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



Gene: uxuR Accession Numbers: EG20249 (EcoCyc), b4324, ECK4315

Regulation Summary Diagram: ?

Component of: UxuR-fructuronate

Summary:
The "hexuronate regulator," UxuR, is a transcriptional factor. This protein negatively regulates its own synthesis, and in the absence of fructuronate it represses transcription of the cluster of operons involved in transport and degradation of the sugar acids β-D-glucuronides, glucuronate, and gluconate [Ritzenthaler82, RobertBaudouy81, Rodionov00, Bates04, Blanco86]. This regulator is subject to catabolic repression in the presence of glucose and at low levels of cyclic AMP.

Although little is known about the regulating mechanism of UxuR, it has been shown to act as a repressor, binding to a putative inverted repeat sequence from the uid operon in a cooperative process with UidR [Ritzenthaler83, Blanco86a, Blanco87]. In 1986, Blanco et al. proposed that total repression of UxuR is achieved in the presence of UidR, suggesting the possibility that UxuR and UidR form a complex. Independently, each repressor binds to DNA separately [Blanco86a, Blanco85, Blanco87]. On the other hand, UxuR is highly similar to ExuR (49% identity), and apparently both act together, capable of cross talk to regulate expression of the uxuR regulon [Rodionov00].

UxuR is a protein that belongs to the GntR family and participates as a regulator of several genes involved in carbon uptake.

Gene Citations: [Ritzenthaler81]

Locations: cytosol

Map Position: [4,552,599 -> 4,553,372] (98.12 centisomes)
Length: 774 bp / 257 aa

Molecular Weight of Polypeptide: 29.308 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014179 , CGSC:12 , DIP:DIP-11110N , EchoBASE:EB4151 , EcoGene:EG20249 , EcoliWiki:b4324 , ModBase:P39161 , OU-Microarray:b4324 , PortEco:uxuR , PR:PRO_000024208 , Protein Model Portal:P39161 , RefSeq:NP_418744 , RegulonDB:EG20249 , SMR:P39161 , String:511145.b4324 , UniProt:P39161

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR008920 , InterPro:IN-FAMILY:IPR011711 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR027376 , 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)

In Reactions of unknown directionality:

Not in pathways:
D-fructuronate + UxuR = UxuR-fructuronate

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Novel76, Blanco86a, Ritzenthaler83a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm
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 operon
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): ?

Notes:

Essentiality data for uxuR knockouts: ?

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

Subunit of: UxuR-fructuronate

Synonyms: B4324, UxuR

Subunit composition of UxuR-fructuronate = [D-fructuronate][UxuR]
         UxuR DNA-binding transcriptional repressor = UxuR (extended summary available)

Citations: [Blanco86a]

Sequence Length: 257 AAs

Relationship Links: Pfam:IN-FAMILY:PF00392

In Reactions of unknown directionality:

Not in pathways:
D-fructuronate + UxuR = UxuR-fructuronate

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 8 -> 76
[UniProt09]
UniProt: HTH gntR-type;
DNA-Binding-Region 36 -> 55
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4324 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG20249; confirmed by SwissProt match.


References

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

Bates04: Bates Utz C, Nguyen AB, Smalley DJ, Anderson AB, Conway T (2004). "GntP is the Escherichia coli Fructuronic acid transporter and belongs to the UxuR regulon." J Bacteriol 186(22);7690-6. PMID: 15516583

Blanco85: Blanco C, Ritzenthaler P, Mata-Gilsinger M (1985). "Nucleotide sequence of a regulatory region of the uidA gene in Escherichia coli K12." Mol Gen Genet 199(1);101-5. PMID: 3889544

Blanco86: Blanco C, Ritzenthaler P, Kolb A (1986). "The regulatory region of the uxuAB operon in Escherichia coli K12." Mol Gen Genet 1986;202(1);112-9. PMID: 3083215

Blanco86a: Blanco C, Ritzenthaler P, Mata-Gilsinger M (1986). "Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression." Genetics 112(2);173-82. PMID: 3079718

Blanco87: Blanco C (1987). "Transcriptional and translational signals of the uidA gene in Escherichia coli K12." Mol Gen Genet 208(3);490-8. PMID: 2823062

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Novel76: Novel M, Novel G (1976). "Regulation of beta-glucuronidase synthesis in Escherichia coli K-12: pleiotropic constitutive mutations affecting uxu and uidA expression." J Bacteriol 127(1);418-32. PMID: 776934

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

Ritzenthaler82: Ritzenthaler P, Mata-Gilsinger M (1982). "Use of in vitro gene fusions to study the uxuR regulatory gene in Escherichia coli K-12: direction of transcription and regulation of its expression." J Bacteriol 150(3);1040-7. PMID: 6281232

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

Ritzenthaler83a: Ritzenthaler P, Mata-Gilsinger M (1983). "Multiple regulation involved in the expression of the uxuR regulatory gene in Escherichia coli K-12." Mol Gen Genet 189(2);351-4. PMID: 6406797

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.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

MedinaRivera11: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs." Nucleic Acids Res 39(3);808-24. PMID: 20923783

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


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 18.5 on Thu Dec 18, 2014, BIOCYC13A.