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
|
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.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan for this report
- Verify target identity and nomenclature for C. elegans ubl-5 (UniProt P91302) and reconcile known aliases (Hub1/UBL5) with domain annotations.
- Gather recent (2023–2024) and foundational literature on molecular function, localization, pathways (pre-mRNA splicing; UPRmt), and phenotypes.
- Synthesize evidence emphasizing precise molecular mechanisms, cellular location, and pathway role, prioritizing 2023–2024 primary studies/reviews.
- Summarize applications/implementations and quantitative readouts where available.
- Provide a concise evidence table and a narrative research report with URLs, dates, and source-backed citations.
Verification of target identity and scope
- Gene symbol and protein: ubl-5 encodes UBL-5, the C. elegans ortholog of Hub1/UBL5, an atypical ubiquitin-like protein lacking the canonical di-Gly motif and functioning via non-covalent protein–protein interactions. The 2023 FEBS Letters study explicitly refers to the C. elegans protein as Hub1/UBL-5 and demonstrates conserved molecular interactions and functions consistent with the Hub1/Ubl5 domain family, validating the identity and domain-based expectations (IPR039732, IPR000626, IPR029071) in the context of a nematode ortholog (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 1-3, kolathur2023theubiquitin‐likeprotein pages 3-4).
Key concepts and definitions (current understanding)
- Atypical ubiquitin-like protein: 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 (Aug 2021) (chanarat2021ubl5hub1anatypical pages 6-8, chanarat2021ubl5hub1anatypical pages 4-6).
- HIND-mediated interactions: UBL-5 recognizes Hub1-interaction domains (HINDs) in spliceosomal proteins (e.g., Snu66/SART1, Prp38/PRPF38A), with a conserved salt bridge between UBL-5 Asp and HIND Arg, stabilizing the complex and modulating spliceosome assembly/activation (Aug 2021; Dec 2023) (chanarat2021ubl5hub1anatypical pages 6-8, kolathur2023theubiquitin‐likeprotein pages 3-4, chanarat2021ubl5hub1anatypical pages 4-6).
- Non-enzymatic splicing cofactor: UBL-5 can interact with splicing ATPase Prp5/DDX46 and multiple tri-snRNP components to tune splicing efficiency and fidelity; in multicellular organisms, its in vivo splicing role was recently demonstrated in C. elegans (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4, chanarat2021ubl5hub1anatypical pages 4-6).
Recent developments and latest research (2023–2024 prioritized)
- Direct demonstration in C. elegans (FEBS Letters, Dec 2023): Kolathur et al. showed that UBL-5 binds HIND-containing SART-1 and PRP-38, co-IPs with spliceosomal proteins, and is essential for splicing of selected targets; ubl-5 mutant animals arrest at L3 and exhibit accumulation of unspliced transcripts. A C. elegans ubl-5 genomic clone rescues lethality, and UBL-5 complements growth/splicing defects in S. pombe hub1 mutants, supporting strong conservation (https://doi.org/10.1002/1873-3468.14555; Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4, kolathur2023theubiquitin‐likeprotein pages 1-3).
- Stress-pathway integration updates (2024 review): UBL5 is positioned at the interface of splicing and stress signaling, including the mitochondrial UPR (mtUPR) and ER stress PERK arm (mammalian cells). Under ER stress, PERK activation decreases UBL5 stability via a ubiquitin-independent proteasome system, hinting that UBL5 levels are dynamically regulated during stress (https://doi.org/10.3390/v16121922; Dec 2024) (xia2024ubl5andits pages 5-7, xia2024ubl5andits pages 4-5).
Primary molecular function and mechanism (precision, partners)
- Non-enzymatic splicing regulator: UBL-5 functions as a non-covalent cofactor within the spliceosome. In C. elegans, UBL-5 binds the HIND-containing splicing factors Snu66/SART-1 and PRP-38 and associates with additional spliceosomal proteins. Loss of ubl-5 produces intron retention and defective cis- and trans-splicing, with lethality at L3, indicating an essential splicing role (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4, kolathur2023theubiquitin‐likeprotein pages 1-3).
