nud-1

Proposed New Ontology Terms

holdase chaperone activity

Definition: Binding to an unfolded or misfolded protein to prevent its aggregation without actively catalyzing refolding. The holdase maintains the client protein in a soluble, folding-competent state. This is mechanistically distinct from foldase activity (GO:0044183) and from carrier-holdase activity (GO:0140309).

Justification: nud-1: NUD-1 prevents aggregation of citrate synthase and luciferase at stoichiometric concentrations in an ATP-independent manner, comparable to small heat shock proteins. Obsolete GO:0051082 captured binding only; GO:0044183 requires assisting folding, and GO:0140309 (relabelled 'unfolded protein holdase activity') keeps a carrier-specific definition requiring escort to an acceptor molecule or location, which is not demonstrated here. See go-ontology#30552.

Parent term: molecular_function

Supporting Evidence:

PMID:18626791 : We demonstrate that nematode NUD-1 is able to prevent the aggregation of two substrate proteins, citrate synthase (CS) and luciferase, at stoichiometric concentrations.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for cytoplasmic localization, inferred phylogenetically from multiple orthologs including Drosophila, Arabidopsis, and human NudC proteins. Consistent with UniProt subcellular location annotation (Cytoplasm) and the known biology of NudC family proteins as cytoplasmic, microtubule-associated proteins. NUD-1::GFP fusion shows cytoplasmic expression in sensory neurons, embryos, gonad, gut, vulva, ventral cord, and hypodermal seam cells (PMID:11685578). Reason: Cytoplasmic localization is well-established for NUD-1 and the NudC family. The IBA inference is consistent with UniProt annotation and direct GFP expression data in C. elegans (PMID:11685578). Supporting Evidence: PMID:11685578 A C. elegans nud-1::GFP fusion produces sustained fluorescence in sensory neurons and embryos, and transient fluorescence in the gonad, gut, vulva, ventral cord, and hypodermal seam cells.
GO:0006457 protein folding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for involvement in protein folding, inferred phylogenetically. NUD-1 has been demonstrated to exhibit chaperone activity in vitro (PMID:18626791), preventing aggregation of citrate synthase and luciferase. However, NUD-1 functions as a holdase rather than a foldase -- it prevents aggregation of unfolded substrates, which can then be refolded by ATP-dependent chaperones. The IBA annotation is consistent with the experimental evidence from PMID:18626791. Reason: Protein folding is appropriate as a biological process annotation for a holdase chaperone, as NUD-1 maintains unfolded intermediates in a refolding-competent state that can be subsequently refolded by the cellular chaperone machinery (PMID:18626791). The IBA inference is supported by direct experimental evidence. Supporting Evidence: PMID:18626791 In the presence of NUD-1, nearly all of the luciferase activity was regained, indicating that unfolded intermediates complexed with NUD-1 could be refolded.
GO:0051082 unfolded protein binding	IBA GO_REF:0000033	MODIFY	Summary: IBA annotation for unfolded protein binding, inferred phylogenetically from NUD-1 itself (WB:WBGene00003829) and other orthologs. GO:0051082 is now formally obsolete. NUD-1 has been directly demonstrated to prevent aggregation of denaturing citrate synthase and luciferase (PMID:18626791), functioning as an ATP-independent holdase chaperone. However, NUD-1 is not a classical sHSP -- it is a NudC family protein with an HSP20-like fold (CS domain) whose primary role is in nuclear migration and cytoskeletal dynamics. The chaperone activity may be secondary to its role in mitotic complex assembly. Reason: GO:0051082 is now formally obsolete. NUD-1 demonstrates holdase activity in vitro (PMID:18626791), preventing aggregation of denaturing substrates and maintaining them in a refolding-competent state. GO:0140309 (unfolded protein carrier activity) is not appropriate because it is carrier-specific (per go-ontology#30552). The replacement is the proposed holdase chaperone activity NTR (see proposed_new_terms). Proposed replacements: holdase chaperone activity Supporting Evidence: PMID:18626791 We demonstrate that nematode NUD-1 is able to prevent the aggregation of two substrate proteins, citrate synthase (CS) and luciferase, at stoichiometric concentrations.
