RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: osmY
Gene(s): osmY   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Yim HH., et al., 1992
Promoter
Name: osmYp
+1: 4611153
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 243
Sequence: ttgcttatgttttcgctgatatcccgagcggtttcaaaattgtgatctatatttaacaaaGtgatgacatttctgacggcg
                       -35                 -10              +1                   
Note(s): osmY is activated by potassium glutamate but only when σS is used. σ70 and σS recognize the osmYp at low osmolarity, but only σS activates this promoter at high osmolarity. This promoter is not a gearbox promoter.

The osmY gene is positively regulated by RpoS in stationary phase and it is mainly controlled at the level of transcription Phadtare S,2001. The effect by RpoS is likely indirect and might be mediated by an intermediate regulator that itself is directly regulated by RpoS. Phadtare et al. found that CspC and CspE upregulate the expression of dps by regulating the expression of RpoS itself Phadtare S,2001.
Evidence: [HIPP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [2] Bordes P., et al., 2000
[3] Ding Q., et al., 1995
[4] Lange R., et al., 1993
[5] Wise A., et al., 1996
[6] Yim HH., et al., 1994
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
proximal CRP-cAMP1 repressor osmYp 4611130 4611151 -12.5 gcggtttcaaAATTGTGATCTATATTTAACAAagtgatgaca nd [GEA], [HIBSCS], [IHBCE] [4], [8]
proximal CRP-cAMP repressor osmYp 4611143 4611164 1.5 tgtgatctatATTTAACAAAGTGATGACATTTctgacggcgt nd [GEA], [HIBSCS], [IHBCE] [4], [8]
proximal CRP-cAMP3 repressor osmYp 4611154 4611175 12.5 tttaacaaagTGATGACATTTCTGACGGCGTTaaataccgtt nd [GEA], [IHBCE] [4], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor osmYp 4611134 4611153 -10.0 tttcaaaattGTGATCTATATTTAACAAAGtgatgacatt nd [AIBSCS], [GEA] [9]
remote Fis repressor osmYp 4611215 4611234 72.0 tctaaagccgTCGATTGTCATTCTACCGATattaataact nd [AIBSCS], [GEA] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor osmYp nd nd nd nd nd [BPP], [GEA] [10], [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 repressor osmYp 4611050 4611062 -96.5 tcaatttcccTTCCTTATTAGCCgcttacggaa nd [BPP], [GEA], [HIBSCS] [4], [7]
proximal IHF repressor osmYp 4611142 4611154 -5.0 ttgtgatctaTATTTAACAAAGTgatgacattt nd [BCE], [GEA] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 repressor osmYp 4610960 4610974 -186.0 ctggcacaggAACGTTATCCGGACGttcagttcca nd [BPP], [GEA], [HIBSCS] [4], [7]
remote Lrp2 repressor osmYp 4610997 4611011 -149.0 agacccgcgaGCATTAATTCTTGCCtccagggcgc nd [BPP], [GEA], [HIBSCS] [4], [7]
Note(s): 1CRP is not essential for osmotic induction of osmY.
3CRP is not essential for osmotic induction of osmY.1IHF is not essential for osmotic induction of osmY.
1Lrp is not essential for osmotic induction of osmY.
2Lrp is not essential for osmotic induction of osmY.1Lrp is not essential for osmotic induction of osmY.
2Lrp is not essential for osmotic induction of osmY.
3IHF is not essential for osmotic induction of osmY.
4CRP is not essential for osmotic induction of osmY.
8CRP is not essential for osmotic induction of osmY.




Reference(s)    

 [1] Yim HH., Villarejo M., 1992, osmY, a new hyperosmotically inducible gene, encodes a periplasmic protein in Escherichia coli., J Bacteriol 174(11):3637-44

 [2] 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

 [3] Ding Q., Kusano S., Villarejo M., Ishihama A., 1995, Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by E sigma D and E sigma S holoenzymes., Mol Microbiol 16(4):649-56

 [4] Lange R., Barth M., Hengge-Aronis R., 1993, Complex transcriptional control of the sigma s-dependent stationary-phase-induced and osmotically regulated osmY (csi-5) gene suggests novel roles for Lrp, cyclic AMP (cAMP) receptor protein-cAMP complex, and integration host factor in the stationary-phase response of Escherichia coli., J Bacteriol 175(24):7910-7

 [5] Wise A., Brems R., Ramakrishnan V., Villarejo M., 1996, Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S., J Bacteriol 178(10):2785-93

 [6] Yim HH., Brems RL., Villarejo M., 1994, Molecular characterization of the promoter of osmY, an rpoS-dependent gene., J Bacteriol 176(1):100-7

 [7] Colland F., Barth M., Hengge-Aronis R., Kolb A., 2000, sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and lrp transcription factors., EMBO J 19(12):3028-37

 [8] Shimada T., Fujita N., Yamamoto K., Ishihama A., 2011, Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources., PLoS One 6(6):e20081

 [9] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [10] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [11] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93


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