RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: osmE
Gene(s): osmE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Gutierrez C., et al., 1995
Promoter
Name: osmEp
+1: 1822283
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 27
Sequence: aagcggagccgtttcgttcacgggcttgaaaaagcgcccaatgtattccaggcttatctaAcacgctgataaacaagagga
                          -35               -10             +1                   
Note(s): osmEp is recognized by both Eσ70 and EσS. Eσ70 is responsible for osmotic induction of osmEp during the exponential growth phase, while EσS controls its expression during entry into the stationary phase Bordes P,2002.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Bordes P., et al., 2002
[3] Bordes P., et al., 2000
[4] Conter A., et al., 1997
[1] Gutierrez C., et al., 1995
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aggccaaaaaAAACCGGCGCAATGGCCGGTTTccgttgttac
Reference(s): [1] Gutierrez C., et al., 1995
TF binding sites (TFBSs)
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor osmEp 1822251 1822265 26.0 ataaacaagaGGACGGAATATGAACaagaatatgg nd [BPP] [2]
proximal Fis repressor osmEp 1822307 1822321 -31.0 ttcgttcacgGGCTTGAAAAAGCGCccaatgtatt nd [BPP] [2]
proximal Fis3 repressor osmEp 1822362 1822376 -86.0 gcgggctgaaTGGTGGTTAAAACGTcatacaggaa nd [BPP] [2]
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor osmEp 1822273 1822285 4.5 caggcttatcTAACACGCTGATAaacaagagga nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1]
Note(s): 3The transcriptional regulator Fis modulates the osmE gene expression under certain environmental conditions at a particular growth stage by reducing its transcription. Fis can bind to three sites in the transcriptional region of osmEp, but the site centered at -86 with respect to the +1 of the transcription initiation site is of major importance for efficient binding Bordes P,2002.
1IHF inhibits osmEp expression at low osmolarity.1The transcriptional regulator Fis modulates the osmE gene expression under certain environmental conditions at a particular growth stage by reducing its transcription. Fis can bind to three sites in the transcriptional region of osmEp, but the site centered at -86 with respect to the +1 of the transcription initiation site is of major importance for efficient binding Bordes P,2002.

3IHF inhibits osmEp expression at low osmolarity.


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [HIPP] Human inference of promoter position

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

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Gutierrez C., Gordia S., Bonnassie S., 1995, Characterization of the osmotically inducible gene osmE of Escherichia coli K-12., Mol Microbiol 16(3):553-63

 [2] Bordes P., Bouvier J., Conter A., Kolb A., Gutierrez C., 2002, Transient repressor effect of Fis on the growth phase-regulated osmE promoter of Escherichia coli K12., Mol Genet Genomics 268(2):206-13

 [3] Bordes P., Repoila F., Kolb A., Gutierrez C., 2000, Involvement of differential efficiency of transcription by esigmas and esigma70 RNA polymerase holoenzymes in growth phase regulation of the Escherichia coli osmE promoter., Mol Microbiol 35(4):845-53

 [4] Conter A., Menchon C., Gutierrez C., 1997, Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12., J Mol Biol 273(1):75-83

 [5] 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.

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