reactant RbsR protein
product RbsR-ribose complex
reactant ribose simple_molecule
RbsR add add_mRNA
Name: add -> add_mRNA
Description: Transcription of transcription unit add. Reaction activation by RbsR.
Type: transcription
Pathway Components: add - RbsR -> add_mRNA
Components:
Function Name Type
activator RbsR protein
reactant add gene
product add_mRNA RNA
add_mRNA Add
Name: add_mRNA -> Add
Description: Translation of Add
Type: translation
Pathway Components: add_mRNA -> Add
Components:
Function Name Type
product Add protein
reactant add_mRNA RNA
Add deoxyadenosine deoxyinosine + ammonium
Name: deoxyadenosine -> deoxyinosine + ammonium
Description: Reaction transforming deoxyadenosine into deoxyinosine, ammonium
Type: state transition
Pathway Components: deoxyadenosine - Add -> deoxyinosine + ammonium
Components:
Function Name Type
catalyzer Add protein
product ammonium simple_molecule
reactant deoxyadenosine simple_molecule
product deoxyinosine simple_molecule
Add adenosine ammonium + inosine
Name: adenosine -> ammonium + inosine
Description: Reaction transforming adenosine into ammonium, inosine
Type: state transition
Pathway Components: adenosine - Add -> ammonium + inosine
Components:
Function Name Type
catalyzer Add protein
reactant adenosine simple_molecule
product ammonium simple_molecule
product inosine simple_molecule
purHD_mRNA PurH
Name: purHD_mRNA -> PurH
Description: Translation of PurH
Type: translation
Pathway Components: purHD_mRNA -> PurH
Components:
Function Name Type
product PurH protein
reactant purHD_mRNA RNA
PurH 10-formyl-THF mono-L-glutamate + AICAR THF polyglutamate + FAICAR
Name: 10-formyl-THF mono-L-glutamate + AICAR -> THF polyglutamate + FAICAR
Description: Reaction transforming 10-formyl-THF mono-L-glutamate, AICAR into THF polyglutamate, FAICAR
Type: state transition
Pathway Components: 10-formyl-THF mono-L-glutamate + AICAR - PurH -> THF polyglutamate + FAICAR
Components:
Function Name Type
reactant 10-formyl-THF mono-L-glutamate simple_molecule
reactant AICAR simple_molecule
product FAICAR simple_molecule
catalyzer PurH protein
product THF polyglutamate simple_molecule
PurH 5'-IMP FAICAR
Name: 5'-IMP -> FAICAR
Description: Reaction transforming 5'-IMP into FAICAR
Type: state transition
Pathway Components: 5'-IMP - PurH -> FAICAR
Components:
Function Name Type
reactant 5'-IMP simple_molecule
product FAICAR simple_molecule
catalyzer PurH protein
purHD_mRNA PurD
Name: purHD_mRNA -> PurD
Description: Translation of PurD
Type: translation
Pathway Components: purHD_mRNA -> PurD
Components:
Function Name Type
product PurD protein
reactant purHD_mRNA RNA
5-phosphoribosylamine PurD 5-phosphoribosylamine + glycine 5'-p-ribosylglycinamide + phosphate
Name: 5-phosphoribosylamine + glycine -> 5'-p-ribosylglycinamide + phosphate
Description: Reaction transforming 5-phosphoribosylamine, glycine into 5'-p-ribosylglycinamide, phosphate
Type: state transition
Pathway Components: 5-phosphoribosylamine + glycine - PurD - 5-phosphoribosylamine -> 5'-p-ribosylglycinamide + phosphate
Components:
Function Name Type
product 5'-p-ribosylglycinamide simple_molecule
inhibitor 5-phosphoribosylamine simple_molecule
reactant 5-phosphoribosylamine simple_molecule
catalyzer PurD protein
reactant glycine simple_molecule
product phosphate simple_molecule
rbsDACBKR_mRNA RbsD
Name: rbsDACBKR_mRNA -> RbsD
Description: Translation of RbsD
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsD
Components:
Function Name Type
product RbsD protein
reactant rbsDACBKR_mRNA RNA
RbsD beta-D-ribopyranose beta-D-ribofuranose
