HSP-60 is the C. elegans mitochondrial matrix chaperonin, a member of the HSP60/GroEL family. It functions as an ATP-dependent protein folding machine that works in concert with the co-chaperonin HSP-10 to assist folding of newly imported mitochondrial proteins and to refold stress-damaged proteins in the mitochondrial matrix. HSP-60 assembles into double heptameric rings (tetradecamer) forming a central folding chamber, and the ATP hydrolysis cycle drives conformational changes that encapsulate and fold substrate proteins. The hsp-60 gene is a canonical target of the mitochondrial unfolded protein response (UPRmt), regulated by the transcription factor ATFS-1. HSP-60::GFP reporters are widely used as readouts of UPRmt activation. Beyond its chaperone role, a cytosolic fraction of HSP-60 contributes to innate immunity via stabilization of SEK-1 and activation of PMK-1/p38 MAPK signaling.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006457 protein folding | IBA GO_REF:0000033 | ACCEPT | Summary: HSP-60 is a bona fide protein folding chaperone. As a member of the GroEL/Cpn60 family, HSP-60 functions as an ATP-dependent protein folding machine in the mitochondrial matrix, assisting newly imported proteins to achieve their native conformation and refolding stress-damaged proteins (Fink 1999, Singh 2024). The IBA annotation is phylogenetically well-supported given the deep conservation of this function across all domains of life. Reason: Protein folding is the core molecular function of HSP-60. The chaperonin mechanism is highly conserved from bacterial GroEL to mitochondrial HSP60, and C. elegans HSP-60 contains all the canonical Cpn60/GroEL domains required for this function. UniProt annotation confirms this function. Supporting Evidence: PMID:15280428 the mitochondrial matrix HSP70 and HSP60 chaperones, encoded by the Caenorhabditis elegans hsp-6 and hsp-60 genes, were selectively activated by perturbations that impair assembly of multi-subunit mitochondrial complexes or by RNAi of genes encoding mitochondrial chaperones or proteases, which lead to defective protein folding and processing in the organelle |
| GO:0008637 apoptotic mitochondrial changes | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Human HSPD1/HSP60 has been implicated in apoptotic processes, particularly mitochondrial changes during programmed cell death. However, direct evidence for this role in C. elegans HSP-60 is limited. The annotation is based on phylogenetic inference from mammalian studies. Reason: While HSP60 family members have been linked to apoptosis in mammals (e.g., cytoplasmic release during apoptosis), this represents a secondary/downstream consequence rather than a core function of the C. elegans chaperonin. The primary role of HSP-60 is protein folding in the mitochondrial matrix. The annotation is phylogenetically inferred and while not incorrect, represents a non-core function that may be context-dependent. |
| GO:0005743 mitochondrial inner membrane | IBA GO_REF:0000033 | MODIFY | Summary: HSP-60 is primarily localized to the mitochondrial matrix, not the inner membrane. Some association with the inner membrane may occur during protein import assistance, but the functional localization is the matrix compartment. Reason: The primary and well-established localization of HSP-60/Cpn60 family members is the mitochondrial matrix, where they perform their chaperone function. UniProt annotates this as "Mitochondrion matrix." While transient associations with the inner membrane may occur during substrate protein import, the matrix is the canonical functional compartment. The annotation GO:0005759 (mitochondrial matrix) is more accurate. Proposed replacements: mitochondrial matrix |
| GO:0005759 mitochondrial matrix | IBA GO_REF:0000033 | ACCEPT | Summary: The mitochondrial matrix is the canonical localization for HSP-60 where it performs its chaperone function. This is well-supported by the UniProt record and extensive literature on Cpn60/GroEL family chaperonins (Singh 2024, Fink 1999). Reason: HSP-60 is nuclear-encoded, synthesized in the cytosol, and imported into the mitochondrial matrix via an N-terminal targeting presequence, where it folds imported matrix proteins and refolds stress-damaged proteins. This is the correct and primary cellular component annotation. Supporting Evidence: file:worm/hsp-60/hsp-60-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix. |
