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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 [3, 4, 8, 11, 12] 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 [2] 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 [2] An exuR mutant strain grew more quickly than the wild-type strain in a medium with glucuronate as a main source of carbon [2] 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 [4, 8, 9].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
ExuR Functional   [IE] [1]
ExuR-α-D-galacturonate, α-D-glucuronate Functional   nd nd
ExuR-α-D-glucuronate Non-Functional   nd nd
Evolutionary Family: GntR
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 (Confirmed, Strong, Weak) References
  ExuR repressor exuRp2 Sigma70 -193.5 -227.5 exuR
gcagttctggCAGTGTTCGACCTGTTAGgtgcgctggt
3246416 3246433 [BPP], [GEA], [HIBSCS] [2]
  ExuR repressor exuRp2 Sigma70 -4.5 -38.5 exuR
taaactcgcaAAAGTGGTATAACAAATAtagtctgccg
3246605 3246622 [BPP], [GEA], [HIBSCS] [2], [3], [4]
  ExuR repressor exuTp2 nd -143.5 -365.5 exuT
ctttgagagtAATTTTTTTAACTACGTTtattgatcta
3244850 3244867 [AIBSCS] [4], [5]
  ExuR repressor exuTp2 nd -17.5 -239.5 exuT
ggcagaaagaTAACTTGTCATACAACTTtaaaaggtga
3244976 3244993 [AIBSCS], [GEA] [1], [4]
  ExuR-α-D-galacturonate, α-D-glucuronate repressor lgoRp4 Sigma24 132.5 35.5 lgoR
tttacgccacAATGTGATTAACCAGGTCattgatgata
4595807 4595824 [BPP] [6]
  ExuR repressor uxaBp Sigma70 -146.5 -186.5 uxaB
cctggatcatAAAGTGGTAGAACACATTgcattcaaat
1610858 1610875 [GEA], [HIBSCS] [1], [4], [7]
  ExuR repressor uxaCp Sigma70 -127.5 -243.5 uxaC, uxaA
tcaccttttaAAGTTGTATGACAAGTTAtctttctgcc
3244976 3244993 [AIBSCS], [GEA] [1], [4]
  ExuR repressor uxaCp Sigma70 -25.5 -141.5 uxaC, uxaA
aattactctcAAAGTGGTAAATCTCGCTgcaggccgcg
3244874 3244891 [AIBSCS] [5]
  ExuR repressor uxaCp Sigma70 -1.5 -117.5 uxaC, uxaA
tagatcaataAACGTAGTTAAAAAAATTactctcaaag
3244850 3244867 [AIBSCS] [4], [5]
  ExuR repressor uxaCp Sigma70 54.5 -62.5 uxaC, uxaA
gatgctgacaAAGTTATCACACCAATTTccagagtccg
3244795 3244812 [AIBSCS] [5]
  ExuR repressor uxuAp Sigma70 -159.5 -277.5 uxuA, uxuB
tatgttatgtAAATTGGTCAACCATTGTtgcgatgaat
4551350 4551367 [GEA] [4], [8]
  ExuR repressor uxuAp Sigma70 -53.5 -171.5 uxuA, uxuB
aaattcttgtGATGTGGTTAACCAATTTcagaattcgg
4551456 4551473 [GEA], [HIBSCS] [4], [8]
  ExuR repressor uxuRp Sigma70 -46.5 -164.5 uxuR
atcaaactgaTATTTGGTTGACCAGTTTtcgttttttt
4554403 4554420 [AIBSCS], [GEA] [4], [9], [10]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  ExuR-α-D-galacturonate, α-D-glucuronate repressor lgoD nd nd 4595807 4595824 [AISGDTU] nd


Alignment and PSSM for ExuR TFBSs    

Aligned TFBS of ExuR   
  Sequence
  ATGTGTTCTACCACTTT
  ATTGGTGTGATAACTTT
  ATTTTTTTAACTACGTT
  GCGAGATTTACCACTTT
  ACTTGTCATACAACTTT
  ATTTGTTATACCACTTT
  CAATGGTTGACCAATTT
  ATGTGGTTAACCAATTT
  ATTTGGTTGACCAGTTT

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

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    

 [IE] Inferred from experiment

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AISGDTU] Automated inference that a single-gene directon is a transcription unit



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [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] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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



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