hsp-3 (C. elegans) — Research Notes

Gene: hsp-3 / HSP70C / C15H9.6 / WBGene00002007
UniProt: P27420 (HSP7C_CAEEL), 661 aa precursor
Taxon: NCBITaxon:6239 (Caenorhabditis elegans)

Identity / one-line summary

hsp-3 is one of the two C. elegans endoplasmic-reticulum (ER)-resident HSP70/BiP
(GRP78/KAR2) orthologs; the other is hsp-4 (F43E2.8, WBGene00002008, P20163). HSP-3 is
an ATP-dependent chaperone of the ER lumen that assists folding/quality control of secretory
and membrane proteins. HSP-3 is generally regarded as the more constitutively expressed
BiP paralog, whereas hsp-4 is the strongly stress-inducible paralog and the source of the
canonical hsp-4::GFP ER-stress reporter.

KNOWN (well-grounded)

Molecular architecture / family

• UniProt: RecName: Full=Heat shock 70 kDa protein C; Flags: Precursor; — belongs to the
  HSP70 family. Signal peptide 1–17; C-terminal ER-retention motif (residues 658–661,
  MOTIF ... "Prevents secretion from ER"; the sequence ends ...DDKDEL, so the functional
  retention tetrapeptide is KDEL — note HSP-4 instead uses HDEL). Canonical HSP70
  nucleotide-binding domain (NBD) + substrate-binding domain (SBD) architecture (InterPro
  BIP_NBD IPR042050; CDD ASKHA_NBD_HSP70_BiP). [UniProt:P27420]
• ATP binding / ATP hydrolysis are family-level MFs (UniProt KW ATP-binding, Nucleotide-binding;
  GOA IBA GO:0016887, IEA GO:0005524, ISS GO:0016887 by similarity to yeast KAR2 P16474).

Localization

• ER lumen. UniProt: SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. Directly stated for
  HSP-3 in the FIC-1 paper: PMID:27138431. The signal peptide + DDKDEL retention motif are consistent.
• The pan-HSP70 IBA also propagated cytoplasm, nucleus, and membrane to HSP-3. These are
  ancestral/aspecific localizations of the broad HSP70 family (which includes cytosolic and
  nuclear members); for a dedicated ER-lumenal BiP with a cleaved signal peptide and DDKDEL
  motif, these are over-propagations, not the functional site.

Function — ER protein folding chaperone

• UniProt FUNCTION (by similarity): Probably plays a role in facilitating the assembly of multimeric protein complexes inside the ER. [UniProt:P27420]
• The two worm BiPs are treated as chaperones that cross-compensate:
  PMID:27138431.
• GOA: protein folding chaperone (GO:0044183, IBA), protein refolding (GO:0042026, IBA),
  ATP hydrolysis activity (GO:0016887), heat shock protein binding (GO:0031072, co-chaperone
  interactions), endoplasmic reticulum chaperone complex (GO:0034663), ERAD pathway
  (GO:0036503, IBA).

Function — UPR / ER stress

• HSP-3 (with HSP-4) is part of the BiP-type repressive brake on the three UPR sensors:
  PMID:27138431.
• hsp-3 is itself an ER-stress/UPR target. In the Urano et al. genome-wide microarray, the gene
  C15H9.6 (= hsp-3) appears in Table I (genes whose tunicamycin induction is attenuated in
  xbp-1(zc12) mutants): induction in N2 = 1.32 ± 0.06 (log2), reduced to 0.68 ± 0.05 in the
  xbp-1 mutant — i.e. hsp-3 IS ER-stress-inducible and xbp-1/ire-1-dependent, though more
  modestly than hsp-4 (F43E2.8; 1.92 → 0.44) and the sHSPs. [PMID:12186849 — Table I lists
  C15H9.6 ... 1.32 ± 0.06 ... 0.68 ± 0.05; general framing: "in C. elegans, the ire-1 and
  xbp-1 pathway has retained its essential role in upregulating expression of many UPR target
  genes that are similarly upregulated by the homologous pathway in yeast"].
  NOTE (paralog caution): the extracted Urano Table I places the display label "HSP-4" next to
  cosmid C15H9.6, but C15H9.6 is unambiguously hsp-3 per WormBase/UniProt ORFName; the GOA
  IEP/HEP annotation of hsp-3 to UPR is therefore based on the gene actually assayed, not a
  mislabel.
• GOA IEP GO:0030968 / GO:0036498 from Shen et al. 2001 PMID:11779465 (abstract-only in cache;
  curator read full text — the foundational C. elegans UPR paper that established
  ire-1/xbp-1-dependent UPR-target transcription). Defer to curator.

