SSB2 review notes

2026-08-12 re-review

• Identity verified as Saccharomyces cerevisiae SSB2/YNL209W, UniProt P40150,
  the canonical ribosome-associated Ssb-type Hsp70 paralog of SSB1/P11484.
• Ssb2 directly binds nascent chains at the cytosolic 60S tunnel exit. RAC's
  Zuo1 J-domain stimulates Ssb ATP hydrolysis, driving the NBD/SBD cycle used for
  ATP-dependent cotranslational folding. PMID:9670014
• GO:0044183 is modified to the more specific GO:0140662, consistent with the
  existing unfolded-protein-binding annotations and SSB1 project decision.
• ATP binding and hydrolysis are genuine core biochemical activities. Broad
  nucleotide-binding and hydrolase parents are over-annotated, while protein
  refolding is retained only as a plausible non-core general Hsp70 capability.
  PMID:9860955
• Plasma-membrane localization is unsupported for this soluble cytosolic Hsp70;
  the IBA transfer is audited against its PANTHER family node. Cytoplasm is true
  but less specific than the core cytosolic ribosome localization.
• The consolidated core function combines GO:0140662 with de novo
  cotranslational folding and cytosolic localization. Translational fidelity,
  frameshifting, and glucose-starvation responses remain supported annotations
  but are not modeled as processes directly carried out by the chaperone MF;
  PMID:15456889 describes fidelity as extending beyond the nascent-chain
  chaperone role.
• Roughly half of cellular Ssb is ribosome-associated, but this is dynamic rather
  than stable complex membership, so the core function uses cytosol as location
  and describes the 60S tunnel-exit position in prose instead of in_complex.

2026-08-28 completion audit

• Reconciled every distinct GOA assertion and added the original qualifiers.
• Audited all eight IBA rows against their actual GOA PAINT nodes:
  PTN002500132 for nucleus, plasma membrane, and cytosol; PTN002321897 for
  cytoplasm; and PTN000452648 for ATP hydrolysis, heat-shock-protein binding,
  protein-folding chaperone activity, and protein refolding.
• The plasma-membrane IBA is a compartment-mismatch propagation failure. The
  independent HDA row from PMID:16622836 is instead retained as an
  over-annotated bulk-fraction observation, using the paper's exact abstract
  description of a stripped plasma-membrane fraction.
• GO:0042026 protein refolding restores activity to an already unfolded or
  misfolded protein; GO:0051083 describes folding a ribosome-bound nascent chain.
  Because the direct Ssb evidence establishes the latter rather than the former,
  the IBA refolding row is modified to GO:0051083 rather than retained as a
  generic Hsp70 capability. PMID:9670014
• Added machine-readable NEW proposals for GO:0043022 ribosome binding and
  GO:0022626 cytosolic ribosome, both directly supported by PMID:9670014 and
  consistent with PMID:1394434. These are missing from the current SSB2 GOA set.

Full annotation re-review — 2026-09-20

Re-read all 41 annotation rows, the cited primary literature, UniProt and the Falcon report. Restored broad cytoplasm, nucleotide-binding, hydrolase and protein-folding-chaperone assertions; retained translation and experimentally recorded plasma-membrane association as non-core. The main cytosolic/ribosomal pool does not disprove a smaller peripheral membrane-associated pool. PMID:16622836 explicitly analyzed proteins from a stripped plasma membrane fraction; there is no basis to assert contamination from the abstract alone.

Traced PAINT PTN002500132 (compartments), PTN002321897 (cytoplasm) and PTN000452648 (Hsp70 functions). Current raw IBD.gaf explicitly records NOT/IRD GO:0042026 at fungal PTN001065099, sourced from PTN000452648 and dated 2026-06-16. The same node records generalized GO:0006457, and current SSB2 leaf PTN000453235 carries that protein-folding descent. Therefore the older refolding IBA is generalized to protein folding; this does not establish zero in-vitro refolding capacity. Current PAINT lacks the older plasma-membrane IBD, but this version discrepancy is not biological refutation of the independent HDA annotation.

Read the complete existing SSB1-versus-SSB2 OpenScientist hypothesis report and reused its substantive finding that paralog-specific substrate/mechanistic differences have not been demonstrated. Its caveat is "absence of evidence for divergence is not the same as proof of perfect functional identity". Primary shared nascent-chain/folding studies support the common function; the report does not investigate refolding and is not treated as an adjudication of that term. Root agreed the explicit current fungal IRD supports the broader-process update without a duplicate SSB2 report.