RegulonDB RegulonDB 11.1: 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: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gutierrez C., et al., 1995
Promoter
Name: osmEp
+1: 1822283
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: aagcggagccgtttcgttcacgggcttgaaaaagcgcccaatgtattccaggcttatctaAcacgctgataaacaagagga
                                      -35                   +10                  
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
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] Huerta AM., et al., 2003
[6] Maciag A., et al., 2011
[7] 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 Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor osmEp 1822251 1822265 26.0 ataaacaagaGGACGGAATATGAACaagaatatgg nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
proximal Fis repressor osmEp 1822307 1822321 -31.0 ttcgttcacgGGCTTGAAAAAGCGCccaatgtatt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
proximal Fis repressor osmEp 1822362 1822376 -86.0 gcgggctgaaTGGTGGTTAAAACGTcatacaggaa nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
[IHF,-] 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 IHF repressor osmEp 1822273 1822285 4.5 caggcttatcTAACACGCTGATAaacaagagga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]


Transcription unit          
Name: osmE
Gene(s): osmE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gutierrez C., et al., 1995
Promoter
Name: osmEp2
+1: 1822283
Sigma Factor: Sigma38 Sigmulon
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
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] Huerta AM., et al., 2003
[6] Maciag A., et al., 2011
[7] 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 Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor osmEp2 1822251 1822265 26.0 ataaacaagaGGACGGAATATGAACaagaatatgg nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
proximal Fis repressor osmEp2 1822307 1822321 -31.0 ttcgttcacgGGCTTGAAAAAGCGCccaatgtatt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
proximal Fis repressor osmEp2 1822362 1822376 -86.0 gcgggctgaaTGGTGGTTAAAACGTcatacaggaa nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
[IHF,-] 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 IHF repressor osmEp2 1822273 1822285 4.5 caggcttatcTAACACGCTGATAaacaagagga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [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] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] 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] 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

 [6] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [7] 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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