GO:0045202 synapse	IEA GO_REF:0000108	KEEP AS NON CORE	Summary: IEA annotation for synaptic localization, inferred automatically from the GO:0051932 (synaptic transmission, GABAergic) annotation via inter-ontology logical inference. NUD-1 depletion causes defective GABA synaptic vesicle trafficking (PMID:16996038), which supports a role at synapses. However, this is an indirect inference -- NUD-1 may affect synaptic vesicle trafficking through its role in cytoskeletal dynamics (dynein/microtubule-dependent transport) rather than being a resident synaptic protein. Reason: The inference from GABAergic synaptic transmission to synaptic localization is logically valid. NUD-1 depletion disrupts GABA synaptic vesicle trafficking (PMID:16996038), suggesting functional involvement at synapses. However, NUD-1 is primarily a cytoplasmic, microtubule-associated protein and its synaptic role is secondary to its core function in nuclear migration and chaperone activity.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for cytoplasmic localization based on UniProt subcellular location mapping. Consistent with the IBA annotation for the same term and direct GFP expression data (PMID:11685578). Reason: Cytoplasmic localization is well-established. This IEA annotation is consistent with the IBA annotation and experimental evidence. Acceptable as automated confirmation.
GO:0006457 protein folding	IDA PMID:18626791 The microtubule-associated protein, NUD-1, exhibits chaperon...	ACCEPT	Summary: IDA annotation for involvement in protein folding based on Faircloth et al. 2009 (PMID:18626791). The study demonstrated that recombinant NUD-1 prevents aggregation of citrate synthase and luciferase, protects native CS from thermal inactivation, and maintains unfolded luciferase intermediates in a refolding-competent state. This is directly supported by the luciferase refolding assay showing that unfolded intermediates complexed with NUD-1 could be refolded by rabbit reticulocyte lysate plus ATP. Reason: Strong experimental evidence directly in C. elegans NUD-1 demonstrating chaperone activity that facilitates the protein folding process. NUD-1 acts as a holdase maintaining substrates in a refolding-competent state, which is part of the protein folding pathway (PMID:18626791). Supporting Evidence: PMID:18626791 In the presence of NUD-1, nearly all of the luciferase activity was regained, indicating that unfolded intermediates complexed with NUD-1 could be refolded. PMID:18626791 NUD-1 also protects the native state of CS from thermal inactivation by significantly reducing the inactivation rate of this enzyme.
GO:0044183 protein folding chaperone	IDA PMID:18626791 The microtubule-associated protein, NUD-1, exhibits chaperon...	KEEP AS NON CORE	Summary: IDA annotation for protein folding chaperone molecular function based on Faircloth et al. 2009 (PMID:18626791). The study directly demonstrated that NUD-1 possesses ATP-independent chaperone activity comparable to small heat shock proteins and cochaperones. NUD-1 prevents aggregation of denaturing citrate synthase and luciferase at stoichiometric concentrations, and maintains substrates in a refolding-competent state. This is a more informative molecular function annotation than GO:0051082 (unfolded protein binding), but NUD-1 does not itself refold clients: refolding of NUD-1-bound luciferase required reticulocyte lysate plus ATP. Reason: Experimental curator annotation, retained. GO:0044183 ("assist the protein folding process") is defensible because NUD-1-bound luciferase intermediates remained refolding-competent (PMID:18626791), but the activity NUD-1 performs is in-situ holdase activity, not foldase activity, so the core molecular function is recorded as the proposed holdase chaperone activity term (see proposed_new_terms) rather than GO:0044183. Supporting Evidence: PMID:18626791 NUD-1 possesses ATP-independent chaperone activity comparable to that of small heat shock proteins and cochaperones and that changes in phosphorylation state functionally alter chaperone activity in a phosphomimetic NUD-1 mutant. PMID:18626791 We demonstrate that nematode NUD-1 is able to prevent the aggregation of two substrate proteins, citrate synthase (CS) and luciferase, at stoichiometric concentrations. file:worm/nud-1/nud-1-deep-research-falcon.md NUD-1 is described as a microtubule-associated protein with in vitro chaperone activity, preventing heat-induced aggregation of citrate synthase and luciferase
GO:0051082 unfolded protein binding	IDA PMID:18626791 The microtubule-associated protein, NUD-1, exhibits chaperon...	MODIFY	Summary: IDA annotation for unfolded protein binding based on Faircloth et al. 2009 (PMID:18626791). The study demonstrated that NUD-1 binds denaturing proteins (citrate synthase and luciferase) and prevents their aggregation. GO:0051082 is now formally obsolete. GO:0044183 (protein folding chaperone) is annotated with IDA evidence from the same publication but describes foldase-type assistance, and the carrier-specific GO:0140309 does not fit, so the holdase function needs the proposed holdase chaperone activity NTR. Reason: GO:0051082 is now formally obsolete. The holdase activity demonstrated in PMID:18626791 is not well captured by GO:0140309 (carrier-specific, per go-ontology#30552), and GO:0044183 (protein folding chaperone) implies foldase activity. The replacement is the proposed holdase chaperone activity NTR (see proposed_new_terms). Proposed replacements: holdase chaperone activity Supporting Evidence: PMID:18626791 We demonstrate that nematode NUD-1 is able to prevent the aggregation of two substrate proteins, citrate synthase (CS) and luciferase, at stoichiometric concentrations.
