RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: dpiBA
Gene(s): dpiB, dpiA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The genes of the dpiBA operon codes for proteins of two-component regulatory system, the sensor kinase (DpiB) and the response regulator (DpiA). These proteins induce the SOS response Miller C,2004.
Transcription of the citCDEFXG operon is dependent on CitB when E. coli is grown in the presence of citrate and the absence of nitrate and oxygen Scheu PD,2012. Yamamoto et al. in 2008 showed that CitB (DpiA), in the presence of citrate, activates the transcription of three promoters, citCp2, citCp1, and citAp (dpiBp), in the intergenic region located between the citC and citA genes (dpiB) Yamamoto K,2008. But they have not shown the mechanism of action of CitB in the activation of the divergent operons.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Miller C., et al., 2004
Promoter
Name: dpiBp1
+1: 651984
Distance from start of the gene: 251
Sequence: tgataaccttttattttcacttgggagaaagggggtgatcgaggtatatctttttctcctTtcgctatacatcctaaggag
Note(s): Mandin and Gottesman (2009) reported the possibility that dpiBp1 ( 41 start site) is generated by RNA processing Mandin P,2009
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Yamamoto K., et al., 2008
TF binding sites (TFBSs)
[ArcA,+] 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 ArcA-phosphorylated activator dpiBp1 651884 651894 -95.5 aggtgcatgtTGTTATCGATTtgcaacgaat nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
[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
remote CRP-cyclic-AMP repressor dpiBp1 652018 652039 45.5 ttcggcgtgaAATTTTGATTTATTTCACATAGagttagtggt nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]
[DpiA,+] 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 DpiA-phosphorylated activator dpiBp1 652049 652072 77.0 gagttagtggTTTTTTATTTATTTAATGATTTTAagttttttaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [4], [5]
remote DpiA-phosphorylated activator dpiBp1 652076 652099 104.0 gattttaagtTTTTTAATTAATGTAATTACGAAAtgactcgcag nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [4], [5]
remote DpiA-phosphorylated activator dpiBp1 652118 652141 146.0 aggtttaagtGATTTAATTGATTTAATGAATAAAatttgccacg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [4], [5]
[FNR,-] 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 FNR repressor dpiBp1 652022 652035 45.5 gcgtgaaattTTGATTTATTTCACatagagttag nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]
[NarL,-] 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 NarL-phosphorylated repressor dpiBp1 652000 652007 20.0 atacatcctaAGGAGTATttcggcgtga nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA ChiX dpiBA repressor 652198 652209 CCGUCAAAGAGG nd [EXP-IGI], [EXP-IMP-SITE-MUTATION] [3]


Transcription unit          
Name: dpiBA
Gene(s): dpiB, dpiA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Miller C., et al., 2004
Promoter
Name: dpiBp2
+1: 652172
Distance from start of the gene: 63
Sequence:
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Mandin P., et al., 2009
TF binding sites (TFBSs)
[DcuR,+] 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 DcuR-phosphorylated activator dpiBp2 652066 652083 -98.0 tttatttaatGATTTTAAGTTTTTTAATtaatgtaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
proximal DcuR-phosphorylated activator dpiBp2 652127 652144 -37.0 tgatttaattGATTTAATGAATAAAATTtgccacgatc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
[NarL,-] 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 NarL-phosphorylated repressor dpiBp2 652193 652200 25.0 acattttaatTACATCCGtcaaagaggc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]


Evidence    

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

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

 [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-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IGI] Inferred from genetic interaction

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Miller C., Thomsen LE., Gaggero C., Mosseri R., Ingmer H., Cohen SN., 2004, SOS response induction by beta-lactams and bacterial defense against antibiotic lethality., Science 305(5690):1629-31

 [2] Yamamoto K., Matsumoto F., Oshima T., Fujita N., Ogasawara N., Ishihama A., 2008, Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli., Biosci Biotechnol Biochem 72(11):3011-4

 [3] Mandin P., Gottesman S., 2009, A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system., Mol Microbiol 72(3):551-65

 [4] Scheu PD., Witan J., Rauschmeier M., Graf S., Liao YF., Ebert-Jung A., Basche T., Erker W., Unden G., 2012, CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo., J Bacteriol 194(3):636-45

 [5] Ingmer H., Miller CA., Cohen SN., 1998, Destabilized inheritance of pSC101 and other Escherichia coli plasmids by DpiA, a novel two-component system regulator., Mol Microbiol 29(1):49-59

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