RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: osmC
Gene(s): osmC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: osmCp1
+1: 1556596
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: gccggattttattcggaatatcctgcttatcctcgtgctgtttctcacgtagtctataatTtcctttttaagcccacagga
                             -35                       -10  +1                   
Note(s): The osmCp1 activity is normally independent of σS and it leads to a basal level of expression during exponential phase. osmCp1 and osmCp2 overlap, but they appear to be independent of one another. The two promoters are both growth phase and osmotically regulated. They are sensitive to the action of the global regulators H-NS and Lrp, but the H-NS negative effect on these promoters could be indirect, because there are no putative binding sites of H-NS in the promoter region.
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bouvier J., et al., 1998
[2] Gordia S., et al., 1996
[3] Gutierrez C., et al., 1991
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor osmCp1 nd nd nd nd nd [GEA] [1]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp1 repressor osmCp1 1556537 1556551 -52.0 aatattttcgCCGGATTTTATTCGGaatatcctgc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1]
[NhaR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NhaR-Na+ activator osmCp1 1556546 1556563 -42.0 gccggattttATTCGGAATATCCTGCTTatcctcgtgc nd [BCE], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [5], [6]
[RcsB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-Pasp56 activator osmCp1 1556548 1556561 -41.5 cggattttatTCGGAATATCCTGCttatcctcgt nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [7], [8]
Note(s): 1Bouvier J,1998mentioned that they do not know if the inhibitory effect of H-NS on transcription from osmCp1 is direct or indirect. The effect on osmCp1 was independent of σS.1Lrp affected the expression of osmCp1 since it repressed the transcription of osmCp1. This regulator hampers E-sigma S action on osmCp1. Lrp is an important factor in the shift of the effect on the transcription by E-sigma S of osmCp1 (repressor) and osmCp2 (activator) Bouvier J,19981Lrp affected the expression of osmCp1 since it repressed the transcription of osmCp1. This regulator hampers E-sigma S action on osmCp1. Lrp is an important factor in the shift of the effect on the transcription by E-sigma S of osmCp1 (repressor) and osmCp2 (activator) Bouvier J,1998
4Bouvier J,1998mentioned that they do not know if the inhibitory effect of H-NS on transcription from osmCp1 is direct or indirect. The effect on osmCp1 was independent of σS.


Transcription unit          
Name: osmC
Gene(s): osmC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: osmCp2
+1: 1556606
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 19
Sequence: attcggaatatcctgcttatcctcgtgctgtttctcacgtagtctataatttcctttttaAgcccacaggagagcaacaat
                       -35              -10                 +1                   
Note(s): This promoter is induced during the decelerating phase. osmCp1 and osmCp2 overlap, but they appear to be independent of one another. The two promoters are both growth-phase and osmotically regulated. They are sensitive to the action of the global regulators H-NS and Lrp, but the H-NS negative effect on these promoters could be indirect, because there are no putative binding sites of H-NS in the promoter region.
Evidence: [HIPP]
[TIM]
Reference(s): [9] Bordes P., et al., 2000
[1] Bouvier J., et al., 1998
[2] Gordia S., et al., 1996
[3] Gutierrez C., et al., 1991
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor osmCp2 nd nd nd nd nd [GEA] [1]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp1 activator osmCp2 1556537 1556551 -62.0 aatattttcgCCGGATTTTATTCGGaatatcctgc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1]
Note(s): 1When H-NS was absent, transcription from osmCp2 was stimulated but remained totally σS dependent. 1Lrp affected the expression of osmCp2 since it activated the transcription of osmCp2. Lrp is an important factor in the shift of the effect on the transcription by E-sigma S of osmCp1 (repressor) and osmCp2 (activator) Bouvier J,19981Lrp affected the expression of osmCp2 since it activated the transcription of osmCp2. Lrp is an important factor in the shift of the effect on the transcription by E-sigma S of osmCp1 (repressor) and osmCp2 (activator) Bouvier J,1998
2When H-NS was absent, transcription from osmCp2 was stimulated but remained totally σS dependent.


Evidence    

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

 [CV(TA/TIM)] cross validation(TA/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

 [GEA] Gene expression analysis

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

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [SM] Site mutation

 [BCE] Binding of cellular extracts


Reference(s)    

 [1] Bouvier J., Gordia S., Kampmann G., Lange R., Hengge-Aronis R., Gutierrez C., 1998, Interplay between global regulators of Escherichia coli: effect of RpoS, Lrp and H-NS on transcription of the gene osmC., Mol Microbiol 28(5):971-80

 [2] Gordia S., Gutierrez C., 1996, Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12., Mol Microbiol 19(4):729-36

 [3] Gutierrez C., Devedjian JC., 1991, Osmotic induction of gene osmC expression in Escherichia coli K12., J Mol Biol 220(4):959-73

 [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] Sturny R., Cam K., Gutierrez C., Conter A., 2003, NhaR and RcsB independently regulate the osmCp1 promoter of Escherichia coli at overlapping regulatory sites., J Bacteriol 185(15):4298-304

 [6] Toesca I., Perard C., Bouvier J., Gutierrez C., Conter A., 2001, The transcriptional activator NhaR is responsible for the osmotic induction of osmC(p1), a promoter of the stress-inducible gene osmC in Escherichia coli., Microbiology 147(Pt 10):2795-803

 [7] Davalos-Garcia M., Conter A., Toesca I., Gutierrez C., Cam K., 2001, Regulation of osmC gene expression by the two-component system rcsB-rcsC in Escherichia coli., J Bacteriol 183(20):5870-6

 [8] Francez-Charlot A., Castanie-Cornet MP., Gutierrez C., Cam K., 2005, Osmotic regulation of the Escherichia coli bdm (biofilm-dependent modulation) gene by the RcsCDB His-Asp phosphorelay., J Bacteriol 187(11):3873-7

 [9] 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

RegulonDB