nce101 (SPAC12G12.17) is a small (58 amino acid) membrane-associated microprotein of fission yeast and the sole S. pombe member of the NCE101 family (InterPro IPR024242, Pfam PF11654, PANTHER PTHR28011), orthologous to Saccharomyces cerevisiae NCE101 (NCE1). The protein carries a single predicted transmembrane helix (residues 10-27) and a short, basic-residue-enriched C-terminal tail, features consistent with a single-pass membrane protein, though its topology and precise subcellular localization have not been experimentally determined. The founding member of the family, budding yeast NCE1, was recovered in a genetic screen for factors affecting a signal-sequence-independent ("non-classical") protein export pathway, and the family is therefore annotated to protein secretion/transport; the original study could not distinguish whether the small protein is part of the export machinery or is itself a non-classically secreted substrate. No molecular activity, interaction partner, or catalytic motif has been identified for the S. pombe protein, and it is classified as a conserved protein of unknown biological role. Genome-wide deletion profiling of the nce101 deletion reports only broad, pleiotropic chemical-stress sensitivity and resistance phenotypes, none of which isolate a specific molecular function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009306 protein secretion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic (IBA) propagation of protein secretion across the NCE101 family (PANTHER PTN001997334), seeded by S. cerevisiae NCE101 whose own annotation derives from the Cleves et al. 1996 non-classical export screen (IGI:SGD, PMID:8655575). This is a defensible family-level inference and there is no positive evidence against it, so it is retained; however it is an indirect inference for a gene with no direct functional data, and even in the founding study the protein's role (machinery versus substrate) was ambiguous, so it should not be treated as an experimentally established core function. Reason: Reasonable phylogenetic inference for an uncharacterized family member, but not demonstrated for the S. pombe protein and interpretively ambiguous at source; keep as a non-core, low-confidence functional context rather than a core function. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: SOURCE EVIDENCE WEAK Sources checked: UniProtKB:Q02820 · S. cerevisiae NCE101 (NCE1) SOURCE WEAK OR INFERRED The OpenScientist database audit identifies the seed annotation as IGI from a single overexpression screen (PMID:8655575) in which the small NCE1 protein's role was ambiguous (machinery versus exported substrate). Supporting Evidence: PMID:8655575 A screen for components of the export machinery has identified genes that are involved in nonclassical export. file:SCHPO/nce101/nce101-deep-research-falcon.md Direct experimental studies on *S. pombe* nce101 are essentially absent from the literature. |
| GO:0009306 protein secretion | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping of the NCE101 family signature (IPR024242) to protein secretion. This is the same family-level inference as the IBA annotation, mapped from the domain model rather than the phylogenetic tree, and is redundant with it. Accurate at the family level but uninformative about the specific molecular function of the S. pombe protein. Reason: Correct family-signature-to-GO mapping but redundant with the IBA and not evidence of a demonstrated function; retain as non-core. |
| GO:0016020 membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Membrane localization mapped from the UniProtKB subcellular-location keyword, which itself rests on a single predicted transmembrane helix (residues 10-27, ECO:0000255) and the curator-inferred single-pass membrane assignment (ECO:0000305). Consistent with the sequence but not experimentally verified; note the S. cerevisiae ortholog also carries a cytosol (HDA) annotation, so the localization is not firmly established. This is an accurate but low-information cellular-component term. Reason: Localization is only predicted (single TM helix) and not experimentally confirmed; the term is not wrong but is uninformative and non-core. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root molecular_function term with the ND (no biological data) evidence code, correctly recording that no molecular function has been experimentally determined for nce101. There is no biochemical activity, ligand, substrate, or catalytic motif described for this protein or its family, so ND is the honest and appropriate annotation. Reason: ND correctly captures a genuine molecular-function knowledge gap; retaining it is the accurate curatorial choice for a dark gene. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: Root cellular_component term with ND evidence, from PomBase. The only localization signal is the predicted transmembrane helix (captured separately by the UniProt SubCell membrane IEA); no experimental localization has been reported, so PomBase's ND annotation reflects the absence of curated CC evidence. Retained as an honest record of the gap. Reason: Accurately records that no experimentally supported cellular component is curated; consistent with a conserved-unknown-function gene. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Root biological_process term with ND evidence. No biological process has been experimentally established for the S. pombe gene; deletion phenotypes are limited to broad, pleiotropic chemical-stress sensitivities and resistances that do not define a specific pathway, and the family-level protein secretion inference is captured by the IBA/IEA annotations. ND appropriately marks the absence of a curated process. Reason: ND honestly records an unknown biological process; the pleiotropic drug phenotypes do not support a specific BP annotation. |
Loading supporting content…
Download this section (compressed HTML)Q: Does S. pombe possess a non-classical (signal-sequence-independent) protein export pathway, and if so does nce101 contribute to it?
