TrpI (PA0037) is a LysR-type transcriptional regulator of Pseudomonas aeruginosa PAO1 encoded divergently from trpBA, the genes for the two tryptophan synthase subunits. TrpI binds two adjacent sites in the trpI-trpBA intergenic region. Without the inducer indoleglycerol phosphate (InGP), a tryptophan-pathway intermediate, it occupies site I (-52 to -77 of trpBA); InGP promotes binding of a second TrpI molecule at site II, extending the footprint to -32 and activating transcription initiation at the trpBA promoter. Purified TrpI with InGP activates trpBA and represses its own overlapping promoter in vitro. TrpI thereby couples tryptophan synthase expression to the supply of its substrate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA DNA-binding TF activity from the LysR node PTN000794521. Reason: TrpI binds its operator and directly activates trpBA transcription in a purified in vitro system, so the inherited TF activity is confirmed for this gene. Supporting Evidence: PMID:1904858 purified TrpI protein and indoleglycerol phosphate (InGP) activate transcription initiation at the trpBA promoter (trpPB) and repress initiation at the trpI promoter (trpPI) |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO DNA-binding TF activity (LysR HTH). Reason: Consistent with the direct evidence. Supporting Evidence: PMID:1904858 activation of trpPB is mediated by a direct effect of TrpI on transcription initiation at trpPB |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: IBA regulation of transcription from PTN000794521; TrpI is one of six seeds. Reason: Sound. TrpI's own PseudoCAP IDA is among the seeds as expected. TrpI activates trpBA and represses trpI, so the undirected term is the right level. Supporting Evidence: PMID:1904858 purified TrpI protein and indoleglycerol phosphate (InGP) activate transcription initiation at the trpBA promoter (trpPB) and repress initiation at the trpI promoter (trpPI) |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:1904858 Activation of the trpBA promoter of Pseudomonas aeruginosa b... | ACCEPT | Summary: PseudoCAP IDA regulation of transcription from an in vitro transcription system with purified TrpI; a seed of the PTN000794521 IBD. Reason: The abstract states the decisive fact: purified TrpI plus InGP activates trpBA and represses trpI transcription initiation in vitro, and the effect at trpPB is direct. Supporting Evidence: PMID:1904858 purified TrpI protein and indoleglycerol phosphate (InGP) activate transcription initiation at the trpBA promoter (trpPB) and repress initiation at the trpI promoter (trpPI) PMID:1904858 activation of trpPB is mediated by a direct effect of TrpI on transcription initiation at trpPB |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA regulation of transcription. Reason: Consistent with the direct evidence. Supporting Evidence: PMID:1904858 activation of trpPB is mediated by a direct effect of TrpI on transcription initiation at trpPB |
| GO:0032993 protein-DNA complex | IPI PMID:2107533 The roles of indoleglycerol phosphate and the TrpI protein i... | KEEP AS NON CORE | Summary: CollecTF IPI protein-DNA complex; TrpI-operator complexes in gel retardation and footprinting. Reason: True (TrpI forms two InGP-dependent complexes with trpBA promoter DNA), but a transient regulator-operator complex is peripheral to the TF function captured by the MF rows. Supporting Evidence: PMID:2107533 two major, slow moving protein-DNA complexes are seen in gel retardation assays |
| GO:0043565 sequence-specific DNA binding | IPI PMID:2107533 The roles of indoleglycerol phosphate and the TrpI protein i... | MODIFY | Summary: CollecTF IPI sequence-specific DNA binding at the trpBA promoter. Reason: Correct but general. The bound sequence is the cis-regulatory region of trpBA (-32 to -77), so the specific descendant GO:0000976 transcription cis-regulatory region binding is supported. Proposed replacements: transcription cis-regulatory region binding Supporting Evidence: PMID:2107533 in the absence of InGP, the binding site of TrpI is located in the -52 to -77 region of the trpBA promoter; in the presence of InGP, the binding region is extended to the -32 region |
| GO:2000284 positive regulation of amino acid biosynthetic process | IMP PMID:1904858 Activation of the trpBA promoter of Pseudomonas aeruginosa b... | ACCEPT | Summary: PseudoCAP IMP positive regulation of amino acid biosynthesis; TrpI activates trpBA. Reason: TrpI activates the tryptophan synthase genes, which is positive regulation of tryptophan biosynthesis; GO has no tryptophan-specific regulation term, so this is the most specific available. The abstract describes promoter mutations and in vitro transcription rather than a trpI mutant, so IMP may not be the best code; the full text was not available to check. Supporting Evidence: PMID:1904858 purified TrpI protein and indoleglycerol phosphate (InGP) activate transcription initiation at the trpBA promoter (trpPB) |
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Download this section (compressed HTML)Q: Should GO add regulation terms for L-tryptophan biosynthesis (positive and negative), so that TrpI and the TrpR-type regulators of other species can be annotated precisely?
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