- Structural interaction logic: The HIND–UBL-5 interface is characterized by a conserved salt bridge and hydrophobic contacts; UBL-5 binding can stabilize HIND motifs and modulate splicing ATPases (e.g., Prp5/DDX46) to promote splicing efficiency, with overexpression generally relaxing splice-site stringency as shown in other systems (Aug 2021) (chanarat2021ubl5hub1anatypical pages 4-6, chanarat2021ubl5hub1anatypical pages 6-8).
- 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 (Aug 2021) (chanarat2021ubl5hub1anatypical pages 6-8).
Subcellular localization
- Nuclear accumulation with spliceosome association: UBL-5 accumulates in the nucleus, associates with spliceosomal complexes, and can redistribute under stress. Human UBL5 has been observed near Cajal bodies, consistent with a role at spliceosome-related subnuclear structures; C. elegans UBL-5 shows stress-induced nuclear accumulation (Aug 2021; Dec 2024) (chanarat2021ubl5hub1anatypical pages 6-8, xia2024ubl5andits pages 4-5, xia2024ubl5andits pages 2-4).
Roles in signaling and biochemical pathways
- Pre-mRNA splicing pathway: UBL-5 integrates at the level of spliceosome assembly/activation by binding HIND-containing factors (SART-1/Snu66, PRP-38/PRPF38A) and potentially modulating helicase activity (Prp5/DDX46), thereby influencing intron recognition and splicing fidelity in vivo in C. elegans (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4).
- Mitochondrial unfolded protein response (UPRmt): In C. elegans, UBL-5 has been linked as a cofactor with DVE-1 to promote transcription of mitochondrial chaperones (hsp-6, hsp-60) during mtUPR; RNAi against ubl-5 reduces hsp-6p::gfp and hsp-60 reporter activation and lowers endogenous chaperone mRNAs, with effects on mitochondrial morphology and complex assembly (Sep 2014; Dec 2024) (bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5).
- UPRmt and longevity nuance: Genetic studies indicate that while UBL-5 participates in mtUPR readouts, activation of mtUPR is neither necessary nor sufficient for lifespan extension across conditions, cautioning against equating UBL-5’s mtUPR role with longevity causality (Mar 2014; review perspective Sep 2014) (xia2024ubl5andits pages 5-7, bennett2014searchingforthe pages 3-5).
- ER stress/PERK arm (mammalian data, mechanistic relevance): UBL5 is degraded downstream of PERK via UIPS, suggesting a conserved logic where stress pathways tune UBL5 abundance to limit prolonged stress signaling; this offers a mechanistic backdrop for stress–splicing crosstalk potentially relevant across metazoans (Dec 2024) (xia2024ubl5andits pages 5-7).
- Genetic screen intersections: Genome-wide RNAi screens for UPRmt regulators in C. elegans uncovered links between splicing factors and UPRmt modulation; overlap between ubl-5 interactors and screen hits supports a mechanistic bridge between splicing and mitochondrial stress responses (Mar 2021; synthesis with Dec 2023 findings) (kolathur2023theubiquitin‐likeprotein pages 3-4, chanarat2021ubl5hub1anatypical pages 4-6).
Key phenotypes upon loss-of-function
- Developmental arrest: ubl-5 mutants arrest at the L3 larval stage and are inviable; lethality is rescued by a genomic ubl-5 transgene, defining an essential developmental requirement (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4).
- Splicing defects: Splicing-sensitive arrays reveal accumulation of unspliced intron-containing RNAs and defects in both cis- and trans-splicing in ubl-5 mutants, consistent with impaired spliceosome function (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4).
- UPRmt reporters and mitochondrial homeostasis: RNAi knockdown of ubl-5 suppresses mtUPR reporters (hsp-6p::gfp, hsp-60) and reduces endogenous chaperone gene expression; concomitant changes in mitochondrial morphology and multi-subunit complex assembly have been reported (Sep 2014; Dec 2024) (bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5).
Current applications and real-world implementations
- C. elegans toolkits: Functional analyses employ RNAi against ubl-5, mtUPR reporter strains (hsp-6p::gfp; hsp-60 reporters), GFP-tagged UBL-5 for localization, and genetic mutants complemented by genomic rescue; cross-species complementation in S. pombe validates conservation (Dec 2023; Sep 2014; Dec 2024) (kolathur2023theubiquitin‐likeprotein pages 3-4, bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5).
