AtuR (PA2885) is a TetR-family transcriptional repressor of Pseudomonas aeruginosa that controls the atuABCDEFGH gene cluster, which encodes most enzymes of acyclic terpene (citronellol, geraniol) utilization, including the geranyl-CoA carboxylase subunits AtuC and AtuF. AtuR binds as a homodimer to two 13-bp inverted repeats separated by 40 bp in the atuR-atuA intergenic operator/promoter region. In an atuR insertion mutant the Atu proteins are expressed constitutively, so AtuR keeps the terpene catabolic genes off in the absence of inducer.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (7 seeds). atuR sits inside this TetR clade. atuR binds an inverted-repeat operator in its target promoter. Reason: Correct and appropriate for the node, but binding to a defined inverted-repeat operator supports the child GO:0000987 cis-regulatory region sequence-specific DNA binding for this gene (the same refinement used for mexZ, which shares the node). The generic term stays right for the node. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HZW2 · atuR (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:20487029 Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) |
| GO:0003677 DNA binding | IDA PMID:20487029 AtuR is a repressor of acyclic terpene utilization (Atu) gen... | MODIFY | Summary: PseudoCAP IDA: EMSA of purified AtuR on the atuR-atuA intergenic region, mapped to two 13-bp inverted repeats. Reason: Correct but general; sequence-specific binding at the atuA operator supports GO:0000987. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:20487029 Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: InterPro/UniRule mapping from the TetR HTH (TetR_N) domain. True. Reason: DNA binding is correct but general; atuR binds a defined operator, which supports GO:0000987. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:20487029 Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (7 seeds). atuR is a DNA-binding TetR-family repressor. Reason: Correct but general. The gene-level evidence (operator binding plus derepression in the mutant) supports GO:0001217 DNA-binding transcription repressor activity. The generic term remains right for the node. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HZW2 · atuR (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:20487029 Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR050109 TetR-like regulator) mapping. True. Reason: Correct but general; the gene-level evidence supports GO:0001217 DNA-binding transcription repressor activity. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:20487029 Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (19 seeds). atuR is one of them, which is expected, not circular. The IBD stands on the other 18 seeds as well. Reason: Correct and appropriate for the node, but atuR is a repressor; GO:0045892 negative regulation of DNA-templated transcription is supported by the gene's own experimental rows. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HZW2 · atuR (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR050109) mapping. True. Reason: Correct but general; atuR is shown to be a repressor, so GO:0045892 applies. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster |
| GO:0045827 negative regulation of isoprenoid metabolic process | IMP PMID:16820476 Identification of genes and proteins necessary for catabolis... | ACCEPT | Summary: PseudoCAP IMP: atuR negatively regulates the acyclic terpene utilization (atu) gene cluster. Reason: Acyclic monoterpenes (citronellol, geraniol) are isoprenoids, and AtuR directly represses the genes for their catabolism, so negative regulation of isoprenoid metabolic process is the process AtuR's target genes carry out. GO has no terpene-catabolism regulation term. Supporting Evidence: PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster PMID:20487029 The atuR-atuABCDEFGH gene cluster is essential for acyclic terpene utilization (Atu) |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:20487029 AtuR is a repressor of acyclic terpene utilization (Atu) gen... | ACCEPT | Summary: PseudoCAP IMP and one of the 19 seeds of the PTN004738546 GO:0006355 IBD. Atu proteins are expressed constitutively in the atuR insertion mutant, and AtuR binds the atuA operator. Seed verdict SOUND. Reason: Direct repressor of the atu operon; core BP. Supporting Evidence: PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) PMID:16820476 A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster |
| GO:0046247 terpene catabolic process | IDA PMID:20487029 AtuR is a repressor of acyclic terpene utilization (Atu) gen... | REMOVE | Summary: PseudoCAP IDA to terpene catabolic process, from the AtuR repressor paper. Reason: AtuR is a TetR-family repressor; the paper's evidence (sequence similarity, constitutive Atu expression in the mutant, EMSA binding) is regulatory. AtuR does not catalyse any step of terpene catabolism, and the IDA code reflects an EMSA. Its regulatory role is captured by GO:0045827 and GO:0045892. Supporting Evidence: PMID:20487029 AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA) |
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Download this section (compressed HTML)Q: Which metabolite (citronellol, geraniol, or a CoA-thioester intermediate) binds AtuR and induces the atu genes?
Experiment: EMSA and thermal-shift assays of purified AtuR with acyclic terpenes and their CoA intermediates.
Type: ligand screening
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