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Zur DNA-binding transcriptional repressor

Synonyms: Zur, Zur-Zn2+
Summary:
Zur, "zinc uptake regulator," regulates genes involved in the Zn2+ ABC transporter uptake system and genes involved in the expression of alternative ribosomal proteins [2, 5, 9] The active conformation of Zur is observed when it is in a reduced form and when it is bound to Zn(II). The oxidized form of Zur does not bind to DNA or zinc. [2, 9, 12] Zur is not autoregulated [12] Zur, which belongs to the Fur family [9], appears to have a DNA-binding site in the N-terminal domain, around residue 65, and a signal-recognition site in the C-terminal domain. This protein has two Zn(II)-binding sites: site A, which only binds to Zn(II), and site B (the sensor site), which binds to Zn(II) and Co(II) with high and low affinities, respectively [1] Zur is able to form dimers, even in the absence of zinc [2]. The 23-bp palindrome consensus sequence for Zur-binding sites of gamma-proteobacteria, including Escherichia coli, has been determined by computational analysis [5] The thermodynamic profile of Zur-DNA interactions directly correlates with the physiological response at different promoters [11] Tyr45 and Arg65 interactions with Zur-box purines define the recognition motif [11] Zurs unbinding rate from DNA is sensitive to Zur concentration in a biphasic way; this was the first reporting of such a biphasic manner [13] These kinds of mechanisms could facilitate transcription switching between repression and derepression [13] A zur mutant enhanced cell survival when cells were exposed to biocides [14]. Read more >


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
Zur Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1], [2]
Zur-Zn2+ Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1], [2]
Evolutionary Family: Fur
TFBs length: 23
Connectivity class: Local Regulator
Gene name: zur
  Genome position: 4259488-4260003
  Length: 516 bp / 171 aa
Operon name: zur
TU(s) encoding the TF:
Transcription unit        Promoter
zur
 


Regulon       
Regulated gene(s) ykgM, ykgO, zinT, znuA, znuB, znuC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
ribosomal proteins (2)
adaptations (2)
ABC superfamily, periplasmic binding component (1)
ABC superfamily, membrane component (1)
membrane (1)
Read more >
Regulated operon(s) ykgMO, zinT, znuA, znuCB
First gene in the operon(s) ykgM, zinT, znuA, znuC
Simple and complex regulons Fur,OxyR,SoxS,Zur
OxyR,Zur
Zur
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Zur,-](4)


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
  Zur-Zn2+ repressor ykgMp Sigma70 11.0 -18.0 ykgM, ykgO
gtatctttatGGTTATGTTATAACATAACAGGTAaaaatgatga
 312784 312807 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX] S [3], [4], [4], [5], [5], [6], [7]
  Zur-Zn2+ repressor zinTp Sigma70 -16.0 -45.0 zinT
tgcattttgcTATATGTTACAATATAACATTACacatcatata
 2041319 2041341 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5], [5]
  Zur-Zn2+ repressor znuAp Sigma38 38.0 -41.0 znuA
gcagtagtcaTGAAATGTTATAATATCACACTTCtcatattcat
 1942613 1942636 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [8], [8], [9], [10], [10]
  Zur-Zn2+ repressor znuCp Sigma70 -10.0 -38.0 znuC, znuB
atgaatatgaGAAGTGTGATATTATAACATTTCAtgactactgc
 1942613 1942636 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [8], [8], [9], [10]



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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  Zur-Zn2+ repressor pliG Transcription-Unit nd
gttcagaatgAGTACGATGAACTGTTATAATATAacaatcccta
1227495 1227518 1227506.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]


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


Evidence    

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

 [EXP-IPI] Inferred from physical interaction

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Outten CE., Tobin DA., Penner-Hahn JE., O'Halloran TV., 2001, Characterization of the metal receptor sites in Escherichia coli Zur, an ultrasensitive zinc(II) metalloregulatory protein., Biochemistry 40(35):10417-23

 [2] Patzer SI., Hantke K., 2000, The zinc-responsive regulator Zur and its control of the znu gene cluster encoding the ZnuABC zinc uptake system in Escherichia coli., J Biol Chem 275(32):24321-32

 [3] Aseev LV., Koledinskaya LS., Boni IV., 2020, Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b., RNA 26(7):814-826

 [4] Hemm MR., Paul BJ., Miranda-Rios J., Zhang A., Soltanzad N., Storz G., 2010, Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies., J Bacteriol 192(1):46-58

 [5] Panina EM., Mironov AA., Gelfand MS., 2003, Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins., Proc Natl Acad Sci U S A 100(17):9912-7

 [6] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [7] Ishihama A, Shimada T, Yamazaki Y, 2016, Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors., Nucleic Acids Res, 44(5):2058 10.1093/nar/gkw051

 [8] Outten CE., O'Halloran TV., 2001, Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis., Science 292(5526):2488-92

 [9] Patzer SI., Hantke K., 1998, The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli., Mol Microbiol 28(6):1199-210

 [10] Warner DM., Levy SB., 2012, SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model., J Bacteriol 194(5):1177-85

 [11] Gilston BA., Wang S., Marcus MD., Canalizo-Hernandez MA., Swindell EP., Xue Y., Mondragon A., O'Halloran TV., 2014, Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon., PLoS Biol 12(11):e1001987

 [12] Hantke K., 2002, Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein., J Mol Microbiol Biotechnol 4(3):217-22

 [13] Jung W, Sengupta K, Wendel BM, Helmann JD, Chen P, 2020, Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria., Nucleic Acids Res, 48(5):2199 10.1093/nar/gkaa056

 [14] Merchel Piovesan Pereira B, Wang X, Tagkopoulos I, 2020, Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis., Appl Environ Microbiol, 86(14):None 10.1128/AEM.00708-20


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