SSA3 review notes

Description cleanup note

The YAML description field was revised to keep it as a standalone biological summary. Project-specific curation framing moved here instead.

• Moved out of the YAML description: wording was adjusted from cytosol/nucleus proteostasis network to avoid confusion with project-specific Proteostasis Network terminology.

2026-08-22 re-review

• Identity was rechecked as Saccharomyces cerevisiae SSA3/YBL075C, UniProt
  P09435: the stress-inducible cytosolic Ssa-family Hsp70 paralog. SSA3 is
  normally expressed at very low levels but can provide essential Ssa function
  when expressed constitutively. PMID:3302682
• The core function is consolidated as ATP-dependent protein folding chaperone
  activity (GO:0140662) in cytosolic folding/refolding. The broader
  GO:0044183 IBA is modified to that mechanistically precise child term, and
  generic nucleotide binding is marked over-annotated because ATP binding and
  ATP hydrolysis are already represented. SSA-family Hsp70 is experimentally
  required for folding newly translated cytosolic proteins. PMID:9789005
• The two GO:0006616 annotations are modified rather than simply retained as
  non-core. Becker et al. tested precursor import into the ER and mitochondria,
  with the strongest rapid direct effect on ER prepro-alpha-factor import. The
  replacement therefore uses the ER-scoped post-translational sibling
  GO:0031204, not the existing SRP-dependent cotranslational label; the separate
  mitochondrial phenotype is not encoded by that replacement. PMID:8754838
• The plasma-membrane IBA is removed as a stale PAINT transfer. The pinned 2025
  GOA row points to PTN002500132, but the current local PTHR19375 PAINT snapshot
  carries nucleus and cytosol at that node and no longer carries GO:0005886.
  This is a current-node comparison, not an inference from donor count. UniProt
  and the SSA3-focused literature consistently identify Ssa3 as cytosolic; no
  target-specific plasma-membrane evidence was found. A
  targeted OpenScientist hypothesis run independently preferred REMOVE because
  it found no SSA3-specific experimental support. Its live QuickGO claims that
  the P09435 IBA had been retired and that Ssa4 lacked the same IBA conflict with
  the repository's pinned GOA snapshots, so those claims are explicitly marked
  disputed and are not used in the decision. [file:yeast/SSA3/SSA3-hypotheses/existing-go-0005886-keep-as-non-core/openscientist.md
  "The plasma-membrane assignment is a phylogenetic (IBA) inference only"]
• The PMID:10745074 cached abstract is not treated as a direct SSA3 localization
  experiment: it describes cytoplasmic Ssa-family Hsp70s but reports the detailed
  transport/localization results for Ssa1/2. The cytosol annotation remains
  accepted because that location is independently established and the curator
  had access to more evidence than the cached abstract.
• The UNFOLDED_PROTEIN_BINDING project row now uses GO:0140662 for SSA3, aligning
  the project decision with the review's ATP-dependent Hsp70 mechanism.

2026-08-27 row-completeness follow-up

• The review was promoted from DRAFT to COMPLETE after restoring one review
  record for every one of the 55 pinned GOA rows. Repeated IPI and IGI rows are retained
  separately by reference and WITH/FROM partner rather than collapsed.
• Generic nucleotide binding is now MODIFY to the existing specific ATP-binding
  term GO:0005524, matching the treatment of the same parent term in SSA4.

2026-09-29 IBA follow-up

• Rechecked all eight GO_REF:0000033 IBA rows against
  interpro/panther/PTHR19375/PTHR19375-paint.tsv. The accepted nucleus,
  cytoplasm, cytosol, ATPase, heat-shock-protein-binding, protein-folding
  chaperone, and protein-refolding transfers all still trace to current PAINT
  rows; the pinned plasma-membrane IBA remains stale because current
  PTN002500132 carries only GO:0005634 nucleus and GO:0005829 cytosol.
• Recorded the 2026 fungal PTN001065099 GO:0042026 protein refolding NOT/IRD
  and retained the SSA3 transfer because the pinned row still descends from the
  PTN000452648 refolding IBD and has no GO:0006457 protein folding
  replacement IBA.
• Added missing propagation_review.source_entities blocks for the accepted
  IBA rows and expanded the PTN-only chaperone IBA with representative current
  donors from PTN000452648.
• Searched PubMed for exact SSA3/Ssa3/YBL075C mentions in 2025-2026 and
  found no new exact-match papers that change the Ssa3 curation.
• Converted the legacy bare GO:0005515 protein binding rows from generic
  high-throughput interaction datasets to REMOVE; the two Hsp70-paralog
  interaction rows remain MODIFY to GO:0030544 Hsp70 protein binding.

2026-10-01 current-GOA refresh follow-up

• Forced a current fetch-gene refresh because live GOA for SSA3 has moved from
  55 historical rows to 19 rows. The review now keeps all historical source
  assertions and marks rows that no longer exactly match live GOA as
  retired: true rather than losing the earlier curation.
• Reviewed all newly exact current rows: the refreshed PTN002321897
  GO:0005737 cytoplasm and PTN000452648 GO:0016887 ATP hydrolysis activity
  IBAs are accepted as supported inherited Ssa/Hsp70 assertions, the refreshed
  PTN000452648 GO:0044183 protein folding chaperone IBA remains a sound
  transfer but is narrowed to GO:0140662 ATP-dependent protein folding chaperone, InterPro2GO GO_REF:0000002 now provides the ATP-binding and
  ATP-hydrolysis IEAs, and the new ARBA GO:0030163 protein catabolic process
  row is kept as non-core because degradation is a contextual branch of Ssa
  client handling.
• The 2026 PAINT rows still use SSA3 itself as a descendant evidence source for
  cytoplasm and ATP hydrolysis. This is correct for an inherited IBA grounded in
  target-family experimental evidence, not circular support.
• Searched PubMed for exact SSA3/Ssa3/YBL075C mentions in 2025-2026.
  The only exact hit was PMID:41314856, a Saccharomyces boulardii
  gastric/intestinal stress proteomics study that mentions APJ1 and SSA3 as
  condition-specific chaperone hubs in the abstract; it did not change the
  S. cerevisiae S288C GO review.