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PuuR DNA-binding transcriptional repressor

Synonyms: PuuR-putrescine, PuuR
Summary:
PuuR is a transcription repressor that regulates transcription of several genes and operons involved in putrescine utilization and transport [3, 4] Transcription of puuA was induced in a puuR deletion mutant [1]. This regulator is comprised of two domains: the carboxy-terminal domain, which is similar to cupin superfamily proteins, and the amino-terminal domain, which has high similarity to regulators of the HTH-XRE family [3] Nemoto et al. showed that this regulator binds to four target sites in the divergent region located between the operons puuA and puuDR. Its regulator represses transcription by overlapping the promoters puuAp and puuDp, and the binding targets for PuuR consist of 15 nucleotides, with the following recognition sequence: AAAATATAATGAACA [3] The transcription of the puu genes occurs when putrescine interacts with PuuR; this effect changes the conformation of PuuR, and its regulator dissociates from the binding sites.
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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
PuuR Functional   Apo nd nd nd
PuuR-putrescine Non-Functional   Holo nd nd nd
Evolutionary Family: HTH_3
TFBs length: 20
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: puuR
  Genome position: 1361911-1362468
  Length: 558 bp / 185 aa
Operon name: puuDRCBE
TU(s) encoding the TF:
Transcription unit        Promoter
puuDRCBE
puuDp


Regulon       
Regulated gene(s) puuA, puuB, puuC, puuD, puuE, puuP, puuR, ymjE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amines (5)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
transcriptional level (1)
Regulated operon(s) puuA-ymjE-puuP, puuDRCBE
First gene in the operon(s) puuA, puuD
Simple and complex regulons ArcA,CRP,PuuR
ArcA,FNR,PuuR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PuuR,-](2)


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
  PuuR repressor puuAp Sigma38 -161.5 -221.5 puuA, ymjE, puuP
gataaccggaTTGTTCATTATATTTTCCATgctcaatctc
 1361120 1361139 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]
  PuuR repressor puuAp Sigma38 -126.5 -186.5 puuA, ymjE, puuP
atctcacaaaGTGGACTAAATTATCGCCATtactgcgctt
 1361085 1361104 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] C [1], [2], [3], [3]
  PuuR repressor puuAp Sigma38 -84.5 -144.5 puuA, ymjE, puuP
aatgacctttATGTTCAATATTTTTTCAATctagcagtgg
 1361043 1361062 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]
  PuuR repressor puuAp Sigma38 11.5 -49.5 puuA, ymjE, puuP
gattcgaatgGTGGTCATTATATTTTACGCtttgataacg
 1360948 1360967 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]
  PuuR repressor puuDp Sigma38 -94.5 -162.5 puuD, puuR, puuC, puuB, puuE
cgttatcaaaGCGTAAAATATAATGACCACcattcgaatc
 1360948 1360967 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]
  PuuR repressor puuDp Sigma38 1.5 -67.5 puuD, puuR, puuC, puuB, puuE
ccactgctagATTGAAAAAATATTGAACATaaaggtcatt
 1361043 1361062 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]
  PuuR repressor puuDp Sigma38 43.5 -25.5 puuD, puuR, puuC, puuB, puuE
aagcgcagtaATGGCGATAATTTAGTCCACtttgtgagat
 1361085 1361104 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] C [1], [2], [3], [3]
  PuuR repressor puuDp Sigma38 78.5 10.5 puuD, puuR, puuC, puuB, puuE
gagattgagcATGGAAAATATAATGAACAAtccggttatc
 1361120 1361139 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] S [1], [2], [3], [3]


Alignment and PSSM for PuuR TFBSs    

Aligned TFBS of PuuR   
  Sequence
  AGCATGGAAAATATAATGAACA
  AAAGCGTAAAATATAATGACCA
  AAAGTGGACTAAATTATCGCCA
  TAGATTGAAAAAATATTGAACA

Position weight matrix (PWM). PuuR matrix-quality result    
A	3	3	2	2	0	0	0	4	3	3	4	2	4	0	3	3	0	0	3	2	0	4
C	0	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	2	4	0
G	0	1	1	2	0	3	3	0	0	0	0	0	0	0	0	0	0	3	1	0	0	0
T	1	0	0	0	3	1	1	0	0	1	0	2	0	4	1	1	4	0	0	0	0	0

Consensus    
;	consensus.strict             	aaagtGGAaaAaATaaTGacCA
;	consensus.strict.rc          	TGGTCATTATTTTTTCCACTTT
;	consensus.IUPAC              	arvryGGAmaAwATaaTSrmCA
;	consensus.IUPAC.rc           	TGKYSATTATWTTKTCCRYBYT
;	consensus.regexp             	a[ag][acg][ag][ct]GGA[ac]aA[at]ATaaT[CG][ag][ac]CA
;	consensus.regexp.rc          	TG[GT][CT][CG]ATTAT[AT]TT[GT]TCC[AG][CT][CGT][CT]T

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

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

 [IC] Inferred by curator

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Kurihara S., Oda S., Tsuboi Y., Kim HG., Oshida M., Kumagai H., Suzuki H., 2008, gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12., J Biol Chem 283(29):19981-90

 [2] Kurihara S., Tsuboi Y., Oda S., Kim HG., Kumagai H., Suzuki H., 2009, The putrescine Importer PuuP of Escherichia coli K-12., J Bacteriol 191(8):2776-82

 [3] Nemoto N., Kurihara S., Kitahara Y., Asada K., Kato K., Suzuki H., 2012, Mechanism for regulation of the putrescine utilization pathway by the transcription factor PuuR in Escherichia coli K-12., J Bacteriol 194(13):3437-47

 [4] Kurihara S., Oda S., Kato K., Kim HG., Koyanagi T., Kumagai H., Suzuki H., 2005, A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12., J Biol Chem 280(6):4602-8


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