ExsA (PA1713) is a sequence-specific DNA-binding transcriptional activator of the AraC/XylS family and the master regulator of the Pseudomonas aeruginosa type III secretion system (T3SS). Its C-terminal domain carries two helix-turn-helix motifs that recognise a conserved consensus (a GnC and a TGnnA element) centred about 51 bp upstream of the start site. Two ExsA monomers are recruited sequentially to adjacent sites overlapping the -35 region and activate transcription of the T3SS operons. The N-terminal domain mediates self-association and binding of the anti-activator ExsD, which holds ExsA in a DNA-binding-incompetent complex; ExsC, released when ExsE leaves the cell under low calcium or host-cell contact, binds ExsD and frees ExsA. Transcription of exsA is activated by the cAMP-dependent regulator Vfr.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002457187; among the seeds for this term are E. coli AraC and ChbR and ExsA itself. Stands without ExsA. Reason: ExsA binds defined cis-regulatory sites in T3SS promoters. Supporting Evidence: PMID:18373522 ExsA(His) specifically bound T3SS promoters with high affinity as determined by electrophoretic mobility shift assays (EMSA). PMID:22408165 Each ExsA-dependent promoter contains two adjacent binding sites for monomeric ExsA. |
| GO:0000976 transcription cis-regulatory region binding | IMP PMID:22408165 The distal ExsA-binding site in Pseudomonas aeruginosa type ... | ACCEPT | Summary: CollecTF: binding-site mutations abolish ExsA binding and activation. Reason: Promoter-specific DNA binding. Supporting Evidence: PMID:22408165 Each ExsA-dependent promoter contains two adjacent binding sites for monomeric ExsA. |
| GO:0001216 DNA-binding transcription activator activity | IMP PMID:22408165 The distal ExsA-binding site in Pseudomonas aeruginosa type ... | ACCEPT | Summary: CollecTF: ExsA activates T3SS promoters through its binding sites. Reason: Core activity: a sequence-specific DNA-binding transcriptional activator. Supporting Evidence: PMID:19376850 we show that the CTD of ExsA binds to ExsA-dependent promoters in vitro and activates transcription from ExsA-dependent promoters both in vitro and in vivo PMID:24142246 Mutations that disrupt the ExsA consensus binding sites in both P. aeruginosa and Y. pestis T3SS promoters prevent activation by ExsA and LcrF. |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN002457187, an AraC/XylS clade (166 leaves, 24 taxa) with ten GO:0006355 seeds, nine of them E. coli or Yersinia regulators with their own experimental annotations (AraC, MelR, RhaS, ChbR, AdiY, GadW, YdeO, AppY, RclR, LcrF). ExsA is one seed. Generic transcription-factor activity at the node. Reason: Entailed by GO:0001216 DNA-binding transcription activator activity (is_a GO:0003700), accepted above. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro HTH_AraC mapping. Reason: Entailed by GO:0001216, accepted above. |
| GO:0005515 protein binding | IPI PMID:20008065 ExsD inhibits expression of the Pseudomonas aeruginosa type ... | REMOVE | Summary: IntAct IPI for the ExsA-ExsD interaction. ExsD is the anti-activator that holds ExsA off DNA. Reason: Bare protein binding is uninformative (protein-binding policy). The functional content of the ExsA-ExsD interaction is the anti-activation mechanism, described in the record; removal does not deny the interaction. Supporting Evidence: PMID:20008065 find that the ExsD.ExsA complex lacks DNA binding activity |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN002457187, an AraC/XylS clade (166 leaves, 24 taxa) with ten GO:0006355 seeds, nine of them E. coli or Yersinia regulators with their own experimental annotations (AraC, MelR, RhaS, ChbR, AdiY, GadW, YdeO, AppY, RclR, LcrF). ExsA is one seed. Node verdict SOUND: generic regulation of transcription is the right level for this broad AraC clade. Reason: True, but entailed by the more specific GO:2000144 positive regulation of DNA-templated transcription initiation, asserted below. The IBD at the generic term is sound for the clade; only this gene's row is refined. |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:7635828 Analyses of the DNA-binding and transcriptional activation p... | TOO GENERAL | Summary: PseudoCAP IDA seed row (PMID:7635828). Seed verdict SOUND: purified ExsA binds its promoters and activates transcription. Reason: The seed is correct but under-specific; GO:2000144 (asserted below) entails it. The seed supports the generic node term. No defect on the seed. Supporting Evidence: PMID:7635828 ExsA was produced and purified as a fusion protein, MALA3A2, which was shown to bind specifically to promoter regions |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro HTH_AraC mapping. Reason: Entailed by GO:2000144, asserted below. |