| GO:0034514 mitochondrial unfolded protein response | IBA GO_REF:0000033 | ACCEPT | Summary: HSP-60 is a core effector and transcriptional target of the UPRmt. The hsp-60 promoter is activated during mitochondrial stress as part of the ATFS-1-dependent transcriptional program. HSP-60::GFP reporters are canonical readouts of UPRmt activation (Haynes 2022, Yoneda 2004, Benedetti 2006). Reason: This is one of the core functions of HSP-60 in C. elegans. The hsp-60 gene is a canonical UPRmt target, and hsp-60p::GFP reporters are among the most widely used tools for monitoring UPRmt activation. HSP-60 protein functions as an effector that helps restore mitochondrial proteostasis during stress. Supporting Evidence: PMID:15280428 hsp-6 and hsp-60 induction was specific to perturbed mitochondrial protein handling, as neither heat-shock nor endoplasmic reticulum stress nor manipulations that impair mitochondrial steps in intermediary metabolism or ATP synthesis activated the mitochondrial chaperone genes. These observations support the existence of a mitochondrial unfolded protein response PMID:16816413 RNAi of ubl-5, a gene encoding a ubiquitin-like protein, suppresses activation of the UPR(mt) markers hsp-60::gfp and hsp-6::gfp by the zc32 mutation and by other manipulations that promote mitochondrial protein misfolding |
| GO:0045041 protein import into mitochondrial intermembrane space | IBA GO_REF:0000033 | MODIFY | Summary: HSP-60 is implicated in assisting the folding of proteins imported into mitochondria, but its primary role is in the matrix, not specifically the intermembrane space (IMS). The annotation may be too specific regarding the compartment. Reason: HSP-60 assists protein folding in the mitochondrial matrix and can assist newly imported proteins. However, proteins destined for the IMS use distinct import pathways (MIA/CHCHD4 pathway) and HSP-60 primarily functions in the matrix. A more general term related to mitochondrial protein import or matrix protein folding would be more accurate. Proposed replacements: protein folding |
| GO:0051087 protein-folding chaperone binding | IBA GO_REF:0000033 | ACCEPT | Summary: HSP-60 binds to its co-chaperonin HSP-10 (Cpn10/GroES family) to form the functional chaperone complex. This interaction is essential for the ATP-dependent protein folding cycle. The annotation reflects the physical interaction between HSP-60 and HSP-10. Reason: The HSP-60/HSP-10 interaction is a fundamental aspect of chaperonin function. HSP-10 (Cpn10) is a heptameric lid that binds to the apical domains of HSP-60 to cap the folding chamber. This is well-established from structural and biochemical studies of the GroEL/GroES system and conserved in mitochondrial chaperonins. Supporting Evidence: file:worm/hsp-60/hsp-60-deep-research-falcon.md HSP-60/Cpn60 forms a double-ring (two heptameric rings) folding cage that captures non-native substrates; HSP-10 (Cpn10/GroES) caps the cavity and an ATP-binding/hydrolysis cycle drives conformational changes to permit folding and release |
| GO:0000166 nucleotide binding | IEA GO_REF:0000043 | ACCEPT | Summary: HSP-60 binds ATP as part of its chaperone cycle. The annotation is correct but overly general - ATP binding (GO:0005524) is a more specific and informative annotation. Reason: While correct, this annotation is subsumed by the more specific ATP binding annotation. HSP-60 contains the conserved ATP-binding equatorial domain of Cpn60/GroEL chaperonins. The annotation can be retained as it is not incorrect, though ATP binding is more informative. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: HSP-60 binds ATP in its equatorial domain, and ATP hydrolysis drives the conformational changes necessary for protein folding. This is a core molecular function of all Cpn60/GroEL family chaperonins. Reason: ATP binding and hydrolysis are essential for HSP-60 function. The ATP-driven conformational cycle is fundamental to chaperonin-assisted protein folding. UniProt lists ATP-binding as a keyword for this protein. Supporting Evidence: file:worm/hsp-60/hsp-60-uniprot.txt KW ATP-binding; Chaperone; Mitochondrion; Nucleotide-binding |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Duplicate annotation with IBA evidence above. The mitochondrial matrix localization is well-supported and correct. Reason: Consistent with IBA annotation and UniProt record. Multiple evidence sources converging on the same correct annotation strengthens confidence. |
| GO:0006457 protein folding | IEA GO_REF:0000002 | ACCEPT | Summary: Duplicate annotation with IBA evidence above. Protein folding is the core function of HSP-60. The InterPro-based annotation supports the phylogenetic inference. Reason: Consistent with IBA annotation. The convergence of phylogenetic and domain-based evidence strengthens the annotation. |
| GO:0042026 protein refolding | IEA GO_REF:0000002 | ACCEPT | Summary: HSP-60 assists in refolding stress-damaged proteins in the mitochondrial matrix. This is consistent with its role as a chaperonin and its induction during mitochondrial stress. Reason: Protein refolding under stress conditions is a well-established function of HSP60 family chaperonins. UniProt states HSP-60 "may also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix." Supporting Evidence: file:worm/hsp-60/hsp-60-uniprot.txt May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix |
