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Escherichia coli K-12 substr. MG1655 Protein: GntR-gluconate



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

Regulation Summary Diagram

Regulation summary diagram for gntR

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

Gene Citations: [Izu97, Tong96]

Map Position: [3,577,731 <- 3,578,726] (77.08 centisomes, 277°)
Length: 996 bp / 331 aa

Molecular Weight: 34.607 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011226, CGSC:667, EchoBASE:EB2514, EcoGene:EG12630, OU-Microarray:b3438, PortEco:gntR, RefSeq:NP_417895, RegulonDB:EG12630, String:511145.b3438

Relationship Links: Pfam:IN-FAMILY:PF00356

In Paralogous Gene Group: 30 (25 members)

Reactions known to both consume and produce the compound:

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

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for gntR

MultiFun Terms: information transferRNA relatedTranscription related
regulationgenetic unit regulatedoperon
regulationtype of regulationtranscriptional levelrepressor


Subunit of GntR-gluconate: GntR DNA-binding transcriptional repressor

Synonyms: GntR

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

Locations: cytosol

Sequence Length: 331 AAs

Molecular Weight: 36.422 kD (from nucleotide sequence)

pI: 6.7


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0045892 - negative regulation of transcription, DNA-templated [Tsunedomi03]
Inferred from experimentGO:0045893 - positive regulation of transcription, DNA-templated [Tsunedomi03]
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0046177 - D-gluconate catabolic process [UniProtGOA12]
Molecular Function:
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0003700 - transcription factor activity, sequence-specific DNA binding [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transferRNA relatedTranscription related
regulationgenetic unit regulatedoperon
regulationtype of regulationtranscriptional levelrepressor

Unification Links: DIP:DIP-9822N, EcoliWiki:b3438, ModBase:P0ACP5, PR:PRO_000022826, Pride:P0ACP5, Protein Model Portal:P0ACP5, RefSeq:YP_026222, SMR:P0ACP5, 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

Reactions known to both consume and produce the compound:

Not in pathways:
GntR + D-gluconate ↔ 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 inducer, D-gluconate, and in the absence of glucose. In the absence of inducer, 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].

Citations: [Zwaig73]

Essentiality data for gntR knockouts:

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

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

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

GOA01a: 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

UniProtGOA11a: 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."

Zwaig73: Zwaig N, Nagel de Zwaig R, Isturiz T, Wecksler M (1973). "Regulatory mutations affecting the gluconate system in Escherichia coli." J Bacteriol 114(2);469-73. PMID: 4574690


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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 Pathway Tools version 20.0 (software by SRI International) on Fri May 6, 2016, BIOCYC14.