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UxuR DNA-binding transcriptional repressor

Synonyms: UxuR-α-D-galacturonate,α-D-glucuronate, UxuR, UxuR-fructuronate


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
UxuR Functional   Apo [GEA], [IMP] [1]
UxuR-α-D-galacturonate,α-D-glucuronate     nd nd
UxuR-fructuronate Non-Functional Allosteric Holo [GEA], [IMP] [1]
Evolutionary Family: GntR
Connectivity class: Local Regulator
Gene name: uxuR
  Genome position: 4554576-4555349
  Length: 774 bp / 257 aa
Operon name: uxuR
TU(s) encoding the TF:
Transcription unit        Promoter
uxuR
uxuRp


Regulon       
Regulated gene(s) exuR, gntP, lgoR, uidA, uidB, uidC, uxuA, uxuB, uxuR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (6)
Transcription related (2)
repressor (2)
Porters (Uni-, Sym- and Antiporters) (2)
membrane (2)
Read more >
Regulated operon(s) exuR, gntP, lgoR, uidABC, uxuAB, uxuR
First gene in the operon(s) exuR, gntP, lgoR, uidA, uxuA, uxuR
Simple and complex regulons CRP,ExuR,OxyR,UxuR
CRP,ExuR,UxuR
CRP,OxyR,UxuR
CRP,UidR,UxuR
ExuR,UxuR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[UxuR,-](6)


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
  UxuR repressor exuRp2 Sigma70 -193.5 -227.5 exuR
gcagttctggCAGTGTTCGACCTGTTAGgtgcgctggt
3246416 3246433 [HIBSCS] [2], [3]
  UxuR repressor gntPp Sigma70 -130.5 -168.5 gntP
ccgaattctgAAATTGGTTAACCACATCacaagaattt
4551456 4551473 [GEA], [HIBSCS] [1], [4], [5]
  UxuR repressor gntPp Sigma70 -24.5 -62.5 gntP
attcatcgcaACAATGGTTGACCAATTTacataacata
4551350 4551367 [BPP], [GEA], [HIBSCS], [SM] [5], [6]
  UxuR-α-D-galacturonate,α-D-glucuronate repressor lgoRp4 Sigma24 132.5 35.5 lgoR
tttacgccacAATGTGATTAACCAGGTCattgatgata
4595807 4595824 [BPP], [GEA] [7], [8]
  UxuR repressor uidAp nd 28.5 -53.5 uidA, uidB, uidC
gtgcaacacaGAATTGGTTAACTAATCAgattaaaggt
1696116 1696133 [GEA], [HIBSCS] [5], [9], [10], [11]
  UxuR repressor uxuAp Sigma70 -159.5 -277.5 uxuA, uxuB
tatgttatgtAAATTGGTCAACCATTGTtgcgatgaat
4551350 4551367 [BPP], [GEA], [HIBSCS], [SM] [5], [6]
  UxuR repressor uxuAp Sigma70 -53.5 -171.5 uxuA, uxuB
aaattcttgtGATGTGGTTAACCAATTTcagaattcgg
4551456 4551473 [GEA], [HIBSCS] [1], [4], [5], [12]
  UxuR repressor uxuRp Sigma70 -66.5 -184.5 uxuR
ccctacagacTTACTGGTCAATCAAACTgatatttggt
4554383 4554400 [AIBSCS] [13]
  UxuR repressor uxuRp Sigma70 -46.5 -164.5 uxuR
atcaaactgaTATTTGGTTGACCAGTTTtcgttttttt
4554403 4554420 [AIBSCS], [GEA] [5], [12], [13]
  UxuR repressor uxuRp Sigma70 93.5 -25.5 uxuR
atccggcaaaAATTTGATTAACCGCACCtaacggacac
4554542 4554559 [AIBSCS], [GEA] [13]


Alignment and PSSM for UxuR TFBSs    

Aligned TFBS of UxuR   
  Sequence
 

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

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

 [IMP] Inferred from mutant phenotype

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] Ritzenthaler P., Mata-Gilsinger M., 1982, Use of in vitro gene fusions to study the uxuR regulatory gene in Escherichia coli K-12: direction of transcription and regulation of its expression., J Bacteriol. 150(3):1040-7

 [2] Barrett TG., Vaughan Williams CH., 1989, Use of a questionnaire to obtain an alcohol history from those attending an inner city accident and emergency department., Arch Emerg Med. 6(1):34-40

 [3] 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

 [4] 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

 [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] Bates Utz C., Nguyen AB., Smalley DJ., Anderson AB., Conway T., 2004, GntP is the Escherichia coli Fructuronic acid transporter and belongs to the UxuR regulon., J Bacteriol. 186(22):7690-6

 [7] Suvorova IA., Tutukina MN., Ravcheev DA., Rodionov DA., Ozoline ON., Gelfand MS., 2011, Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria., J Bacteriol. 193(15):3956-63

 [8] 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

 [9] Blanco C., 1987, Transcriptional and translational signals of the uidA gene in Escherichia coli K12., Mol Gen Genet. 208(3):490-8

 [10] Blanco C., Mata-Gilsinger M., Ritzenthaler P., 1985, The use of gene fusions to study the expression of uidR, a negative regulatory gene of Escherichia coli K-12., Gene. 36(1-2):159-67

 [11] Blanco C., Ritzenthaler P., Mata-Gilsinger M., 1986, Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression., Genetics. 112(2):173-82

 [12] 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

 [13] 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



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