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GntR DNA-binding transcriptional repressor

Synonyms: GntR, 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 [4, 7, 12, 13] . This regulator is part of the gntRKU operon, yet it can also be constitutively expressed as an independent ARRAY(0x28cac88) transcription unit [1, 6] . Gluconate I is considered the main system for transport of D-gluconate and contains genes that encode high- and low-affinity gluconate transporters [4, 8, 9, 11, 14] . 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 [4, 7, 12, 13] . 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.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
GntR Functional   Apo [GEA], [IEP] [1]
GntR-gluconate Non-Functional Allosteric Holo [GEA], [IEP] [1]
Evolutionary Family: GalR/LacI
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: gntR
  Genome position: 3577731-3578726
  Length: 996 bp / 331 aa
Operon name: gntRKU
TU(s) encoding the TF:
Transcription unit        Promoter
gntR
gntRp2
gntR
gntRp3
gntR
gntRp4
gntRKU
null


Regulon       
Regulated gene(s) eda, edd, gntK, gntT, gntU, gntX, idnD, idnK, idnO, idnR, idnT, nfuA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (5)
Porters (Uni-, Sym- and Antiporters) (3)
membrane (3)
Entner-Doudoroff (2)
glyoxylate degradation (1)
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Regulated operon(s) edd-eda, gntRKU, gntT, gntX-nfuA, idnDOTR, idnK
First gene in the operon(s) edd, gntK, gntK, gntT, gntT, gntT, gntX, idnD, idnK
Simple and complex regulons CRP,GntR
CRP,GntR,IdnR
Cra,GntR,KdgR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GntR,-](8)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  GntR repressor eddp1 Sigma70 -93.5 -202.5 edd, eda
tcctttatggTTATTTTACCGGTAACATGAtcttgcgcag
1934797 1934816 [AIBSCS], [BPP], [HIBSCS] [2], [3], [4], [5]
  GntR repressor eddp1 Sigma70 128.5 18.5 edd, eda
tatgaatccaCAATTGTTACGCGTAACAAAtcgaatcatt
1934576 1934595 [BPP], [HIBSCS], [SM] [2], [3], [4]
  GntR repressor gntKp Sigma70 2.5 -51.5 gntK, gntU
tccggctggaCAATGTTACCGATAACAGTTacccgtaaca
3577634 3577653 [AIBSCS], [BPP], [GEA], [HIBSCS], [SM] [1], [4], [5], [6], [7]
  GntR repressor gntKp Sigma70 15.5 -38.5 gntK, gntU
tgttaccgatAACAGTTACCCGTAACATTTttaattcttg
3577621 3577640 [AIBSCS], [BPP], [GEA], [HIBSCS], [SM] [4], [5], [7]
  GntR repressor gntTp1 Sigma70 -14.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
3546381 3546400 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [8], [9], [10]
  GntR repressor gntTp1 Sigma70 127.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
3546522 3546541 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [9], [10]
  GntR repressor gntTp2 nd -55.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
3546381 3546400 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [8], [9], [10]
  GntR repressor gntTp2 nd 86.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
3546522 3546541 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [9], [10]
  GntR repressor gntTp3 nd -58.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
3546381 3546400 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [8], [9], [10]
  GntR repressor gntTp3 nd 83.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
3546522 3546541 [AIBSCS], [BPP], [GEA], [HIBSCS], [TASES] [4], [5], [9], [10]
  GntR repressor gntXp Sigma70 -15.0 -230.5 gntX, nfuA
ctgttgcagcACGGCTTCGGCCATATCAGCaagtgacagc
3544642 3544661 [AIBSCS] [11]
  GntR repressor idnDp nd -108.5 -137.5 idnD, idnO, idnT, idnR
cacgttttttTATTTCTACTGATAAGAATTacaaggcaca
4494534 4494553 [AIBSCS], [GEA], [HIBSCS] [5], [12]
  GntR repressor idnDp nd -78.5 -107.5 idnD, idnO, idnT, idnR
acaaggcacaTCACGTTATGCGTAACATAGtaatgtaaca
4494504 4494523 [AIBSCS], [GEA], [HIBSCS] [4], [5], [12]
  GntR repressor idnDp nd -58.5 -87.5 idnD, idnO, idnT, idnR
cgtaacatagTAATGTAACAATTTTCTGACgtgatcttca
4494484 4494503 [GEA], [HIBSCS] [12]
  GntR repressor idnKp Sigma70 -103.5 -129.5 idnK
tgaagatcacGTCAGAAAATTGTTACATTActatgttacg
4494484 4494503 [GEA], [HIBSCS] [12]
  GntR repressor idnKp Sigma70 -83.5 -109.5 idnK
tgttacattaCTATGTTACGCATAACGTGAtgtgccttgt
4494504 4494523 [AIBSCS], [GEA], [HIBSCS] [4], [5], [12]
  GntR repressor idnKp Sigma70 -53.5 -79.5 idnK
tgtgccttgtAATTCTTATCAGTAGAAATAaaaaaacgtg
4494534 4494553 [AIBSCS], [GEA], [HIBSCS] [5], [12]


Alignment and PSSM for GntR TFBSs    

Aligned TFBS of GntR   
  Sequence
 

Position weight matrix (PWM).   
A	3	6	0	0	0	2	8	0	1	1	2	0	8	5	1	7	2	5
C	3	0	3	0	0	1	0	6	4	6	0	0	0	0	8	0	0	1
G	3	1	0	8	0	0	1	1	3	2	5	0	0	0	0	0	4	0
T	0	2	6	1	9	6	0	2	1	0	2	9	1	4	0	2	3	3

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [TASES] Traceable author statement to experimental support



Reference(s)    

 [1] 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

 [2] Egan SE., Fliege R., Tong S., Shibata A., Wolf RE., Conway T., 1992, Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon., J Bacteriol. 174(14):4638-46

 [3] Murray EL., Conway T., 2005, Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli., J Bacteriol. 187(3):991-1000

 [4] 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

 [5] Suvorova IA., Korostelev YD., Gelfand MS., 2015, GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution., PLoS One. 10(7):e0132618

 [6] 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. 178(11):3260-9

 [7] 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

 [8] 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

 [9] 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. 180(7):1777-85

 [10] Peekhaus N., Conway T., 1998, What's for dinner?: Entner-Doudoroff metabolism in Escherichia coli., J Bacteriol. 180(14):3495-502

 [11] 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

 [12] 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

 [13] 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. 180(14):3704-10

 [14] 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. 179(5):1584-90



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