APS1 (P35181, YLR170C) notes

2026-10-21 — Full re-review, independent of the ProtNLM2 predictions

Context: APS1 is the experimentally characterised S. cerevisiae relative of S. pombe vas2/Aps1 (Q9P7N2).
ProtNLM2 output was not consulted.

just fetch-gene yeast APS1 created the stub (32 GOA rows).
just deep-research-falcon yeast APS1 --fallback perplexity-lite FAILED: falcon failed and the
perplexity-lite fallback timed out after 600 s. No deep-research file exists. The review is built from
cached literature that I read directly.
Extra papers cached: PMID:8157009 (Phan 1994), PMID:8373805 (YAP19 cloning), PMID:11879634
(Valdivia 2002), PMID:26658609 (Whitfield 2016, full text), PMID:19624755 (S. pombe AP-1, Ma 2009),
PMID:16823372 (S. pombe ORFeome).

UniProt: "Belongs to the adaptor complexes small subunit family." PANTHER family PTHR11753; according to the
task brief, PANTHER 19 places APS1 and S. pombe Q9P7N2 together in PTHR11753:SF5 "AP COMPLEX SUBUNIT SIGMA".
I did not re-query this myself; the SF5 name is confirmed in interpro/panther/panther.obo.
PAINT (interpro/panther/PTHR11753/PTHR11753-paint.tsv): the only IBD nodes are at the root PTN000204281, for
GO:0016192 vesicle-mediated transport and GO:0043231 intracellular membrane-bounded organelle. SGD:S000004160
(APS1) is itself an experimental donor. PAINT propagated no AP-1-specific term (such as AP-1 adaptor complex)
from the root, which is correct because the root covers sigma1/2/3/4 and COPI zeta.
The ISS localization rows come from S. pombe Q9P7N2, which is in the same subfamily. The Golgi, endosome and
CCV localizations in pombe come from the AP-1 subunit study PMID:19624755. The nucleus and
cytoplasm localizations come only from the genome-wide ORFeome GFP screen (PMID:16823372). I therefore
marked nucleus as over-annotated.

AP-1 subunit composition, including Aps1, by co-IP; only AP-1 binds clathrin PMID:10564262. Abstract only.
Aps1 co-fractionates with CCVs. aps1 deletion has no phenotype alone, but it worsens chc1-ts growth and
alpha-factor maturation PMID:8157009.
Aps1 is shared by AP-1 and AP-1R PMID:26658609. The aps1 deletion
raises surface levels of the Snc1 reporter GSS PMID:26658609.
AP-1 retains Chs3 and Tlg1 in the TGN/early endosome PMID:11879634. The abstract speaks of AP-1 in general, not of
aps1 specifically.
AP-1 mutants fail to deliver ubiquitylated cargo to the vacuole lumen. The paper attributes this to defective
Fab1 activation (PMID:17003107). I kept the IMP Golgi to vacuole transport row, as non-core.

Dileucine-signal recognition by the gamma/sigma hemicomplex. In yeast this is stated by analogy
PMID:26658609. It has not been mutationally mapped to Aps1. Hence contributes_to clathrin-cargo adaptor activity.

AP-1 adaptor complex (EXP/IDA/NAS/IEA) and CCV membrane: ACCEPT.
Clathrin-cargo adaptor activity (IEA): ACCEPT. ND root: MODIFY to GO:0035615.
10 bare protein-binding IPI rows (all with other AP-1 subunits): REMOVE under the protein-binding policy.
Golgi apparatus, endosome: ACCEPT. Cytoplasm and membrane coat: TOO_GENERAL, since both are entailed by
AP-1 adaptor complex. Nucleus: MARK_AS_OVER_ANNOTATED.
Intracellular protein transport and vesicle-mediated transport (IBA and IEA): ACCEPT. Protein transport:
TOO_GENERAL. Intercellular transport (ARBA): REMOVE. Golgi to vacuole transport (IMP): KEEP_AS_NON_CORE.
No NEW terms. UniProt also carries GO:0048203 (vesicle targeting, trans-Golgi to endosome; IMP from
ComplexPortal), but it is not in the GOA set and I did not add it. Valdivia's model is endosome-to-TGN
recycling, so the direction is not settled.