| GO:0032993 protein-DNA complex | IMP PMID:19376850 Functional domains of ExsA, the transcriptional activator of... | ACCEPT | Summary: CollecTF: ExsA forms a complex on promoter DNA (EMSA/footprint). Reason: ExsA binds promoter DNA as a protein-DNA complex. Supporting Evidence: PMID:18373522 ExsA(His) specifically bound T3SS promoters with high affinity as determined by electrophoretic mobility shift assays (EMSA). |
| GO:0032993 protein-DNA complex | IMP PMID:22408165 The distal ExsA-binding site in Pseudomonas aeruginosa type ... | ACCEPT | Summary: CollecTF: ExsA-DNA complex on T3SS promoters. Reason: Protein-DNA complex on the promoter. Supporting Evidence: PMID:22408165 Each ExsA-dependent promoter contains two adjacent binding sites for monomeric ExsA. |
| GO:0032993 protein-DNA complex | IPI PMID:18373522 Characterization of ExsA and of ExsA-dependent promoters req... | ACCEPT | Summary: CollecTF IPI: ExsA bound to promoter DNA. Reason: Protein-DNA complex on the promoter. Supporting Evidence: PMID:18373522 ExsA(His) specifically bound T3SS promoters with high affinity as determined by electrophoretic mobility shift assays (EMSA). |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to sequence-specific DNA binding. Reason: Entailed by GO:0000976 transcription cis-regulatory region binding (is_a GO:0043565), accepted above. |
| GO:0043565 sequence-specific DNA binding | IMP PMID:19376850 Functional domains of ExsA, the transcriptional activator of... | TOO GENERAL | Summary: CollecTF: ExsA binds its consensus sequence. Reason: Entailed by GO:0000976, accepted above. |
| GO:0043565 sequence-specific DNA binding | IPI PMID:18373522 Characterization of ExsA and of ExsA-dependent promoters req... | TOO GENERAL | Summary: CollecTF IPI: sequence-specific binding by ExsA. Reason: Entailed by GO:0000976, accepted above. |
| GO:0050709 negative regulation of protein secretion | IMP PMID:1655713 Cloning and sequence analysis of a trans-regulatory locus re... | REMOVE | Summary: PseudoCAP IMP (PMID:1655713). An exsA mutant is defective in expression and secretion of T3SS products; the abstract states ExsA is required for (activates) the pathway. Reason: Wrong term for a transcriptional activator: ExsA regulates transcription of the secretion genes, not secretion itself, and the sign is inverted (ExsA activates). The transcriptional role is captured by GO:2000144 / GO:0001216. PSEUDOCAP WRONG_TERM defect. Supporting Evidence: PMID:1655713 The ExsA gene product appeared to be required for induction of exoenzyme S synthesis above a low basal level. |
| GO:2000144 positive regulation of DNA-templated transcription initiation | IDA PMID:24142246 ExsA and LcrF recognize similar consensus binding sites, but... | ACCEPT | Summary: CACAO IDA (PMID:24142246). ExsA activates transcription initiation at T3SS promoters; consensus-site mutations block it. Reason: Core process: positive regulation of transcription initiation. Supporting Evidence: PMID:24142246 Mutations that disrupt the ExsA consensus binding sites in both P. aeruginosa and Y. pestis T3SS promoters prevent activation by ExsA and LcrF. PMID:19376850 we show that the CTD of ExsA binds to ExsA-dependent promoters in vitro and activates transcription from ExsA-dependent promoters both in vitro and in vivo |
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Download this section (compressed HTML)Q: Should bacterial transcriptional activators of secretion systems ever carry regulation-of-secretion terms (e.g. GO:0050709) directly, or only regulation-of-transcription terms, with the secretion effect left as an indirect phenotype?
Experiment: Map the full ExsA regulon by ChIP-seq and RNA-seq in low- and high-calcium conditions to separate directly activated promoters from indirect effects.
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