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DcuR DNA-binding transcriptional activator

Synonyms: DcuR-phosphorylated, DcuR
Summary:
DcuR regulates several genes involved in C4-dicarboxylate metabolism [4]. 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 [4, 7]. 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 [2, 5, 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 [4, 7].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
DcuR Non-Functional   Apo nd nd nd
DcuR-phosphorylated Functional Covalent Holo nd nd nd
Evolutionary Family: OmpR
TFBs length: 17
TFBs symmetry: inverted-repeat
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) aspA, dctA, dcuA, dcuB, dpiA, dpiB, frdA, frdB, frdC, frdD, fumB, pck
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (6)
fermentation (5)
anaerobic respiration (4)
electron acceptors (4)
carbon compounds (3)
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Regulated operon(s) aspA-dcuA, dctA, dcuB-fumB, dpiBA, frdABCD, pck
First gene in the operon(s) aspA, dctA, dcuB, dpiB, frdA, pck
Simple and complex regulons ArcA,CRP,DcuR
CRP,Cra,DcuR
CRP,DcuR,FNR,NarL
DcuR
DcuR,FNR,NarL
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DcuR,+](7)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  DcuR-phosphorylated activator aspAp Sigma70 -161.0 -266.0 aspA, dcuA
cgaatcgcgtTTAGCTTATATTGTGGTCattagcaaaa
 4368585 4368602 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  DcuR-phosphorylated activator aspAp Sigma70 -75.0 -180.0 aspA, dcuA
atctatttcaCAAATTAATAATTAAGGGgtaaaaaccg
 4368499 4368516 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  DcuR-phosphorylated activator dctAp Sigma70 -106.0 -157.0 dctA
aaactgattaCAAAACTTTAAAAAGTGctggtttgtg
 3683596 3683612 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2], [3], [4], [5]
  DcuR-phosphorylated activator dcuBp2 nd -63.0 -410.0 dcuB, fumB
ggtgaacggtGTTTTTAATTTCAAAACgctaacaaaa
 4349146 4349162 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [5], [5], [6], [6]
  DcuR-phosphorylated activator dcuBp2 nd -41.0 -388.0 dcuB, fumB
aaaacgctaaCAAAAGTTAATTAACTAttatgtcacc
 4349124 4349140 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [5], [5], [6], [6]
  DcuR-phosphorylated activator dpiBp2 nd -98.0 -161.0 dpiB, dpiA
tttatttaatGATTTTAAGTTTTTTAATtaatgtaatt
 652066 652083 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  DcuR-phosphorylated activator dpiBp2 nd -37.0 -100.0 dpiB, dpiA
tgatttaattGATTTAATGAATAAAATTtgccacgatc
 652127 652144 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  DcuR-phosphorylated activator frdAp Sigma70 -104.0 -198.0 frdA, frdB, frdC, frdD
cgatctgatgGTTTAGTAATTAAATTAatcatcttca
 4382508 4382524 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [4], [5], [7]
  DcuR-phosphorylated activator frdAp2 Sigma38 -104.0 -198.0 frdA, frdB, frdC, frdD
cgatctgatgGTTTAGTAATTAAATTAatcatcttca
 4382508 4382524 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [4], [5], [7]
  DcuR-phosphorylated activator pckp Sigma70 -64.0 -203.0 pck
atattcccgcCATATAAACCAAGATTTAaccttttgag
 3532607 3532624 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  DcuR-phosphorylated activator pckp Sigma70 -13.0 -152.0 pck
cctaaaatgcTATTTCTGCGATAATAGCaaccgtttcg
 3532658 3532675 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]


Alignment and PSSM for DcuR TFBSs    

Aligned TFBS of DcuR   
  Sequence
  TGATTAATTTAATTACTAAAC
  TAATGATTTTAAGTTTTTTAA
  TAATTGATTTAATGAATAAAA
  CGGTGTTTTTAATTTCAAAAC
  TAGTTAATTAACTTTTGTTAG
  GCACTTTTTAAAGTTTTGTAA

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

Consensus    
;	consensus.strict             	taattaaTTtAatttttaaAa
;	consensus.strict.rc          	TTTTAAAAATTAAATTAATTA
;	consensus.IUPAC              	trrtkwwTTwAaktwytwwAm
;	consensus.IUPAC.rc           	KTWWARWAMTTWAAWWMAYYA
;	consensus.regexp             	t[ag][ag]t[gt][at][at]TT[at]Aa[gt]t[at][ct]t[at][at]A[ac]
;	consensus.regexp.rc          	[GT]T[AT][AT]A[AG][AT]A[AC]TT[AT]AA[AT][AT][AC]A[CT][CT]A

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    

 [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


Reference(s)    

 [1] Surmann K., Stopp M., Worner S., Dhople VM., Volker U., Unden G., Hammer E., 2020, Fumarate dependent protein composition under aerobic and anaerobic growth conditions in Escherichia coli., J Proteomics 212:103583

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [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 10.1074/jbc.M204482200

 [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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