Escherichia coli K-12 substr. MG1655 Polypeptide: ExuR DNA-binding transcriptional repressor

Gene: exuR Accession Numbers: EG12739 (EcoCyc), b3094, ECK3085

Synonyms: negative regulator of exu regulon, exuT, uxaAC, and uxuB

Regulation Summary Diagram: ?

Regulation summary diagram for exuR

The Exuronate repressor," ExuR, is a DNA-binding transcription factor that negatively regulates its own synthesis and represses transcription of the operons involved in transport and catabolism of galacturonate and glucuronate [HugovieuxCotteP82, Rodionov00, Ritzenthaler81, RobertBaudouy81, HugouvieuxCotte81, Nemoz76].

On the other hand, ExuR is similar to UxuR (49% of identity), and apparently both act together and are capable of cross-talk to regulate expression of the uxu operon [Rodionov00, RobertBaudouy81, Ritzenthaler83, Ritzenthaler85]. For this reason, there is the possibility that these regulators bind the same sites with different affinities.

Currently, no DNA-binding sites for this regulator have been reported in the literature, and although little is known about the regulating mechanism of ExuR, it has been shown to act as a repressor that binds to a putative inverted repeat sequence [Rodionov00]. Comparative analysis of intergenic DNA sequences showed the consistent occurrence of ExuR possible binding sites upstream of the genes related to the transport of gluconate (gntP) and with the transport and degradation of glucuronides (uidAB) [Rodionov00].

Citations: [MataGilsinger83]

Locations: cytosol

Map Position: [3,244,674 -> 3,245,450] (69.93 centisomes, 252°)
Length: 777 bp / 258 aa

Molecular Weight of Polypeptide: 29.836 kD (from nucleotide sequence)

pI: 5.57

Unification Links: ASAP:ABE-0010176 , CGSC:801 , EchoBASE:EB2595 , EcoGene:EG12739 , EcoliWiki:b3094 , ModBase:P0ACL2 , OU-Microarray:b3094 , PortEco:exuR , PR:PRO_000022557 , Pride:P0ACL2 , Protein Model Portal:P0ACL2 , RefSeq:NP_417565 , RegulonDB:EG12739 , SMR:P0ACL2 , String:511145.b3094 , UniProt:P0ACL2

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR008920 , InterPro:IN-FAMILY:IPR011711 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00392 , Pfam:IN-FAMILY:PF07729 , Prints:IN-FAMILY:PR00035 , Prosite:IN-FAMILY:PS50949 , Smart:IN-FAMILY:SM00345 , Smart:IN-FAMILY:SM00895

In Paralogous Gene Group: 38 (9 members) , 491 (2 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for exuR

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [RobertBaudouy81]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
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: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level repressor

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: aaaTTGGTtaACCAAttt

Regulated Transcription Units (6 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for exuR 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]

Sequence Features

Protein sequence of ExuR DNA-binding transcriptional repressor with features indicated

Feature Class Location Citations Comment
Conserved-Region 7 -> 75
UniProt: HTH gntR-type;
DNA-Binding-Region 35 -> 54
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3094 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12739; confirmed by SwissProt match.


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

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."

HugouvieuxCotte81: Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1981). "Isolation of fusions between the lac genes and several genes of the exu regulon: analysis of their regulation, determination of the transcription direction of the uxaC-uxaA operon, in Escherichia coli K-12." Mol Gen Genet 182(2);279-87. PMID: 7026975

HugovieuxCotteP82: Hugovieux-Cotte-Pattat N, Robert-Baudouy J (1982). "Regulation and transcription direction of exuR, a self-regulated repressor in escherichia coli K-12." J Mol Biol 156(1);221-8. PMID: 6808145

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

MataGilsinger83: Mata-Gilsinger M, Ritzenthaler P, Blanco C (1983). "Characterization of the operator sites of the exu regulon in Escherichia coli K-12 by operator-constitutive mutations and repressor titration." Genetics 1983;105(4);829-42. PMID: 6357945

Nemoz76: Nemoz G, Robert-Baudouy J, Stoeber F (1976). "Physiological and genetic regulation of the aldohexuronate transport system in Escherichia coli." J Bacteriol 1976;127(2);706-18. PMID: 783117

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Ritzenthaler81: Ritzenthaler P, Mata-Gilsinger M, Stoeber F (1981). "Molecular cloning of Escherichia coli K-12 hexuronate system genes: exu region." J Bacteriol 145(1);181-90. PMID: 6450743

Ritzenthaler83: Ritzenthaler P, Blanco C, Mata-Gilsinger M (1983). "Interchangeability of repressors for the control of the uxu and uid operons in E. coli K12." Mol Gen Genet 191(2);263-70. PMID: 6353163

Ritzenthaler85: Ritzenthaler P, Blanco C, Mata-Gilsinger M (1985). "Genetic analysis of uxuR and exuR genes: evidence for ExuR and UxuR monomer repressors interactions." Mol Gen Genet 199(3);507-11. PMID: 3929016

RobertBaudouy81: Robert-Baudouy J, Portalier R, Stoeber F (1981). "Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products." J Bacteriol 145(1);211-20. PMID: 7007313

Rodionov00: Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS (2000). "Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria." Mol Microbiol 38(4);673-83. PMID: 11115104

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297

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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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