RegulonDB RegulonDB 10.10:Regulon Page

UxuR DNA-binding transcriptional repressor

Synonyms: UxuR, UxuR-D-fructuronate, UxuR-α-D-glucuronate-α-D-galacturonate
The "hexuronate regulator," UxuR, is a transcriptional factor. This protein negatively regulates its own synthesis, and in the absence of fructuronate it represses transcription of the cluster of operons involved in transport and degradation of the sugar acids β-D-glucuronides, glucuronate, and gluconate [1, 3, 4, 10, 11]. This regulator is subject to catabolic repression in the presence of glucose and at low levels of cyclic AMP. Although little is known about the regulating mechanism of UxuR, it has been shown to act as a repressor, binding to a putative inverted repeat sequence from the uid operon in a cooperative process with UidR [7, 12, 13]. In 1986, Blanco et al. proposed that total repression of UxuR is achieved in the presence of UidR, suggesting the possibility that UxuR and UidR form a complex. Independently, each repressor binds to DNA separately [7, 13, 14]. On the other hand, UxuR is highly similar to ExuR (49% identity), and apparently both act together and are capable of cross talk to regulate expression of the uxuR regulon [10].
Read more >

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-glucuronate-α-D-galacturonate Non-Functional   Holo nd nd
UxuR-D-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

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
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  UxuR repressor exuRp2 Sigma70 -193.5 -227.5 exuR
3246416 3246433 [GEA], [APIORCISFBSCS], [BPP] [2]
  UxuR repressor gntPp Sigma70 -130.5 -168.5 gntP
4551456 4551473 [GEA], [APIORCISFBSCS] [1], [3]
  UxuR repressor gntPp Sigma70 -24.5 -62.5 gntP
4551350 4551367 [GEA], [APIORCISFBSCS], [BPP], [SM] [4]
  UxuR repressor lgoRp4 Sigma24 132.5 36.5 lgoR
4595807 4595824 [GEA], [BPP] [5]
  UxuR repressor uidAp nd 28.5 -53.5 uidA, uidB, uidC
1696116 1696133 [GEA], [APIORCISFBSCS] [6], [7]
  UxuR repressor uxuAp Sigma70 -159.5 -277.5 uxuA, uxuB
4551350 4551367 [GEA], [APIORCISFBSCS], [BPP], [SM] [4]
  UxuR repressor uxuAp Sigma70 -53.5 -171.5 uxuA, uxuB
4551456 4551473 [GEA], [APIORCISFBSCS] [1], [3], [8]
  UxuR repressor uxuRp Sigma70 -66.5 -184.5 uxuR
4554383 4554400 [AIBSCS] [9]
  UxuR repressor uxuRp Sigma70 -46.5 -164.5 uxuR
4554403 4554420 [GEA], [AIBSCS] [8], [9]
  UxuR repressor uxuRp Sigma70 93.5 -25.5 uxuR
4554542 4554559 [GEA], [AIBSCS] [9]

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 (Confirmed, Strong, Weak) References
  UxuR repressor yjjN Transcription-Unit -174.5
4595807 4595824 4595815.5 nd [GEA], [BPP] [5]

Alignment and PSSM for UxuR TFBSs    

Aligned TFBS of UxuR   

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

;	consensus.strict             	agTGGTcAACCAaattggtGc
;	consensus.strict.rc          	GCACCAATTTGGTTGACCACT
;	consensus.IUPAC              	asTGGTyAAYCAawttkgkGy
;	consensus.IUPAC.rc           	RCMCMAAWTTGRTTRACCAST
;	consensus.regexp             	a[cg]TGGT[ct]AA[CT]CAa[at]tt[gt]g[gt]G[ct]
;	consensus.regexp.rc          	[AG]C[AC]C[AC]AA[AT]TTG[AG]TT[AG]ACCA[CG]T

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


 [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] 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] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] Blanco C., Ritzenthaler P., Kolb A., 1986, The regulatory region of the uxuAB operon in Escherichia coli K12., Mol Gen Genet 202(1):112-9

 [12] 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

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

 [14] Blanco C, Ritzenthaler P, Mata-Gilsinger M, 1985, Nucleotide sequence of a regulatory region of the uidA gene in Escherichia coli K12., Mol Gen Genet, 199(1):101 10.1007/BF00327517