- Screening paradigms: Genome-wide RNAi screens and cross-species modifier screens connect splicing factors (including UBL-5 interactors) to mtUPR regulation, enabling systems-level dissection of mitochondrial stress signaling (Mar 2021; synthesis with Dec 2023) (chanarat2021ubl5hub1anatypical pages 4-6, kolathur2023theubiquitin‐likeprotein pages 3-4).
Expert opinions and analysis from authoritative sources
- Mechanistic synthesis: Reviews emphasize that UBL-5/Hub1 is a stress-responsive, non-enzymatic UBL-like factor that primarily regulates pre-mRNA splicing via direct interactions with spliceosomal components and that its roles in mitochondrial stress signaling likely emerge from its impact on nuclear RNA processing rather than a dedicated enzymatic function (Aug 2021; Dec 2024) (chanarat2021ubl5hub1anatypical pages 6-8, xia2024ubl5andits pages 5-7, xia2024ubl5andits pages 4-5).
- Longevity context: Expert commentary argues mtUPR activation is not a reliable proxy for longevity extension, cautioning against over-attributing lifespan effects to UBL-5–dependent mtUPR readouts in the absence of rigorous genetic controls (Mar 2014; Sep 2014) (xia2024ubl5andits pages 5-7, bennett2014searchingforthe pages 3-5).
Relevant statistics and data from recent studies
- Essentiality and stage specificity: ubl-5 null mutants arrest at L3, and ubl-5 expression is elevated at L3, aligning with a critical developmental window for its splicing function (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4).
- Molecular interaction specificity: The UBL-5–SART-1 interaction depends on a conserved salt bridge (UBL-5 Asp22–SART-1 Arg62) demonstrated in binding assays; co-IP/MS showed enrichment of spliceosomal proteins in UBL-5 complexes in C. elegans (Dec 2023) (kolathur2023theubiquitin‐likeprotein pages 3-4).
- Reporter and expression effects: In C. elegans mtUPR paradigms, ubl-5 RNAi reduces hsp-6p::gfp and hsp-60 signals and lowers endogenous hsp-6/hsp-60 mRNAs; under stress, UBL-5-GFP accumulates in nuclei (Sep 2014; Dec 2024) (bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5, xia2024ubl5andits pages 2-4).
Concise evidence table
| Aspect | Key finding (1-2 sentences) | Experimental details / quantitative notes | Organism / context | Source (authors, year) | Journal | URL | Publication date (Month Year) | Citation ID(s) available |
|---|---|---:|---|---|---|---|---|---|
| Primary molecular function | UBL-5 is an atypical, non-enzymatic ubiquitin-like protein that acts via non-covalent protein–protein interactions with spliceosomal factors (HIND-containing proteins) and can modulate splicing machinery (e.g., PRP-38 / SART-1 binding). | Biochemical binding (Y2H, GST pulldown), co-IP/MS identifying spliceosomal partners; structural/biophysical evidence for HIND salt-bridge interactions. | Caenorhabditis elegans (functional conservation shown across species) | Kolathur et al., 2023; Chanarat, 2021 | FEBS Letters; Int. J. Mol. Sci. | https://doi.org/10.1002/1873-3468.14555; https://doi.org/10.3390/ijms22179384 | Dec 2023; Aug 2021 | (kolathur2023theubiquitin‐likeprotein pages 1-3, chanarat2021ubl5hub1anatypical pages 6-8) |
| Role in pre-mRNA splicing | 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. | Splicing-sensitive microarray and rescue assays; ubl-5 mutants accumulate unspliced RNAs; genomic ubl-5 clone rescues lethality; complementation of S. pombe hub1 mutants. | C. elegans (developmental L3 arrest phenotype) and cross-species complementation | Kolathur et al., 2023 | FEBS Letters | https://doi.org/10.1002/1873-3468.14555 | Dec 2023 | (kolathur2023theubiquitin‐likeprotein pages 3-4) |
| Subcellular localization | UBL-5 accumulates in the nucleus and associates with spliceosomal complexes; localizes near Cajal bodies in other systems and shows stress-induced nuclear redistribution. | GFP-fusion localization (nuclear accumulation under stress), co-IP with spliceosome components, microscopy showing proximity to Cajal body markers in other species. | Observed in C. elegans (stress-induced nuclear accumulation) and human/yeast models for localization context | Chanarat, 2021; Xia, 2024 | Int. J. Mol. Sci.; Viruses | https://doi.org/10.3390/ijms22179384; https://doi.org/10.3390/v16121922 | Aug 2021; Dec 2024 | (chanarat2021ubl5hub1anatypical pages 6-8, xia2024ubl5andits pages 2-4) |
