PtxS (PA2259) is a LacI/GalR-family transcriptional repressor of Pseudomonas aeruginosa that controls 2-ketogluconate catabolism and modulates exotoxin A expression. It carries an N-terminal lacI-type helix-turn-helix domain and a C-terminal periplasmic-binding-protein-like effector domain that binds 2-ketogluconate. PtxS binds a 14-bp palindromic operator (TGAAACCGGTTTCA) upstream of its own gene and represses itself, and binds near the -10 region of the kgu and gad catabolic operon promoters, occluding RNA polymerase. PtxS does not bind the toxA promoter; instead it binds the divergently encoded activator PtxR with nanomolar affinity and blocks PtxR-dependent activation of toxA, and at the kgu and gad promoters the two DNA-bound regulators interact to form a DNA loop. 2-Ketogluconate disrupts the PtxS-PtxR interaction and releases PtxS from DNA.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001248758; PtxS is itself a seed and binds defined operators. Reason: Directly supported: footprinted operators at PptxS, Pkgu and Pgad. Supporting Evidence: PMID:22844393 PtxS operates as a repressor that binds to the -10 region of the target promoters and occludes RNA polymerase access PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction; agrees with the experimental rows. Reason: Same claim as the experimental rows. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0000976 transcription cis-regulatory region binding | IMP PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | ACCEPT | Summary: Operator mutagenesis abolishes PtxS binding to the ptxS upstream region. Reason: Direct operator-binding evidence. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:10438759 The Pseudomonas aeruginosa exotoxin A regulatory gene, ptxS:... | ACCEPT | Summary: PtxS-dependent gel shift of a 52-bp ptxS upstream fragment, lost in the mutant. Reason: Direct binding evidence with genetic controls. Supporting Evidence: PMID:10438759 The gel shift band was not detected when the 52-bp fragment was incubated with the lysate of the ptxS isogenic mutant PAO1::ptxS. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | ACCEPT | Summary: PtxS binds the 14-bp palindrome. Reason: Direct binding evidence. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:22844393 Genes for carbon metabolism and the ToxA virulence factor in... | ACCEPT | Summary: PtxS footprints at Pkgu and Pgad. Reason: Direct binding evidence. Supporting Evidence: PMID:22844393 the PtxS operator site is located 50 bp downstream from the PtxR site |
| GO:0001217 DNA-binding transcription repressor activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction; agrees with the experimental rows. Reason: PtxS is a repressor of its own gene and of the kgu and gad operons. Supporting Evidence: PMID:22844393 PtxS operates as a repressor that binds to the -10 region of the target promoters and occludes RNA polymerase access |
| GO:0001217 DNA-binding transcription repressor activity | IMP PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | ACCEPT | Summary: Operator deletion raises ptxS expression: repression through the bound site. Reason: Binding plus loss-of-repression evidence. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. PMID:10894751 the deletion of the 14-bp sequence caused a significant enhancement in ptxS expression |
| GO:0001217 DNA-binding transcription repressor activity | IPI PMID:10438759 The Pseudomonas aeruginosa exotoxin A regulatory gene, ptxS:... | ACCEPT | Summary: PtxS binds its own upstream region; ptxS-lacZ is higher in the ptxS mutant. Reason: Binding plus derepression in the mutant. Supporting Evidence: PMID:10438759 The gel shift band was not detected when the 52-bp fragment was incubated with the lysate of the ptxS isogenic mutant PAO1::ptxS. PMID:10438759 was four- to fivefold higher than that produced by PAO1 carrying the same plasmid |
| GO:0001217 DNA-binding transcription repressor activity | IPI PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | ACCEPT | Summary: PtxS binds the palindromic operator that mediates autorepression. Reason: Binding plus derepression on operator deletion. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. PMID:10894751 the deletion of the 14-bp sequence caused a significant enhancement in ptxS expression |
