RegulonDB RegulonDB 11.1: 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: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
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: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] 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                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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 Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine activator astCp2 1832083 1832100 -47.5 tccagttagcCTCCGCCGTTTATGCACTtttatcactg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArgR-L-arginine activator astCp2 1832114 1832131 -78.5 atgcatatggTTTGGTTATAACTCCTTGatttccagtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote ArgR-L-arginine activator astCp2 1832135 1832152 -99.5 ttcactttatATGCACTTTAAATGCATAtggtttggtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote ArgR-L-arginine activator astCp2 1832157 1832174 -121.5 attcacccacATCGCAAACGTATTCACTttatatgcac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [5]
[NtrC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-phosphorylated activator astCp2 1832269 1832285 -233.0 tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote NtrC-phosphorylated activator astCp2 1832289 1832305 -253.0 gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote NtrC-phosphorylated activator astCp2 1832311 1832327 -275.0 gttgttaatgATGTCAACGATGGCGCAaaaaatgccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-EXO] high throughput 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

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