| UPRmt pathway role | UBL-5 has been implicated as a cofactor with DVE-1 in activating mitochondrial chaperone genes (hsp-6, hsp-60) in UPRmt models, but its UPRmt role may be mediated via effects on pre-mRNA splicing rather than a separate enzymatic activity. | Reporter assays (hsp-6p::gfp, hsp-60), RNAi knockdown reducing reporter activation and endogenous chaperone mRNAs; genetic studies linking UBL-5 to UPRmt readouts but with caveats about causality for longevity. | C. elegans UPRmt models and reporter assays | Bennett et al., 2014; Kolathur et al., 2023; Xia, 2024 | Worm; FEBS Lett; Viruses | https://doi.org/10.4161/21624046.2014.959404; https://doi.org/10.1002/1873-3468.14555; https://doi.org/10.3390/v16121922 | Sep 2014; Dec 2023; Dec 2024 | (bennett2014searchingforthe pages 3-5, kolathur2023theubiquitin‐likeprotein pages 1-3, xia2024ubl5andits pages 4-5) |
| Links to ER stress / PERK and degradation | In mammalian studies UBL5 levels are regulated by ER stress (PERK arm) and UBL5 can be degraded via a ubiquitin-independent proteasome pathway, suggesting UBL5 levels are stress-regulated and that turnover modulates downstream responses. | Cellular assays showing PERK-dependent decreases in UBL5 stability and UIPS-mediated degradation (mammalian). | Mammalian cell models (implications for conserved stress regulation) | Xia, 2024 | Viruses | https://doi.org/10.3390/v16121922 | Dec 2024 | (xia2024ubl5andits pages 5-7) |
| Genetic screens linking splicing to UPRmt | Genome-wide RNAi and cross-species screens identified splicing factors and UBL-5 interactors as modifiers of UPRmt, suggesting a functional link between splicing machinery and mitochondrial stress signaling. | RNAi suppressor/enhancer screens for UPRmt regulators; overlap observed between UBL-5 interactors and screen hits. | C. elegans genetic screens for UPRmt regulators (fusion-defective and other models) | Bennett et al., 2014; Kolathur et al., 2023 | Worm; FEBS Lett | https://doi.org/10.4161/21624046.2014.959404; https://doi.org/10.1002/1873-3468.14555 | Sep 2014; Dec 2023 | (bennett2014searchingforthe pages 3-5, kolathur2023theubiquitin‐likeprotein pages 3-4) |
| Applications / implementations in C. elegans | UBL-5 has been studied using RNAi, hsp-6/hsp-60 reporter assays, GFP fusions, loss-of-function mutants (L3 arrest), and cross-species complementation (S. pombe), enabling functional dissection and in vivo validation. | RNAi reporter knockdowns, transgenic GFP localization, mutant phenotyping (developmental arrest), and genetic rescue/complementation experiments. | Experimental tools applied in C. elegans research | Kolathur et al., 2023; Bennett et al., 2014; Xia, 2024 | FEBS Lett; Worm; Viruses | https://doi.org/10.1002/1873-3468.14555; https://doi.org/10.4161/21624046.2014.959404; https://doi.org/10.3390/v16121922 | Dec 2023; Sep 2014; Dec 2024 | (kolathur2023theubiquitin‐likeprotein pages 3-4, bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5) |
| Recent 2023–2024 updates (C. elegans-specific) | Dec 2023 FEBS Lett. study provided direct, in vivo evidence that C. elegans UBL-5 is a conserved spliceosome-associated factor essential for proper splicing and development; 2024 reviews expand UBL5 links to stress responses, UPRmt, ER stress, and viral contexts. | FEBS Lett.: splicing arrays and genetic rescue in C. elegans; 2024 reviews compile mechanistic hypotheses and stress-regulatory observations (reporter and RNAi data summarized). | Primary C. elegans experimental data (2023) and 2024 integrative reviews | Kolathur et al., 2023; Xia, 2024 | FEBS Letters; Viruses | https://doi.org/10.1002/1873-3468.14555; https://doi.org/10.3390/v16121922 | Dec 2023; Dec 2024 | (kolathur2023theubiquitin‐likeprotein pages 1-3, xia2024ubl5andits pages 4-5) |
Table: Concise, source-backed summary of key findings about Caenorhabditis elegans ubl-5 (UniProt P91302), including molecular function, splicing role, localization, pathway links, experimental evidence, and recent (2023–2024) updates; useful for quick reference and citation tracking.
