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ExuR DNA-binding transcriptional repressor

Synonyms: ExuR-α-D-galacturonate, α-D-glucuronate, ExuR-α-D-glucuronate, ExuR
Summary:
The "Exuronate" repressor ExuR, is a DNA-binding transcription factor that negatively regulates its own synthesis and represses transcription of the operons involved in transport and catabolism of galacturonate and glucuronate [2, 3, 9, 12, 13, 14] ExuR binds to the exuR regulatory region in the presence of glucuronate and inhibits the expression of exuR. This repression is partially affected by the presence of UxuR, since UxuR is capable of binding to the same regulatory region as ExuR [1] The promoter activity of exuR was increased during cell growth in the presence of glucuronate compared to growth with glucose as a main carbon source. Higher activities were found also in a uxuR mutant strain grown in the presence of glucose as a carbon source. However, this response was not observed in an exuR mutant strain. On the other hand, the promoter activity was increased in a crp mutant strain, independent of whether the carbon source was glucose or glucuronate [1] An exuR mutant strain grew more quickly than the wild-type strain in a medium with glucuronate as a main source of carbon [1] On the other hand, ExuR is similar to UxuR (49% of identity), and apparently both act together and are capable of cross-talk to regulate expression of the uxu operon [3, 9, 10, 15].
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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
ExuR Functional   nd nd nd
ExuR-α-D-galacturonate, α-D-glucuronate Functional   nd nd nd
ExuR-α-D-glucuronate Non-Functional   nd nd nd
Evolutionary Family: GntR
TFBs length: 18
TFBs symmetry: inverted-repeat
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: exuR
  Genome position: 3246652-3247428
  Length: 777 bp / 258 aa
Operon name: exuR
TU(s) encoding the TF:
Transcription unit        Promoter
exuR
exuRp2


Regulon       
Regulated gene(s) exuR, exuT, lgoR, uxaA, uxaB, uxaC, uxuA, uxuB, uxuR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (8)
Transcription related (2)
repressor (2)
regulon (1)
Porters (Uni-, Sym- and Antiporters) (1)
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Regulated operon(s) exuR, exuT, lgoR, uxaB, uxaCA, uxuAB, uxuR
First gene in the operon(s) exuR, exuT, lgoR, uxaB, uxaC, uxuA, uxuR
Simple and complex regulons CRP,DpiA,ExuR
CRP,ExuR
CRP,ExuR,FNR
CRP,ExuR,OxyR,UxuR
CRP,ExuR,UxuR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[ExuR,-](7)


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
  ExuR repressor exuRp2 Sigma70 -193.5 -227.5 exuR
gcagttctggCAGTGTTCGACCTGTTAGgtgcgctggt
 3246416 3246433 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  ExuR repressor exuRp2 Sigma70 -4.5 -38.5 exuR
taaactcgcaAAAGTGGTATAACAAATAtagtctgccg
 3246605 3246622 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [3], [3]
  ExuR repressor exuTp2 nd -143.5 -365.5 exuT
tagatcaataAACGTAGTTAAAAAAATTactctcaaag
 3244850 3244867 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [3], [4]
  ExuR repressor exuTp2 nd -17.5 -239.5 exuT
tcaccttttaAAGTTGTATGACAAGTTAtctttctgcc
 3244976 3244993 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [3], [5], [6]
  ExuR-α-D-galacturonate, α-D-glucuronate repressor lgoRp4 Sigma24 132.5 36.5 lgoR
tttacgccacAATGTGATTAACCAGGTCattgatgata
 4595807 4595824 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [7], [7]
  ExuR repressor uxaBp Sigma70 -146.5 -186.5 uxaB
atttgaatgcAATGTGTTCTACCACTTTatgatccagg
 1610858 1610875 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [5], [8]
  ExuR repressor uxaCp2 Sigma70 -127.5 -243.5 uxaC, uxaA
ggcagaaagaTAACTTGTCATACAACTTtaaaaggtga
 3244976 3244993 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [3], [3], [5], [6]
  ExuR repressor uxaCp2 Sigma70 -25.5 -141.5 uxaC, uxaA
cgcggcctgcAGCGAGATTTACCACTTTgagagtaatt
 3244874 3244891 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  ExuR repressor uxaCp2 Sigma70 -1.5 -117.5 uxaC, uxaA
ctttgagagtAATTTTTTTAACTACGTTtattgatcta
 3244850 3244867 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [3], [4], [4]
  ExuR repressor uxaCp2 Sigma70 54.5 -62.5 uxaC, uxaA
cggactctggAAATTGGTGTGATAACTTtgtcagcatc
 3244795 3244812 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  ExuR repressor uxuAp Sigma70 -159.5 -277.5 uxuA, uxuB
tatgttatgtAAATTGGTCAACCATTGTtgcgatgaat
 4551350 4551367 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [3], [9], [9]
  ExuR repressor uxuAp Sigma70 -53.5 -171.5 uxuA, uxuB
aaattcttgtGATGTGGTTAACCAATTTcagaattcgg
 4551456 4551473 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [9]
  ExuR repressor uxuRp Sigma70 -46.5 -164.5 uxuR
atcaaactgaTATTTGGTTGACCAGTTTtcgttttttt
 4554403 4554420 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [10], [11]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  ExuR-α-D-galacturonate, α-D-glucuronate repressor yjjN Transcription-Unit nd
tatcatcaatGACCTGGTTAATCACATTgtggcgtaaa
4595807 4595824 4595815.5 nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [7]


