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DpiA DNA-binding transcriptional dual regulator

Synonyms: DpiA, DpiA-Pasp
Summary:
CitB/DpiA is a dual transcriptional regulator involved in anaerobic citrate catabolism. In the presence of citrate and under anaerobic conditions it activates genes for citrate fermentation, the citCDEFXGT operon, the citAB operon, and mdh, as well as the exuTR operon for dissimilation of hexuronate |CITS:[18997424]|.
Due to the ability of CitB/DpiA to bind to A/T-rich sequences, multiple other roles have been assigned to CitB. When overexpressed in E. coli, it destabilizes plasmid inheritance, represses transcription of appY, encoding a regulator of anaerobic metabolism, and induces the SOS response by competing with DnaA and DnaB in binding to A/T-rich sequences at the replication origin |CITS: [9701802][14526013]|. Moreover, inactivation of penicillin-binding protein 3, FtsI, either chemically or genetically, induces SOS in E. coli. This induction requires dpiBA |CITS:[15308764]|.
CitB/DpiA belongs to the two-component system DpiB/DpiA, or CitBA. The operon containing both genes, citB (dpiA), encoding the response regulator, and citA (dpiB), encoding the sensor kinase, is transcribed divergently to the citCDEFXGT operon. CitA (DpiB) binds citrate with its periplasmic domain |CITS:[11889485]| and senses reduced conditions using a single Cys residue in vitro |CITS:[19202292]|. The cytoplasmic domain is involved in autophosphorylation and phosphotransfer to CitB (DpiA) |CITS:[19202292]|.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
DpiA Non-Functional   Apo [IEP], [SM] [1]
DpiA-Pasp Functional Covalent Holo nd nd
Evolutionary Family: HTH_11
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: dpiA
  Genome position: 653862-654542
  Length: 681 bp / 226 aa
Operon name: dpiBA
TU(s) encoding the TF:
Transcription unit        Promoter
dpiBA
dpiBp
dpiBA
dpiBp2


Regulon       
Regulated gene(s) appY, citC, citD, citE, citF, citG, citX, dpiA, dpiB, exuT, mdh
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
posttranslational modification (3)
unassigned reversible reactions (3)
Transcription related (2)
activator (2)
covalent modification, demodification, maturation (2)
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Regulated operon(s) appY, citCDEFXG, dpiBA, exuT, mdh
First gene in the operon(s) appY, citC, citC, dpiB, exuT, exuT, mdh, mdh
Simple and complex regulons ArcA,CRP,DpiA,FNR,NarL
ArcA,CRP,DpiA,FlhDC
ArcA,DpiA
CRP,DpiA,ExuR
CRP,DpiA,FNR,NarL
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DpiA,+](3)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  DpiA-Pasp repressor appYp Sigma70 nd nd appY nd nd [GEA], [HIBSCS] [1]
  DpiA-Pasp activator citCp1 nd -177.0 -273.0 citC, citD, citE, citF, citX, citG
gtggcaaattTTATTCATTAAATCAATTAAATCacttaaacct
652118 652140 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator citCp1 nd -135.0 -231.0 citC, citD, citE, citF, citX, citG
tgcgagtcatTTCGTAATTACATTAATTAAAAAacttaaaatc
652076 652098 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator citCp1 nd -108.0 -204.0 citC, citD, citE, citF, citX, citG
taaaaaacttAAAATCATTAAATAAATAAAAAAccactaactc
652049 652071 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator citCp2 nd -90.0 -273.0 citC, citD, citE, citF, citX, citG
gtggcaaattTTATTCATTAAATCAATTAAATCacttaaacct
652118 652140 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator citCp2 nd -48.0 -231.0 citC, citD, citE, citF, citX, citG
tgcgagtcatTTCGTAATTACATTAATTAAAAAacttaaaatc
652076 652098 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator citCp2 nd -21.0 -204.0 citC, citD, citE, citF, citX, citG
taaaaaacttAAAATCATTAAATAAATAAAAAAccactaactc
652049 652071 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator dpiBp nd 77.0 -175.0 dpiB, dpiA
gagttagtggTTTTTTATTTATTTAATGATTTTaagtttttta
652049 652071 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator dpiBp nd 104.0 -148.0 dpiB, dpiA
gattttaagtTTTTTAATTAATGTAATTACGAAatgactcgca
652076 652098 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator dpiBp nd 146.0 -106.0 dpiB, dpiA
aggtttaagtGATTTAATTGATTTAATGAATAAaatttgccac
652118 652140 [BPP], [GEA], [HIBSCS] [1], [2], [3]
  DpiA-Pasp activator exuTp1 nd nd nd exuT nd nd [BPP], [GEA] [3]
  DpiA-Pasp activator exuTp2 nd nd nd exuT nd nd [BPP], [GEA] [3]
  DpiA-Pasp activator mdhp1 Sigma70 nd nd mdh nd nd [BPP], [GEA] [3]
  DpiA-Pasp activator mdhp2 nd nd nd mdh nd nd [BPP], [GEA] [3]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [IEP] Inferred from expression pattern

 [SM] Site mutation

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins



Reference(s)    

 [1] 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

 [2] 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

 [3] 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



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