| GO:0140662 ATP-dependent protein folding chaperone | IEA GO_REF:0000002 | ACCEPT | Summary: This molecular function annotation accurately captures the core enzymatic/chaperone activity of HSP-60 - ATP-dependent protein folding. Reason: This is an accurate and informative molecular function annotation for HSP-60. The chaperonin uses ATP binding and hydrolysis to drive conformational changes that facilitate protein folding in the chamber formed between the two heptameric rings. |
| GO:0005739 mitochondrion | IDA PMID:17189267 Knockdown of mitochondrial heat shock protein 70 promotes pr... | ACCEPT | Summary: Kimura et al. (2007) studied HSP-6 (mtHsp70) knockdown effects and showed that HSP-60 levels are reduced along with other mitochondrial proteins, demonstrating HSP-60's mitochondrial localization. This provides experimental support for mitochondrial localization. Reason: The IDA evidence from PMID:17189267 supports mitochondrial localization. While the more specific term "mitochondrial matrix" is also annotated, the general mitochondrion term is not incorrect and represents valid experimental evidence. Supporting Evidence: PMID:17189267 Knockdown of HSP-6 by RNA interference in young adult nematodes caused a reduction in the levels of ATP-2, HSP-60 and CLK-1, leading to abnormal mitochondrial morphology |
| GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding | IPI PMID:17925224 ClpP mediates activation of a mitochondrial unfolded protein... | UNDECIDED | Summary: WormBase IPI annotation (WITH/FROM WB:WBGene00022861, dve-1) asserting that HSP-60 binds the homeodomain transcription factor DVE-1. WormBase curated the reciprocal row from the same paper, dve-1 enables GO:0051087 protein-folding chaperone binding (IPI, WITH WB:WBGene00002025 = hsp-60), and separately recorded the DVE-1/UBL-5 complex as GO:0005667 (IPI, WITH UniProtKB:P91302), so the curator recorded a physical HSP-60/DVE-1 interaction distinct from the UBL-5 complex. The abstract of Haynes et al. (2007) does not describe this interaction; only the abstract is cached (full_text_available false) and the full text could not be retrieved (Cell Press/ScienceDirect return 403; not in PMC). Reason: The reciprocal pair of binding-MF IPI rows is the signature of a curated protein-protein interaction, and the curator read the full text, which we cannot see; the experimental annotation is therefore not removed. It is left UNDECIDED rather than accepted because the assay that established the interaction cannot be identified from the abstract, and it is not clear how a mitochondrial matrix chaperonin contacts a nuclear homeodomain factor (for example, an in vitro or co-immunoprecipitation result, or a non-mitochondrial pool of HSP-60). The quoted abstract sentence is context (DVE-1 regulating the hsp-60 promoter), not direct support for the binding. Not part of the core function in any case. Supporting Evidence: PMID:17925224 Activation of the UPR(mt) correlates temporally and spatially with nuclear redistribution of DVE-1 and with its enhanced binding to the promoters of mitochondrial chaperone genes |
| GO:0034514 mitochondrial unfolded protein response | IEP PMID:15280428 Compartment-specific perturbation of protein handling activa... | ACCEPT | Summary: Yoneda et al. (2004) showed hsp-60 gene expression is induced during UPRmt. This IEP (Inferred from Expression Pattern) annotation is appropriate as hsp-60 expression correlates with UPRmt activation. Reason: The IEP evidence is valid - hsp-60 expression is upregulated during mitochondrial stress as part of the UPRmt transcriptional program. This is a landmark paper establishing the UPRmt in C. elegans. Supporting Evidence: PMID:15280428 the mitochondrial matrix HSP70 and HSP60 chaperones, encoded by the Caenorhabditis elegans hsp-6 and hsp-60 genes, were selectively activated by perturbations that impair assembly of multi-subunit mitochondrial complexes |
| GO:0034514 mitochondrial unfolded protein response | IMP PMID:15280428 Compartment-specific perturbation of protein handling activa... | ACCEPT | Summary: The IMP (Inferred from Mutant Phenotype) annotation suggests functional involvement in UPRmt was demonstrated through genetic manipulation. Yoneda et al. (2004) showed that RNAi of mitochondrial chaperones/proteases activates hsp-60 expression. Reason: HSP-60 is both a transcriptional target and functional effector of the UPRmt. The protein helps restore proteostasis in the mitochondrial matrix during stress. Multiple evidence types (IBA, IEP, IMP) converge on this annotation. Supporting Evidence: PMID:15280428 RNAi of genes encoding mitochondrial chaperones or proteases, which lead to defective protein folding and processing in the organelle [activate hsp-60/hsp-6] |
