RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit       
Name: astCADBE
Gene(s): astE, astB, astD, astA, astC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 1998
Promoter
Name: astCp1
+1: 1832013
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: ggctggcacgaaccctgcaatctacatttacagcgcaaacattacttattattaacatatAaataacgaattatttactgt
                      -35                      -10          +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Fraley CD., et al., 1998
[3] Huerta AM., et al., 2003


Transcription unit       
Name: astCADBE
Gene(s): astE, astB, astD, astA, astC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 1998
Promoter
Name: astCp3
+1: 1832039
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 57
Sequence: tccgccgtttatgcacttttatcactggctggcacgaaccctgcaatctacatttacagcGcaaacattacttattattaa
                         -35                -10             +1                   
Note(s): The expression of this promoter is induced in cells in stationary phase in nitrogen-limited medium lacking glucose.
Evidence: [CV(RPF/TIM)]
[HIPP]
[ICWHO]
[RPF]
[TIM]
Reference(s): [2] Fraley CD., et al., 1998
[3] Huerta AM., et al., 2003
[4] Kiupakis AK., et al., 2002


Transcription unit          
Name: astCADBE
Gene(s): astE, astB, astD, astA, astC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 1998
Promoter
Name: astCp2
+1: 1832044
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 62
Sequence: tagcctccgccgtttatgcacttttatcactggctggcacgaaccctgcaatctacatttAcagcgcaaacattacttatt
                                   -24         -12          +1                   
Note(s): The expression of this promoter is induced in cells growing exponentially in nitrogen-limited minimal medium Fraley CD,1998
Evidence: [CV(RPF/TIM)]
[HIPP]
[ICWHO]
[RPF]
[TIM]
Reference(s): [2] Fraley CD., et al., 1998
[3] Huerta AM., et al., 2003
[4] Kiupakis AK., et al., 2002
TF binding sites (TFBSs)
[ArgR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine1 activator astCp2 1832083 1832100 -47.5 ttccagttagCCTCCGCCGTTTATGCACTtttatcactg nd [AIBSCS], [BPP], [GEA] [4]
proximal ArgR-L-arginine2 activator astCp2 1832114 1832131 -78.5 aatgcatatgGTTTGGTTATAACTCCTTGatttccagtt nd [AIBSCS], [BPP], [GEA] [4]
remote ArgR-L-arginine3 activator astCp2 1832135 1832152 -99.5 attcactttaTATGCACTTTAAATGCATAtggtttggtt nd [AIBSCS], [BPP], [GEA] [4]
remote ArgR-L-arginine4 activator astCp2 1832157 1832174 -121.5 tattcacccaCATCGCAAACGTATTCACTttatatgcac nd [EME], [AIBSCS], [AIBSPD], [BPP], [CEE], [GEA] [4], [5]
[NtrC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-phosphorylated activator astCp2 1832269 1832285 -233.0 ttggtgcgcgCTGCGTCAGAATGGCGCAgtaatttcca nd [AIBSCS], [BPP], [GEA] [4]
remote NtrC-phosphorylated activator astCp2 1832289 1832305 -253.0 ggcgcaaaaaATGCCCGCTTTTGGTGCGcgctgcgtca nd [AIBSCS], [BPP], [GEA] [4]
remote NtrC-phosphorylated activator astCp2 1832311 1832327 -275.0 ggttgttaatGATGTCAACGATGGCGCAaaaaatgccc nd [AIBSCS], [BPP], [GEA] [4]
Note(s): 1ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
2ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
3ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
4ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.4ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
5ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
6ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.
7ArgR enhances expression from the astCp2 promoter but is not essential for its expression Kiupakis AK,2002.


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [CV(RPF/TIM)] cross validation(RPF/TIM)

 [RPF] RNA polymerase footprinting

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [EME] Expression microarray evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CEE] ChIP-exo evidence


Reference(s)    

 [1] Schneider BL., Kiupakis AK., Reitzer LJ., 1998, Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli., J Bacteriol 180(16):4278-86

 [2] Fraley CD., Kim JH., McCann MP., Matin A., 1998, The Escherichia coli starvation gene cstC is involved in amino acid catabolism., J Bacteriol 180(16):4287-90

 [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] Kiupakis AK., Reitzer L., 2002, ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli., J Bacteriol 184(11):2940-50

 [5] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

RegulonDB