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ZraR DNA-binding transcriptional activator

Synonyms: ZraR-phosphorylated, ZraR
Summary:
ZraR, "zinc resistance-associated regulator," controls the expression of genes involved in tolerance to high zinc concentrations. Based on chromatin immunoprecipitation followed by sequencing (ChIp-Seq) and RT-qPCR, 25 new genes regulated by ZraR were identified. The genes encode proteins of diverse functions that may be critical to maintain envelope integrity and cell survival under stressful conditions; they are mostly involved in the response against stress [2]. The genes of the ZraR regulon are also involved in replication and protein synthesis [2].The protein ZraR also appears to be involved in palladium ion reduction [3]. This regulator is a member of the two-component regulatory system ZraS/ZraR. The operon contains both genes zraR, which encodes the response regulator, and zraS, which encodes the sensor kinase, and is located next to and in the opposite direction to zraP, a gene regulated by ZraR. It has been suggested that ZraS functions as a zinc receptor [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
ZraR Non-Functional   Apo nd nd
ZraR-phosphorylated Functional Covalent Holo nd nd
Evolutionary Family: EBP
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: zraR
  Genome position: 4203320-4204645
  Length: 1326 bp / 441 aa
Operon name: zraSR
TU(s) encoding the TF:
Transcription unit        Promoter
zraSR
zraSp


Regulon       
Regulated gene(s) zraP, zraR, zraS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
fermentation (2)
two component regulatory systems (external signal) (2)
osmotic pressure (1)
pH (1)
protection (1)
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Regulated operon(s) zraP, zraSR
First gene in the operon(s) zraP, zraS
Simple and complex regulons CRP,ZraR
ZraR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[ZraR,+](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 (Confirmed, Strong, Weak) References
  ZraR-phosphorylated activator zraPp Sigma54 -107.0 -131.0 zraP
aagtttcaatGAGTAAAAATGACTCGCtacccgcagc
 4201811 4201827 [GEA], [BPP] [1]
  ZraR-phosphorylated activator zraPp Sigma54 -78.0 -102.0 zraP
cccgcagcagGCGAGTCATTTTTACTCgtttatcatg
 4201782 4201798 [GEA], [APIORCISFBSCS], [BPP] [1]
  ZraR-phosphorylated activator zraSp Sigma54 -115.0 -136.0 zraS, zraR
catgataaacGAGTAAAAATGACTCGCctgctgcggg
 4201782 4201798 [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] [1]
  ZraR-phosphorylated activator zraSp Sigma54 -86.0 -107.0 zraS, zraR
gctgcgggtaGCGAGTCATTTTTACTCattgaaactt
 4201811 4201827 [GEA], [BPP] [1]



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
  ZraR-phosphorylated activator yjjY Transcription-Unit -162.5
tcatagccttCCGCTTCGAAAATACTTTtcaacgtgtt
4640231 4640249 4640239.5 nd [IEP], [CSE], [ICWHO] [2]
  ZraR-phosphorylated activator cspB Transcription-Unit -98.5
agttctcattTCAGGTGTTATTCACTTAttccttcttt
1641644 1641662 1641652.5 nd [IEP], [CSE], [ICWHO] [2]
  ZraR-phosphorylated activator yrdD-rimN-aroE-yrdB Transcription-Unit -34.5
agtgaatgaaGGTATGCTGCATTAATCAtttctttaat
3431988 3432006 3431996.5 nd [IEP], [CSE], [ICWHO] [2]


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


Evidence    

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [IEP] Inferred from expression pattern

 [CSE] ChIP-seq evidence

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Leonhartsberger S., Huber A., Lottspeich F., Bock A., 2001, The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system., J Mol Biol 307(1):93-105

 [2] Rome K., Borde C., Taher R., Cayron J., Lesterlin C., Gueguen E., De Rosny E., Rodrigue A., 2018, The Two-Component System ZraPSR Is a Novel ESR that Contributes to Intrinsic Antibiotic Tolerance in Escherichia coli., J Mol Biol 430(24):4971-4985

 [3] Matsumoto T, Kamino M, Yamada R, Konishi Y, Ogino H, 2020, Identification of genes responsible for reducing palladium ion in Escherichia coli., J Biotechnol, 324(None):7 10.1016/j.jbiotec.2020.09.015

 [4] Stoker K., Reijnders WN., Oltmann LF., Stouthamer AH., 1989, Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12., J Bacteriol 171(8):4448-56

 [5] Sallai L, Tucker PA, 2005, Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR., J Struct Biol, 151(2):160 10.1016/j.jsb.2005.05.006

 [6] Naughtin M, Haftek-Terreau Z, Xavier J, Meyer S, Silvain M, Jaszczyszyn Y, Levy N, Miele V, Benleulmi MS, Ruff M, Parissi V, Vaillant C, Lavigne M, 2015, DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity., PLoS One, 10(6):e0129427 10.1371/journal.pone.0129427

 [7] Sevier SA, Levine H, 2018, Properties of gene expression and chromatin structure with mechanically regulated elongation., Nucleic Acids Res, 46(12):5924 10.1093/nar/gky382

 [8] Lee LJ., Barrett JA., Poole RK., 2005, Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc., J Bacteriol 187(3):1124-34

 [9] Mendez-Ortiz MM., Hyodo M., Hayakawa Y., Membrillo-Hernandez J., 2006, Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid., J Biol Chem 281(12):8090-9


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