Conclusion
In Caenorhabditis elegans, ubl-5 encodes UBL-5, a conserved, non-enzymatic ubiquitin-like protein whose primary molecular role is to act as a spliceosome-associated cofactor that promotes proper pre-mRNA splicing through specific non-covalent interactions with HIND-containing spliceosomal proteins and splicing ATPases. Its nuclear localization and stress-responsive accumulation, together with genetic and reporter evidence, explain why UBL-5 contributes to mtUPR transcriptional outputs, but recent work indicates that its fundamental, essential function is splicing rather than a dedicated mitochondrial stress enzymatic role. Loss-of-function causes L3 lethality and splicing defects; RNAi reduces mtUPR reporter activation and mitochondrial chaperone expression. These findings, anchored by 2023 C. elegans genetics and biochemistry, position UBL-5 as a core splicing regulator that interfaces with broader stress-response networks through its control of nuclear RNA processing (Dec 2023; Mar/Sep 2014; Dec 2024) (kolathur2023theubiquitin‐likeprotein pages 3-4, xia2024ubl5andits pages 5-7, bennett2014searchingforthe pages 3-5, xia2024ubl5andits pages 4-5).
References
(kolathur2023theubiquitin‐likeprotein pages 1-3): Kiran Kumar Kolathur, Pallavi Sharma, Nagesh Y. Kadam, Navneet Shahi, Ane Nishitha, Kavita Babu, and Shravan Kumar Mishra. The ubiquitin‐like protein hub1/
(kolathur2023theubiquitin‐likeprotein pages 3-4): Kiran Kumar Kolathur, Pallavi Sharma, Nagesh Y. Kadam, Navneet Shahi, Ane Nishitha, Kavita Babu, and Shravan Kumar Mishra. The ubiquitin‐like protein hub1/
(chanarat2021ubl5hub1anatypical pages 6-8): Sittinan Chanarat. Ubl5/hub1: an atypical ubiquitin-like protein with a typical role as a stress-responsive regulator. International Journal of Molecular Sciences, 22:9384, Aug 2021. URL: https://doi.org/10.3390/ijms22179384, doi:10.3390/ijms22179384. This article has 21 citations and is from a poor quality or predatory journal.
(chanarat2021ubl5hub1anatypical pages 4-6): Sittinan Chanarat. Ubl5/hub1: an atypical ubiquitin-like protein with a typical role as a stress-responsive regulator. International Journal of Molecular Sciences, 22:9384, Aug 2021. URL: https://doi.org/10.3390/ijms22179384, doi:10.3390/ijms22179384. This article has 21 citations and is from a poor quality or predatory journal.
(xia2024ubl5andits pages 5-7): Liancheng Xia, Yanhua He, Yifan Sui, Xijia Feng, Xijing Qian, Yangang Liu, and Zhongtian Qi. Ubl5 and its role in viral infections. Viruses, 16:1922, Dec 2024. URL: https://doi.org/10.3390/v16121922, doi:10.3390/v16121922. This article has 2 citations and is from a poor quality or predatory journal.
(xia2024ubl5andits pages 4-5): Liancheng Xia, Yanhua He, Yifan Sui, Xijia Feng, Xijing Qian, Yangang Liu, and Zhongtian Qi. Ubl5 and its role in viral infections. Viruses, 16:1922, Dec 2024. URL: https://doi.org/10.3390/v16121922, doi:10.3390/v16121922. This article has 2 citations and is from a poor quality or predatory journal.