Q: Is nce101 a component of a transport/export machinery or is it itself a secreted or membrane-cargo substrate, as the ambiguity in the founding budding-yeast study implies?
Q: What is the true subcellular localization and membrane topology of the Nce101 protein?
Experiment: Determine the endogenous subcellular localization and membrane topology of Nce101 by tagging (avoiding tag-induced mislocalization of a 58-aa protein), fluorescence microscopy, and protease-protection / carbonate-extraction membrane fractionation.
Type: Fluorescence microscopy and membrane fractionation
Experiment: Identify physical interaction partners by co-immunoprecipitation/mass spectrometry or proximity labeling to test the export-machinery hypothesis, and perform secretome analysis of nce101-delta versus wild type to test whether it affects non-classical protein secretion.
Type: Affinity purification / mass spectrometry and secretome analysis
Experiment: Characterize nce101-delta (and combinations with related small membrane proteins, to control for redundancy) under the stress conditions flagged by chemical-genomics screens to connect the pleiotropic phenotypes to a defined cellular process.
Type: Genetic / phenotypic characterization
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular function of nce101 is undetermined: no biochemical activity, ligand, substrate, catalytic residue, or diagnostic sequence motif has been identified for the protein or the NCE101 family.
OPEN BIOLOGY MF_DARK
What is known: The protein is a defined 58-aa NCE101-family member with a single predicted transmembrane helix; its only functional association (protein secretion / non-classical export) is an indirect inference from an overexpression/genetic screen of the S. cerevisiae ortholog, in which the founding authors could not determine whether the small protein acts as part of the export machinery or is itself a non-classically secreted substrate.
Gap: The biological process in which nce101 participates in S. pombe is unknown, and it has not been shown that fission yeast operates a non-classical protein export pathway through nce101.
OPEN BIOLOGY BP_DARK
What is known: Genome-wide deletion profiling of nce101-delta reports only broad, pleiotropic chemical-stress phenotypes (sensitivity to cadmium, diamide, valproate and vanadate; resistance to lithium, MMS, tert-butyl hydroperoxide, EGTA, amorolfine, and various salt/SDS combinations) that do not point to a single pathway.
Gap: The subcellular localization and membrane topology of Nce101 are experimentally undetermined: it is unclear whether the protein is stably membrane-integral, which membrane it occupies, and in what orientation (N-in versus N-out, signal-anchored versus tail-anchored).
OPEN BIOLOGY CC_DARK
What is known: Membrane association is inferred solely from a single predicted transmembrane helix (residues 10-27) and a curator-assigned single-pass membrane annotation; the S. cerevisiae ortholog additionally carries a high-throughput cytosol annotation.
Gap: No loss-of-function phenotype isolates a specific molecular or cellular role, and no interacting partners, complex membership, or regulatory context are known; it is also unresolved whether nce101 is functionally redundant with other small membrane microproteins, which would mask deletion phenotypes.
OPEN BIOLOGY WHOLLY_DARK
What is known: A viable deletion strain exists and has been chemically profiled, but the resulting phenotypes are pleiotropic and non-diagnostic.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)