ROF1 (YHR177W) is a putative sequence-specific DNA-binding transcription factor of the fungal Gti1/Pac2 (WOPR-domain) family. Its N-terminal WOPR domain (residues ~6-201) has been crystallized in complex with a preferred DNA site, establishing it as a bona fide sequence-specific DNA-binding protein, and the protein is a paralog of the S. cerevisiae pseudohyphal-growth regulator Mit1 and an ortholog of the Candida albicans white-opaque master regulator Wor1. Rof1 acts in the nucleus as a regulator of the transcriptional program controlling filamentous/pseudohyphal growth and complex (biofilm-like "fluffy") colony morphology: its overexpression represses the FLO11/flocculin and filamentation-MAPK regulon and flattens complex colony structure, while its deletion can increase colony structure. The direction of its transcriptional effect on direct targets, and its physiological trigger, remain incompletely defined.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) propagation from the Gti1/Pac2 (WOPR) family. Family members (Wor1, Mit1, Ryp1) are sequence-specific DNA-binding transcription factors, and the ROF1 WOPR domain has been crystallized bound to DNA (PMID:24994900). Domain- and structure-defensible core molecular function. Supporting Evidence: PMID:22095082 recognize the same DNA sequence |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization is expected for a sequence-specific DNA-binding transcription factor and is consistent with the curator IC nucleus annotation. Retained as the core site of action. |
| GO:0043565 sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Directly supported by the co-crystal structure of the ROF1 WOPR domain with a preferred DNA site (PMID:24994900) and by the shared sequence-specific recognition of the Wor1/Mit1/Ryp1 family. Core molecular function. Supporting Evidence: PMID:22095082 recognize the same DNA sequence |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: ROF1 is a transcriptional regulator, so involvement in regulation of RNA polymerase II transcription is well supported. However, the POSITIVE direction is not established for ROF1 in S. cerevisiae: the direct budding-yeast data show ROF1 overexpression REPRESSING the FLO11/flocculin and filamentation-MAPK program, and the IBA/ISS positive direction derives from the C. albicans activator Wor1. The regulatory role is real but its direction on direct targets is a knowledge gap; kept as non-core, and a direction-neutral parent term is proposed as a better fit. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:28673928 as regulators of |
| GO:0003677 DNA binding | IDA PMID:24994900 Structure of a new DNA-binding domain which regulates pathog... | ACCEPT | Summary: Direct experimental evidence: the ROF1 WOPR domain (PDB 4M8B, residues 6-201 of P38867) was crystallized in complex with its preferred DNA sequence. GO:0043565 (sequence-specific DNA binding) is the more precise term for the same activity; this general parent is retained as accurate. Supporting Evidence: PMID:24994900 WOPR-domain proteins are found throughout the fungal kingdom where they function |
| GO:0005634 nucleus | IC PMID:24994900 Structure of a new DNA-binding domain which regulates pathog... | ACCEPT | Summary: Curator inference (IC) of nuclear localization from the transcription-factor role. Appropriate for a sequence-specific DNA-binding transcription factor; the core cellular location. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | ISS PMID:24994900 Structure of a new DNA-binding domain which regulates pathog... | KEEP AS NON CORE | Summary: ISS from C. albicans Wor1 (with/from UniProtKB:Q5AP80), an activator of opaque-phase genes. The orthology is genuine (both are WOPR-family regulators), but the transferred POSITIVE direction is Wor1-specific; ROF1 experimental data in S. cerevisiae point to repression of the filamentation/FLO11 program. Not removed (well-grounded curator ISS), but the direction is uncertain, so kept as non-core and flagged in knowledge_gaps. Supporting Evidence: PMID:22095082 recognize the same DNA sequence |
| GO:1900428 regulation of filamentous growth of a population of unicellular organisms | IMP PMID:28673928 Transcriptional Profiling of Biofilm Regulators Identified b... | NEW | Summary: Proposed NEW annotation not currently in GOA. ROF1 was identified in an overexpression screen as a regulator of complex ("fluffy") colony morphology: overexpression reduces, and deletion increases, complex colony structure, and the overexpression transcriptional profile represses the FLO11/flocculin and filamentation-MAPK regulon. This establishes ROF1 as a regulator of the filamentous/pseudohyphal growth program in S. cerevisiae. A direction-neutral term is used because the direct-target direction (activation vs repression) is a knowledge gap. Supporting Evidence: PMID:28673928 as regulators of |
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Download this section (compressed HTML)Q: Does Rof1 bind the FLO11 promoter directly, or does it act indirectly through shared targets with its paralog Mit1?
