AI GO-annotation review of the understudied fission-yeast gene ahk1 (PomBase standard
name; systematic name SPAC7D4.03c; UniProt O14260, entry name YFP3_SCHPO). This is a
"dark gene": PomBase characterisation status is "biological role inferred" and all of its
functional GO annotations are transferred by orthology (ISO), not experimentally determined in
S. pombe.
name: ahk1, product: "MAP kinase cascade scaffold protein Ahk1",characterisation_status: "biological role inferred", deletion_viability: viable,taxonomic_distribution: fungi only (PomBase JSON API, gene SPAC7D4.03c, latest dataset).RecName: Full=UPF0592 membrane protein C7D4.03c; 886 aa;PE 3: Inferred from homology. Belongs to the UPF0592 family (-!- SIMILARITY, ECO:0000305).Membrane; Multi-pass membrane protein (ECO:0000305, inferred).Both functional GO annotations on S. pombe ahk1 are ISO (inferred from sequence orthology),
with-from SGD:S000002231:
- GO:0005078 "MAP kinase scaffold activity" — ISO, GO_REF:0000024, with SGD:S000002231.
- GO:0000165 "MAPK cascade" — ISO, PMID:26787842, with SGD:S000002231.
- PomBase ortholog_annotations lists YDL073W (S. cerevisiae AHK1) as ortholog via
InterPro:IPR013887 (the UPF0592 family), and SJAG_04503 (S. japonicus) via
PMID:21511999. PomBase orthogroup SOG_0639. (Note the curated orthologs list is empty; the
cross-species relationship is captured as an InterPro-family-based ortholog_annotation, i.e. it
is a domain-family/homology call, not a 1:1 syntenic ortholog assertion.)
S. cerevisiae AHK1 (YDL073W, SGD:S000002231) is a Verified ORF described by SGD as
"Scaffold protein in the HKR1 sub-branch of the Hog1p-signaling pathway; physically interacts with
the cytoplasmic domain of Hkr1p, and with Sho1p, Pbs2p, and Ste11p; prevents cross-talk signaling
from Hkr1p of the osmotic stress MAPK cascade to the Kss1p MAPK cascade; non-essential"
(yeastgenome.org locus S000002231).
PMID:26787842 is entirely about the budding-yeast (S. cerevisiae) Ahk1:
- PMID:26787842
- PMID:26787842
- PMID:26787842
- PMID:26787842
This paper does NOT assay the S. pombe protein. Cache marks full_text_available: false
(abstract only). The paper is the experimental basis for the S. cerevisiae annotation that is
then transferred to S. pombe by ISO.
17 single-locus (ahk1Δ) phenotypes are recorded in PomBase, all from systematic screens
(no gene-focused study). References and phenotype highlights:
- PMID:20473289 — genome-wide deletion set (Kim et al.). ahk1Δ viable.
- PMID:23697806 — cell-cycle/cell-shape genome-wide resource.
- PMID:28410370 — systematic screen of sexual-reproduction morphology (identifies mating/shmoo
abnormalities): abnormal shmoo morphology (FYPO:0000357), shmoo formation at cell side
(FYPO:0006011), promiscuous mating (FYPO:0006014).
- PMID:34250083 — chronological lifespan barcode screen: loss of viability in stationary phase
(FYPO:0000245) (ageing-associated).
- PMID:35820914 — yeast-ageing protease study.
- PMID:37787768 — broad phenomics/machine-learning functional profiling: stress sensitivities and
resistances — sensitive to caffeine (FYPO:0000097), cycloheximide (FYPO:0000104), hydroxyurea
(FYPO:0000088), tunicamycin (FYPO:0001457), KCl+SDS (FYPO:0007924); resistant to MMS
(FYPO:0000725), vanadate (FYPO:0000830), lithium (FYPO:0001583), LiCl+SDS (FYPO:0009085),
MgCl2+SDS (FYPO:0009087).
Interpretation: the deletion phenotype fingerprint (osmotic/salt/cell-wall-stress, caffeine,
mating/shmoo abnormalities) is broadly consistent with a role in stress-responsive signaling,
which fits the orthology-based MAPK-scaffold assignment. But NONE of these screens establishes a
molecular mechanism, a direct binding partner, or a specific, non-redundant place in the Sty1/Spc1
(Hog1-like) SAPK pathway for the S. pombe protein.
KNOWN (or well-supported):
- Fungal-only protein of the UPF0592/DUF1765 family; large (886 aa); predicted multi-pass membrane
protein with a disordered region. (UniProt, InterPro, PANTHER.)
- Non-essential (ahk1Δ viable). (PMID:20473289.)
- Deletion perturbs stress responses and sexual-reproduction morphology in genome-wide screens.
- Its S. cerevisiae homolog (AHK1/YDL073W) is an experimentally validated scaffold in the HKR1
sub-branch of the Hog1 osmostress MAPK pathway. (PMID:26787842.)
NOT KNOWN (the deliverable knowledge gaps):
- Whether S. pombe ahk1 actually functions as a MAPK scaffold, or is a scaffold at all — this is
purely an orthology transfer via the shared UPF0592 domain family (IPR013887), never tested in
S. pombe.
- Its direct binding partners in S. pombe (does it bind Sty1/Spc1, Wis1, Win1/Wak1, Sho1-like
components, or the Wsc1/Mtl2 osmosensors?). Unknown.
- Whether it has any specific, non-redundant role in the Sty1/Spc1 SAPK pathway (the pombe
osmostress core is Wis1→Sty1; there is no exact Hkr1/Kss1 cross-talk architecture in pombe, so
the budding-yeast "prevents Hkr1→Kss1 cross-talk" role may not map directly).
- Its precise molecular activity (DUF1765 has no assigned biochemical function).
- Its subcellular localization in S. pombe (membrane prediction only; not experimentally shown).
scripts/deep_research_wrapper.py SCHPO SPAC7D4.03c falcon --fallback perplexity-lite was run in
the foreground twice; it hung (exit 124 / 550s timeout) after emitting only the
"Using SPAC7D4.03c as gene symbol" line, producing no report. Per project policy, no
-deep-research-*.md file was fabricated; this review is grounded in UniProt + GOA + PomBase +
the cached publication, all with explicit provenance above.