GO:0048489 synaptic vesicle transport	IMP PMID:16996038 Genetic interactions among cortical malformation genes that ...	KEEP AS NON CORE	Summary: IMP annotation for involvement in synaptic vesicle transport based on Locke et al. 2006 (PMID:16996038). The study used fluorescent markers for synaptic vesicle trafficking and found that depletion of NUD-1 (along with other LIS1 pathway components) resulted in defective GABA synaptic vesicle trafficking. This is consistent with NUD-1's role in dynein-dependent transport along microtubules. Reason: The experimental evidence from PMID:16996038 supports involvement in synaptic vesicle transport, likely through NUD-1's role in the dynein motor complex and microtubule-based transport. However, this is a secondary consequence of NUD-1's core function in cytoskeletal dynamics rather than a specialized role in synaptic vesicle trafficking per se. Retained as non-core. Supporting Evidence: PMID:16996038 We found that depletion of LIS1 pathway components resulted in defective GABA synaptic vesicle trafficking.
GO:0051932 synaptic transmission, GABAergic	IGI PMID:16996038 Genetic interactions among cortical malformation genes that ...	KEEP AS NON CORE	Summary: IGI annotation for involvement in GABAergic synaptic transmission based on Locke et al. 2006 (PMID:16996038). The study used genetic interaction experiments with LIS-1 pathway components (indicated by with/from WB:WBGene00003047) and pentylenetetrazole exposure to demonstrate that NUD-1 depletion affects GABAergic neurotransmission, resulting in convulsion susceptibility. Reason: The genetic interaction evidence supports a role in GABAergic synaptic transmission, likely secondary to NUD-1's role in microtubule-dependent transport of synaptic vesicles. This is a non-core function reflecting the downstream effects of disrupted cytoskeletal dynamics on neuronal function. Supporting Evidence: PMID:16996038 Worms depleted for LIS1 pathway components (NUD-1, NUD-2, DHC-1, CDK-5, and CDKA-1) exhibited significant convulsions following PTZ and RNAi treatment.
GO:0040011 locomotion	IMP PMID:11685578 Evolutionarily conserved nuclear migration genes required fo...	KEEP AS NON CORE	Summary: IMP annotation for involvement in locomotion based on Dawe et al. 2001 (PMID:11685578). RNAi knockdown of nud-1 resulted in uncoordinated movement, one of several pleiotropic phenotypes observed. This is a downstream consequence of NUD-1's role in neuronal development and function rather than a direct role in locomotion. Reason: The uncoordinated movement phenotype from nud-1 RNAi (PMID:11685578) is a pleiotropic effect of disrupting this broadly required nuclear migration/ cytoskeletal dynamics gene, not a specific role in locomotion. Retained as non-core. Supporting Evidence: PMID:11685578 Phenotypic analysis of either nud-1 and lis-1 by RNA interference yielded similar phenotypes, including embryonic lethality, sterility, altered vulval morphology, and uncoordinated movement.
GO:0040025 vulval development	IMP PMID:11685578 Evolutionarily conserved nuclear migration genes required fo...	KEEP AS NON CORE	Summary: IMP annotation for involvement in vulval development based on Dawe et al. 2001 (PMID:11685578). RNAi knockdown of nud-1 resulted in altered vulval morphology. nud-1::GFP shows expression in the vulva, and vulval development requires proper cell division and nuclear migration, consistent with NUD-1's core function. Reason: Altered vulval morphology from nud-1 RNAi (PMID:11685578) is a pleiotropic phenotype consistent with disruption of nuclear migration and cell division in vulval precursor cells. nud-1::GFP is expressed in the vulva. Retained as non-core since vulval development is not the primary function of NUD-1. Supporting Evidence: PMID:11685578 Phenotypic analysis of either nud-1 and lis-1 by RNA interference yielded similar phenotypes, including embryonic lethality, sterility, altered vulval morphology, and uncoordinated movement.
GO:0009792 embryo development ending in birth or egg hatching	IMP PMID:11685578 Evolutionarily conserved nuclear migration genes required fo...	ACCEPT	Summary: IMP annotation for involvement in embryo development based on Dawe et al. 2001 (PMID:11685578). RNAi knockdown of nud-1 caused embryonic lethality and nuclear positioning defects in early embryonic cell division similar to dynein/dynactin depletion. This is a core biological process for NUD-1 given its essential role in nuclear migration during cell division. Reason: Embryonic lethality from nud-1 RNAi represents a core phenotype (PMID:11685578). NUD-1 is essential for proper nuclear positioning during early embryonic cell division, and its requirement for embryo development is a direct consequence of its core function in nuclear migration and mitotic progression. Supporting Evidence: PMID:11685578 Digital time-lapse video microscopy was used to determine that RNAi-treated embryos exhibited nuclear positioning defects in early embryonic cell division similar to those reported for dynein/dynactin depletion. file:worm/nud-1/nud-1-deep-research-falcon.md embryos usually arrested between comma and one-fold stages
