CdhR (PA5389) is a 336-residue AraC/XylS-family transcriptional activator of Pseudomonas aeruginosa that controls carnitine catabolism. It has an N-terminal DJ-1/PfpI-like (class I glutamine amidotransferase-like) domain, as in ArgR and GbdR, and a C-terminal AraC-type helix-turn-helix DNA-binding domain. CdhR is required for carnitine to induce the adjacent PA5388-PA5384 (cdh) genes, which encode carnitine dehydrogenase and the other enzymes that convert carnitine via 3-dehydrocarnitine towards glycine betaine. A cdhR mutant cannot grow on carnitine as sole carbon and nitrogen source.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the AraC-type HTH domain signatures. Reason: Correct but general. CdhR induces transcription of the cdh genes, so the specific term is GO:0001216 DNA-binding transcription activator activity, an is_a descendant. Proposed replacements: DNA-binding transcription activator activity Supporting Evidence: file:PSEAE/cdhR/cdhR-uniprot.txt Induces the transcription of the PA5384-PA5388 operon in response to carnitine. file:PSEAE/cdhR/cdhR-uniprot.txt InterPro; IPR018060; HTH_AraC. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN000111456, seeded by CdhR itself (expected self-seed), ArgR, GbdR and S. coelicolor AdpA. Reason: Correct but general for CdhR, which activates transcription; the leaf-level term is GO:0045893 positive regulation of DNA-templated transcription. The general node term is right for a clade of activators and repressors. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000111456 · PTN000111456 SUPPORTS TRANSFER AraC-family regulator node (50 leaves, 13 taxa); the general regulation term transfers correctly, and the activator sign is gene-level. UniProtKB:Q9HTH5 · cdhR (self; PseudoCAP IMP PMID:19406895) SUPPORTS TRANSFER Expected self-seed reflecting CdhR's own mutant evidence. UniProtKB:Q9HTI4 · P. aeruginosa GbdR SUPPORTS TRANSFER Characterised AraC-family regulator of glycine betaine catabolism. UniProtKB:G3XCU2 · P. aeruginosa ArgR SUPPORTS TRANSFER Characterised AraC-family regulator of arginine metabolism. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:19406895 PA5389 is required for induction of the PA5388-PA5384 transcripts in response to carnitine |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | MODIFY | Summary: Electronic regulation of transcription from the AraC HTH signatures. Reason: Correct but general; CdhR is an activator, so GO:0045893. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:19406895 PA5389 is required for induction of the PA5388-PA5384 transcripts in response to carnitine |
| GO:0006355 regulation of DNA-templated transcription | IMP PMID:19406895 Identification of genes required for Pseudomonas aeruginosa ... | MODIFY | Summary: PseudoCAP row and a seed of the PTN000111456 IBD. The cdhR mutant fails to induce the PA5388-PA5384 transcripts in response to carnitine. Reason: Sound seed; the mutant directly shows CdhR controls transcription of the cdh genes. Because CdhR is required for induction, the specific term is GO:0045893 positive regulation of DNA-templated transcription. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:19406895 PA5389 is required for induction of the PA5388-PA5384 transcripts in response to carnitine |
| GO:0009896 positive regulation of catabolic process | IMP PMID:19406895 Identification of genes required for Pseudomonas aeruginosa ... | ACCEPT | Summary: PseudoCAP row. CdhR is required for growth on carnitine and for induction of the carnitine catabolic genes. Reason: The regulator acts on the transcription of the catabolic genes, so a regulation term (not carnitine catabolic process) is right. GO has no regulation term specific to carnitine catabolism, so this is as precise as GO allows. Supporting Evidence: PMID:19406895 The PA5389 and PA1998 transcription factors are required for growth on carnitine. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO sequence-specific DNA binding from the AraC HTH domain. Reason: Expected for an AraC-family HTH regulator; part of its activator function. Supporting Evidence: file:PSEAE/cdhR/cdhR-uniprot.txt PROSITE; PS01124; HTH_ARAC_FAMILY_2; 1. |
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Download this section (compressed HTML)Q: Does CdhR bind carnitine (or a catabolite such as 3-dehydrocarnitine) directly, and where does it bind in the cdh promoter?
Experiment: Electrophoretic mobility shift and DNase I footprinting of purified CdhR on the PA5388 promoter, with and without carnitine, plus ligand binding by isothermal titration calorimetry.
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