UBL-5 is a small ubiquitin-like protein (73 aa) that functions as an atypical, non-enzymatic regulator acting through non-covalent protein-protein interactions. Unlike typical ubiquitin-like proteins, UBL-5/Hub1 lacks the C-terminal di-glycine motif required for covalent conjugation. UBL-5 has two main functional roles: (1) as a spliceosome-associated cofactor that promotes proper pre-mRNA splicing through specific interactions with HIND-containing spliceosomal proteins (SART-1/Snu66, PRP-38), and (2) as a positive regulator of the mitochondrial unfolded protein response (UPR-mt) where it forms a complex with DVE-1 to activate transcription of mitochondrial chaperone genes (hsp-6, hsp-60). Under mitochondrial stress, UBL-5 accumulates in the nucleus. Loss of ubl-5 causes L3 larval arrest and splicing defects.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000398 mRNA splicing, via spliceosome | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation based on phylogenetic inference from Hub1/UBL5 orthologs. Recent direct experimental evidence in C. elegans (Kolathur et al., 2023) demonstrates that UBL-5 binds HIND-containing spliceosomal proteins SART-1 and PRP-38, co-immunoprecipitates with spliceosomal components, and is essential for splicing. Loss of ubl-5 causes accumulation of unspliced transcripts and defects in both cis- and trans-splicing (PMID:16816413, Kolathur et al. 2023). Reason: This annotation is strongly supported by recent C. elegans-specific experimental data. Kolathur et al. (2023) showed UBL-5 binds HIND-containing splicing factors, associates with spliceosome components via co-IP/MS, and ubl-5 mutants accumulate unspliced RNAs. The splicing role is now considered the primary molecular function of UBL-5, with UPR-mt effects potentially being downstream of its nuclear RNA processing role. Supporting Evidence: file:worm/ubl-5/ubl-5-deep-research-falcon.md Loss of ubl-5 causes selective splicing defects (intron retention and trans-/cis-splicing defects) and developmental arrest (L3 lethality), demonstrating an essential splicing role in vivo. 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 |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for nuclear localization based on phylogenetic inference. This is directly supported by experimental evidence in C. elegans showing UBL-5-GFP accumulates in nuclei under mitochondrial stress (PMID:16816413). Reason: Nuclear localization is well-supported by direct experimental evidence. Benedetti et al. (2006) showed that "Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms." The nuclear localization is consistent with UBL-5's role in both splicing (spliceosome is nuclear) and UPR-mt transcriptional regulation. Supporting Evidence: PMID:16816413 Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms, suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for cytoplasmic localization. UBL-5 is present in both cytoplasm and nucleus, with stress-induced nuclear accumulation. UniProt lists cytoplasm based on sequence similarity (ISS evidence). Reason: Cytoplasmic localization is consistent with UBL-5 being present in both compartments and shuttling to the nucleus under stress. The UniProt record indicates "Cytoplasm {ECO:0000250}" and the stress-induced nuclear redistribution implies a basal cytoplasmic pool. This is an appropriate annotation at the correct level of specificity. Supporting Evidence: file:worm/ubl-5/ubl-5-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. |
| GO:0031386 protein tag activity | IBA GO_REF:0000033 | REMOVE | Summary: IBA annotation based on phylogenetic inference from ubiquitin-like protein family. However, UBL-5/Hub1 is atypical - it lacks the C-terminal di-glycine motif required for covalent conjugation and functions via non-covalent protein-protein interactions rather than as a covalent tag. Reason: This annotation is incorrect for UBL-5. The deep research explicitly states: "UBL-5 is an atypical, non-enzymatic ubiquitin-like protein that acts via non-covalent protein-protein interactions" and "Not a covalent modifier: Consistent with atypical UBL classification, UBL-5 does not act through E1-E2-E3 conjugation but via direct protein-protein interactions in the splicing machinery." The protein tag activity term (GO:0031386) is defined as covalent attachment of a small protein tag to another protein, which does not apply to UBL-5. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000315756 · ubiquitin-like PANTHER source node SUPPORTS SOURCE BUT NOT TARGET The source node propagates a covalent protein-tag activity typical of ubiquitin-like modifiers, but the Hub1/UBL5 clade lacks the C-terminal di-glycine conjugation motif and acts non-covalently. SGD:S000007251 · yeast Hub1/UBL5 source gene SUPPORTS SOURCE BUT NOT TARGET Hub1/UBL5 biology supports non-covalent spliceosome-factor binding, not covalent protein tag activity for worm ubl-5. Supporting Evidence: file:worm/ubl-5/ubl-5-goa.tsv UniProtKB P91302 ubl-5 enables GO:0031386 protein tag activity molecular_function ECO:0000318 IBA GO_REF:0000033 PANTHER:PTN000315756|SGD:S000007251 6239 Caenorhabditis elegans GO_Central Ubiquitin-like protein 5 20170228 file:worm/ubl-5/ubl-5-deep-research-falcon.md UBL-5/Hub1 is a ubiquitin-like protein that, unlike many UBLs, lacks the C-terminal di-Gly motif for covalent conjugation and instead acts primarily through non-covalent binding to partner proteins, especially within the spliceosome. file:worm/ubl-5/ubl-5-hypotheses/function-hypothesis-go-0031386/openscientist.md is **not supported** and should be treated as an over-annotation. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation based on UniProt subcellular location vocabulary mapping. This is consistent with the IBA annotation above and with experimental evidence of cytoplasmic presence. Reason: This IEA annotation duplicates the IBA annotation but with different evidence. Both are valid - the protein is present in cytoplasm. While duplicates exist, retaining both preserves the evidence provenance trail. Supporting Evidence: file:worm/ubl-5/ubl-5-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. |
| GO:0034514 mitochondrial unfolded protein response | IMP PMID:23870130 The NAD(+)/Sirtuin Pathway Modulates Longevity through Activ... | ACCEPT | Summary: IMP annotation from Mouchiroud et al. (2013) Cell paper on NAD+/Sirtuin pathway and longevity. This study showed UPR-mt activation through NAD+ modulation involves mitonuclear protein imbalance and stress signaling. Reason: The role of UBL-5 in UPR-mt is well-established through multiple independent studies. While the 2013 Cell paper focuses on NAD+/sirtuin pathway, it demonstrates UPR-mt involvement. The UPR-mt role of UBL-5 is a core function, though recent work suggests it may be partially mediated through its splicing function affecting nuclear RNA processing of stress-responsive genes. Supporting Evidence: PMID:23870130 These effects are dependent upon the protein deacetylase sir-2.1 and involve the induction of mitonuclear protein imbalance as well as activation of stress signaling via the mitochondrial unfolded protein response (UPR(mt)) |
| GO:0034514 mitochondrial unfolded protein response | IMP PMID:17925224 ClpP mediates activation of a mitochondrial unfolded protein... | ACCEPT | Summary: IMP annotation from Haynes et al. (2007) Dev Cell paper. This is the key paper establishing UBL-5 as a UPR-mt regulator, showing DVE-1/UBL-5 complex formation under mitochondrial stress. Reason: This is foundational experimental evidence for UBL-5's role in UPR-mt. The paper demonstrated that "Unfolded protein stress in the mitochondria correlates with complex formation between a homeodomain-containing transcription factor DVE-1 and the small ubiquitin-like protein UBL-5, both of which are encoded by genes required for signaling the UPR(mt)." Supporting Evidence: PMID:17925224 Unfolded protein stress in the mitochondria correlates with complex formation between a homeodomain-containing transcription factor DVE-1 and the small ubiquitin-like protein UBL-5, both of which are encoded by genes required for signaling the UPR(mt). |
| GO:0005667 transcription regulator complex | IPI PMID:17925224 ClpP mediates activation of a mitochondrial unfolded protein... | ACCEPT | Summary: IPI annotation indicating UBL-5 is part of a transcription regulator complex, based on its physical interaction with DVE-1, a homeodomain transcription factor. This complex regulates mitochondrial chaperone gene expression. Reason: The DVE-1/UBL-5 complex functions as a transcriptional regulatory unit for UPR-mt target genes. Haynes et al. (2007) showed that "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." UBL-5 forms a complex with DVE-1 that binds these promoters. 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. file:worm/ubl-5/ubl-5-uniprot.txt Interacts with dve-1; the interaction occurs in a mitochondrial stress-dependent manner. |
| GO:0034514 mitochondrial unfolded protein response | IMP PMID:16816413 Ubiquitin-like protein 5 positively regulates chaperone gene... | ACCEPT | Summary: IMP annotation from Benedetti et al. (2006) Genetics paper. This was the first paper to identify UBL-5 as a positive regulator of UPR-mt through an RNAi screen for suppressors of UPR-mt activation. Reason: This is the original discovery paper for UBL-5's role in UPR-mt. The study showed that "RNAi of ubl-5 suppresses activation of the UPR(mt) markers hsp-60::gfp and hsp-6::gfp" and that UBL-5 is required for induction of endogenous mitochondrial chaperone genes. This represents core UBL-5 function. Supporting Evidence: 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. ubl-5 (RNAi) inhibits the induction of endogenous mitochondrial chaperone encoding genes hsp-60 and hsp-6 and compromises the ability of animals to cope with mitochondrial stress. |