PTM

• HSP-3 is a direct substrate of the FIC-1 AMPylase (covalent AMP addition). UniProt: PTM: AMPylated by fic-1. {ECO:0000269|PubMed:27138431}. Direct MS evidence:
  PMID:27138431.

Physiology (hsp-3-specific)

• HSP-3 contributes to tolerance of chronic ER stress and innate immunity:
  PMID:27138431.
• Recent paralog-resolved work (Urban et al. 2025, Nat Commun 10.1038/s41467-025-65998-0; bioRxiv
  2025.01.14.633073) shows the two BiPs are functionally diversified: HSP-3 carries the more
  canonical ER-folding role while HSP-4 is specialized for interorganellar signaling / ER-phagy
  (Sec-62/C18E9.2) and ER-stress mitigation, together controlling body growth, reproduction,
  stress resistance, aging, and autophagy. (DOI-level; not in local PMID cache.)

NOT known / gaps

• The molecular basis of the hsp-3 vs hsp-4 division of labor — differential client
  repertoire, tissue programs, and signaling interfaces — is unresolved; the paralogs are still
  largely "assumed to cross-compensate" PMID:27138431. Which clients specifically require
  HSP-3 (vs HSP-4) is not established.
• The functional consequence of HSP-3 AMPylation by FIC-1 (does it inhibit/tune HSP-3
  chaperone/ATPase activity in vivo, and under what conditions?) is unknown:
  PMID:27138431; and
  PMID:27138431.
• Whether the classic BiP→UPR-sensor repression mechanism is exerted specifically by HSP-3 (vs
  HSP-4, or requiring both) in worms is inferred from mammalian precedent (ref [23] in the FIC-1
  paper) rather than shown directly for HSP-3.

Annotation-review plan (21 GOA annotations)

MF/biology core (ACCEPT): GO:0005788 ER lumen (IBA+IEA); GO:0016887 ATP hydrolysis (IBA/IEA/ISS);
GO:0005524 ATP binding (IEA); GO:0044183 protein folding chaperone (IBA); GO:0042026 protein
refolding (IBA); GO:0031072 heat shock protein binding (IBA); GO:0034663 ER chaperone complex
(IBA+ISS).

UPR (ACCEPT, hsp-3 assayed/part of machinery): GO:0030968 ER UPR (IBA/IEA/IEP×1/HEP×1);
GO:0036498 IRE1-mediated UPR (IEP+HEP).

Non-core (KEEP_AS_NON_CORE): GO:0036503 ERAD pathway (IBA — genuine BiP QC role but no
hsp-3-specific evidence, peripheral to the constitutive folding role).

Over-propagations from pan-HSP70 IBA (MARK_AS_OVER_ANNOTATED): GO:0005737 cytoplasm; GO:0005634
nucleus; GO:0016020 membrane — HSP-3 is a soluble ER-lumen protein (signal peptide + DDKDEL).

Additional findings surfaced by falcon deep research (hsp-3-deep-research-falcon.md)

The falcon report (real output, 28 citations; verified against primary sources where cached)
corroborates and extends the above. Notable additional, literature-grounded points (cited to
the report's own sources — not all are in the local PMID cache, so treated as context, not as
GOA-annotation evidence):
- AMPylation site mapped to Thr176 in the NBD; consequences for HSP-3 chaperone activity
"remain to be fully elucidated"; FIC-1 selectively AMPylates HSP-3 (not HSP-4)
(truttmann2016; camara2022). Reinforces knowledge-gap 2.
- HSP-3 is ~5-fold more abundant than HSP-4 basally and only ~2-fold DTT-inducible (vs ~9-fold
for hsp-4); IRE-1 is required for hsp-3 basal expression (urban2025; shen2001).
Confirms hsp-3 = the constitutive paralog.
- UPR-independent, infection-specific immune role: Couillault et al. 2012 place HSP-3
downstream of NIPI-3 / upstream of TPA-1 in epidermal nlp-29 antimicrobial-peptide control
during Drechmeria coniospora fungal infection — not shared with HSP-4, not via canonical
UPR. (Not in GOA; noted for completeness.)
- BiP as a temperature sensor (Shi et al. 2024): at 30°C, folding demand sequesters BiP
(hsp-3/hsp-4), lowering free BiP and driving ERAD-dependent degradation of TRA-2 to promote
male germline fate. Provides worm-specific ERAD context (kept hsp-3 ERAD as non-core since
attributed to BiP collectively).
- Germline-specific hsp-3 ablation shortens lifespan; intestine-specific loss does not
(urban2025) — tissue-specific physiology.

