Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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



Gene: gntR Accession Numbers: EG12630 (EcoCyc), b3438, ECK3423

Regulation Summary Diagram: ?

Component of: GntR-gluconate

Summary:
The Gluconate repressor," GntR, is a transcription factor that negatively regulates the operon involved in the catabolism of d-gluconate via the Entner-Doudoroff pathway and also represses genes involved in two different systems related to d-gluconate uptake: gluconate I and gluconate II [Rodionov00, Tsunedomi03, Tsunedomi03a, Bausch98]. This regulator is part of the gntRKU operon, yet it can also be constitutively expressed as an independent (gntR) transcription unit [Izu97, Tong96].

Gluconate I is considered the main system for transport of d-gluconate and contains genes that encode high- and low-affinity gluconate transporters [Rodionov00, Porco97, Porco98, Izu97a, Peekhaus98]. The d-gluconate II system is capable of transport of l-idonate and also is regulated by IdnR; the genes involved in this system encode another high-affinity gluconate transporter [Rodionov00, Tsunedomi03, Tsunedomi03a, Bausch98].

In addition, the genes regulated are induced when Escherichia coli is grown in the presence of the inductor, d-gloconate, and in the absence of glucose. In the absence of inductor, this repressor binds in tandem to inverted repeat sequences that consist of 20-nucleotide-long DNA target sites [Rodionov00]. Binding of GntR to DNA is diminished in the presence of the inducer d-gluconate.

GntR is closely homologous to IdnR (53% identity) and belongs to the LacI/GalR family of transcriptional regulators [Rodionov00, Tong96, Izu97]. 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 effector binding and oligomerization [Izu97].

Locations: cytosol

Map Position: [3,575,754 <- 3,576,749] (77.07 centisomes)
Length: 996 bp / 331 aa

Molecular Weight of Polypeptide: 36.422 kD (from nucleotide sequence)

pI: 6.7

Unification Links: ASAP:ABE-0011226 , CGSC:667 , EchoBASE:EB2514 , EcoGene:EG12630 , EcoliWiki:b3438 , ModBase:P0ACP5 , OU-Microarray:b3438 , PortEco:gntR , PR:PRO_000022826 , Pride:P0ACP5 , Protein Model Portal:P0ACP5 , RefSeq:YP_026222 , RegulonDB:EG12630 , SMR:P0ACP5 , String:511145.b3438 , UniProt:P0ACP5

Relationship Links: InterPro:IN-FAMILY:IPR000843 , InterPro:IN-FAMILY:IPR001761 , InterPro:IN-FAMILY:IPR010982 , InterPro:IN-FAMILY:IPR028082 , Pfam:IN-FAMILY:PF00356 , Pfam:IN-FAMILY:PF00532 , Prosite:IN-FAMILY:PS00356 , Prosite:IN-FAMILY:PS50932 , Smart:IN-FAMILY:SM00354

In Paralogous Gene Group: 30 (25 members)

In Reactions of unknown directionality:

Not in pathways:
GntR + D-gluconate = GntR-gluconate

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Tsunedomi03]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Tsunedomi03]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046177 - D-gluconate catabolic process Inferred by computational analysis [UniProtGOA12]
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 from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer RNA related Transcription related
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: taaTGTTACCGGTAACAttt

Regulated Transcription Units (9 total): ?

Notes:

Essentiality data for gntR 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: GntR-gluconate

Synonyms: B3438, GntR

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

Sequence Length: 331 AAs

Molecular Weight: 34.607 kD (from nucleotide sequence)

Unification Links: RefSeq:NP_417895

Relationship Links: Pfam:IN-FAMILY:PF00356

In Reactions of unknown directionality:

Not in pathways:
GntR + D-gluconate = GntR-gluconate

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


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 6 -> 60
[UniProt09]
UniProt: HTH lacI-type;
DNA-Binding-Region 8 -> 27
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Martin Peralta on Fri Oct 29, 2004:
The start site of this gene was originally assigned solely on the basis of sequence considerations (Blattner et al, 1997, PubMed: 9278503). However, it was changed because Tong et al,1996, determined the nucleotide sequence of gntR, starting with an ATG start codon, from wich deduced its amino acid sequence (PMID:8655507). The demonstration is based on (a) comparisons of the new gene sequence with homologous proteins, (b) determination of the mRNA size (Northern blot), plus (c) identification of both a plausible ribosome binding site and a promoter at an appropriate distance from the new start site. The promoter was identified using primer extension analysis.
10/20/97 Gene b3438 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12630; 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

Bausch98: Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T (1998). "Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli." J Bacteriol 1998;180(14);3704-10. PMID: 9658018

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

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Izu97: Izu H, Adachi O, Yamada M (1997). "Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli." J Mol Biol 267(4);778-93. PMID: 9135111

Izu97a: Izu H, Kawai T, Yamada Y, Aoshima H, Adachi O, Yamada M (1997). "Characterization of the gntT gene encoding a high-affinity gluconate permease in Escherichia coli." Gene 199(1-2);203-10. PMID: 9358057

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Peekhaus98: Peekhaus N, Conway T (1998). "Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex." J Bacteriol 1998;180(7);1777-85. PMID: 9537375

Porco97: Porco A, Peekhaus N, Bausch C, Tong S, Isturiz T, Conway T (1997). "Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism." J Bacteriol 1997;179(5);1584-90. PMID: 9045817

Porco98: Porco A, Alonso G, Isturiz T (1998). "The gluconate high affinity transport of GntI in Escherichia coli involves a multicomponent complex system." J Basic Microbiol 38(5-6);395-404. PMID: 9871335

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

Tong96: Tong S, Porco A, Isturiz T, Conway T (1996). "Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism." J Bacteriol 1996;178(11);3260-9. PMID: 8655507

Tsunedomi03: Tsunedomi R, Izu H, Kawai T, Yamada M (2003). "Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli." J Mol Microbiol Biotechnol 6(1);41-56. PMID: 14593252

Tsunedomi03a: Tsunedomi R, Izu H, Kawai T, Matsushita K, Ferenci T, Yamada M (2003). "The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli." J Bacteriol 185(6);1783-95. PMID: 12618441

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.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


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 Wed Nov 26, 2014, biocyc13.