| GO:0005634 nucleus | IDA PMID:16816413 Ubiquitin-like protein 5 positively regulates chaperone gene... | ACCEPT | Summary: IDA annotation for nuclear localization from Benedetti et al. (2006). Direct visualization of GFP-tagged UBL-5 accumulating in nuclei under mitochondrial stress. Reason: This is direct experimental evidence (IDA) for nuclear localization. The paper explicitly states that "Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms." Nuclear localization is essential for both UBL-5's splicing and transcriptional regulatory functions. Supporting Evidence: PMID:16816413 Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms, suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding. |
| GO:0005829 cytosol | IDA PMID:16816413 Ubiquitin-like protein 5 positively regulates chaperone gene... | ACCEPT | Summary: IDA annotation for cytosolic localization from Benedetti et al. (2006). The paper shows UBL-5 is present in cytoplasm and redistributes to nucleus under stress, implying baseline cytosolic presence. Reason: The stress-induced nuclear accumulation implies UBL-5 must be present in the cytosol under basal conditions before translocating to the nucleus. Cytosol (GO:0005829) is more specific than cytoplasm (GO:0005737) but appropriate here as UBL-5 is a soluble protein that shuttles between compartments. Supporting Evidence: PMID:16816413 Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms [implying baseline cytoplasmic/cytosolic presence before nuclear redistribution] |
| GO:1990935 splicing factor binding | IDA file:worm/ubl-5/ubl-5-deep-research-falcon.md | NEW | Summary: NEW annotation based on 2023 FEBS Letters study (Kolathur et al.) demonstrating that UBL-5 directly binds HIND-containing spliceosomal proteins SART-1 and PRP-38 via co-immunoprecipitation and binding assays. This molecular function term captures UBL-5's role as a non-enzymatic splicing cofactor. Reason: UBL-5's molecular function as a splicing factor binding protein is well-supported by recent C. elegans experimental data showing direct interaction with spliceosomal components. This is more specific than the existing IBA annotation for the biological process (mRNA splicing) and accurately reflects UBL-5's non-covalent binding mechanism. Supporting Evidence: file:worm/ubl-5/ubl-5-deep-research-falcon.md UBL-5 binds HIND-containing spliceosomal proteins SART-1 and PRP-38, co-IPs with spliceosomal proteins... co-IP/MS showed enrichment of spliceosomal proteins in UBL-5 complexes in C. elegans |
| GO:0003713 transcription coactivator activity | IDA PMID:17925224 ClpP mediates activation of a mitochondrial unfolded protein... | NEW | Summary: NEW annotation based on UBL-5's role as a cofactor with DVE-1 in activating transcription of mitochondrial chaperone genes during UPR-mt. UBL-5 forms a stress-dependent complex with DVE-1 that binds to and activates promoters of hsp-6 and hsp-60 genes. Reason: UBL-5 functions as a transcription coactivator by forming a complex with the transcription factor DVE-1. This complex is required for activation of UPR-mt target genes. The evidence from PMID:17925224 shows that UBL-5 is required for DVE-1-mediated transcriptional activation of mitochondrial chaperone genes. Supporting Evidence: PMID:17925224 Unfolded protein stress in the mitochondria correlates with complex formation between a homeodomain-containing transcription factor DVE-1 and the small ubiquitin-like protein UBL-5, both of which are encoded by genes required for signaling the UPR(mt) 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 |
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Download this section (compressed HTML)Q: Is the UPR-mt role of UBL-5 mechanistically dependent on its splicing function, or are these independent pathways? Recent work suggests UBL-5's effects on nuclear RNA processing (splicing) may contribute to its UPR-mt phenotypes, but the DVE-1 interaction appears to be a distinct function.
Experiment: Test whether splicing-defective UBL-5 mutants (disrupting HIND-binding) retain ability to interact with DVE-1 and activate UPR-mt reporters. This would distinguish whether the splicing and UPR-mt functions are mechanistically linked or represent independent activities of UBL-5.
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