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



Gene: glpR Accession Numbers: EG10400 (EcoCyc), b3423, ECK3409

Regulation Summary Diagram: ?

Component of:
GlpR-glycerol
GlpR-glycerol-3-phosphate (summary available)

Summary:
The sn-Glycerol-3-phosphate repressor," GlpR, acts as the repressor of the glycerol-3-phosphate regulon, which is organized in different operons [Larson87, Lin76, Larson92, Yang97, Truniger92, Weissenborn92, Yang96]. This regulator is part of the glpEGR operon, yet it can also be constitutively expressed as an independent (glpR) transcription unit [Yang98, Schweizer85].

In addition, the operons regulated are induced when Escherichia coli is grown in the presence of inductor, glycerol, or glycerol-3-phosphate (G3P), and the absence of glucose [Lin76]. In the absence of inductor, this repressor binds in tandem to inverted repeat sequences that consist of 20-nucleotide-long DNA target sites [Zhao94, Larson92, Lin76]. Binding of GlpR to DNA is diminished in the presence of the inducers glycerol or G3P.

GlpR belongs to the DeoR family of transcriptional regulators [Zeng96]. Accordingly, this transcriptional repressor family protein is composed of two domains: a conserved N-terminal domain which contains the DNA-binding region, and the carboxy-terminal domain, which is involved in oligomerization and binding of the inducer [Zeng96].

Resequencing of multiple isolates of the MG1655 strain has identified several genetic variations compared to the reference sequence, including a 1-bp deletion in glpR in strain ATCC700926 [Freddolino12]. This EcoliWiki page summarizes these sequence differences.

Gene Citations: [Choi91]

Locations: cytosol

Map Position: [3,557,870 <- 3,558,628] (76.68 centisomes)
Length: 759 bp / 252 aa

Molecular Weight of Polypeptide: 28.048 kD (from nucleotide sequence)

pI: 6.07

Unification Links: ASAP:ABE-0011176 , CGSC:688 , EchoBASE:EB0395 , EcoGene:EG10400 , EcoliWiki:b3423 , ModBase:P0ACL0 , OU-Microarray:b3423 , PortEco:glpR , PR:PRO_000022799 , Pride:P0ACL0 , Protein Model Portal:P0ACL0 , RefSeq:NP_417881 , RegulonDB:EG10400 , SMR:P0ACL0 , String:511145.b3423 , UniProt:P0ACL0

Relationship Links: InterPro:IN-FAMILY:IPR001034 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014036 , InterPro:IN-FAMILY:IPR018356 , 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:
GlpR + glycerol = GlpR-glycerol
GlpR + sn-glycerol 3-phosphate = GlpR-glycerol-3-phosphate

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Zhao94]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Inferred from experiment [Larson87]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
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:0005622 - intracellular Inferred by computational analysis [GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon anaerobic respiration
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: naTGCGCGataaCGCGCAtn

Regulated Transcription Units (4 total): ?

Notes:

Essentiality data for glpR 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]

Subunit of: GlpR-glycerol

Subunit composition of GlpR-glycerol = [GlpR][glycerol]
         GlpR DNA-binding transcriptional repressor = GlpR (extended summary available)

Citations: [Lin76]

Sequence Length: 252 AAs

In Reactions of unknown directionality:

Not in pathways:
GlpR + glycerol = GlpR-glycerol

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon anaerobic respiration
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Subunit of: GlpR-glycerol-3-phosphate

Synonyms: B3423, GlpR

Subunit composition of GlpR-glycerol-3-phosphate = [GlpR][sn-glycerol 3-phosphate]
         GlpR DNA-binding transcriptional repressor = GlpR (extended summary available)

Summary:
When glycerol-3-phosphate is bound to GlpR, the affinity of the protein for the operators is reduced [Lemieux04].

