ICY1 (YMR195W) is a small (127-residue, ~14 kDa) protein of the budding yeast Saccharomyces cerevisiae whose molecular function is undetermined. It is a moderately abundant protein (~4050 molecules per cell in log-phase minimal medium) that has been reported both in the cytosol and, in a genome-wide GFP localization screen, at the vacuole (fungal-type vacuole) membrane as a peripheral membrane protein. Genetically, ICY1 is required for viability of cells that lack mitochondrial DNA: its overexpression rescues the petite-negative phenotype of mutants defective in mitochondrial protein import, and deletion of ICY1 renders cells unable to grow without mitochondrial DNA. Cells lacking ICY1 also show an invasive-growth defect with elongated cell morphology, and ICY1 transcription is induced by amino-acid starvation; its promoter is also reported as a target of carbon-source / respiratory-state transcriptional regulators (Ert1 and related factors), linking its expression to the fermentation-to-respiration transition. The protein has no recognizable catalytic motif or characterized domain, and its whole-genome-duplication paralog ATG41/ICY2 acts in autophagosome formation, a role that ICY1 (which has low sequence similarity to the paralog) does not appear to share. The direct molecular activity, binding partners, and mechanism underlying its phenotypes remain unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005774 vacuolar membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic annotation propagated from the UniProtKB Subcellular Location keyword (Vacuole membrane; Peripheral membrane protein). This is the IEA/SubCell shadow of the experimental GFP localization; the general "vacuolar membrane" term is a valid location but redundant with, and less specific than, the experimental fungal-type vacuole membrane annotation. Reason: Localization, not molecular function; supported indirectly through the same GFP evidence that underlies the more specific HDA term. Kept as non-core because ICY1's location is real but does not define its function, and the cytosolic pool reported by Dunn & Jensen 2003 leaves the functionally relevant compartment unresolved. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast. |
| GO:0000329 fungal-type vacuole membrane | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | KEEP AS NON CORE | Summary: High-throughput direct assay (genome-wide GFP-fusion screen) localizing Icy1p to the fungal-type vacuole membrane. This is the single positive experimental localization for ICY1 and the most specific, defensible cellular-component annotation. Reason: Well-supported experimental localization, but a compartment call rather than a molecular function; retained as non-core. Note the literature also reports a cytosolic pool (Dunn & Jensen 2003), so the functionally active compartment is not fully settled. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root molecular_function term with ND (No biological Data available) evidence, correctly recording that ICY1 has no experimentally or computationally determined molecular activity. No catalytic motif or characterized domain is present in the sequence, and the only functional data (a genetic high-copy-suppressor relationship and mutant phenotypes) do not pin a biochemical activity. Reason: ND on the MF root is the appropriate representation for a gene whose molecular function is genuinely undetermined; there is no defensible specific MF term to substitute. This is a real molecular-function knowledge gap (see knowledge_gaps), not a curation omission. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Root biological_process term with ND evidence. Although ICY1 has associated phenotypes (petite-negativity, invasive-growth defect, amino-acid-starvation induction), these are genetic/indirect and do not identify the pathway in which ICY1 acts directly; SGD therefore records the process as undetermined. Reason: ND on the BP root is appropriate. The available phenotypes are consequences that could arise indirectly and do not, on current evidence, justify a specific process annotation. Represented as a knowledge gap rather than an invented process term. |
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Download this section (compressed HTML)Q: Does Icy1p have any detectable biochemical activity or a stable protein/RNA partner that would define a molecular function, and does it physically associate with the cytoskeleton as its name implies?
Suggested experts: Dunn CD, Jensen RE
Q: Is ICY1's requirement for viability of rho0 cells due to a direct effect on mitochondrial inner-membrane potential/protein import, or an indirect cytosolic role shared with the co-identified suppressors?
Suggested experts: Dunn CD, Jensen RE
Experiment: Delete and overexpress ICY1 in import-machinery mutant backgrounds (e.g. tim18delta) and measure mitochondrial inner-membrane potential and in vivo/in vitro protein-import efficiency, testing epistasis with the co-identified suppressors CCT6, SSB1, TIP41 and PBP1.
Hypothesis: Icy1p acts as a non-catalytic factor that supports mitochondrial protein import or inner-membrane potential when import is compromised.
