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DcuR DNA-binding transcriptional activator

Synonyms: DcuR-Phosphorylated, DcuR
Summary:
DcuR regulates several genes involved in C4-dicarboxylate metabolism [2]. In addition, a recent microarray-based global transcriptional profiling study suggested that the DcuR regulon could comprise at least 39 genes, including some involved in lipopolysaccharide biosynthesis and some involved in anaerobic nitrate and nitrite respiration [8]. DcuR is the response regulator in the two-component regulatory system DcuR/DcuS and is a member of the CitAB subfamily of His protein kinases [2, 5]. Autophosphorylation of DcuS is stimulated by C4-dicarboxylates such as fumarate or succinate, and the phosphate group is transferred to DcuR, which is converted to a dimeric form [1, 3, 9]. This protein contains an N-terminal receiver domain that includes the aspartate residue (Asp-56) for phosphorylation and a C-terminal domain that contains a helix-turn-helix motif for DNA binding [2, 5].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
DcuR Non-Functional   Apo [BPP] [1]
DcuR-Phosphorylated Functional Covalent Holo [AIFS], [BPP], [GEA], [IEP], [IPI] [1], [2], [3], [4], [5]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: dcuR
  Genome position: 4349315-4350034
  Length: 720 bp / 239 aa
Operon name: dcuSR
TU(s) encoding the TF:
Transcription unit        Promoter
dcuR
dcuRp
dcuSR
dcuSp


Regulon       
Regulated gene(s) dctA, dcuB, dpiA, dpiB, frdA, frdB, frdC, frdD, fumB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (5)
fermentation (5)
anaerobic respiration (4)
electron acceptors (4)
carbon compounds (2)
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Regulated operon(s) dctA, dcuB-fumB, dpiBA, frdABCD
First gene in the operon(s) dctA, dcuB, dpiB, frdA
Simple and complex regulons ArcA,CRP,DcuR
DcuR
DcuR,FNR,NarL
DcuR,NarL
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DcuR,+](4)


Transcription factor regulation    


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
  DcuR-Phosphorylated activator dctAp Sigma70 -106.0 -157.0 dctA
cacaaaccagCACTTTTTAAAGTTTTGtaatcagttt
3683596 3683612 [BPP], [GEA] [1], [2], [3], [6]
  DcuR-Phosphorylated activator dcuBp2 nd -63.0 -410.0 dcuB, fumB
ttttgttagcGTTTTGAAATTAAAAACaccgttcacc
4349146 4349162 [BPP], [GEA] [1], [3], [7]
  DcuR-Phosphorylated activator dcuBp2 nd -41.0 -388.0 dcuB, fumB
ggtgacataaTAGTTAATTAACTTTTGttagcgtttt
4349124 4349140 [BPP], [GEA] [1], [3], [7]
  DcuR-Phosphorylated activator dpiBp2 nd -98.0 -160.5 dpiB, dpiA
tttatttaatGATTTTAAGTTTTTTAAttaatgtaat
652066 652083 [BPP], [HIBSCS] [7]
  DcuR-Phosphorylated activator dpiBp2 nd -37.0 -99.5 dpiB, dpiA
tgatttaattGATTTAATGAATAAAATttgccacgat
652127 652144 [BPP], [HIBSCS] [7]
  DcuR-Phosphorylated activator frdAp Sigma70, Sigma38 -104.0 -198.0 frdA, frdB, frdC, frdD
tgaagatgatTAATTTAATTACTAAACcatcagatcg
4382508 4382524 [BPP], [GEA] [1], [2], [3], [5]


Alignment and PSSM for DcuR TFBSs    

Aligned TFBS of DcuR   
  Sequence
  ATTAATTAAAAAACTTA
  TTTAATGAATAAAATTT
  AGCACTTTTTAAAGTTT
  AATAGTTAATTAACTTT
  TTTAATTTCAAAACGCT
  TTTAATTACTAAACCAT

Position weight matrix (PWM).   
A	3	1	0	6	4	0	0	4	3	2	5	6	6	1	0	1	1
C	0	0	1	0	1	0	0	0	2	0	0	0	0	4	1	1	0
G	0	1	0	0	1	0	1	0	0	0	0	0	0	1	1	0	0
T	3	4	5	0	0	6	5	2	1	4	1	0	0	0	4	4	5

PWM logo   


 


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


Evidence    

 [BPP] Binding of purified proteins

 [AIFS] Automated inference of function from sequence

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [HIBSCS] Human inference based on similarity to consensus sequences



Reference(s)    

 [1] Abo-Amer AE., Munn J., Jackson K., Aktas M., Golby P., Kelly DJ., Andrews SC., 2004, DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli., J Bacteriol 186(6):1879-89

 [2] Golby P., Davies S., Kelly DJ., Guest JR., Andrews SC., 1999, Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli., J Bacteriol 181(4):1238-48

 [3] Janausch IG., Garcia-Moreno I., Lehnen D., Zeuner Y., Unden G., 2004, Phosphorylation and DNA binding of the regulator DcuR of the fumarate-responsive two-component system DcuSR of Escherichia coli., Microbiology 150(Pt 4):877-83

 [4] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem 280(2):1448-56

 [5] Zientz E., Bongaerts J., Unden G., 1998, Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR genes) two-component regulatory system., J Bacteriol 180(20):5421-5

 [6] Davies SJ., Golby P., Omrani D., Broad SA., Harrington VL., Guest JR., Kelly DJ., Andrews SC., 1999, Inactivation and regulation of the aerobic C(4)-dicarboxylate transport (dctA) gene of Escherichia coli., J Bacteriol 181(18):5624-35

 [7] 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

 [8] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [9] Janausch IG., Garcia-Moreno I., Unden G., 2002, Function of DcuS from Escherichia coli as a fumarate-stimulated histidine protein kinase in vitro., J Biol Chem 277(42):39809-14

 [10] Oyamada T., Yokoyama K., Morinaga M., Suzuki M., Makino K., 2007, Expression of Escherichia coli DcuS-R two-component regulatory system is regulated by the secondary internal promoter which is activated by CRP-cAMP., J Microbiol 45(3):234-40

 [11] Goh EB., Bledsoe PJ., Chen LL., Gyaneshwar P., Stewart V., Igo MM., 2005, Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system., J Bacteriol 187(14):4890-9

 [12] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Bacteriol 185(6):1851-6



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