| GO:0001217 DNA-binding transcription repressor activity | IPI PMID:22844393 Genes for carbon metabolism and the ToxA virulence factor in... | ACCEPT | Summary: PtxS binds at -10 of Pkgu/Pgad and occludes RNA polymerase. Reason: Core molecular function. Supporting Evidence: PMID:22844393 PtxS operates as a repressor that binds to the -10 region of the target promoters and occludes RNA polymerase access |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro HTH_LacI mapping to generic DNA binding. Reason: Entailed by GO:0000976, accepted here (is_a GO:0003677). |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN001248758 (11 seeds, including PtxS itself). Reason: True but entailed by GO:0001217 DNA-binding transcription repressor activity, accepted here (is_a GO:0003700). Node-level claim not disputed. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN001248758, the node that this gene's PseudoCAP GO:0045892 IDA row seeds (with 18 other LacI-family seeds). Seed SOUND. Reason: True but entailed by GO:0045892 negative regulation of DNA-templated transcription, accepted here. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping; agrees with the IBA. Reason: Entailed by GO:0045892, accepted here. |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA prediction of protein-DNA complex. Reason: True of a repressor bound at its operator, but a transient state rather than a location; kept as non-core, as for the CollecTF rows. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0032993 protein-DNA complex | IMP PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | KEEP AS NON CORE | Summary: CollecTF protein-DNA complex row from operator mutagenesis. Reason: CollecTF convention for a TF-operator complex; true but not informative as a location. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0032993 protein-DNA complex | IPI PMID:10438759 The Pseudomonas aeruginosa exotoxin A regulatory gene, ptxS:... | KEEP AS NON CORE | Summary: CollecTF protein-DNA complex row from gel shift. Reason: As above. Supporting Evidence: PMID:10438759 The gel shift band was not detected when the 52-bp fragment was incubated with the lysate of the ptxS isogenic mutant PAO1::ptxS. |
| GO:0032993 protein-DNA complex | IPI PMID:10894751 Autoregulation of the Pseudomonas aeruginosa protein PtxS oc... | KEEP AS NON CORE | Summary: CollecTF protein-DNA complex row. Reason: As above. Supporting Evidence: PMID:10894751 PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. |
| GO:0032993 protein-DNA complex | IPI PMID:22844393 Genes for carbon metabolism and the ToxA virulence factor in... | KEEP AS NON CORE | Summary: CollecTF protein-DNA complex row from footprints. Reason: As above. Supporting Evidence: PMID:22844393 the PtxS operator site is located 50 bp downstream from the PtxR site |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:22844393 Genes for carbon metabolism and the ToxA virulence factor in... | ACCEPT | Summary: PseudoCAP IDA seed of the PTN001248758 GO:0006355 IBD. PtxS footprints at the -10 region of Pkgu and Pgad and represses them; it also represses its own promoter and, through binding PtxR, toxA. Reason: Seed SOUND (full text read): DNA binding plus repression in lacZ fusions in the deletion background. Supporting Evidence: PMID:22844393 PtxS operates as a repressor that binds to the -10 region of the target promoters and occludes RNA polymerase access PMID:22844393 PtxS with 2-ketogluconate is the regulator of the gluconate degradation pathway and controls expression from its own promoter and also from the P(gad) and P(kgu) for the catabolic operons |
| GO:0140297 DNA-binding transcription factor binding | IDA PMID:22844393 Genes for carbon metabolism and the ToxA virulence factor in... | NEW | Summary: Proposed. ITC shows purified PtxS binds the DNA-binding transcription factor PtxR with nanomolar affinity, abolished by 2-ketogluconate; EMSA shows PtxS acting on PtoxA only through PtxR. Reason: This interaction is how PtxS controls toxA, a promoter it does not bind; it is the mechanism named in the paper's title and is not captured by any existing row. Supporting Evidence: PMID:22844393 In vitro, PtxS recognises PtxR with nanomolar affinity, but this interaction does not occur in the presence of 2-ketogluconate, the specific effector of PtxS. PMID:22844393 PtxR binds to the -35 region of the P(toxA) promoter in front of the exotoxin A gene, whereas PtxS does not bind to this promoter |
Loading supporting content…
Download this section (compressed HTML)Q: Is the PtxS-PtxR complex the only way PtxS influences toxA, or does PtxS also act through regA or other regulators?
Experiment: Map PtxS-PtxR contact residues and test whether contact mutants that keep DNA binding lose toxA repression in vivo.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)