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GntR DNA-binding transcriptional repressor

Synonyms: GntR-D-gluconate, GntR
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 [5, 7, 13, 14]. This regulator is part of the gntRKU operon, yet it can also be constitutively expressed as an independent (gntR) transcription unit [1, 8]. Gluconate I is considered the main system for transport of D-gluconate and contains genes that encode high- and low-affinity gluconate transporters [5, 9, 10, 12, 15]. 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 [5, 7, 13, 14]. 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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
GntR Functional   Apo [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
GntR-D-gluconate Non-Functional Allosteric Holo [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
Evolutionary Family: GalR/LacI
TFBs length: 20
TFBs symmetry: inverted-repeat
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
 


Regulon       
Regulated gene(s) eda, edd, gntK, gntT, gntU, idnD, idnK, idnO, idnR, idnT, nfuA, yhgH
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, idnDOTR, idnK, yhgH-nfuA
First gene in the operon(s) edd, gntK, gntT, yhgH, 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 regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  GntR repressor eddp Sigma70 -93.5 -202.5 edd, eda
tcctttatggTTATTTTACCGGTAACATGAtcttgcgcag
 1934797 1934816 [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [4], [5], [6]
  GntR repressor eddp Sigma70 128.5 19.5 edd, eda
tatgaatccaCAATTGTTACGCGTAACAAAtcgaatcatt
 1934576 1934595 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [4], [5]
  GntR repressor gntKp Sigma70 2.5 -51.5 gntK, gntU
tccggctggaCAATGTTACCGATAACAGTTacccgtaaca
 3577634 3577653 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [3], [5], [6], [7], [7], [8]
  GntR repressor gntKp Sigma70 15.5 -38.5 gntK, gntU
tgttaccgatAACAGTTACCCGTAACATTTttaattcttg
 3577621 3577640 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5], [6], [7], [7]
  GntR repressor gntTp1 Sigma70 -14.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
 3546381 3546400 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [9], [9], [10], [10], [11], [11]
  GntR repressor gntTp1 Sigma70 127.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
 3546522 3546541 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [10], [10], [11], [11]
  GntR repressor gntTp2 nd -55.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
 3546381 3546400 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [9], [9], [10], [10], [11], [11]
  GntR repressor gntTp2 nd 86.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
 3546522 3546541 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [10], [10], [11], [11]
  GntR repressor gntTp3 nd -58.5 -168.5 gntT
ctcaaacgccAGATGTTACCCGTATCATTCacatgggtac
 3546381 3546400 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [9], [9], [10], [10], [11], [11]
  GntR repressor gntTp3 nd 83.5 -27.5 gntT
gtcagaaaatTGACGTTACCCATAACAAATgaaaggccag
 3546522 3546541 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-TAS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-TAS] C [3], [5], [6], [10], [10], [11], [11]
  GntR repressor gntXp Sigma70 -15.0 -230.0 yhgH, nfuA
ctgttgcagcACGGCTTCGGCCATATCAGCaagtgacagc
 3544642 3544661 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [12]
  GntR repressor idnDp nd -108.5 -137.5 idnD, idnO, idnT, idnR
cacgttttttTATTTCTACTGATAAGAATTacaaggcaca
 4494534 4494553 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6], [13], [13]
  GntR repressor idnDp nd -78.5 -107.5 idnD, idnO, idnT, idnR
acaaggcacaTCACGTTATGCGTAACATAGtaatgtaaca
 4494504 4494523 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [5], [6], [13], [13]
  GntR repressor idnDp nd -58.5 -87.5 idnD, idnO, idnT, idnR
cgtaacatagTAATGTAACAATTTTCTGACgtgatcttca
 4494484 4494503 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [13], [13]
  GntR repressor idnKp Sigma70 -103.5 -129.5 idnK
tgaagatcacGTCAGAAAATTGTTACATTActatgttacg
 4494484 4494503 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [13], [13]
  GntR repressor idnKp Sigma70 -83.5 -109.5 idnK
tgttacattaCTATGTTACGCATAACGTGAtgtgccttgt
 4494504 4494523 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [5], [6], [13], [13]
  GntR repressor idnKp Sigma70 -53.5 -79.5 idnK
tgtgccttgtAATTCTTATCAGTAGAAATAaaaaaacgtg
 4494534 4494553 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6], [13], [13]


Alignment and PSSM for GntR TFBSs    

Aligned TFBS of GntR   
  Sequence
  CAGTTACCCGTAACATTTTTAA
  ATGTTACCGGTAAAATAACCAT
  ATGTTACCCGTATCATTCACAT
  ACGTTACCCATAACAAATGAAA
  ACGTTATGCGTAACATAGTAAT
  TTGTTACGCGTAACAAATCGAA
  TTGTAATTCTTATCAGTAGAAA
  CAGAAAATTGTTACATTACTAT
  ACGGCTTCGGCCATATCAGCAA

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

Consensus    
;	consensus.strict             	acGttAccCGTaaCAtaagcAa
;	consensus.strict.rc          	TTGCTTATGTTACGGGTAACGT
;	consensus.IUPAC              	myGttAysSGTaaCAtwwsmAw
;	consensus.IUPAC.rc           	WTKSWWATGTTACSSRTAACRK
;	consensus.regexp             	[ac][ct]GttA[ct][cg][CG]GTaaCAt[at][at][cg][ac]A[at]
;	consensus.regexp.rc          	[AT]T[GT][CG][AT][AT]ATGTTAC[CG][CG][AG]TAAC[AG][GT]

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    

 [EXP-IEP] Inferred from expression pattern

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-TAS] 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] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

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

 [5] 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

 [6] 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

 [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] 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

 [9] 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

 [10] 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

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

 [12] 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

 [13] 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

 [14] 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

 [15] 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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