RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
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
Reference(s): [1] Almiron M., et al., 1992
[2] Altuvia S., et al., 1994
Promoter
Name: dpsp
+1: 848950
Sigma Factor: Sigma70 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]
[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
[6] Salgado H, et al., 2012
TF binding sites (TFBSs)
[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 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]
[H-NS,-] 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 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]
[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 activator dpsp 849042 849054 -98.5 tatatctaacTCATTGAATCTTTattagttttg nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd nd
[MntR,-] 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 MntR-Mn2+ repressor dpsp 848957 848978 -17.5 gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8]
[OxyR,+] 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 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


Transcription unit          
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
Reference(s): [1] Almiron M., et al., 1992
[2] Altuvia S., et al., 1994
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
TF binding sites (TFBSs)
[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 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]
[H-NS,-] 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 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]
[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 activator dpsp2 849042 849054 -98.5 tatatctaacTCATTGAATCTTTattagttttg nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd nd
[MntR,-] 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 MntR-Mn2+ repressor dpsp2 848957 848978 -17.5 gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8]
[OxyR,+] 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 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


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [EXP-IPI] Inferred from physical interaction


Reference(s)    

 [1] Almiron M., Link AJ., Furlong D., Kolter R., 1992, A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli., Genes Dev 6(12B):2646-54

 [2] Altuvia S., Almiron M., Huisman G., Kolter R., Storz G., 1994, The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase., Mol Microbiol 13(2):265-72

 [3] 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

 [4] Lacour S., Landini P., 2004, SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences., J Bacteriol 186(21):7186-95

 [5] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [6] 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.

 [7] Grainger DC., Goldberg MD., Lee DJ., Busby SJ., 2008, Selective repression by Fis and H-NS at the Escherichia coli dps promoter., Mol Microbiol 68(6):1366-77

 [8] Yamamoto K., Ishihama A., Busby SJ., Grainger DC., 2011, The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein., J Bacteriol 193(6):1477-80

 [9] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [10] Peano C., Wolf J., Demol J., Rossi E., Petiti L., De Bellis G., Geiselmann J., Egli T., Lacour S., Landini P., 2015, Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis., Sci Rep 5:10469

RegulonDB