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Name: | dps | ||||||||||
Synonym(s): | OP00242 | ||||||||||
Gene(s): | dps Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | dps is induced by l-ascorbate through OxyR during early exponential phase Campos E,2007 Fis represses thedps promoter by trapping RNA polymerase contained at the promoter. The Fis-Eσ70 promoter complex, which can block transcription by Eσ38, acts as a corepressor of dps transcription Grainger DC,2008 The transcript of dps is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020. MntR represses dps expression during stationary phase Yamamoto K,2011 Fis also has a dual role in Dps control, repressing its transcription and promoting the Dps-mediated hypercondensation of the nucleoid The transcription of the gene dps is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013 |
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Reference(s): |
[1] Almiron M., et al., 1992 [2] Altuvia S., et al., 1994 |
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Promoter | |||||||||||
Name: | dpsp | ||||||||||
+1: | 848950 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 39 | ||||||||||
Sequence: |
attagtgtgataggaacagccagaatagcggaacacatagccggtgctatacttaatctcGttaattactgggacataaca -35 -10 +1 |
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Note(s): | Results suggest that the dps promoter is recognized by both the σ70 holoenzyme and σS holoenzyme, since OxyR acts on σ70, and in addition the starts of the OxyR-dependent and the σS-dependent transcripts are identical. This promoter displays an unusual form of regulation. If cells are treated with hydrogen peroxide during exponential growth, dps transcription is induced by OxyR, which activates σ70 RNA polymerase. Surprisingly, the same promoter is also activated by IHF and σS at the onset of the stationary phase. It is assumed that both OxyR and IHF bind upstream of the dps promoter and that the mechanisms of activation act independently of each other. The promoter has a a sequence that conforms to the consensus -10, but no obvious -35 sequence is present. Possibly, the dps promoter is not ideally bound by either holoenzyme, leading to the need for IHF to enhance the binding of σS RNA polymerase and of OxyR to enhance the binding of σ70 RNA polymerase. The dpS 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. (2001) found that CspC and CspE upregulate the expression of dps by regulating the expression of RpoS itself Phadtare S,2001. Fis and H-NS control σ factor selection at the dps promoter Grainger DC,2008 This promoter appears to be activated during σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020. |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [RS-EPT-CBR] |
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Reference(s): |
[2] Altuvia S., et al., 1994 [3] Huerta AM., et al., 2003 [4] Lacour S., et al., 2004 [5] Maciag A., et al., 2011 [6] Salgado H, et al., 2012 |
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 | dpsp | 848953 | 848967 | -10.0 | cacatagccgGTGCTATACTTAATCtcgttaatta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [8] |
proximal | Fis | repressor | dpsp | 848969 | 848983 | -26.0 | agccagaataGCGGAACACATAGCCggtgctatac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [8] |
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 | H-NS | repressor | dpsp | 848943 | 848953 | 3.5 | tatacttaatCTCGTTAATTActgggacata | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
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 | activator | dpsp | 849042 | 849054 | -98.5 | tatatctaacTCATTGAATCTTTattagttttg | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
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 | MntR-Mn2+ | repressor | dpsp | 848957 | 848978 | -17.5 | gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [8] |
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 | OxyR | activator | dpsp | 848959 | 848975 | -17.0 | tagcggaacaCATAGCCGGTGCTATACttaatctcgt | nd | [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] | S | [9] |
proximal | OxyR | activator | dpsp | 848986 | 849002 | -44.0 | ctattagtgtGATAGGAACAGCCAGAAtagcggaaca | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
proximal | OxyR | activator | dpsp | 849008 | 849024 | -66.0 | ttgtttttcaCGCTTGTTACCACTATTagtgtgatag | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
Name: | dps | ||||||||||
Synonym(s): | OP00242 | ||||||||||
Gene(s): | dps Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | dps is induced by l-ascorbate through OxyR during early exponential phase Campos E,2007 Fis represses thedps promoter by trapping RNA polymerase contained at the promoter. The Fis-Eσ70 promoter complex, which can block transcription by Eσ38, acts as a corepressor of dps transcription Grainger DC,2008 The transcript of dps is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020. MntR represses dps expression during stationary phase Yamamoto K,2011 The dps gene is positively regulated by Crl under nitrogen starvation Zafar MA,2014. Fis also has a dual role in Dps control, repressing its transcription and promoting the Dps-mediated hypercondensation of the nucleoid The transcription of the gene dps is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013 |
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Reference(s): |
[1] Almiron M., et al., 1992 [2] Altuvia S., et al., 1994 |
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Promoter | |||||||||||
Name: | dpsp2 | ||||||||||
+1: | 848950 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 39 | ||||||||||
Sequence: |
attagtgtgataggaacagccagaatagcggaacacatagccggtgctatacttaatctcGttaattactgggacataaca -35 -10 +1 |
||||||||||
Note(s): | Results suggest that the dps promoter is recognized by both the σ70 holoenzyme and σS holoenzyme, since OxyR acts on σ70, and in addition the starts of the OxyR-dependent and the σS-dependent transcripts are identical. This promoter displays an unusual form of regulation. If cells are treated with hydrogen peroxide during exponential growth, dps transcription is induced by OxyR, which activates σ70 RNA polymerase. Surprisingly, the same promoter is also activated by IHF and σS at the onset of the stationary phase. It is assumed that both OxyR and IHF bind upstream of the dps promoter and that the mechanisms of activation act independently of each other. The promoter has a a sequence that conforms to the consensus -10, but no obvious -35 sequence is present. Possibly, the dps promoter is not ideally bound by either holoenzyme, leading to the need for IHF to enhance the binding of σS RNA polymerase and of OxyR to enhance the binding of σ70 RNA polymerase. The dpS 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. (2001) found that CspC and CspE upregulate the expression of dps by regulating the expression of RpoS itself Phadtare S,2001. Fis and H-NS control σ factor selection at the dps promoter Grainger DC,2008 This promoter appears to be activated during σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020. |
||||||||||
Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IPI] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[2] Altuvia S., et al., 1994 [3] Huerta AM., et al., 2003 [4] Lacour S., et al., 2004 [5] Maciag A., et al., 2011 [10] Peano C., et al., 2015 [6] Salgado H, et al., 2012 |
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 | dpsp2 | 848953 | 848967 | -10.0 | cacatagccgGTGCTATACTTAATCtcgttaatta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [8] |
proximal | Fis | repressor | dpsp2 | 848969 | 848983 | -26.0 | agccagaataGCGGAACACATAGCCggtgctatac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [8] |
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 | H-NS | repressor | dpsp2 | 848943 | 848953 | 3.5 | tatacttaatCTCGTTAATTActgggacata | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
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 | activator | dpsp2 | 849042 | 849054 | -98.5 | tatatctaacTCATTGAATCTTTattagttttg | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
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 | MntR-Mn2+ | repressor | dpsp2 | 848957 | 848978 | -17.5 | gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [8] |
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 | OxyR | activator | dpsp2 | 848959 | 848975 | -17.0 | tagcggaacaCATAGCCGGTGCTATACttaatctcgt | nd | [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] | S | [9] |
proximal | OxyR | activator | dpsp2 | 848986 | 849002 | -44.0 | ctattagtgtGATAGGAACAGCCAGAAtagcggaaca | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
proximal | OxyR | activator | dpsp2 | 849008 | 849024 | -66.0 | ttgtttttcaCGCTTGTTACCACTATTagtgtgatag | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
Reference(s) |
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