GO:0035046 pronuclear migration	IMP PMID:11685578 Evolutionarily conserved nuclear migration genes required fo...	ACCEPT	Summary: IMP annotation for involvement in pronuclear migration based on Dawe et al. 2001 (PMID:11685578). RNAi knockdown of nud-1 caused nuclear positioning defects in early embryonic cell division. Pronuclear migration is a dynein-dependent process, and NUD-1 functions with the dynein motor complex. This is a core biological process directly reflecting NUD-1's primary molecular role in nuclear migration. Reason: Pronuclear migration is a core function of NUD-1, directly reflecting its primary role in nuclear migration via the dynein motor complex. The nuclear positioning defects observed after nud-1 RNAi (PMID:11685578) are consistent with the conserved role of NudC family proteins in nuclear migration from fungi to humans. The gene name itself (nuclear distribution) reflects this function. Supporting Evidence: PMID:11685578 Digital time-lapse video microscopy was used to determine that RNAi-treated embryos exhibited nuclear positioning defects in early embryonic cell division similar to those reported for dynein/dynactin depletion. PMID:11685578 Heterologous expression of the C. elegans nudC ortholog, nud-1, complements the A. nidulans nudC3 mutant, demonstrating evolutionary conservation of function. file:worm/nud-1/nud-1-deep-research-falcon.md pronuclei moved inward but failed to rotate onto the anterior-posterior axis; nuclear envelope breakdown occurred on the dorsal-ventral axis
GO:0051932 synaptic transmission, GABAergic	IMP PMID:16996038 Genetic interactions among cortical malformation genes that ...	KEEP AS NON CORE	Summary: IMP annotation for involvement in GABAergic synaptic transmission based on Locke et al. 2006 (PMID:16996038). NUD-1-depleted worms exhibited significant convulsions following PTZ treatment, and fluorescent markers showed defective GABA synaptic vesicle trafficking. This is a separate evidence line (IMP vs IGI) from the other GO:0051932 annotation for the same gene from the same paper. Reason: This IMP annotation provides independent evidence from the IGI annotation for the same term. The convulsion susceptibility phenotype after NUD-1 depletion (PMID:16996038) supports involvement in GABAergic signaling, but this is a secondary function stemming from NUD-1's role in microtubule-based transport. Retained as non-core. Supporting Evidence: PMID:16996038 Worms depleted for LIS1 pathway components (NUD-1, NUD-2, DHC-1, CDK-5, and CDKA-1) exhibited significant convulsions following PTZ and RNAi treatment.
GO:0000281 mitotic cytokinesis	IMP PMID:12679384 Role for NudC, a dynein-associated nuclear movement protein,...	NEW	Summary: NEW annotation proposed from Aumais et al. 2003 (PMID:12679384), which was not represented in the original GOA/UniProt set. RNAi gene silencing of nud-1 in C. elegans caused loss of midzone microtubules and rapid regression of the cleavage furrow, producing one-celled embryos containing two nuclei - a defining cytokinesis-failure phenotype. The falcon deep research synthesis further quantifies this (midzone microtubules absent in 26% and weak in 74% of one-cell embryos) and frames NUD-1 as required for late cytokinesis via midzone microtubule organization, mechanistically consistent with the conserved NudC-family role in midzone/midbody microtubule organization during cell division. Reason: Aumais et al. (PMID:12679384) provide direct experimental (RNAi) evidence in C. elegans that NUD-1 is required for completion of the first embryonic cytokinesis: its depletion blocks midzone microtubule formation and causes cleavage-furrow regression, yielding binucleate one-cell embryos. The phenotype occurs in the early embryonic mitotic division, so the directly-annotatable term GO:0000281 (mitotic cytokinesis) is appropriate. IMP with a verified primary PMID is a valid evidence/reference pairing for this RNAi loss-of-function phenotype. This complements the existing pronuclear-migration/nuclear-positioning annotations and captures the second worm-established arm of NUD-1 function. Supporting Evidence: PMID:12679384 Gene silencing of nud-1, the Caenorhabditis elegans ortholog of NudC, led to a loss of midzone microtubules and the rapid regression of the cleavage furrow, which resulted in one-celled embryos containing two nuclei. file:worm/nud-1/nud-1-deep-research-falcon.md cleavage furrows stalled or regressed, producing multinucleated one-cell embryos file:worm/nud-1/nud-1-deep-research-falcon.md Midzone microtubules were absent in 26% (10/39) of one-cell embryos and weak/poorly defined in 74% (29/39)