RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: phoBR
Synonym(s): OP00072, phoB
Gene(s): phoB, phoR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the operon phoBR is increased under phosphate starvation Ulu?eker C, Torres-Bacete J, García JL, Hanczyc MM, Nogales J, Kahramano?ullar? O,2019 and 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
The transcript that contains phoB is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Reference(s): [1] Wanner BL., et al., 1987
Promoter
Name: phoBp
+1: 417101
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: tgaagatatgtgcgacgagcttttcataaatctgtcataaatctgacgcataatgacgtcGcattaatgatcgcaacctat
                       -35                       -10        +1                   
Evidence: [AS-NAS]
[COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Huerta AM., et al., 2003
[3] Makino K., et al., 1986
Terminator(s)
Type: rho-independent
Sequence: ttaatccgccTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTcaaaatacgg
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[AlpA,-] 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 AlpA repressor phoBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[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 phoBp 417061 417079 -31.0 tgcgacgagcTTTTCATAAATCTGTCATAaatctgacgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7]


Evidence    

 [AS-NAS] Non-traceable author statement

 [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-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] Wanner BL., Chang BD., 1987, The phoBR operon in Escherichia coli K-12., J Bacteriol 169(12):5569-74

 [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] Makino K., Shinagawa H., Amemura M., Nakata A., 1986, Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12., J Mol Biol 190(1):37-44

 [4] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [5] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [6] 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

 [7] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

 [8] Song S., Kim JS., Yamasaki R., Oh S., Benedik MJ., Wood TK., 2021, Escherichia coli cryptic prophages sense nutrients to influence persister cell resuscitation., Environ Microbiol 23(11):7245-7254

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