GbdR (PA5380) is an AraC-family transcriptional activator of Pseudomonas aeruginosa that senses the choline catabolites glycine betaine and dimethylglycine. It binds direct-repeat sites in target promoters and activates about 25 genes from 11 promoters, covering choline acquisition from host phospholipids (the hemolytic phospholipase C plcH, the phosphorylcholine phosphatase pchP and the acetylcholine esterase choE), quaternary amine uptake (betX, cbcXWV) and the full catabolic route from glycine betaine through dimethylglycine, sarcosine, glycine and serine to pyruvate. A gbdR mutant cannot grow on glycine betaine or dimethylglycine and fails to induce plcH and pchP in lung surfactant.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IMP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | ACCEPT | Summary: CollecTF row. MBP-GbdR shifts the plcH and pchP promoters, and a 2-bp site mutation abolishes binding and induction. Reason: Direct promoter binding is the core molecular activity. Supporting Evidence: PMID:19103776 In electrophoretic mobility shift assays, a GbdR-maltose binding protein fusion bound specifically to both the plcH and pchP promoters. |
| GO:0001216 DNA-binding transcription activator activity | IMP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | ACCEPT | Summary: CollecTF row; GbdR binds and activates the plcH and pchP promoters. Reason: Core activity; GbdR is an activator with no demonstrated repressor role. Supporting Evidence: PMID:19103776 Here we report that the induction of plcH and pchP transcription by glycine betaine is mediated by GbdR, an AraC family transcription factor. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the AraC HTH domain. Reason: Entailed by the accepted GO:0001216 (is_a GO:0003700). |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN000111456, seeded by this gene's own PseudoCAP rows (expected self-appearance), P. aeruginosa ArgR and CdhR and S. coelicolor AdpA. Sound at the node. Reason: True, but entailed by the accepted GO:0045893 on this gene. |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:17951379 Identification of two gene clusters and a transcriptional re... | TOO GENERAL | Summary: PseudoCAP seed row for PTN000111456. The abstract identifies GbdR as a regulator required for induction of gbcAB and dgcAB. Seed verdict SOUND. Reason: True, but entailed by the accepted GO:0045893 (is_a GO:0006355). |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | TOO GENERAL | Summary: Combined IEA from the AraC HTH domain. Reason: Entailed by the accepted GO:0045893. |
| GO:0006355 regulation of DNA-templated transcription | IMP PMID:24097953 Characterization of the GbdR regulon in Pseudomonas aerugino... | TOO GENERAL | Summary: PseudoCAP seed row for PTN000111456. Full text defines the regulon with in vitro binding to 11 promoters. Seed verdict SOUND. Reason: True, but entailed by the accepted GO:0045893. |
| GO:0009896 positive regulation of catabolic process | IMP PMID:17951379 Identification of two gene clusters and a transcriptional re... | ACCEPT | Summary: PseudoCAP row. GbdR is required for induction of the GB and DMG catabolic genes, and later directly activates every step from GB to pyruvate. Reason: Correct regulatory role. GO has no positive regulation of glycine betaine catabolic process term, so this is as precise as GO allows. Supporting Evidence: PMID:24097953 as it directly regulates transcription of the genes involved in all steps of conversion from GB to pyruvate |
| GO:0010518 positive regulation of phospholipase activity | IMP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | REMOVE | Summary: PseudoCAP row. The gbdR mutant has 95% less PlcH activity because it cannot induce plcH transcription. Reason: GbdR acts on plcH transcription, not on the phospholipase. Regulating the expression of an enzyme is not regulation of its activity; the transcriptional role is captured by GO:0045893. Supporting Evidence: PMID:19103776 Here we report that the induction of plcH and pchP transcription by glycine betaine is mediated by GbdR, an AraC family transcription factor. |
| GO:0010922 positive regulation of phosphatase activity | IMP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | REMOVE | Summary: PseudoCAP row; GbdR is required for induction of pchP transcription. Reason: GbdR activates pchP transcription and does not act on the PchP enzyme; this is transcriptional regulation, not regulation of phosphatase activity. Supporting Evidence: PMID:19103776 Here we report that the induction of plcH and pchP transcription by glycine betaine is mediated by GbdR, an AraC family transcription factor. |
| GO:0031457 glycine betaine catabolic process | IMP PMID:17951379 Identification of two gene clusters and a transcriptional re... | MODIFY | Summary: PseudoCAP row. The gbdR mutant cannot grow on GB because it cannot induce the catabolic genes; the demethylations are performed by GbcAB and DgcAB. Reason: A transcriptional regulator of the pathway does not take part in it. The sound claim is positive regulation of the catabolic process, which the gene already carries (GO:0009896). Proposed replacements: positive regulation of catabolic process Supporting Evidence: PMID:24097953 as it directly regulates transcription of the genes involved in all steps of conversion from GB to pyruvate |
| GO:0032993 protein-DNA complex | IMP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | KEEP AS NON CORE | Summary: CollecTF standard row recording the GbdR-promoter complex. Reason: True (EMSA complexes) but adds little beyond the cis-regulatory binding row. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the AraC HTH domain. Reason: Entailed by the accepted GO:0000976 (is_a GO:0043565). |
| GO:0045764 positive regulation of amino acid metabolic process | IMP PMID:17951379 Identification of two gene clusters and a transcriptional re... | KEEP AS NON CORE | Summary: PseudoCAP row. GbdR activates the DMG, sarcosine, glycine and serine catabolic genes (dgc, soxBDAG, glyA1, sdaB). Reason: True, and as precise as GO allows, but a side view of the glycine betaine regulon captured by GO:0009896. Supporting Evidence: PMID:24097953 as it directly regulates transcription of the genes involved in all steps of conversion from GB to pyruvate |
| GO:0045893 positive regulation of DNA-templated transcription | EXP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | ACCEPT | Summary: CollecTF row; GbdR activates plcH and pchP transcription. Reason: Core process, shown by reporter fusions, promoter mutation and EMSA. Supporting Evidence: PMID:19103776 Here we report that the induction of plcH and pchP transcription by glycine betaine is mediated by GbdR, an AraC family transcription factor. |
| GO:0045893 positive regulation of DNA-templated transcription | IEP PMID:19103776 GbdR regulates Pseudomonas aeruginosa plcH and pchP transcri... | ACCEPT | Summary: CollecTF row for the same claim. Reason: Consistent with the EXP row. Supporting Evidence: PMID:19103776 Here we report that the induction of plcH and pchP transcription by glycine betaine is mediated by GbdR, an AraC family transcription factor. |
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