(xia2024ubl5andits pages 2-4): Liancheng Xia, Yanhua He, Yifan Sui, Xijia Feng, Xijing Qian, Yangang Liu, and Zhongtian Qi. Ubl5 and its role in viral infections. Viruses, 16:1922, Dec 2024. URL: https://doi.org/10.3390/v16121922, doi:10.3390/v16121922. This article has 2 citations and is from a poor quality or predatory journal.
(bennett2014searchingforthe pages 3-5): Christopher F Bennett, Haeri Choi, and Matt Kaeberlein. Searching for the elusive mitochondrial longevity signal in c. elegans. Worm, 3:e959404, Sep 2014. URL: https://doi.org/10.4161/21624046.2014.959404, doi:10.4161/21624046.2014.959404. This article has 8 citations.
Focus: function-assignment — does the gene product directly have GO:0031386 "protein tag activity"?
Source annotation: existing_annotations[4].function_hypothesis, evidence IBA, GO_REF:0000033.
Verdict: REFUTED (over-annotated).
The seed hypothesis — that ubl-5 has protein tag activity (GO:0031386) — is not supported and should be treated as an over-annotation. Three independent, mutually reinforcing lines of evidence converge:
The IBA annotation is a phylogenetic carry-over from the broad ubiquitin superfamily that fails to account for the well-characterized, conjugation-independent divergence of the Hub1/UBL5 clade. The genuinely supported function is non-covalent binding to HIND-motif spliceosomal factors, contributing to mRNA splicing (GO:0000398) — already annotated (IBA) — not protein tag activity.
Most important caveat: UniProt's human UBL5 entry still carries the legacy keyword "Ubl conjugation pathway," and older yeast reports (early 2000s) initially suggested Hub1 conjugation; these were superseded. This legacy is the likely origin of the over-annotation and should not be weighted against the direct non-covalent evidence.
| Citation | Evidence type | Stance | Claim tested | Key finding | Context | Confidence / limitations |
|---|---|---|---|---|---|---|
| This report (UniProt P91302 FASTA) | Structural/evolutionary (computed) | Refutes | Does UBL-5 have a conjugation-competent C-terminus? | 73 aa, C-terminus …ELYYQ; no C-terminal GG; contrasts ubiquitin/SUMO/NEDD8/ISG15 which all end in GG | Sequence-level, worm + human ortholog | High; sequence-based inference of mechanism |
| Ammon et al. 2014, PMID 24872507 | Direct assay / cell biology | Refutes | Is Hub1/UBL5 a covalent tag? | "Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently"; modulator of alternative splicing | Human + yeast | High; explicit statement of binding mode |
| Mishra et al. 2011, PMID 21614000 | Structural + biochemical | Refutes / re-assigns | Binding mode & function | Hub1 "binds non-covalently to a conserved element termed HIND" (Snu66/Prp38); "non-covalent modification of the spliceosome by an unconventional ubiquitin-like modifier" | S. cerevisiae, structural | High; foundational mechanistic paper |
| Kolathur et al. 2023, PMID 36480405 | Mutant phenotype + interaction | Refutes (organism-specific) / re-assigns | Worm UBL-5 binding mode & role | "Hub1/UBL-5 associates with proteins non-covalently"; binds HIND factors Snu66/SART-1 and PRP-38; ubl-5 mutants die at L3 with splicing defects | C. elegans | High; the directly relevant organism |
| Oka et al. 2014, PMID 25092792 | Depletion / functional assay | Qualifies (re-assigns) | Metazoan UBL5 function | UBL5 "primarily associates with spliceosomal proteins"; depletion → intron retention, loss of sister-chromatid cohesion via Sororin | Human cells | High; function is splicing, not tagging |
| Karaduman et al. 2017, PMID 28712727 | Biochemical | Qualifies (re-assigns) | Molecular mechanism | Hub1 binds DEAD-box helicase Prp5 and stimulates its ATPase → error-prone splicing | S. cerevisiae | High; non-covalent partner regulation |
| Haynes et al. 2007, PMID 17925224 (UniProt FUNCTION) | Mutant phenotype | Competing (downstream BP) | Worm-specific role | ubl-5 required for mitochondrial UPR (mtUPR); interacts with dve-1 under stress | C. elegans | Downstream biological process, not an MF |
| QuickGO GO:0031386 (definition) | Database / ontology | Sets the bar | What the term requires | "covalently attached (…conjugated) to another protein"; comment: "annotate conjugated tags" | Ontology | Definitional; decisive for the call |
Lead (requires curator verification): REMOVE / do-not-annotate GO:0031386 (protein tag activity) for ubl-5.