Q: Under what physiological condition is Rof1 activity required, and is it functionally antagonistic, redundant, or parallel to Mit1?
Experiment: Genome-wide ChIP-seq/CUT&RUN of epitope-tagged Rof1 under filamentation-inducing conditions, integrated with RNA-seq of rof1 deletion and overexpression, and compared to Mit1 binding maps, to define direct targets and the activation/repression direction.
Experiment: Epistasis and expression analysis of rof1, mit1, and rof1 mit1 mutants across colony-morphology conditions and strain backgrounds to resolve the paralog relationship and a clean loss-of-function phenotype.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The direct in vivo target genes of Rof1 in S. cerevisiae are undetermined. No genome-wide Rof1 ChIP dataset has been reported (unlike its paralog Mit1); the available data are downstream expression changes from overexpression, not direct binding, and SGD lists zero known targets.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Rof1 is established as a sequence-specific DNA-binding protein (WOPR domain co-crystallized with DNA) and its paralog Mit1 binds the control regions of known pseudohyphal-growth regulators and flocculin genes, so a plausible target space is the FLO11/filamentation regulon - but ROF1's own direct binding sites are unmapped.
Significance: Without direct targets, ROF1's placement in the filamentous-growth regulatory network (and whether it acts on FLO11 directly or via Mit1-shared sites) cannot be fixed.
What would resolve it: Genome-wide ChIP-seq / CUT&RUN for tagged Rof1 under filamentation-inducing conditions, compared with Mit1 binding maps.
Provenance (the field's own admissions):
Gap: Whether Rof1 functions as a transcriptional activator or repressor of its direct targets in S. cerevisiae is unresolved. GO annotations encode positive regulation (transferred from the C. albicans activator Wor1), yet the budding-yeast phenotypic and expression data indicate repression of the complex-colony/FLO11 program.
OPEN BIOLOGY MF_DARK
What is known: It is firmly established that ROF1 overexpression reduces complex "fluffy" colony morphology and that its deletion can increase colony structure, and that the overexpression profile is dominated by repression of FLO11, FLO10 and TEC1. The mechanistic direction on genes it binds directly is not established.
Significance: Activator-vs-repressor identity determines how ROF1 is wired into the filamentous-growth circuit and how it relates functionally to the activator paralog Mit1 and to Wor1.
What would resolve it: Direct-target reporter/expression assays with DNA-binding-competent vs -defective Rof1 alleles, and Rof1 ChIP integrated with target expression.
Provenance (the field's own admissions):
Gap: Rof1 has no penetrant, condition-independent loss-of-function phenotype, and the physiological signal or condition that activates it is unknown. Single-deletion effects on colony morphology are strain-background dependent and conflicting between studies.
OPEN BIOLOGY BP_DARK
What is known: Deletion increases colony structure in one background and suppresses hog1-driven hyper-filamentation in another, and overexpression reduces complex colony morphology; but a clean, condition-independent single-deletion phenotype has not been established.
Significance: A defined activating condition and a clean phenotype are prerequisites for placing ROF1 in a specific signaling pathway (HOG / filamentation-MAPK / cAMP-PKA) rather than the broad morphology network.
What would resolve it: Systematic phenotyping of rof1 deletion (and rof1 mit1 double mutants) across nutrient/stress conditions and strain backgrounds; identification of upstream regulators.
Provenance (the field's own admissions):
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