Provenance index (cached publications used)

• PMID:27138431 — FIC-1 AMPylase paper (full text). HSP-3-specific: ER-lumen localization,
  AMPylation, UPR-sensor complex, ER-stress/immunity role. HIGH relevance.
• PMID:12186849 — Urano et al. 2002, JCB (full text). Microarray; C15H9.6/hsp-3 is an
  xbp-1-dependent UPR target (Table I). HIGH relevance.
• PMID:11779465 — Shen et al. 2001, Cell (abstract-only). Foundational C. elegans UPR paper;
  source of IEP UPR annotations. MEDIUM–HIGH relevance.
• PMID:2225768 — Heschl & Baillie 1990, review (abstract-only). HSP70 multigene family; ISS
  source for ATP hydrolysis. LOW–MEDIUM relevance.
  
  

2026-09-21 full-gene re-review

All21 original assertions preserved. One old NEW folding parent was withdrawn as redundant with existing refolding; function remains in the synthesis. Actual PTHR19375 target PTN000452754 is below cytoplasm PTN002321897 and BiP node PTN001834223, which carries ER lumen, nucleus, membrane, ERAD and chaperone-complex inferences. No loss was recovered. Nuclear/membrane donors are BiP-family proteins, not a spurious arbitrary cytosolic-HSP70 transfer. Cytoplasm includes the ER. Membrane GO:0016020 includes attached proteins. Nucleus includes nuclear envelope/perinuclear space; donor PMID:1373379 explicitly observes BiP in nuclear envelope. Thus cytoplasm/membrane/ERAD restored core, nuclear retained as contextual inference, without asserting worm nucleoplasmic localization.

Falcon narrative/tables read and new primary leads fetched. Full PMID:41387410 Results/Methods/Discussion give HSP-3/HSP-4 expression and perturbation phenotypes; Discussion calls canonical HSP-3 refolding a model. There are no purified refolding/ATPase measurements; direct BiP/IRE1/Sec62 co-IP is human A549. Full PMID:39134659 shows Hsp-4 RNAi can suppress both paralogs, uses double-mutant dosage to establish redundancy, and directly co-IPs TRA-2 with HSP-4 in HEK293 cells. That is not direct HSP-3 binding or disposal by HSP-3; no new germline process annotation manufactured. Full PMID:22546897 says “It is conceivable that HSP-3 has a UPR-independent function outside the ER.” This is a hypothesis, not an observed extra-ER pool; infection phenotypes are retained in the description/references without NEW.

Full PMID:27138431 and itsS2 assay caption separate worm-lysate incubation with recombinant FIC-1 from intact-animal evidence. Thr176 modification is established with purified protein, not a demonstrated in-vivo site. The old direct-localization and triple-UPR-sensor-complex claims were background extrapolations; corrected findings/reasons preserve conserved function with honest assay scope. No exact OpenScientist report existed; verified primary and BiP source topology resolved the over-harsh disputed calls, so no overlapping new request was necessary.

Recovery PR follow-up (2026-09-22)

Restored readable GO/PMID/PTN identifiers in curation prose. For DCV1, core
localization cites the recorded UniProt topology and SGD-attributed observation;
the unrelated Rim101 report sentence no longer supports plasma-membrane location.
For YAR1, unanswered report questions are not positive evidence. For SSQ1, the
located Nop1 association remains recorded while its generic binding label is removed.
The annotation changes apply only to the relevant gene; no inherited location is
rejected solely from its best-characterized compartment.