Name: beta-D-ribopyranose -> beta-D-ribofuranose
Description: Reaction transforming beta-D-ribopyranose into beta-D-ribofuranose
Type: state transition
Pathway Components: beta-D-ribopyranose - RbsD -> beta-D-ribofuranose
Components:
Function Name Type
catalyzer RbsD protein
product beta-D-ribofuranose simple_molecule
reactant beta-D-ribopyranose simple_molecule
rbsDACBKR_mRNA RbsA
Name: rbsDACBKR_mRNA -> RbsA
Description: Translation of RbsA
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsA
Components:
Function Name Type
product RbsA protein
reactant rbsDACBKR_mRNA RNA
RbsA + RbsB + RbsC RbsA-RbsC-RbsB
Name: RbsA + RbsB + RbsC -> RbsA-RbsC-RbsB
Description: Reaction transforming RbsA, RbsB, RbsC into RbsA-RbsC-RbsB
Type: state transition
Pathway Components: RbsA + RbsB + RbsC -> RbsA-RbsC-RbsB
Components:
Function Name Type
reactant RbsA protein
product RbsA-RbsC-RbsB complex
reactant RbsB protein
reactant RbsC protein
RbsA-RbsC-RbsB beta-D-ribopyranose_Ext beta-D-ribopyranose
Name: beta-D-ribopyranose_Ext -> beta-D-ribopyranose
Description: Transport of beta-D-ribopyranose_Ext through a bacterial membrane, leading to the presence of beta-D-ribopyranose inside the cell.
Type: transport
Pathway Components: beta-D-ribopyranose_Ext - RbsA-RbsC-RbsB -> beta-D-ribopyranose
Components:
Function Name Type
catalyzer RbsA-RbsC-RbsB complex
product beta-D-ribopyranose simple_molecule
reactant beta-D-ribopyranose_Ext simple_molecule
rbsDACBKR_mRNA RbsC
Name: rbsDACBKR_mRNA -> RbsC
Description: Translation of RbsC
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsC
Components:
Function Name Type
product RbsC protein
reactant rbsDACBKR_mRNA RNA
rbsDACBKR_mRNA RbsB
Name: rbsDACBKR_mRNA -> RbsB
Description: Translation of RbsB
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsB
Components:
Function Name Type
product RbsB protein
reactant rbsDACBKR_mRNA RNA
rbsDACBKR_mRNA RbsK
Name: rbsDACBKR_mRNA -> RbsK
Description: Translation of RbsK
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsK
Components:
Function Name Type
product RbsK protein
reactant rbsDACBKR_mRNA RNA
RbsK α D-ribose α-D-ribose 5-phosphate
Name: α D-ribose -> α-D-ribose 5-phosphate
Description: Reaction transforming α D-ribose into α-D-ribose 5-phosphate
Type: state transition
Pathway Components: α D-ribose - RbsK -> α-D-ribose 5-phosphate
Components:
Function Name Type
reactant α D-ribose simple_molecule
product α-D-ribose 5-phosphate simple_molecule
catalyzer RbsK protein
rbsDACBKR_mRNA RbsR
Name: rbsDACBKR_mRNA -> RbsR
Description: Translation of RbsR
Type: translation
Pathway Components: rbsDACBKR_mRNA -> RbsR
Components:
Function Name Type
product RbsR protein
reactant rbsDACBKR_mRNA RNA
5'-p-ribosylglycinamide AICAR
Name: 5'-p-ribosylglycinamide -> AICAR
Description: Transformation of 5'-p-ribosylglycinamide into AICAR by one or more reactions not shown.
Type: complementary pathway reaction
Pathway Components: 5'-p-ribosylglycinamide / GARTRANSFORMYL2-RXN / FGAMSYN-RXN / AIRS-RXN / RXN0-742 / RXN0-743 / SAICARSYN-RXN / AICARSYN-RXN / AICAR
Components:
Function Name Type
reactant 5'-p-ribosylglycinamide simple_molecule
product AICAR simple_molecule
beta-D-ribofuranose α D-ribose
Name: beta-D-ribofuranose -> α D-ribose
Description: Transformation of beta-D-ribofuranose into α D-ribose by one or more reactions not shown.
Type: complementary pathway reaction
Pathway Components: beta-D-ribofuranose / RXN-14904 / α D-ribose
Components:
Function Name Type
product α D-ribose simple_molecule
reactant beta-D-ribofuranose simple_molecule



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