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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 |CITS:[23301696]|.
PgrR negatively controls ycjY-ymjD-ymjC-mpaA operon expression and binds to the palindromic sequence ATCATTT-AAATGAT |CITS:[23301696]|. 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 |CITS:[23301696]|.
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 |CITS:[23301696]|.
PgrR, Peptide glycan recycling Regulator.
A ycjZ mutant shows a defect in swarming motility, but no defect in swimming motility |CITS: [17122336]|.


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PgrR     nd nd
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)
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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 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 nd tyrR nd nd [BPP], [GEA], [IGI] [1]
  PgrR repressor ycjGp nd nd nd ycjG nd nd [BPP], [GEA], [IGI] [1]
  PgrR repressor ycjXp Sigma32 nd nd ycjX, ycjF, tyrR nd nd [BPP], [GEA], [IGI] [1]
  PgrR repressor ycjYp6 Sigma32 113.5 -106.5 ycjY, ymjD, ymjC, mpaA
caatctattaATCATTTAAATGATaggtctaatc
1391953 1391966 [BPP], [GEA], [IGI] [1], [2]


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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction



Reference(s)    

 [1] 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)

 [2] 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



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