ParR (PA1799) is the cytoplasmic response regulator of the ParR-ParS two-component system of Pseudomonas aeruginosa. It is a 235-residue OmpR/PhoB-family protein with an N-terminal receiver (REC) domain that accepts a phosphoryl group from its cognate membrane sensor kinase ParS (PA1798) and a C-terminal winged-helix domain that binds promoter DNA. The system senses subinhibitory concentrations of polymyxins and cationic antimicrobial peptides and switches on the arnBCADTEF-ugd operon, which aminoarabinosylates lipid A and so lowers the negative charge of the outer membrane; this is the main route to adaptive resistance to polymyxin B and colistin, and it also raises resistance to aminoglycosides. The ParR regulon is wide and condition-dependent, including both activated genes (the arn operon, mexXY, mexEF-oprN) and repressed genes (notably the porin gene oprD), so ParR acts as both a transcriptional activator and a repressor depending on the promoter.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000156 phosphorelay response regulator activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN000724188 IBD, the OmpR/PhoB response-regulator node. The IBD has ten seeds, including the experimentally characterised E. coli regulators ArcA (P0A9Q1), OmpR (P0AA16) and CpxR (P0AE88). ParR has the receiver domain and sits next to its cognate sensor kinase ParS, so it is inside the clade that inherited the activity. Q9I2U3 appearing in its own WITH/FROM reflects its PseudoCAP experimental row and is expected, not circular. Reason: Sound phylogenetic inference at the right level for this node; the activity is the defining one of the family. Supporting Evidence: PMID:24034668 As is typical of TCST systems, the ParS/ParR system consists of a membrane-bound histidine sensor kinase (ParS) and a cytoplasmic response regulator (ParR). |
| GO:0000156 phosphorelay response regulator activity | IMP PMID:20547815 Adaptive resistance to the "last hope" antibiotics polymyxin... | ACCEPT | Summary: PseudoCAP row, and one of the ten seeds of the GO:0000156 IBD. The cited paper shows that deleting parR abolishes peptide-induced arn expression and adaptive polymyxin resistance. That is a mutant phenotype of the system, not a demonstration that ParR itself accepts a phosphoryl group, so the molecular function is being read off the phenotype plus the domain architecture. The claim is almost certainly correct - receiver domain, winged-helix output domain, cognate kinase encoded next to it - so the row is kept. Reason: Right gene and right activity; deferring to the curator on a claim this well supported by architecture and by the family. The reservation is about the evidence code, recorded as a source defect rather than by changing the action. Supporting Evidence: PMID:20547815 Here we describe the identification and characterization of a novel P. aeruginosa two-component regulator affecting polymyxin-adaptive resistance, ParR-ParS (PA1799-PA1798). |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the receiver and winged-helix domain signatures. ParR is the regulator half of a genuine two-component system. Reason: Correct and informative for this protein; the cognate sensor kinase ParS is encoded immediately upstream. Supporting Evidence: PMID:24034668 As is typical of TCST systems, the ParS/ParR system consists of a membrane-bound histidine sensor kinase (ParS) and a cytoplasmic response regulator (ParR). |
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from a twelve-seed IBD at the same node, seeded by E. coli and other response regulators with demonstrated promoter binding. ParR has the family's winged-helix output domain and controls a large regulon, so the inherited DNA-binding claim holds. Reason: Well-seeded node assertion; consistent with the transcriptome evidence that ParR activates and represses specific operons. Supporting Evidence: PMID:24034668 data from all three studies indicate that ParS/ParR are responsible for the repression of the oprD gene |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the OmpR/PhoB-type winged-helix DNA-binding domain. Agrees with the IBA row on the same term. Reason: Consistent electronic assertion of the same, well-supported claim. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | TOO GENERAL | Summary: Generic DNA binding from the winged-helix signature and a UniRule. True, but the more specific GO:0000976 accepted above entails it. Reason: Uninformative given the accepted cis-regulatory region binding term. