RegulonDB RegulonDB 11.1: Operon Form
   

phoA-psiF operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: phoA-psiF
Synonym(s): OP00071, phoA
Gene(s): phoA, psiF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene phoA 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
Reference(s): [1] Wanner BL., et al., 1981
[2] Yamada M., et al., 1989
Promoter
Name: phoAp
+1: 401707
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: aaagttaatcttttcaacagctgtcataaagttgtcacggccgagacttatagtcgctttGtttttattttttaatgtatt
                          -35                    -10        +1                   
Evidence: [AS-NAS]
[COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Huerta AM., et al., 2003
[4] Makino K., et al., 1986
[5] Shuttleworth H., et al., 1986
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 phoAp 401667 401685 -31.0 ttttcaacagCTGTCATAAAGTTGTCACGgccgagactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W [6]


Transcription unit       
Name: psiF
Gene(s): psiF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s):
Promoter
Name: psiFp
+1: 403231
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 50
Sequence: ccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcAgatcacgggcgcatacgctc
                         -35                        -10     +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
Reference(s):


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -26.0 403163 403206 ctgaaataaaACCGCGCCCGGCAGTGAATTTTCGCTGCCGGGTGGTTTTTTTGctgttagcaa
  anti-terminator -13.0 403139 403184 tacaccatgaAAGCCGCTCTGGGGCTGAAATAAAACCGCGCCCGGCAGTGAATTTtcgctgccgg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence


Reference(s)    

 [1] Wanner BL., Wieder S., McSharry R., 1981, Use of bacteriophage transposon Mu d1 to determine the orientation for three proC-linked phosphate-starvation-inducible (psi) genes in Escherichia coli K-12., J Bacteriol 146(1):93-101

 [2] 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

 [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] 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

 [5] Shuttleworth H., Taylor J., Minton N., 1986, Sequence of the gene for alkaline phosphatase from Escherichia coli JM83., Nucleic Acids Res 14(21):8689

 [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] null, 2018, Erratum., J Am Geriatr Soc 66(12):2436

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