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



Gene: ulaR Accession Numbers: G7854 (EcoCyc), b4191, ECK4187

Synonyms: yjfQ

Regulation Summary Diagram: ?

Component of: UlaR-L-ascorbate-6P

Summary:
UlaR is a DNA-binding transcription factor of 251 amino acids that is expressed constitutively and that coordinately represses transcription of a divergent operon (ula) involved in transport and utilization of L-ascorbate catabolism [Zhang03, Campos02, Campos07, Hvorup03]. Synthesis of these genes is induced when Escherichia coli is grown in the absence of glucose, and under anaerobic conditions it can ferment L-ascorbate; under aerobic conditions it is functional in the presence of casein acid hydrolysate [Campos04, Yew02, Campos07].

L-Ascorbate-6-P is the effector of the UlaR transcriptional repressor, and when this small molecule binds to UlaR, it severely impairs the formation of UlaR cognate operator sites, since they form a stable complex [Garces08]. L-Ascorbate-6-P weakens the affinity of UlaR for DNA and displaces the UlaR oligomer state from a transcription-silencing tetrameric form to a transcription-activating dimeric form [Garces08]. UlaR activity is also controlled by homotypic tetramer-dimer transitions regulated by L-ascorbate-6-P [Garces08].

UlaR binds to four inverted repeat motifs in the divergent intergenic region ulaG-ulaA and overlaps its target promoters to repress transcription by blocking the interaction of the RNA polymerase with ulaGp and ulaAp [Campos04]. Here, the presence of L-ascorbate-6-P breaks this configuration down into DNA-free UlaR homodimers and allows transcription to proceed [Garces08]. At concentrations of >2 nM, L-ascorbate-6-P displaces UlaR from its operator site [Garces08].

In this system the full repression of the ula regulon requires IHF and binding of UlaR to four operator sites, possibly involving UlaR-mediated DNA loop formation [Campos04].

The UlaR transcriptional repressor belongs to the DeoR family, and accordingly, this transcriptional repressor family protein is composed of two domains: an N-terminal HTH domain (residues 1-62), which contains the DNA-binding region [Campos02], and the C-terminal sugar-phosphate-binding domain (residues 69-251), which is responsible for dimerization and inducer binding [Anantharaman06]. The C-terminal sugar-phosphate-binding domain belongs to the DeoR-C family of the ISOCOT superfamily and is structurally related to E. coli D-ribose-5-P isomerase [Anantharaman06]. Asp206 and Lys209 are directly involved in binding L-ascorbate-6-P [Garces08].

Review: [Amouyal05].

Locations: cytosol

Map Position: [4,415,721 <- 4,416,476] (95.17 centisomes)
Length: 756 bp / 251 aa

Molecular Weight of Polypeptide: 27.602 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013713 , DIP:DIP-47874N , EchoBASE:EB2384 , EcoGene:EG12491 , EcoliWiki:b4191 , Mint:MINT-1221501 , ModBase:P0A9W0 , OU-Microarray:b4191 , PortEco:ulaR , PR:PRO_000024181 , Pride:P0A9W0 , Protein Model Portal:P0A9W0 , RefSeq:NP_418612 , RegulonDB:G7854 , SMR:P0A9W0 , String:511145.b4191 , UniProt:P0A9W0

Relationship Links: InterPro:IN-FAMILY:IPR001034 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014036 , InterPro:IN-FAMILY:IPR018356 , InterPro:IN-FAMILY:IPR023711 , Pfam:IN-FAMILY:PF00455 , Pfam:IN-FAMILY:PF08220 , Prints:IN-FAMILY:PR00037 , Prosite:IN-FAMILY:PS00894 , Prosite:IN-FAMILY:PS51000 , Smart:IN-FAMILY:SM00420

In Paralogous Gene Group: 375 (8 members)

In Reactions of unknown directionality:

Not in pathways:
UlaR + L-ascorbate 6-phosphate = UlaR-L-ascorbate-6P

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Campos02]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05, Arifuzzaman06]
GO:0031418 - L-ascorbic acid binding Inferred from experiment [Garces08]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01a]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level repressor

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: tGATTAnTcatgAatAATCa

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for ulaR 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: UlaR-L-ascorbate-6P

Synonyms: YjfQ, B4191, UlaR

Subunit composition of UlaR-L-ascorbate-6P = [UlaR][L-ascorbate 6-phosphate]
         UlaR DNA-binding transcriptional repressor = UlaR (extended summary available)

Sequence Length: 251 AAs

Relationship Links: Pfam:IN-FAMILY:PF00455

In Reactions of unknown directionality:

Not in pathways:
UlaR + L-ascorbate 6-phosphate = UlaR-L-ascorbate-6P

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Common Name Citations Comment
DNA-Binding-Region 1 -> 62 N-terminal H-T-H domain
[Campos02, Campos02]
 
Conserved-Region 3 -> 58  
[UniProt09]
UniProt: HTH deoR-type;
DNA-Binding-Region 20 -> 39  
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 69 -> 251 C-terminal sugar-phosphate-binding domain
[Anantharaman06, Anantharaman06]
 
Phosphorylation-Modification 206 L-ascorbate-6-P-binding
[Garces08, Garces08]
 
Phosphorylation-Modification 209 L-ascorbate-6-P-binding
[Garces08, Garces08]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Amouyal05: Amouyal M (2005). "Gene regulation at-a-distance in E. coli: new insights." C R Biol 328(1);1-9. PMID: 15714875

Anantharaman06: Anantharaman V, Aravind L (2006). "Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase." J Mol Biol 356(3);823-42. PMID: 16376935

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Campos02: Campos E, Aguilar J, Baldoma L, Badia J (2002). "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli." J Bacteriol 184(21);6065-8. PMID: 12374842

Campos04: Campos E, Baldoma L, Aguilar J, Badia J (2004). "Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in LaAscorbate dissimilation in Escherichia coli." J Bacteriol 186(6);1720-8. PMID: 14996803

Campos07: Campos E, Montella C, Garces F, Baldoma L, Aguilar J, Badia J (2007). "Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli." Microbiology 153(Pt 10);3399-408. PMID: 17906139

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

Garces08: Garces F, Fernandez FJ, Gomez AM, Perez-Luque R, Campos E, Prohens R, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC (2008). "Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli." Biochemistry 47(44);11424-33. PMID: 18844374

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hvorup03: Hvorup R, Chang AB, Saier MH (2003). "Bioinformatic analyses of the bacterial L-ascorbate phosphotransferase system permease family." J Mol Microbiol Biotechnol 6(3-4);191-205. PMID: 15153772

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

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."

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

Yew02: Yew WS, Gerlt JA (2002). "Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons." J Bacteriol 2002;184(1);302-6. PMID: 11741871

Zhang03: Zhang Z, Aboulwafa M, Smith MH, Saier MH (2003). "The ascorbate transporter of Escherichia coli." J Bacteriol 185(7);2243-50. PMID: 12644495


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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 Fri Dec 19, 2014, BIOCYC13B.