GntR (PA2320) is a LacI/GalR-family transcriptional repressor of Pseudomonas aeruginosa that controls gluconate uptake, one of the routes feeding glucose-derived carbon into the Entner-Doudoroff pathway. It has an N-terminal lacI-type helix-turn-helix DNA-binding domain and a C-terminal periplasmic-binding-protein-like effector domain. GntR binds an operator (consensus AC-N-AAG-N-TAGCGCT) that overlaps the RNA polymerase binding site at its own promoter and at the promoter of the gluconate permease gene gntP, and represses both. Gluconate and 6-phosphogluconate bind the GntR-DNA complex and release the repressor (effector-mediated de-repression). GntR is a paralog of PtxS and, unlike PtxS, does not affect exotoxin A (toxA) expression.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from LacI-family node PTN001248758; GntR binds operators at PgntR and PgntP. Reason: Directly supported for this gene: purified GntR binds both promoters at a defined operator. Supporting Evidence: PMID:28752954 GntR was found to bind to promoters PgntR and PgntP |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro HTH_LacI mapping to generic DNA binding. Reason: True but entailed by GO:0000976 transcription cis-regulatory region binding, accepted here (is_a GO:0003677). Supporting Evidence: PMID:28752954 GntR was found to bind to promoters PgntR and PgntP |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN001248758 with 11 LacI-family seeds, including this gene's own PseudoCAP IDA (expected self-seed). Reason: Correct but general for GntR, which acts as a repressor of its own gene and of gntP. GO:0001217 DNA-binding transcription repressor activity (is_a GO:0003700) is the specific term. The node-level claim is not disputed; GO:0003700 is the right level for a clade with activators and repressors. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001248758 · PTN001248758 SUPPORTS TRANSFER LacI/GalR-family node with 11 seeds for GO:0003700 (E. coli LacI, MalI, XylR, RbsR, PurR, AscG, TreR, B. subtilis CcpA, Shewanella NagR, P. aeruginosa PtxS and GntR). The generic node term suits the clade; most members are repressors, but the node term need not say so. UniProtKB:Q9I1F6 · gntR (self; PseudoCAP IDA PMID:28752954) SUPPORTS TRANSFER Expected self-seed reflecting this gene's own DNA-binding and repression data. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:28752954 GntR repressed its own expression as well as that of the GntP gluconate permease. PMID:28752954 GntR was found to bind to promoters PgntR and PgntP |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:28752954 Identification of GntR as regulator of the glucose metabolis... | MODIFY | Summary: PseudoCAP IDA seed of the PTN001248758 IBD. Purified GntR binds its operators at PgntR and PgntP, and gluconate/6-phosphogluconate release it; in vivo it represses both promoters. Reason: Seed is SOUND: DNA binding plus repression is direct evidence for a DNA-binding transcription factor. The precise term is GO:0001217 DNA-binding transcription repressor activity. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:28752954 GntR was found to bind to promoters PgntR and PgntP PMID:28752954 GntR repressed its own expression as well as that of the GntP gluconate permease. PMID:28752954 we show that GntR employs an effector mediated de-repression mechanism |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN001248758 (19 LacI-family seeds). Reason: Correct but general. GntR represses transcription of gntR and gntP, so GO:0045892 negative regulation of DNA-templated transcription (is_a GO:0006355) is the specific term. Node-level claim not disputed. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001248758 · PTN001248758 SUPPORTS TRANSFER LacI/GalR node with 19 experimentally characterized seeds (E. coli LacI, PurR, RbsR, MalI, CytR, GalR/GalS and others, B. subtilis CcpA, P. aeruginosa PtxS). Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:28752954 GntR repressed its own expression as well as that of the GntP gluconate permease. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | MODIFY | Summary: Automated InterPro/ARBA mapping; agrees with the IBA. Reason: As for the IBA row: GntR is a repressor, so GO:0045892 is the specific term. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:28752954 GntR repressed its own expression as well as that of the GntP gluconate permease. |
| GO:0010906 regulation of glucose metabolic process | IMP PMID:28752954 Identification of GntR as regulator of the glucose metabolis... | KEEP AS NON CORE | Summary: PseudoCAP IMP row. GntR controls the gluconate permease gene gntP; in pseudomonads glucose is partly oxidized to gluconate in the periplasm and taken up as gluconate before entering the Entner-Doudoroff pathway. Reason: A fair organism-level description of the regulatory role, since gluconate uptake is one route of glucose catabolism in Pseudomonas, but it is a consequence of transcriptional repression of gntP rather than the gene's core activity. Not a PAINT seed. Supporting Evidence: PMID:28752954 GntR repressed its own expression as well as that of the GntP gluconate permease. PMID:28752954 glucose metabolism in pseudomonads occurs exclusively through the Entner-Doudoroff (ED) pathway |
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Download this section (compressed HTML)Q: Does GntR regulate genes beyond gntR and gntP (for example glucose or gluconate kinase genes), and how does it share targets with PtxS, HexR and GtrS/GltR?
Experiment: ChIP-seq or RNA-seq of a gntR deletion strain grown on glucose versus gluconate to define the full GntR regulon.
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