Sequence Length: 252 AAs

Molecular Weight: 28.048 kD (from nucleotide sequence)

Relationship Links: Pfam:IN-FAMILY:PF00455

In Reactions of unknown directionality:

Not in pathways:
GlpR + sn-glycerol 3-phosphate = GlpR-glycerol-3-phosphate

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon anaerobic respiration
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
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;
Sequence-Conflict 155
[Choi88, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 2);
Sequence-Conflict 235
[Choi88, UniProt10]
Alternate sequence: P → PP; UniProt: (in Ref. 2);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3423 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10400.


References

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

Choi88: Choi YL, Kawase S, Nishida T, Sakai H, Komano T, Kawamukai M, Utsumi R, Kohara Y, Akiyama K (1988). "Nucleotide sequence of the glpR gene encoding the repressor for the glycerol-3-phosphate regulon of Escherichia coli K12." Nucleic Acids Res 16(15);7732. PMID: 3045764

Choi91: Choi YL, Kawase S, Kawamukai M, Sakai H, Komano T (1991). "Regulation of glpD and glpE gene expression by a cyclic AMP-cAMP receptor protein (cAMP-CRP) complex in Escherichia coli." Biochim Biophys Acta 1991;1088(1);31-5. PMID: 1846566

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

Freddolino12: Freddolino PL, Amini S, Tavazoie S (2012). "Newly identified genetic variations in common Escherichia coli MG1655 stock cultures." J Bacteriol 194(2);303-6. PMID: 22081388

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

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

Larson87: Larson TJ, Ye SZ, Weissenborn DL, Hoffmann HJ, Schweizer H (1987). "Purification and characterization of the repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K12." J Biol Chem 1987;262(33);15869-74. PMID: 3316209

Larson92: Larson TJ, Cantwell JS, van Loo-Bhattacharya AT (1992). "Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12." J Biol Chem 1992;267(9);6114-21. PMID: 1556120

Lemieux04: Lemieux MJ, Huang Y, Wang DN (2004). "Glycerol-3-phosphate transporter of Escherichia coli: structure, function and regulation." Res Microbiol 155(8);623-9. PMID: 15380549

Lin76: Lin EC (1976). "Glycerol dissimilation and its regulation in bacteria." Annu Rev Microbiol 1976;30;535-78. PMID: 825019

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Schweizer85: Schweizer H, Boos W, Larson TJ (1985). "Repressor for the sn-glycerol-3-phosphate regulon of Escherichia coli K-12: cloning of the glpR gene and identification of its product." J Bacteriol 161(2);563-6. PMID: 3881401

Truniger92: Truniger V, Boos W, Sweet G (1992). "Molecular analysis of the glpFKX regions of Escherichia coli and Shigella flexneri." J Bacteriol 174(21);6981-91. PMID: 1400248

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Weissenborn92: Weissenborn DL, Wittekindt N, Larson TJ (1992). "Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12." J Biol Chem 1992;267(9);6122-31. PMID: 1372899

Yang96: Yang B, Larson TJ (1996). "Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 178(24);7090-8. PMID: 8955388

Yang97: Yang B, Gerhardt SG, Larson TJ (1997). "Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12." Mol Microbiol 24(3);511-21. PMID: 9179845

Yang98: Yang B, Larson TJ (1998). "Multiple promoters are responsible for transcription of the glpEGR operon of Escherichia coli K-12." Biochim Biophys Acta 1998;1396(1);114-26. PMID: 9524241

Zeng96: Zeng G, Ye S, Larson TJ (1996). "Repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12: primary structure and identification of the DNA-binding domain." J Bacteriol 1996;178(24);7080-9. PMID: 8955387

Zhao94: Zhao N, Oh W, Trybul D, Thrasher KS, Kingsbury TJ, Larson TJ (1994). "Characterization of the interaction of the glp repressor of Escherichia coli K-12 with single and tandem glp operator variants." J Bacteriol 176(8);2393-7. PMID: 8157609

Other References Related to Gene Regulation

Ye88: Ye SZ, Larson TJ (1988). "Structures of the promoter and operator of the glpD gene encoding aerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 1988;170(9);4209-15. PMID: 3045087


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 Sun Nov 23, 2014, BIOCYC14B.