RegulonDB RegulonDB 11.1: 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
Note(s):
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for osmY . 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.
Reference(s): [1] Yim HH., et al., 1992
Promoter
Name: osmYp2
+1: 4611153
Sigma Factor: Sigma38 Sigmulon
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Bordes P., et al., 2000
[3] Ding Q., et al., 1995
[4] Huerta AM., et al., 2003
[5] Lange R., et al., 1993
[6] Wise A., et al., 1996
[7] Yim HH., et al., 1994
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor osmYp2 4611130 4611151 -12.5 gcggtttcaaAATTGTGATCTATATTTAACAAagtgatgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [10]
proximal CRP-cyclic-AMP repressor osmYp2 4611143 4611164 1.5 tgtgatctatATTTAACAAAGTGATGACATTTctgacggcgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [10]
proximal CRP-cyclic-AMP repressor osmYp2 4611154 4611175 12.5 tttaacaaagTGATGACATTTCTGACGGCGTTaaataccgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF] W [5], [10]
[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 osmYp2 4611134 4611153 -10.0 tttcaaaattGTGATCTATATTTAACAAAGtgatgacatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]
remote Fis repressor osmYp2 4611215 4611234 72.0 tctaaagccgTCGATTGTCATTCTACCGATattaataact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]
[FliZ,-] 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
nd FliZ repressor osmYp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [12], [13]
[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
remote IHF repressor osmYp2 4611050 4611062 -96.5 tcaatttcccTTCCTTATTAGCCgcttacggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8]
proximal IHF repressor osmYp2 4611142 4611154 -5.0 ttgtgatctaTATTTAACAAAGTgatgacattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W nd
[Lrp,-] 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
remote Lrp repressor osmYp2 4610960 4610974 -186.0 ctggcacaggAACGTTATCCGGACGttcagttcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8], [9]
remote Lrp repressor osmYp2 4610997 4611011 -149.0 agacccgcgaGCATTAATTCTTGCCtccagggcgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8], [9]


Transcription unit          
Name: osmY
Gene(s): osmY   Genome Browser M3D Gene expression COLOMBOS
Note(s):
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for osmY . 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.
Reference(s): [1] Yim HH., et al., 1992
Promoter
Name: osmYp
+1: 4611153
Sigma Factor: Sigma70 Sigmulon
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Bordes P., et al., 2000
[3] Ding Q., et al., 1995
[4] Huerta AM., et al., 2003
[5] Lange R., et al., 1993
[6] Wise A., et al., 1996
[7] Yim HH., et al., 1994
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor osmYp 4611130 4611151 -12.5 gcggtttcaaAATTGTGATCTATATTTAACAAagtgatgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [10]
proximal CRP-cyclic-AMP repressor osmYp 4611143 4611164 1.5 tgtgatctatATTTAACAAAGTGATGACATTTctgacggcgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [10]
proximal CRP-cyclic-AMP repressor osmYp 4611154 4611175 12.5 tttaacaaagTGATGACATTTCTGACGGCGTTaaataccgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF] W [5], [10]
[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 osmYp 4611134 4611153 -10.0 tttcaaaattGTGATCTATATTTAACAAAGtgatgacatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]
remote Fis repressor osmYp 4611215 4611234 72.0 tctaaagccgTCGATTGTCATTCTACCGATattaataact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]
[FliZ,-] 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
nd FliZ repressor osmYp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [12], [13]
[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
remote IHF repressor osmYp 4611050 4611062 -96.5 tcaatttcccTTCCTTATTAGCCgcttacggaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8]
proximal IHF repressor osmYp 4611142 4611154 -5.0 ttgtgatctaTATTTAACAAAGTgatgacattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W nd
[Lrp,-] 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
remote Lrp repressor osmYp 4610960 4610974 -186.0 ctggcacaggAACGTTATCCGGACGttcagttcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8], [9]
remote Lrp repressor osmYp 4610997 4611011 -149.0 agacccgcgaGCATTAATTCTTGCCtccagggcgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [8], [9]


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-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-CHIP-PCR-MANUAL] ChIP-PCR evidence used in manual assertion

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence


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] 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] 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

 [6] 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

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

 [8] 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

 [9] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [10] 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

 [11] 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

 [12] 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

 [13] 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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