Net: the protein-tag MF should be removed/generalized away; the splicing BP and localization CC annotations carry the real function.
…IHEGFNFELYYQ; no C-terminal Gly-Gly.FNFELYYQ (no GG), UBL5_human MNLELYYQ (no GG) vs. ubiquitin …LRGG, SUMO1 …QTGG, NEDD8 …LRGG, ISG15 …LRGG (all GG).id: P91302
gene_symbol: ubl-5
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:6239
label: Caenorhabditis elegans
description: '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.'
existing_annotations:
- term:
id: GO:0000398
label: mRNA splicing, via spliceosome
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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).
action: ACCEPT
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.
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
supporting_text: 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.
- reference_id: PMID:16816413
supporting_text: 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
- term:
id: GO:0005634
label: nucleus
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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).
action: ACCEPT
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.
supported_by:
- reference_id: PMID:16816413
supporting_text: 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.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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).
action: ACCEPT
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.
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.'
- term:
id: GO:0031386
label: protein tag activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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.
action: REMOVE
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.'
additional_reference_ids:
- file:worm/ubl-5/ubl-5-goa.tsv
- file:worm/ubl-5/ubl-5-hypotheses/function-hypothesis-go-0031386/openscientist.md
propagation_review:
root_cause: PROPAGATION_BAD
failure_modes:
- PSEUDO_OR_SUBACTIVITY_LOSS
- FUNCTIONAL_DIVERGENCE
source_entities:
- source_id: PANTHER:PTN000315756
source_label: ubiquitin-like PANTHER source node
source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
comment: 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.
- source_id: SGD:S000007251
source_label: yeast Hub1/UBL5 source gene
source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
comment: Hub1/UBL5 biology supports non-covalent spliceosome-factor binding,
not covalent protein tag activity for worm ubl-5.
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-goa.tsv
supporting_text: "UniProtKB\tP91302\tubl-5\tenables\tGO:0031386\tprotein tag activity\tmolecular_function\tECO:0000318\tIBA\tGO_REF:0000033\tPANTHER:PTN000315756|SGD:S000007251\t6239\tCaenorhabditis elegans\tGO_Central\tUbiquitin-like protein 5\t20170228"
- reference_id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
supporting_text: 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.
- reference_id: file:worm/ubl-5/ubl-5-hypotheses/function-hypothesis-go-0031386/openscientist.md
supporting_text: is **not supported** and should be treated as an over-annotation.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.'
- term:
id: GO:0034514
label: mitochondrial unfolded protein response
evidence_type: IMP
original_reference_id: PMID:23870130
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:23870130
supporting_text: 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))
- term:
id: GO:0034514
label: mitochondrial unfolded protein response
evidence_type: IMP
original_reference_id: PMID:17925224
review:
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.
action: ACCEPT
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)."
supported_by:
- reference_id: PMID:17925224
supporting_text: 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).
- term:
id: GO:0005667
label: transcription regulator complex
evidence_type: IPI
original_reference_id: PMID:17925224
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:17925224
supporting_text: 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.
- reference_id: file:worm/ubl-5/ubl-5-uniprot.txt
supporting_text: Interacts with dve-1; the interaction occurs in a
mitochondrial stress-dependent manner.
- term:
id: GO:0034514
label: mitochondrial unfolded protein response
evidence_type: IMP
original_reference_id: PMID:16816413
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:16816413
supporting_text: 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.
- term:
id: GO:0005634
label: nucleus
evidence_type: IDA
original_reference_id: PMID:16816413
review:
summary: IDA annotation for nuclear localization from Benedetti et al.
(2006). Direct visualization of GFP-tagged UBL-5 accumulating in nuclei
under mitochondrial stress.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:16816413
supporting_text: 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.