Alignment and PSSM for ExuR TFBSs    

Aligned TFBS of ExuR   
  Sequence
  AAAGTGGTAGAACACATTGC
  AAACTGGTCAACCAAATATC
  AAATTGGTTAACCACATCAC
  AAAGTGGTATAACAAATATA
  AAAGTGGTAAATCTCGCTGC
  GACCTGGTTAATCACATTGT
  ACAATGGTTGACCAATTTAC
  AACGTAGTTAAAAAAATTAC
  AAAGTTGTATGACAAGTTAT
  AAAGTTATCACACCAATTTC
  TAACAGGTCGAACACTGCCA

Position weight matrix (PWM). ExuR matrix-quality result    
A	9	10	9	1	1	1	1	0	4	6	9	6	1	9	6	7	0	2	4	2
C	0	1	2	3	0	0	0	0	3	0	1	3	10	1	5	0	1	2	1	7
G	1	0	0	6	0	8	10	0	0	3	1	0	0	0	0	2	1	0	3	0
T	1	0	0	1	10	2	0	11	4	2	0	2	0	1	0	2	9	7	3	2

Consensus    
;	consensus.strict             	aAagTGGTcaaaCacattgC
;	consensus.strict.rc          	GCAATGTGTTTGACCACTTT
;	consensus.IUPAC              	aAasTGGThramCamattrC
;	consensus.IUPAC.rc           	GYAATKTGKTYDACCASTTT
;	consensus.regexp             	aAa[cg]TGGT[act][ag]a[ac]Ca[ac]att[ag]C
;	consensus.regexp.rc          	G[CT]AAT[GT]TG[GT]T[CT][AGT]ACCA[CG]TTT

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-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

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

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

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

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


Reference(s)    

 [1] Tutukina MN., Potapova AV., Cole JA., Ozoline ON., 2016, Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation., Microbiology 162(7):1220-31

 [2] Hugovieux-Cotte-Pattat N., Robert-Baudouy J., 1982, Regulation and transcription direction of exuR, a self-regulated repressor in escherichia coli K-12., J Mol Biol 156(1):221-8

 [3] 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

 [4] Medina-Rivera A., Abreu-Goodger C., Thomas-Chollier M., Salgado H., Collado-Vides J., van Helden J., 2011, Theoretical and empirical quality assessment of transcription factor-binding motifs., Nucleic Acids Res 39(3):808-24

 [5] Mata-Gilsinger M., Ritzenthaler P., Blanco C., 1983, Characterization of the operator sites of the exu regulon in Escherichia coli K-12 by operator-constitutive mutations and repressor titration., Genetics 105(4):829-42

 [6] 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

 [7] Tutukina MN., Potapova AV., Vlasov PK., Purtov YA., Ozoline ON., 2016, Structural modeling of the ExuR and UxuR transcription factors of E. coli: search for the ligands affecting their regulatory properties., J Biomol Struct Dyn :1-9

 [8] Blanco C., Mata-Gilsinger M., Ritzenthaler P., 1983, Construction of hybrid plasmids containing the Escherichia coli uxaB gene: analysis of its regulation and direction of transcription., J Bacteriol 153(2):747-55

 [9] Robert-Baudouy J., Portalier R., Stoeber F., 1981, Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products., J Bacteriol 145(1):211-20

 [10] Ritzenthaler P., Blanco C., Mata-Gilsinger M., 1985, Genetic analysis of uxuR and exuR genes: evidence for ExuR and UxuR monomer repressors interactions., Mol Gen Genet 199(3):507-11

 [11] Ritzenthaler P., Mata-Gilsinger M., 1983, Multiple regulation involved in the expression of the uxuR regulatory gene in Escherichia coli K-12., Mol Gen Genet 189(2):351-4

 [12] Ritzenthaler P., Mata-Gilsinger M., Stoeber F., 1981, Molecular cloning of Escherichia coli K-12 hexuronate system genes: exu region., J Bacteriol 145(1):181-90

 [13] Hugouvieux-Cotte-Pattat N, Robert-Baudouy J, 1981, Isolation of fusions between the lac genes and several genes of the exu regulon: analysis of their regulation, determination of the transcription direction of the uxaC-uxaA operon, in Escherichia coli K-12., Mol Gen Genet, 182(2):279 10.1007/BF00269671

 [14] Nemoz G., Robert-Baudouy J., Stoeber F., 1976, Physiological and genetic regulation of the aldohexuronate transport system in Escherichia coli., J Bacteriol 127(2):706-18

 [15] Ritzenthaler P, Blanco C, Mata-Gilsinger M, 1983, Interchangeability of repressors for the control of the uxu and uid operons in E. coli K12., Mol Gen Genet, 191(2):263 10.1007/BF00334824


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