RegulonDB RegulonDB 10.10: 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
Note(s): The osmC gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The osmC gene is upregulated at 1.25 M MgSO4 (Magnesium Sulfate); this upregulatioin may arise from increased production of RpoS and the transcription of osmC from osmCp2, or in a RpoS-independent way from osmCp1 during the exponential growth phase. Another possibility is the downregulation of H-NS and LrP or decreased binding affinities to both promoters Nepal S, Kumar P,2020
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for osmC . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [AISGDTU] 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                   
Evidence: [HIPP]
[ICWHO]
[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] Huerta AM., et al., 2003
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor osmCp1 nd nd nd nd nd [GEA], [BPP] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp repressor osmCp1 1556537 1556551 -52.0 aatattttcgCCGGATTTTATTCGGaatatcctgc nd [GEA], [APIORCISFBSCS], [BPP], [SM] [1]
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 [GEA], [BCE], [SM] [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcsB-phosphorylated activator osmCp1 1556548 1556561 -41.5 cggattttatTCGGAATATCCTGCttatcctcgt nd [GEA], [BPP], [SM] [8], [9]


Transcription unit          
Name: osmC
Gene(s): osmC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The osmC gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The osmC gene is upregulated at 1.25 M MgSO4 (Magnesium Sulfate); this upregulatioin may arise from increased production of RpoS and the transcription of osmC from osmCp2, or in a RpoS-independent way from osmCp1 during the exponential growth phase. Another possibility is the downregulation of H-NS and LrP or decreased binding affinities to both promoters Nepal S, Kumar P,2020
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for osmC . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [AISGDTU] 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                   
Evidence: [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM]
Reference(s): [10] Bordes P., et al., 2000
[1] Bouvier J., et al., 1998
[2] Gordia S., et al., 1996
[3] Gutierrez C., et al., 1991
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor osmCp2 nd nd nd nd nd [GEA], [BPP] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp activator osmCp2 1556537 1556551 -62.0 aatattttcgCCGGATTTTATTCGGaatatcctgc nd [GEA], [APIORCISFBSCS], [BPP], [SM] [1]




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] 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

 [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.

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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


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