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UvrY DNA-binding transcriptional activator

Synonyms: UvrY-phosphorylated, UvrY
Summary:
The protein belongs to the LuxR/UhpA family. This regulator participates in controlling several genes involved in the DNA repair system and carbon metabolism. UvrY has been shown to be the cognate response regulator for the BarA sensor protein. UvrY phosphorylated at the conserved Asp54 residue is the active form [1]. Z nucleotides [ZMP (5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5-monophosphate) and/or ZTP (5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5-triphosphate)] can act as direct phosphodonors to UvrY in vivo, activating it in a BarA-independent manner [1]. UvrY requires the presence of IHF for binding to csrB but not csrC [2] The genes regulated by this two-component sytem have yet to be identified. The signal the system responds to is also not known, but may be associated with hydrogen peroxide-mediated stress [5]. However, it has been reported that UvrY is phosphorylated at the transition from the exponential to stationary phase of growth (OD600 1.3) [1]. Only two targets of UvrY were found in a Genomic SELEX screening; they are located upstream of the genes csrB and csrC [6]. 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
UvrY Non-Functional   Apo nd nd nd
UvrY-phosphorylated Functional   Holo nd nd nd
Evolutionary Family: LuxR/UhpA
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: uvrY
  Genome position: 1994703-1995359
  Length: 657 bp / 218 aa
Operon name: uvrYC
TU(s) encoding the TF:
Transcription unit        Promoter
uvrYC
uvrYp2


Regulon       
Regulated gene(s) csrB, csrC, luxS, uhpT, ydeP
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
RNA degradation (1)
posttranscriptional (1)
RNA related (1)
quorum sensing (1)
carbon compounds (1)
Read more >
Regulated operon(s) csrB, csrC, luxS, uhpT, ydeP
First gene in the operon(s) csrB, csrC, luxS, uhpT, ydeP
Simple and complex regulons CRP,UhpA,UvrY
CRP,UvrY
EvgA,H-NS,NagC,NarL,NarP,PhoP,RcsB,UvrY
IHF,UvrY
UvrY
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[UvrY,+](5)


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
  UvrY-phosphorylated activator csrBp Sigma70 -183.0 -183.0 csrB
ccccatctggTTGTGAGAGATCTCTTACAgactctgtag
 2924698 2924716 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]
  UvrY-phosphorylated activator csrCp nd -159.0 -159.0 csrC
ccatacgcttTGTGAGACATTGCCGATAGtctttatgcg
 4050868 4050886 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  UvrY-phosphorylated activator luxSp2 nd nd nd luxS
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  UvrY-phosphorylated activator uhpTp Sigma70 nd nd uhpT
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4]
  UvrY-phosphorylated activator ydePp Sigma70 nd nd ydeP
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [4]


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

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

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


Reference(s)    

 [1] Vazquez-Ciros OJ., Alvarez AF., Georgellis D., 2020, Identification of Z nucleotides as an ancient signal for two-component system activation in bacteria., Proc Natl Acad Sci U S A 117(52):33530-33539

 [2] Zere TR., Vakulskas CA., Leng Y., Pannuri A., Potts AH., Dias R., Tang D., Kolaczkowski B., Georgellis D., Ahmer BM., Romeo T., 2015, Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems., PLoS One 10(12):e0145035

 [3] Mitra A., Herren CD., Patel IR., Coleman A., Mukhopadhyay S., 2016, Integration of AI-2 Based Cell-Cell Signaling with Metabolic Cues in Escherichia coli., PLoS One 11(6):e0157532

 [4] Yoshida M., Ishihama A., Yamamoto K., 2015, Cross talk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system., Genes Cells 20(7):601-12

 [5] Pernestig AK., Melefors O., Georgellis D., 2001, Identification of UvrY as the cognate response regulator for the BarA sensor kinase in Escherichia coli., J Biol Chem 276(1):225-31

 [6] Shimada T., Ogasawara H., Kobayashi I., Kobayashi N., Ishihama A., 2021, Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12., Front Microbiol 12:697803


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