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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted DNA-binding transcriptional regulator

Gene: dctR Accession Numbers: EG11889 (EcoCyc), b3507, ECK3491

Synonyms: yhiF

Regulation Summary Diagram: ?

Regulation summary diagram for dctR

DctR is a predicted transcriptional regulator whose target may be dctA. A dctR mutation is the mechanism by which Suc+ reversion mutations suppress the growth defect on C4-dicarboxylates (such as succinate) that is exhibited by atp mutants [Boogerd98].

A slp dctR double mutation suppresses the increased acid resistance of a strain overproducing YdeO [Masuda03] and affects survival in acidified spent minimal E glucose medium, indicating a role in protection against metabolic endproducts that are toxic at low pH [Mates07]. A slp-dctR double mutant exhibited loss of viability during growth in spent LB at pH 2.5 much faster than wild-type [Mates07]. The slp-dctR double mutant was also unable to survive at pH 2.5 in minimal medium when formate, succinate, or lactate were added [Mates07]. The fact that individual slp and dctR mutants retain resistance indicates redundant functions for Slp and DctR in protection against formate, succinate, and lactate at low pH [Mates07].

Overproduction of YdeO [Masuda03] or GadE [Hommais04] result in increased expression of dctR. Overexpression of DctR affects cellular morphology and causes filamentous biofilm formation [Tenorio03].

A yhiF mutation in an enterohemorrhagic E. coli strain causes increased type III secretion and increased cellular adhesion, compared to wild type [Tatsuno03].

DctR: "dicarboxylate transport regulator" [Boogerd98]

Gene Citations: [Alexander94, Tucker03]

Locations: cytosol

Map Position: [3,652,706 -> 3,653,236] (78.73 centisomes, 283°)
Length: 531 bp / 176 aa

Molecular Weight of Polypeptide: 20.408 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011454 , DIP:DIP-12362N , EchoBASE:EB1835 , EcoGene:EG11889 , EcoliWiki:b3507 , ModBase:P37195 , OU-Microarray:b3507 , PortEco:dctR , PR:PRO_000022411 , Protein Model Portal:P37195 , RefSeq:NP_417964 , RegulonDB:EG11889 , SMR:P37195 , String:511145.b3507 , UniProt:P37195

Relationship Links: InterPro:IN-FAMILY:IPR000792 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR016032 , Pfam:IN-FAMILY:PF00196 , Prosite:IN-FAMILY:PS50043 , Smart:IN-FAMILY:SM00421

In Paralogous Gene Group: 535 (2 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for dctR

GO Terms:

Biological Process: GO:0001101 - response to acid chemical Inferred from experiment [Mates07]
GO:0043471 - regulation of cellular carbohydrate catabolic process Inferred from experiment [Boogerd98]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01, Boogerd98]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations pH
regulation type of regulation unknown

Essentiality data for dctR 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]

Curated 14-Feb-2007 by Keseler I , SRI International
Last-Curated ? 16-Apr-2007 by Johnson A , TIGR

Sequence Features

Protein sequence of predicted DNA-binding transcriptional regulator with features indicated

Feature Class Location Citations Comment
Conserved-Region 109 -> 174
UniProt: HTH luxR-type;
DNA-Binding-Region 133 -> 152
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 163 -> 176
[Alexander94, UniProt10a]
UniProt: (in Ref. 1; AAA60371);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3507 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11889; confirmed by SwissProt match.


Alexander94: Alexander DM, St John AC (1994). "Characterization of the carbon starvation-inducible and stationary phase-inducible gene slp encoding an outer membrane lipoprotein in Escherichia coli." Mol Microbiol 1994;11(6);1059-71. PMID: 8022277

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

Boogerd98: Boogerd FC, Boe L, Michelsen O, Jensen PR (1998). "atp Mutants of Escherichia coli fail to grow on succinate due to a transport deficiency." J Bacteriol 180(22);5855-9. PMID: 9811641

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

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

Masuda03: Masuda N, Church GM (2003). "Regulatory network of acid resistance genes in Escherichia coli." Mol Microbiol 48(3);699-712. PMID: 12694615

Mates07: Mates AK, Sayad AK, Foster JW (2007). "Products of the Escherichia coli Acid Fitness Island Attenuate Metabolite Stress at Extreme Low pH and Mediate a Cell Density-Dependent Acid Resistance." J Bacteriol 189(7):2759-68. PMID: 17259322

PerezRueda04: Perez-Rueda E, Collado-Vides J, Segovia L (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea." Comput Biol Chem 28(5-6);341-50. PMID: 15556475

Tatsuno03: Tatsuno I, Nagano K, Taguchi K, Rong L, Mori H, Sasakawa C (2003). "Increased adherence to Caco-2 cells caused by disruption of the yhiE and yhiF genes in enterohemorrhagic Escherichia coli O157:H7." Infect Immun 71(5);2598-606. PMID: 12704134

Tenorio03: Tenorio E, Saeki T, Fujita K, Kitakawa M, Baba T, Mori H, Isono K (2003). "Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation." FEMS Microbiol Lett 225(1);107-14. PMID: 12900028

Tucker03: Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T (2003). "Genes of the GadX-GadW regulon in Escherichia coli." J Bacteriol 185(10);3190-201. PMID: 12730179

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Hirakawa10: Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K (2010). "Indole enhances acid resistance in Escherichia coli." Microb Pathog 49(3);90-4. PMID: 20470880

Johnson11: Johnson MD, Burton NA, Gutierrez B, Painter K, Lund PA (2011). "RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters." J Bacteriol 193(14);3653-6. PMID: 21571995

Krin10: Krin E, Danchin A, Soutourina O (2010). "Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli." BMC Microbiol 10;273. PMID: 21034467

Krin10a: Krin E, Danchin A, Soutourina O (2010). "RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli." Res Microbiol 161(5);363-371. PMID: 20435136

Price00: Price GP, St John AC (2000). "Purification and analysis of expression of the stationary phase-inducible slp lipoprotein in Escherichia coli: role of the Mar system." FEMS Microbiol Lett 193(1);51-6. PMID: 11094278

Seoane95a: Seoane AS, Levy SB (1995). "Identification of new genes regulated by the marRAB operon in Escherichia coli." J Bacteriol 177(3);530-5. PMID: 7836283

Tramonti08: Tramonti A, De Canio M, De Biase D (2008). "GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites." Mol Microbiol 70(4);965-82. PMID: 18808381

Yamanaka14: Yamanaka Y, Oshima T, Ishihama A, Yamamoto K (2014). "Characterization of the YdeO regulon in Escherichia coli." PLoS One 9(11);e111962. PMID: 25375160

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Sep 1, 2015, BIOCYC14B.