TRF2 (MoC19TRF2, MGG_04853) is a 625-residue homeodomain transcription factor of the rice blast fungus Pyricularia oryzae, encoded among the genes flanking the pyriculol polyketide synthase gene MoPKS19. It has a single typical homeodomain (residues 73-132, with the WFQNRR DNA-recognition motif) preceded by a disordered N-terminal region, and a C-terminal PH-like domain (PF24818, PH_TRF2_HOY1) shared with a lineage of fungal homeobox proteins including Neurospora crassa KAL-1 (its one-to-one ortholog) and Yarrowia lipolytica HOY1. Deletion of TRF2, like deletion of the second cluster transcription factor TRF1, increases MoPKS19 transcript levels, so TRF2 acts as a negative regulator of the cluster that makes the lesion-inducing heptaketides pyriculol and pyriculariol. Its DNA-binding specificity, direct target genes and nuclear localisation are inferred from the homeodomain and have not been tested directly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-derived sequence-specific DNA-binding term. TRF2 has a canonical homeodomain (DNA_BIND 73-132) with the WFQNRR helix-3 recognition motif and the canonical I47/Q50/N51/R53 DNA-contacting residues. Reason: Correct but less specific than GO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding), which TRF2 already carries from the PANTHER PTHR24324:SF5 TreeGrafter annotation and which describes how homeodomain transcription factors engage promoter elements. Refine to GO:0000978. No DNA-binding experiment exists for TRF2 itself; the claim rests on the intact homeodomain and subfamily membership. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: file:PYRO7/TRF2/TRF2-uniprot.txt DR Pfam; PF00046; Homeodomain; 1. file:PYRO7/TRF2/TRF2-bioinformatics/RESULTS.md The TRF2 homeodomain (residues 73-132) carries the helix-3 recognition motif WFQNRR (residues 120-125) |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter assignment from PANTHER node PTN004691474 (PTHR24324:SF5). The same PAINT annotations give the N. crassa ortholog KAL-1 its IBA rows; the node is grounded in experimental DNA binding by fission and budding yeast and human SF5 members. Reason: Sequence-specific binding of cis-regulatory DNA is the ancestral homeodomain activity of the SF5 subfamily, and TRF2 is inside that subfamily with an intact recognition helix (WFQNRR, residues 120-125). No TRF2-specific binding site or motif has been determined, so no more specific term is warranted. This is the most precise DNA-binding claim supported and is accepted as core, but it is inferred, not experimentally established in P. oryzae. Supporting Evidence: file:PYRO7/TRF2/TRF2-uniprot.txt DR Pfam; PF00046; Homeodomain; 1. file:PYRO7/TRF2/TRF2-bioinformatics/RESULTS.md The TRF2 homeodomain (residues 73-132) carries the helix-3 recognition motif WFQNRR (residues 120-125) file:PYRO7/TRF2/TRF2-bioinformatics/RESULTS.md Only the shared homeodomain activity |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro (homeobox conserved site) mapping to RNA polymerase II-specific DNA-binding transcription factor activity. Reason: TRF2 is a homeodomain protein with an intact DNA-recognition helix, and deletion of TRF2 raises transcript levels of the cluster polyketide synthase gene MoPKS19 in vivo (PMID:27902426), consistent with action as a transcription factor. A repressor-specific child term (GO:0001227) is not proposed: direct promoter binding was not tested, and overexpression left MoPKS19 transcript essentially unchanged, so the repression could be indirect. Supporting Evidence: file:PYRO7/TRF2/TRF2-uniprot.txt DR Pfam; PF00046; Homeodomain; 1. PMID:27902426 found individually to act as negative regulators repressing gene expression of MoPKS19 file:PYRO7/TRF2/TRF2-uniprot.txt Leads to increased expression of the pyriculol/pyriculariol biosynthesis cluster highly reducing polyketide synthase PKS19 |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro homeodomain (IPR001356) mapping to generic DNA binding. Reason: True but uninformative: the homeodomain binds DNA sequence-specifically at cis-regulatory regions, and TRF2 already carries the specific descendant GO:0000978. Refine to that term. