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BluR DNA-binding transcriptional repressor

Synonyms: BluR
Summary:
BluR is a MerR-like regulator that contains an N-terminal helix-turn-helix DNA-binding region and a ligand-binding region in the C-terminal domain []. BluR functions as a repressor for genes involved in the modulation of biofilm formation and for acid resistance genes [2]. Its expression is strongly induced at low temperatures [2, 4]. BluR is a paralogue of MlrA, and it represses the transcription of the ycgZ-ymgA-ariR-ymgC operon [2, 3]. This operon is transcribed divergently on the opposite strand, under the control of σ38 (RpoS) RNA polymerase [2, 5]. Its gene products are involved in the production of colanic acid, a component of the biofilm matrix, via the Rcs phosphorelay system [6, 7, 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
BluR Functional   [APPH], [HIFS], [IEP] [1], [2]
Evolutionary Family: MerR
Connectivity class: Local Regulator
Gene name: bluR
  Genome position: 1213328-1214059
  Length: 732 bp / 243 aa
Operon name: bluR
TU(s) encoding the TF:
Transcription unit        Promoter
bluR
bluRp


Regulon       
Regulated gene(s) ariR, ycgZ, ymgA, ymgC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
unknown (1)
pH (1)
other (mechanical, nutritional, oxidative stress) (1)
Regulated operon(s) ycgZ-ymgA-ariR-ymgC
First gene in the operon(s) ycgZ
Simple and complex regulons BluR,MarA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[BluR,-](1)


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
  BluR repressor ycgZp Sigma38, Sigma70 -29.5 -66.5 ycgZ, ymgA, ariR, ymgC
atttatcattCTGTACACATATTTCGTACAAgtttgctatt
 1215713 1215733 [BPP], [CV(SM)], [GEA], [SM] [2], [3]


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


Evidence    

 [APPH] Assay of protein purified to homogeneity

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [2] Tschowri N., Busse S., Hengge R., 2009, The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli., Genes Dev 23(4):522-34

 [3] Tschowri N., Lindenberg S., Hengge R., 2012, Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli., Mol Microbiol 85(5):893-906

 [4] White-Ziegler CA, Um S, Pérez NM, Berns AL, Malhowski AJ, Young S, 2008, Low temperature (23 degrees C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12., Microbiology, 2008 Jan

 [5] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [6] Domka J., Lee J., Bansal T., Wood TK., 2007, Temporal gene-expression in Escherichia coli K-12 biofilms., Environ Microbiol 9(2):332-46

 [7] Majdalani N, Gottesman S, 2007, Genetic dissection of signaling through the Rcs phosphorelay., Methods Enzymol, 2007

 [8] Lee J, Page R, García-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W, 2007, Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance., J Mol Biol, 2007 Oct 12

 [9] Attila C, Ueda A, Wood TK, 2009, 5-Fluorouracil reduces biofilm formation in Escherichia coli K-12 through global regulator AriR as an antivirulence compound., Appl Microbiol Biotechnol, 2009 Mar


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