RegulonDB RegulonDB 10.9: Operon Form
   

gntRKU operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: gntRKU
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: gntKU
Synonym(s): OP00323
Gene(s): gntU, gntK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Izu H., et al., 1997
[2] Tong S., et al., 1996
Promoter
Name: gntKp
+1: 3577645
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 53
Sequence: cttatacacttaaggcatggatggatattgcttctgatattgtccggctggacaatgttaCcgataacagttacccgtaac
                            -35                    -10      +1                   
Note(s): Transcription from the gntKp promoter seems to be attenuated at the potential stem-loop structure in front of the gntU gene.
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Izu H., et al., 1997
[2] Tong S., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: tcgaaaagaaCCCGGTAGCGTCACAACTACCGGGcgaacaaact
Reference(s): [1] Izu H., et al., 1997
[2] Tong S., et al., 1996
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator gntKp 3577703 3577724 -68.5 tttaagcccaCAAATTTGAAGTAGCTCACACTTatacacttaa nd [APIORCISFBSCS], [BCE], [GEA] [1]
[GntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GntR repressor gntKp 3577621 3577640 15.5 atgttaccgaTAACAGTTACCCGTAACATTTttaattcttg nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
proximal GntR repressor gntKp 3577634 3577653 2.5 gtccggctggACAATGTTACCGATAACAGTTacccgtaaca nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
[IdnR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IdnR-5-ketogluconate1 repressor gntKp 3577623 3577638 15.5 gttaccgataACAGTTACCCGTAACATttttaattct nd [GEA] [4]
proximal IdnR-5-ketogluconate repressor gntKp 3577636 3577651 2.5 ccggctggacAATGTTACCGATAACAGttacccgtaa nd [GEA] [4]
Note(s): 1IdnR negatively controls the gntK operon, presumably by binding to GntR-binding elements when GntR is released from the operator by interaction with gluconate.
4IdnR negatively controls the gntK operon, presumably by binding to GntR-binding elements when GntR is released from the operator by interaction with gluconate.


Transcription unit          
Name: gntK
Gene(s): gntK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Izu H., et al., 1997
Promoter
Name: gntKp
+1: 3577645
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 53
Sequence: cttatacacttaaggcatggatggatattgcttctgatattgtccggctggacaatgttaCcgataacagttacccgtaac
                            -35                    -10      +1                   
Note(s): Transcription from the gntKp promoter seems to be attenuated at the potential stem-loop structure in front of the gntU gene.
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Izu H., et al., 1997
[2] Tong S., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: catgactaaaAACAGCAGCAGTAAAACAGACCCTACTGCTGTTaaaacaagcg
Reference(s): [1] Izu H., et al., 1997
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator gntKp 3577703 3577724 -68.5 tttaagcccaCAAATTTGAAGTAGCTCACACTTatacacttaa nd [APIORCISFBSCS], [BCE], [GEA] [1]
[GntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GntR repressor gntKp 3577621 3577640 15.5 atgttaccgaTAACAGTTACCCGTAACATTTttaattcttg nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
proximal GntR repressor gntKp 3577634 3577653 2.5 gtccggctggACAATGTTACCGATAACAGTTacccgtaaca nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
[IdnR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IdnR-5-ketogluconate1 repressor gntKp 3577623 3577638 15.5 gttaccgataACAGTTACCCGTAACATttttaattct nd [GEA] [4]
proximal IdnR-5-ketogluconate repressor gntKp 3577636 3577651 2.5 ccggctggacAATGTTACCGATAACAGttacccgtaa nd [GEA] [4]
Note(s): 1IdnR negatively controls the gntK operon, presumably by binding to GntR-binding elements when GntR is released from the operator by interaction with gluconate.
4IdnR negatively controls the gntK operon, presumably by binding to GntR-binding elements when GntR is released from the operator by interaction with gluconate.


Transcription unit       
Name: gntR
Gene(s): gntR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Tong S., et al., 1996
Promoter
Name: gntRp2
+1: 3578818
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 92
Sequence: gcttccggggttttgccgcgtcgttagcacaatgcgatgcaattgatttagtgtatatctAataattgtaaacaagcactg
                        -35                      -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[2] Tong S., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: aagaattaaaAATGTTACGGGTAACTGTTATCGGTAACATTgtccagccgg


Transcription unit       
Name: gntR
Gene(s): gntR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Tong S., et al., 1996
Promoter
Name: gntRp3
+1: 3578862
Distance from start of the gene: 136
Sequence: tttttgcaggcttcctcgctcgctccggtcgcgtgctgatgtacgcttccggggttttgcCgcgtcgttagcacaatgcga
Evidence: [HIPP]
[TIM]
Reference(s): [2] Tong S., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: aagaattaaaAATGTTACGGGTAACTGTTATCGGTAACATTgtccagccgg


Transcription unit       
Name: gntR
Gene(s): gntR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Tong S., et al., 1996
Promoter
Name: gntRp4
+1: 3578880
Distance from start of the gene: 154
Sequence: gcatctttgaagcctgcctttttgcaggcttcctcgctcgctccggtcgcgtgctgatgtAcgcttccggggttttgccgc
Evidence: [TIM]
Reference(s): [2] Tong S., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: aagaattaaaAATGTTACGGGTAACTGTTATCGGTAACATTgtccagccgg


Transcription unit       
Name: gntU
Gene(s): gntU   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Reference(s): [3] Huerta AM., et al., 2003
[1] Izu H., et al., 1997
Terminator(s)
Type: rho-independent
Sequence: tcgaaaagaaCCCGGTAGCGTCACAACTACCGGGcgaacaaact
Reference(s): [1] Izu H., et al., 1997
[2] Tong S., et al., 1996


Transcription unit       
Name: gntRKU
Gene(s): gntU, gntK, gntR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription from the gntRp promoter seems to be terminated by the presence of GntR around the GntR-binding site, which overlaps with the gntKp promoter.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Izu H., et al., 1997
Terminator(s)
Type: rho-independent
Sequence: tcgaaaagaaCCCGGTAGCGTCACAACTACCGGGcgaacaaact
Reference(s): [1] Izu H., et al., 1997
[2] Tong S., et al., 1996


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [HIPP] Human inference of promoter position


Reference(s)    

 [1] Izu H., Adachi O., Yamada M., 1997, Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli., J Mol Biol 267(4):778-93

 [2] Tong S., Porco A., Isturiz T., Conway T., 1996, Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism., J Bacteriol 178(11):3260-9

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] 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

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