SSA1 review notes

2026-08-22 re-review

• Identity was rechecked as Saccharomyces cerevisiae SSA1/YAL005C, UniProt
  P10591: the major constitutively expressed cytosolic Ssa-family Hsp70. The
  standalone description was narrowed to the core ATP-dependent chaperone
  mechanism and no longer presents every reported high-throughput localization
  as an equivalent site of function.
• The core molecular function remains ATP-dependent protein folding chaperone
  (GO:0140662), supported by direct Ssa1 ATPase regulation and Ssa1/2 folding
  and refolding experiments. The broader GO:0044183 IBA is modified to this
  mechanistically precise child, and generic nucleotide binding is marked
  over-annotated. PMID:7737974 PMID:8947547
• The two GO:0006616 annotations are modified to GO:0031204 because the
  SSA/Ydj1 evidence concerns post-translational precursor import rather than
  SRP-dependent cotranslational targeting. The negative cell-free result from
  PMID:8947547 is retained as a scope limitation. PMID:8754838
• Nuclear, vacuolar-membrane, and cell-wall localizations are retained as
  non-core because they have experimental support but are secondary to the
  predominant cytosolic chaperone function. The cell-wall evidence includes
  intact-cell immunofluorescence and extracellular biotinylation; the
  vacuolar-membrane evidence is tied to Ape1 transport. PMID:8755907 PMID:10745074
• The plasma-membrane IBA and HDA rows are now separated by evidence source.
  The pinned IBA cites PTN002500132, but the current local PTHR19375 PAINT
  snapshot has nucleus and cytosol at that node and no GO:0005886; the IBA is
  therefore removed as SOURCE_STALE_OR_MISSING, based on node content rather
  than donor count. The HDA is retained conservatively as non-core.
  The cached PMID:16622836 record is abstract-only and confirms a stripped
  plasma-membrane proteomics workflow but does not itself name Ssa1, so the
  citation is marked UNVERIFIED rather than used to claim a primary functional
  localization. A targeted OpenScientist run independently concluded that
  non-core retention is defensible because the experiment is bulk
  co-purification rather than a demonstrated functional site. Its live QuickGO
  claim that P10591 has no plasma-membrane IBA conflicts with the pinned SSA1
  GOA snapshot, which still contains GO:0005886 IBA from GO_Central dated
  2025-09-03. That claim is marked DISPUTED and is not used to alter the source
  evidence code. [file:yeast/SSA1/SSA1-hypotheses/existing-go-0005886-keep-as-non-core/openscientist.md
  "treating plasma membrane as non-core is the correct handling of the evidence
  weight"]
• The inherited review collapsed 242 pinned GOA rows to 70 review records,
  chiefly by representing eight high-throughput IPI datasets once each. The
  2026-08-27 audit expands every repeated dataset row with its exact WITH/FROM
  identifier and removes a redundant NEW pseudo-row from
  existing_annotations; the review now reconciles exactly 242/242.
• A stricter post-rebase audit also confirmed one-to-one WITH/FROM provenance
  for every IPI row after adding the exact pinned accession to ten singleton
  review summaries.
• PR review follow-up separated two targeted Ssa1-Sse1 biochemical/structural
  studies from bulk interaction screens: the former support refinement of
  generic protein binding to heat shock protein binding, whereas partner
  identity alone does not. The GO:0031072 IBA rationale is now anchored to
  PAINT node PTN000452648 and those targeted studies rather than to discounted
  high-throughput IPI rows. PMID:16688211 PMID:18555782
• The UNFOLDED_PROTEIN_BINDING project row now uses GO:0140662 for SSA1 and
  describes its constitutive cytosolic Hsp70 role. SSA1 is also part of the
  BIOREASON_COMPARISON benchmark, but that project consumes the review through
  generated benchmark outputs rather than a manually maintained per-gene claim.
• Every PMID supporting an experimental, high-throughput, or NAS row now has a
  manual reference_review. Dataset papers and abstract-only records are marked
  UNVERIFIED whenever the SSA1-specific edge or assay is not visible; direct
  Ssa1 experiments are marked VERIFIED only when the cached text exposes the
  relevant evidence. With the exact 242-row reconciliation and all actions
  resolved, the review is promoted to COMPLETE.

2026-09-29 IBA re-review

• All eight IBA rows were rechecked against the GOA WITH/FROM PAINT nodes and
  the current local PTHR19375 cache. PTN000452648 still carries the core ATP
  hydrolysis, heat shock protein binding, protein folding chaperone, and protein
  refolding assertions; PTN002321897 still carries broad cytoplasm; PTN002500132
  still carries nucleus and cytosol but not plasma membrane. The stale
  PTN002500132/GO:0005886 plasma-membrane IBA therefore remains the only IBA
  removal, while the other IBA rows now carry explicit structured
  propagation_review provenance.
• The 189 remaining legacy GO:0005515 high-throughput IPI rows were changed
  from MARK_AS_OVER_ANNOTATED to REMOVE, matching the project rule that
  generic protein binding is uninformative rather than an over-specific
  biological-process claim. The two Ssa1-Sse1 targeted rows stay MODIFY to
  the better-supported GO:0031072 heat shock protein binding term.
• A 2024 PNAS Sup35 amyloid paper and three full-text 2024-2025 Ssa1/Ssa2
  papers were cached and added as manually verified references: PMID:39656207
  maps Sup35 residues 143-164 as an Ssa1/Sis1-dependent amyloid-disaggregation
  determinant; PMID:39795068 maps Ssa1-EEVD/Sis1 contacts by NMR; PMID:40202836
  shows Ssa1, Sis1, and Hsp104 overexpression can limit Pab1 inclusions in
  cells lacking SSA1 and SSA2; and PMID:41390490 places Ssa1 T492 phosphorylation
  downstream of heat-induced Mid2/Pkc1 signaling.

2026-10-01 current-GOA reconciliation

• just fetch-gene yeast SSA1 --force reconciled the review against the live
  70-row GOA feed. The refresh seeded three new current assertions, backfilled
  67 qualifiers and 40 supporting-entity lists, and left 175 exact historical
  assertions from older local GOA snapshots outside the current feed. Those 175
  rows are retained in existing_annotations with retired: true so the source
  provenance remains visible while validation and the rendered review focus on
  the live 70 rows.
• The three new current rows were reviewed from cached evidence rather than left
  PENDING: GO:0005524 ATP binding from InterPro was accepted as a distinct
  nucleotide-binding-domain activity; GO:0017053 Hap1-Ssa-Ydj1-Sro9
  transcription repressor complex was kept as a non-core chaperone context; and
  GO:0070585 protein localization to mitochondrion was kept as non-core because
  PMID:8754838 supports an Ssa/Ydj1 effect on one tested mitochondrial precursor
  but not a general mitochondrial-import role.
• PTHR19375 was refreshed and the seven live IBA rows plus the retired
  historical plasma-membrane IBA were rechecked against PTN000452648,
  PTN002321897, and PTN002500132. The live nodes still support ATP hydrolysis,
  heat-shock-protein binding, protein folding chaperone, protein refolding,
  cytoplasm, cytosol, and nucleus; PTN002500132 still lacks GO:0005886, so the
  historical plasma-membrane IBA remains marked REMOVE as stale.
• Searches for newer Ssa1 papers found no uncached primary paper that changed the
  review. The relevant 2024-2025 papers found in the search were already cached
  and had been reviewed in the 2026-09-29 pass: PMID:39656207, PMID:39795068,
  PMID:40202836, and PMID:41390490.