RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: proP
Synonym(s): OP00211
Gene(s): proP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The mRNA produced by the proP gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Reference(s): [1] Xu J., et al., 1995
Promoter
Name: proPp1
+1: 4330320
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 182
Sequence: tcctaaacgaaatccatgtgtgaagttgatcacaaatttaaacactggtagggtaaaaagGtcattaactgcccaattcag
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Mellies J., et al., 1995
[4] Salgado H, et al., 2012
[1] Xu J., et al., 1995
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor proPp1 4330275 4330296 -34.5 aacgaaatccATGTGTGAAGTTGATCACAAATttaaacactg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W nd


Transcription unit          
Name: proP
Gene(s): proP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The mRNA produced by the proP gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Reference(s): [1] Xu J., et al., 1995
Promoter
Name: proPp2
+1: 4330407
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 95
Sequence: actggtttgattgtacattccttaaccggagggtgtaagcaaacccgctacgcttgttacAgagattgcatcctgcaattc
                          -35               -10             +1                   
Note(s): proPp2 is central to the stationary-phase response. The sequence around the -10 region of the proPp2 promoter has similarity to those of σ70 promoters, but there is no resemblance in the -35 region.
Fis and RpoS are two regulators that control different sets of genes in distinct stages of cellular growth and, in general, function antagonistically. However, proP gene expression at the proPp2 promoter is the unique case, with both regulators collaborating to achieve promoter activation. It is also the only case in which Fis functions as a class II transcription activator with its site centered at -41 (the proP regulatory region presents two sites for Fis, at -41 and -81 with respect to the +1 of transcriptional initiation). The ability of EσS to recognize nonoptimally placed and degenerated -35 elements enables EσS and Fis to control proP expression at proPp2Typas A, Stella S, Johnson RC, Hengge R,2007.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Eguchi Y., et al., 2004
[2] Huerta AM., et al., 2003
[3] Mellies J., et al., 1995
[1] Xu J., et al., 1995
TF binding sites (TFBSs)
[CRP,+] 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
remote CRP-cyclic-AMP activator proPp2 4330274 4330295 -122.5 aaacgaaatcCATGTGTGAAGTTGATCACAAAtttaaacact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Fis,+] 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 Fis activator proPp2 4330319 4330333 -81.0 agggtaaaaaGGTCATTAACTGCCCaattcaggcg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
proximal Fis activator proPp2 4330359 4330373 -41.0 tggtttgattGTACATTCCTTAACCggagggtgta nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [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] Xu J., Johnson RC., 1995, Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli., J Bacteriol 177(18):5222-31

 [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] Mellies J., Wise A., Villarejo M., 1995, Two different Escherichia coli proP promoters respond to osmotic and growth phase signals., J Bacteriol 177(1):144-51

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Eguchi Y., Okada T., Minagawa S., Oshima T., Mori H., Yamamoto K., Ishihama A., Utsumi R., 2004, Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli., J Bacteriol 186(10):3006-14

 [6] McLeod SM., Xu J., Johnson RC., 2000, Coactivation of the RpoS-dependent proP P2 promoter by fis and cyclic AMP receptor protein., J Bacteriol 182(15):4180-7

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