RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: appCBA-yccB
Synonym(s): OP00137, appCBA, cyx-appA, cyxAB-appA
Gene(s): appC, appB, appX, appA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Atlung T., et al., 1994
[2] Dassa J., et al., 1991
Promoter
Name: appCp
+1: 1037710
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: ggcgaatacctctggtcgtagagtttcaggataaagagggagatctaccattatcgggttAtttttctctcttcgcctaca
                        -35                   -10           +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Atlung T., et al., 1994
[3] Atlung T., et al., 1997
[2] Dassa J., et al., 1991
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[AppY,+] 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
nd AppY activator appCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W nd
[ArcA,+] 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
nd ArcA-phosphorylated activator appCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[YdeO,+] 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 YdeO activator appCp 1037672 1037694 -27.5 tggtcgtagaGTTTCAGGATAAAGAGGGAGATCtaccattatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Transcription unit          
Name: appCBA-yccB
Synonym(s): OP00137, appCBA, cyx-appA, cyxAB-appA
Gene(s): appC, appB, appX, appA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Atlung T., et al., 1994
[2] Dassa J., et al., 1991
Promoter
Name: appCp2
+1: 1037710
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 30
Sequence: ggcgaatacctctggtcgtagagtttcaggataaagagggagatctaccattatcgggttAtttttctctcttcgcctaca
                        -35              -10                +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Atlung T., et al., 1994
[3] Atlung T., et al., 1997
[2] Dassa J., et al., 1991
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[AppY,+] 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
nd AppY activator appCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W nd
[ArcA,+] 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
nd ArcA-phosphorylated activator appCp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[YdeO,+] 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 YdeO activator appCp2 1037672 1037694 -27.5 tggtcgtagaGTTTCAGGATAAAGAGGGAGATCtaccattatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Transcription unit       
Name: appA
Gene(s): appA   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Atlung T., et al., 1994
Promoter
Name: appAp
+1: 1040599
Distance from start of the gene: 18
Sequence:
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Dassa J., et al., 1991


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [COMP-HINF] Inferred by a human based on computational evidence

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

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


Reference(s)    

 [1] Atlung T., Brondsted L., 1994, Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase., J Bacteriol 176(17):5414-22

 [2] Dassa J., Fsihi H., Marck C., Dion M., Kieffer-Bontemps M., Boquet PL., 1991, A new oxygen-regulated operon in Escherichia coli comprises the genes for a putative third cytochrome oxidase and for pH 2.5 acid phosphatase (appA), Mol Gen Genet 229(3):341-52

 [3] Atlung T., Knudsen K., Heerfordt L., Brondsted L., 1997, Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation., J Bacteriol 179(7):2141-6

 [4] 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

 [5] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [6] Brondsted L., Atlung T., 1996, Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli., J Bacteriol 178(6):1556-64

RegulonDB