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: file:PYRO7/TRF2/TRF2-uniprot.txt DR Pfam; PF00046; Homeodomain; 1. file:PYRO7/TRF2/TRF2-bioinformatics/RESULTS.md The TRF2 homeodomain (residues 73-132) carries the helix-3 recognition motif WFQNRR (residues 120-125) |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nucleus from the UniProt subcellular-location mapping, itself based on the PROSITE homeobox rule. Reason: A sequence-specific DNA-binding transcription factor acts in the nucleus. No localisation experiment has been done for TRF2, so this is inferred from the homeodomain, but it is the expected and only plausible compartment for the activity. Supporting Evidence: file:PYRO7/TRF2/TRF2-uniprot.txt DR Pfam; PF00046; Homeodomain; 1. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro mapping to the general regulation of DNA-templated transcription. Reason: Correct but general. The experimental evidence for TRF2 is specifically negative: deletion of TRF2 increases MoPKS19 transcript (PMID:27902426), and the activity is RNA polymerase II-specific. Refine to GO:0000122 negative regulation of transcription by RNA polymerase II. Whether the repression is direct has not been tested. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:27902426 found individually to act as negative regulators repressing gene expression of MoPKS19 file:PYRO7/TRF2/TRF2-uniprot.txt Leads to increased expression of the pyriculol/pyriculariol biosynthesis cluster highly reducing polyketide synthase PKS19 |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000118 | MODIFY | Summary: TreeGrafter assignment from PANTHER node PTN004691474 (PTHR24324:SF5) to regulation of transcription by RNA polymerase II. Reason: The family-level claim is sound and TRF2 lies inside the node, but for TRF2 the direction of regulation has been determined experimentally: ΞMoC19TRF2 has raised MoPKS19 transcript (PMID:27902426). Refine to the descendant GO:0000122 negative regulation of transcription by RNA polymerase II. This direction is a TRF2-specific experimental result and should not be assumed for other SF5 members without evidence. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:27902426 found individually to act as negative regulators repressing gene expression of MoPKS19 file:PYRO7/TRF2/TRF2-uniprot.txt Leads to increased expression of the pyriculol/pyriculariol biosynthesis cluster highly reducing polyketide synthase PKS19 |
| GO:0030154 cell differentiation | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: TreeGrafter assignment of cell differentiation from PANTHER node PTN004691474; the node-level term reflects animal developmental homeobox donors (HHEX) and fungal developmental regulators. Reason: No developmental or differentiation phenotype has been reported for TRF2; the only characterised role is repression of the pyriculol polyketide cluster gene MoPKS19 (PMID:27902426). The broad animal-derived developmental term is not supported for this gene. Its N. crassa ortholog KAL-1 has a conidiation phenotype, so a fungal developmental role in this lineage is possible, but it has not been shown in P. oryzae. Supporting Evidence: PMID:27902426 found individually to act as negative regulators repressing gene expression of MoPKS19 |
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Download this section (compressed HTML)Q: Does TRF2 bind the MoPKS19 promoter (and other cluster promoters) directly, and what DNA motif does its homeodomain recognise? Do TRF1 and TRF2 act together or in parallel?
Q: Does loss of TRF2 increase pyriculol and pyriculariol production, as UniProt implies, or only MoPKS19 transcript? Metabolite levels were not reported for the TRF mutants.
Q: What does the C-terminal PF24818 (PH_TRF2_HOY1) PH-like domain contribute, and is repression of secondary-metabolite clusters conserved in the N. crassa ortholog KAL-1?
Experiment: HPLC quantification of pyriculol, pyriculariol and their dihydro derivatives in ΞMoC19TRF2, complemented and overexpression strains, together with RNA-seq to define all genes repressed by TRF2.
Type: metabolite profiling / RNA-seq
Experiment: ChIP-seq or DAP-seq of tagged TRF2, plus a GFP fusion to confirm nuclear localisation, to establish direct binding at cluster promoters and its recognition motif.
Type: ChIP-seq / DAP-seq / localisation
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