RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: phoE
Synonym(s): OP00118
Gene(s): phoE   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene phoE is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Reference(s): [1] Yamada M., et al., 1989
Promoter
Name: phoEp
+1: 260158
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 58
Sequence: ttttaagaatattattaatctgtaatatatctttaacaatctcaggttaaaaactttcctGttttcaacgggactctcccg
                                -35                  -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Tommassen J., et al., 1987
TF binding sites (TFBSs)
[PhoB,+] 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 PhoB-phosphorylated activator phoEp 260181 260199 -32.0 tattattaatCTGTAATATATCTTTAACAatctcaggtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W [5]
proximal PhoB-phosphorylated activator phoEp 260237 260255 -88.0 agcggcagttGTTTACGCTTTTATTACAGatttaataaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W [5]
remote PhoB-phosphorylated activator phoEp 260261 260281 -113.0 ttttgttgcgCGGGATCAGCAAGCCTAGCGGcagttgttta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W [5]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA MicF phoE repressor 260067 260079 CCAUCACCACUAA nd [EXP-IMP] [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IMP] Inferred from mutant phenotype


Reference(s)    

 [1] Yamada M., Makino K., Amemura M., Shinagawa H., Nakata A., 1989, Regulation of the phosphate regulon of Escherichia coli: analysis of mutant phoB and phoR genes causing different phenotypes., J Bacteriol 171(10):5601-6

 [2] 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

 [3] Tommassen J., Koster M., Overduin P., 1987, Molecular analysis of the promoter region of the Escherichia coli K-12 phoE gene. Identification of an element, upstream from the promoter, required for efficient expression of phoE protein., J Mol Biol 198(4):633-41

 [4] Holmqvist E., Unoson C., Reimegard J., Wagner EG., 2012, A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp., Mol Microbiol 84(3):414-27

 [5] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

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