RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: phoH
Gene(s): phoH   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene phoH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kim SK., et al., 1993
Promoter
Name: phoHp1
+1: 1084865
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 127
Sequence: gcacacagcttttttcatcactgtcatcactctgtcatctttccagtagaaactaatgtcActgaaatggtgttttatagt
                                -35                   -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Kim SK., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: gttatcggtgCAGAGCCCGGGCGAACCGGGCTTTGttttgggtgt
Reference(s): [1] Kim SK., et al., 1993
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 phoHp1 1084825 1084843 -31.0 tttttcatcaCTGTCATCACTCTGTCATCtttccagtag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]


Transcription unit       
Name: phoH
Gene(s): phoH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kim SK., et al., 1993
Promoter
Name: phoHp2
+1: 1084938
Distance from start of the gene: 54
Sequence: tttatagttaaatataagtaaatatattgttgcaataaatgcgagatctgttgtacttatTaagtagcagcggaagttccc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Kim SK., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: gttatcggtgCAGAGCCCGGGCGAACCGGGCTTTGttttgggtgt
Reference(s): [1] Kim SK., et al., 1993


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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


Reference(s)    

 [1] Kim SK., Makino K., Amemura M., Shinagawa H., Nakata A., 1993, Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli., J Bacteriol 175(5):1316-24

 [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] 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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