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | TOO GENERAL | Summary: UniProt subcellular-location mapping. ParR is the cytoplasmic half of the two-component pair, but GO:0005829 cytosol, accepted below, is part_of cytoplasm and is already asserted for this gene. Reason: True but uninformative - the accepted cytosol row (GO:0005829 part_of GO:0005737) entails it, and cytosol is where a soluble response regulator acts. Supporting Evidence: PMID:24034668 As is typical of TCST systems, the ParS/ParR system consists of a membrane-bound histidine sensor kinase (ParS) and a cytoplasmic response regulator (ParR). |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from a four-seed IBD at the same node (E. coli ArcA, CpxR and PhoB-family members). Soluble response regulators act in the cytosol, and ParR is explicitly described as the cytoplasmic partner of ParS. Reason: Sound for a soluble regulator; this is where its DNA-binding activity acts. Supporting Evidence: PMID:24034668 As is typical of TCST systems, the ParS/ParR system consists of a membrane-bound histidine sensor kinase (ParS) and a cytoplasmic response regulator (ParR). |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 33-seed GO:0006355 IBD at PTN000724188. ParR controls a large regulon in both directions, so the inherited claim is directly borne out in this organism. Reason: Broadly seeded and true of the gene; ParR activates the arn operon and represses oprD. Supporting Evidence: PMID:24034668 quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis revealed that ParR-dependent genes such as arnBCADTEF-ugd, pmrB, pagL and PA1797 are not induced by ParR in the absence of indolicidin, suggesting that the ParS/ParR system regulates gene expression in an environment-dependent manner |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO assertion of the same process claim as the IBA row above. Reason: Consistent with the accepted IBA row and with the organism's own transcriptome data. |
| GO:0032993 protein-DNA complex | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Seven-seed IBD at the same node. The claim restates, as a complex, that the regulator binds promoter DNA; it adds little beyond GO:0000976 but it is not wrong for a DNA-binding response regulator. Reason: True of any promoter-bound transcription factor and as precise as the evidence allows, but peripheral to what this gene does; the informative claims are the DNA binding and the regulation rows. |
| GO:0071073 positive regulation of phospholipid biosynthetic process | IMP PMID:20547815 Adaptive resistance to the "last hope" antibiotics polymyxin... | ACCEPT | Summary: PseudoCAP row from the same paper, capturing ParR-dependent induction of the arnBCADTEF operon. The wording is surprising but the placement is correct - GO:0009245 lipid A biosynthetic process is a descendant of GO:0008654 phospholipid biosynthetic process, and ParR positively regulates the lipid A modification pathway. ParR does not perform the modification itself, which is exactly what a regulation term says. Reason: Correct and as specific as GO currently allows - no regulation term exists for lipid A biosynthesis (checked against go-basic). Not modified, because the available descendants would be wrong, and not marked too general, because no more specific term is asserted anywhere in this review. Supporting Evidence: PMID:20547815 This system was required for activation of the arnBCADTEF LPS modification operon in the presence of subinhibitory concentrations of polymyxin, colistin, or the bovine peptide indolicidin, leading to increased resistance to various polycationic antibiotics, including aminoglycosides. |
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Download this section (compressed HTML)Q: GO has lipid A biosynthetic process (GO:0009245) but no regulation terms under it, so regulators of the arn operon land on positive regulation of phospholipid biosynthetic process. Should a regulation-of-lipid-A-biosynthesis term be requested?
Q: Has phosphotransfer from ParS to ParR, or binding of phospho-ParR to the arn promoter, been shown biochemically? The GO:0000156 annotation currently rests on mutant phenotypes and domain architecture.
Q: ParR represses oprD and activates the arn operon from the same signal. What distinguishes the two promoter architectures?
Experiment: Phosphorylate purified ParR with acetyl phosphate or with the ParS cytoplasmic domain and test binding to the arnB and oprD promoters by EMSA and DNase I footprinting, comparing the phosphorylated and unphosphorylated forms with a receiver-domain aspartate mutant.
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