Type: genetic and biochemical epistasis / mitochondrial import assay
Experiment: Affinity-purify tagged Icy1p from cells grown in rich medium and under amino-acid starvation, identify co-purifying proteins by mass spectrometry, and specifically probe for cytoskeletal components; validate top hits by reciprocal co-immunoprecipitation and imaging.
Hypothesis: Icy1p has one or more stable interaction partners that reveal its molecular function and test the implied cytoskeletal connection.
Type: affinity purification-mass spectrometry / interaction validation
Experiment: Quantify endogenous Icy1p localization by live-cell microscopy and subcellular fractionation across rich medium, amino-acid starvation, and rho0 backgrounds to determine which compartment correlates with its phenotypes.
Hypothesis: The functionally active pool of Icy1p is condition-dependent (cytosolic vs. vacuole membrane).
Type: quantitative localization / fractionation
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular function of ICY1 is entirely undetermined: no catalytic activity, ligand, RNA/DNA/protein-binding activity, or structural/scaffolding role has been demonstrated or can be inferred from sequence.
OPEN BIOLOGY MF_DARK
What is known: It is firmly established that ICY1 is a small (127 aa) fungal protein, moderately abundant (~4050 molecules/cell), that localizes to the vacuole membrane in a GFP screen and is reported cytosolic elsewhere. What is unknown is the biochemical activity that ICY1 performs.
Significance: Assigning a specific molecular function would let ICY1's MF annotation move off the ND root and would clarify whether its phenotypes reflect a direct biochemical role or an indirect/regulatory one.
What would resolve it: Biochemical characterization (activity assays, affinity purification with mass-spectrometry identification of stable partners, and structural determination) is required, since no domain/motif or informative ortholog provides a functional handle.
Provenance (the field's own admissions):
Gap: The biological process in which ICY1 acts directly is unknown; whether its requirement for viability of mtDNA-less (rho0) cells reflects a direct role in mitochondrial function/protein import or an indirect cytosolic contribution is unresolved.
OPEN BIOLOGY BP_DARK
What is known: Genetically, ICY1 overexpression suppresses the petite-negative phenotype of mitochondrial-import mutants and icy1 deletion makes cells unable to grow without mtDNA. The gap is the mechanistic pathway linking ICY1 to these outcomes.
Significance: Resolving this would determine whether ICY1 warrants a specific biological-process annotation (e.g. related to mitochondrial homeostasis, protein import, or the response to loss of mtDNA) rather than the ND root.
What would resolve it: Epistasis analysis with the co-identified suppressors (CCT6, SSB1, TIP41, PBP1) and with import-machinery components, plus assays of inner-membrane potential and import efficiency in icy1 mutants, would test the proposed import/membrane-potential model.
Provenance (the field's own admissions):
Gap: The gene name "Interacting with cytoskeleton" is not supported by any verified molecular-interaction evidence in the reviewed literature; whether ICY1 physically or functionally associates with the cytoskeleton is unknown.
OPEN BIOLOGYCURATION MF_DARK
What is known: ICY1 mutants show altered cell morphology (elongated cells, invasive-growth defect), which is consistent with, but does not demonstrate, a cytoskeletal connection. No verified direct cytoskeletal partner is documented here.
Significance: Confirming or refuting a cytoskeletal association would either justify a cytoskeleton-related function/process annotation or formally retire an unsupported implication carried by the gene symbol.
What would resolve it: Targeted interaction assays (co-immunoprecipitation, proximity labeling, two-hybrid against cytoskeletal components) and cytoskeleton-morphology imaging in icy1 mutants would test the association directly.
Provenance (the field's own admissions):
Gap: The functionally relevant subcellular compartment for ICY1 is unresolved: it is reported at the vacuole membrane (GFP screen) yet described as cytosolic in the functional genetics study.
OPEN BIOLOGY CC_DARK
What is known: Both localizations are experimentally reported; there is no transmembrane segment or signal peptide in the sequence, so any membrane association is peripheral. Which pool mediates ICY1's function is unknown.
Significance: Clarifying the active compartment would guide interpretation of the vacuole membrane annotation and connect localization to the mtDNA-viability and morphology phenotypes.
What would resolve it: Endogenous-level, quantitative localization (e.g. under amino-acid starvation vs. rich medium, and in rho0 cells) and fractionation would establish which pool is functional and under which conditions.
Provenance (the field's own admissions):
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