Escherichia coli K-12 substr. MG1655 Protein: DcuR-Phosphorylated DNA-binding transcriptional activator

Gene: dcuR Accession Numbers: G7826 (EcoCyc), b4124, ECK4117

Synonyms: yjdG, DcuR response regulator - phosphorylated, DcuR-Pasp56

Regulation Summary Diagram: ?

Regulation summary diagram for dcuR

Subunit composition of DcuR-Phosphorylated DNA-binding transcriptional activator = [DcuR]2

Alternative forms of DcuR: DcuR transcriptional activator

DcuR regulates several genes involved in C4-dicarboxylate metabolism [Golby99]. 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 [Oshima02].

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 [Golby99, Zientz98]. 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 [Janausch04, Janausch02, AboAmer04].

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 [Golby99, Zientz98]. Two directly repeated hexameric DNA sequences that are highly enriched in A/T residues have been proposed to be the sites recognized by a DcuR dimer [AboAmer04].

Both dcuR, encoding the response regulator, and dcuS, encoding the sensor kinase, are organized in an operon that is located upstream of the dcuB-fumB operon, whose expression is activated by DcuR [AboAmer04]. The dcuSR operon contains two promoters, an external one that transcribes both genes and an internal one that only transcribes to dcuR and that is activated by CRP [Oyamada07]. Neither of these two promoters is regulated by DcuR [Goh05]. The full operon is repressed by nitrate acting through the NarXL regulatory system, so that E.coli will use nitrate as a respiratory electron acceptor before fumarate [Goh05].]|

Overproduction of DcuR causes a drug resistance phenotype [Hirakawa03].

Gene Citations: [Salmon03]

Locations: cytosol

Map Position: [4,347,338 <- 4,348,057] (93.7 centisomes, 337°)
Length: 720 bp / 239 aa

Molecular Weight of Polypeptide: 27.488 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013507 , EchoBASE:EB2357 , EcoGene:EG12464 , OU-Microarray:b4124 , PortEco:dcuR , PR:PRO_000025386 , RefSeq:NP_418548 , RegulonDB:G7826

Relationship Links: Pfam:IN-FAMILY:PF00072

In Paralogous Gene Group: 121 (40 members)

Reactions known to produce the compound:

DcuSR Two-Component Signal Transduction System, dicarboxylate-dependent :
DcuR + DcuS sensory histidine kinase - phosphorylated → DcuR-Pasp + DcuS

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for dcuR

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment [Golby99]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment [Oyamada07]
Molecular Function: GO:0000156 - phosphorelay response regulator activity Inferred from experiment [Golby99]
Cellular Component: GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon anaerobic respiration
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

DNA binding site length: 17 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: gtttttaAtTtcaaaac

Regulated Transcription Units (4 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for dcuR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Created 15-Aug-2008 by Gama-Castro S , UNAM
Last-Curated ? 17-Aug-2008 by Gama-Castro S , UNAM

Sequence Features

Protein sequence of DcuR with features indicated

Feature Class Location Citations Comment State
Conserved-Region 1 -> 121
UniProt: Response regulatory;
4-aspartylphosphate-Modification 56
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.
DNA-Binding-Region 181 -> 200
UniProt: H-T-H motif;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


AboAmer04: 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. PMID: 14996819

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Goh05: 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. PMID: 15995204

Golby99: 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 1999;181(4);1238-48. PMID: 9973351

Hirakawa03: 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. PMID: 12618449

Janausch02: 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 2002;277(42);39809-14. PMID: 12167640

Janausch04: 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. PMID: 15073297

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Oshima02: 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. PMID: 12366850

Oyamada07: 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. PMID: 17618229

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

Zientz98: 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 1998;180(20);5421-5. PMID: 9765574

Other References Related to Gene Regulation

AboAmer09: Abo-Amer AE, Altalhi AD (2009). "RpoS-independent and growth phase-dependent expression of dcuSR operon of Escherichia coli." Acta Microbiol Immunol Hung 56(3);211-27. PMID: 19789137

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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