| GO:0002119 nematode larval development | IMP PMID:15280428 Compartment-specific perturbation of protein handling activa... | KEEP AS NON CORE | Summary: Yoneda et al. (2004) demonstrated that perturbing mitochondrial proteostasis affects development, and hsp-60 is involved in the response. This represents a downstream phenotypic consequence rather than a specific molecular function. Reason: While HSP-60 is essential for proper development (as are many mitochondrial proteins), larval development is a broad phenotypic readout rather than a specific molecular function. The annotation reflects pleiotropy - loss of mitochondrial chaperone function affects many processes including development. This is a valid but non-core annotation. Supporting Evidence: PMID:15280428 Jul 27. Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones. |
| GO:0007005 mitochondrion organization | IMP PMID:16816413 Ubiquitin-like protein 5 positively regulates chaperone gene... | ACCEPT | Summary: Benedetti et al. (2006) showed that perturbation of UPRmt signaling (via ubl-5 RNAi) affects mitochondrial morphology and assembly of mitochondrial complexes. HSP-60, as an effector chaperone, contributes to proper mitochondrial organization. Reason: HSP-60 contributes to proper folding and assembly of mitochondrial protein complexes, which is essential for mitochondrial organization. The study shows that compromising UPRmt (and thus chaperone function) leads to abnormal mitochondrial morphology. Supporting Evidence: PMID:16816413 Mitochondrial morphology and assembly of multi-subunit mitochondrial complexes of biotinylated proteins are also perturbed in ubl-5(RNAi) worms, indicating that UBL-5 also counteracts physiological levels of mitochondrial stress |
| GO:0009792 embryo development ending in birth or egg hatching | IMP PMID:15280428 Compartment-specific perturbation of protein handling activa... | KEEP AS NON CORE | Summary: Similar to larval development, this annotation reflects that HSP-60 function is required for normal embryonic development. This is a broad phenotypic consequence of mitochondrial chaperone function. Reason: Embryonic development is a broad biological process affected by mitochondrial dysfunction. While the annotation is valid, it represents pleiotropy rather than a specific molecular role. Essential mitochondrial proteins affect many developmental processes. Supporting Evidence: PMID:15280428 Jul 27. Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones. |
| GO:0045087 innate immune response | TAS PMID:15280428 Compartment-specific perturbation of protein handling activa... | NEW | Summary: Jeong et al. (2017, EMBO J) demonstrated that HSP-60 contributes to antibacterial immunity via the p38 MAPK/PMK-1 pathway. A cytosolic fraction of HSP-60 stabilizes SEK-1 and promotes PMK-1 phosphorylation, enhancing resistance to P. aeruginosa. This function is described in the deep research but the primary paper PMID is not yet in the publications cache. Reason: This represents a significant non-canonical function of HSP-60 supported by direct experimental evidence. The deep research document cites Jeong et al. (2017, EMBO J, doi:10.15252/embj.201694781) showing hsp-60 RNAi reduces PMK-1 activity and pathogen resistance, while cytosolic HSP-60 overexpression improves PA14 resistance. Supporting Evidence: file:worm/hsp-60/hsp-60-deep-research-falcon.md hsp-60 RNAi lowers PMK-1 activity (decreased PMK-1 reporters and phospho-PMK-1) and reduces survival on PA14; cytosolic HSP-60 overexpression improves PA14 resistance, consistent with HSP-60 acting via p38/PMK-1 PMID:15280428 Jul 27. Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones. |
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Download this section (compressed HTML)Q: What is the substrate specificity of C. elegans HSP-60? Are there specific mitochondrial proteins that preferentially require HSP-60 for folding?
Q: How does the cytosolic fraction of HSP-60 contribute to innate immunity? Is this a regulated process or does it occur constitutively?
Q: Does HSP-60 have roles in mitochondrial protein import beyond folding newly imported proteins?
Experiment: Identify HSP-60 client proteins using proximity labeling (BioID/TurboID) in the mitochondrial matrix under normal and stress conditions.
Hypothesis: HSP-60 has specific client proteins in the mitochondrial matrix that require chaperonin assistance for folding.
Experiment: Characterize the cytosolic HSP-60 pool using subcellular fractionation and determine what regulates its distribution between mitochondria and cytosol.
Hypothesis: The cytosolic fraction of HSP-60 is regulated and contributes to innate immunity signaling under specific conditions.
Experiment: Test whether HSP-60 co-localizes with the TIM/TOM import machinery using super-resolution microscopy.
Hypothesis: HSP-60 interacts with the mitochondrial import machinery to assist folding of newly imported proteins.
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