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PgrR DNA-binding transcriptional repressor

Synonyms: PgrR
Summary:
Based on analysis with the Genomic SELEX screening system, PgrR was identified as a repressor of the expression of genes of the initial enzymes for peptidoglycan (PG) peptide degradation as well as genes of the switch control between recycling and degradation of PG peptides, which are induced upon exposure to heat shock or membrane distortion [3] PgrR negatively controls ycjY-ymjD-ymjC-mpaA operon expression and binds to the palindromic sequence ATCATTT-AAATGAT [3] Both the pgrR and ycjY promoters are recognized by RpoH (σ32) and RpoE (σ24), both of which are involved in the heat shock response, and by FecI (σ19), which is involved in the response to extracytoplasmic stimuli [3] Eleven possible targets were predicted to be under PgrR control. These targets were identified by Genomic SELEX analysis and include genes related to membrane formation and function: leuL, leuO, pheP, ycjY, pgrR, yedS, xapR, yfgF, yfgG, rfaL, and rfaS [3] PgrR, Peptide glycan recycling Regulator. A ycjZ mutant shows a defect in swarming motility, but no defect in swimming motility [5]. Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PgrR Functional   [APPPINH], [HIFS] [1], [2], [3]
Evolutionary Family: LysR
Connectivity class: Local Regulator
Gene name: pgrR
  Genome position: 1391991-1392890
  Length: 900 bp / 299 aa
Operon name: pgrR
TU(s) encoding the TF:
Transcription unit        Promoter
pgrR
null


Regulon       
Regulated gene(s) mpaA, tyrR, ycjF, ycjG, ycjX, ycjY, ymjC, ymjD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
proteins/peptides/glycopeptides (1)
murein (1)
Transcription related (1)
activator (1)
repressor (1)
Read more >
Regulated operon(s) ycjG, ycjXF-tyrR, ycjY-ymjDC-mpaA
First gene in the operon(s) tyrR, ycjG, ycjX, ycjY, ycjY
Simple and complex regulons PgrR
PgrR,TyrR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PgrR,-](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
  PgrR repressor tyrRp Sigma70 nd -1386720.0 tyrR nd nd [BPP], [GEA], [IGI] [4]
  PgrR repressor ycjGp nd nd -1388930.0 ycjG nd nd [BPP], [GEA], [IGI] [4]
  PgrR repressor ycjXp Sigma32 nd -1384117.0 ycjX, ycjF, tyrR nd nd [BPP], [GEA], [IGI] [4]
  PgrR repressor ycjYp6 Sigma32 113.5 -107.0 ycjY, ymjD, ymjC, mpaA
gattagacctATCATTTAAATGATtaatagattg
1391953 1391967 [BPP], [GEA], [IGI] [3], [4]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  PgrR repressor mpaA nd nd nd nd [IC], [LTED] [3]
  PgrR repressor mppA nd nd nd nd [ICWHO] nd
Other High-throughput regulatory interactions with weak evidence


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


Evidence    

 [APPPINH] Assay of protein partially-purified from its native host

 [HIFS] Human inference of function from sequence

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction

 [IC] Inferred by curator

 [LTED] Length of transcript experimentally determined

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [2] 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

 [3] Shimada T., Yamazaki K., Ishihama A., 2013, Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli., Genes Cells 18(2):123-34

 [4] Choi U., Park YH., Kim YR., Seok YJ., Lee CR., 2016, Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli., FEMS Microbiol Lett 363(14)

 [5] Inoue T., Shingaki R., Hirose S., Waki K., Mori H., Fukui K., 2007, Genome-wide screening of genes required for swarming motility in Escherichia coli K-12., J Bacteriol 189(3):950-7



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