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: PMID:16816413
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:16816413
supporting_text: Induction of mitochondrial stress promotes accumulation
of GFP-tagged UBL-5 in nuclei of transgenic worms [implying baseline
cytoplasmic/cytosolic presence before nuclear redistribution]
full_text_unavailable: true
- term:
id: GO:1990935
label: splicing factor binding
evidence_type: IDA
original_reference_id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
review:
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.
action: NEW
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.
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
supporting_text: 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
- term:
id: GO:0003713
label: transcription coactivator activity
evidence_type: IDA
original_reference_id: PMID:17925224
review:
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.
action: NEW
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.
supported_by:
- reference_id: PMID:17925224
supporting_text: 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)
- reference_id: PMID:16816413
supporting_text: 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
references:
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular
Location vocabulary mapping
findings: []
- id: PMID:16816413
title: Ubiquitin-like protein 5 positively regulates chaperone gene expression
in the mitochondrial unfolded protein response.
findings:
- statement: First identification of UBL-5 as positive regulator of UPR-mt
supporting_text: 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
- statement: RNAi of ubl-5 suppresses hsp-60::gfp and hsp-6::gfp reporter
activation
supporting_text: 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
- statement: ubl-5 RNAi inhibits induction of endogenous hsp-60 and hsp-6
genes
supporting_text: 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
- statement: Mitochondrial stress promotes nuclear accumulation of GFP-tagged
UBL-5
supporting_text: Induction of mitochondrial stress promotes accumulation of
GFP-tagged UBL-5 in nuclei of transgenic worms
- statement: UBL-5 effects a nuclear step in UPR-mt signaling
supporting_text: UBL-5 effects a nuclear step required for mounting a
response to the threat of mitochondrial protein misfolding
- id: PMID:17925224
title: ClpP mediates activation of a mitochondrial unfolded protein response
in C. elegans.
findings:
- statement: DVE-1 and UBL-5 form a complex during mitochondrial stress
supporting_text: 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
- statement: Both DVE-1 and UBL-5 are required for signaling UPR-mt
supporting_text: DVE-1 and the small ubiquitin-like protein UBL-5, both of
which are encoded by genes required for signaling the UPR(mt)
- statement: DVE-1 nuclear redistribution correlates with UPR-mt activation
supporting_text: Activation of the UPR(mt) correlates temporally and
spatially with nuclear redistribution of DVE-1
- statement: DVE-1 binds promoters of mitochondrial chaperone genes
supporting_text: 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
- id: PMID:23870130
title: The NAD(+)/Sirtuin Pathway Modulates Longevity through Activation of
Mitochondrial UPR and FOXO Signaling.
findings:
- statement: NAD+ restoration promotes longevity via UPR-mt activation
supporting_text: genetic or pharmacological restoration of NAD(+) prevents
age-associated metabolic decline and promotes longevity in worms
- statement: UPR-mt is part of the mitochondrial stress signaling pathway
supporting_text: activation of stress signaling via the mitochondrial
unfolded protein response (UPR(mt)) and the nuclear translocation and
activation of FOXO transcription factor DAF-16
- statement: Links metabolic regulation to mitochondrial proteostasis
supporting_text: augmenting mitochondrial stress signaling through the
modulation of NAD(+) levels may be a target to improve mitochondrial
function
- id: file:worm/ubl-5/ubl-5-goa.tsv
title: GOA annotation export for ubl-5
publication_type: DATABASE
findings:
- statement: GOA records the phylogenetic IBA source for the ubl-5 GO:0031386 annotation.
supporting_text: "UniProtKB\tP91302\tubl-5\tenables\tGO:0031386\tprotein tag activity\tmolecular_function\tECO:0000318\tIBA\tGO_REF:0000033\tPANTHER:PTN000315756|SGD:S000007251\t6239\tCaenorhabditis elegans\tGO_Central\tUbiquitin-like protein 5\t20170228"
- id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
title: Deep research summary for UBL-5
findings:
- statement: UBL-5 binds HIND-containing spliceosomal proteins SART-1 and
PRP-38
supporting_text: UBL-5 binds HIND-containing spliceosomal proteins SART-1
and PRP-38, co-IPs with spliceosomal proteins
- statement: UBL-5 co-immunoprecipitates with spliceosomal components
supporting_text: co-IP/MS showed enrichment of spliceosomal proteins in
UBL-5 complexes in C. elegans
- statement: ubl-5 mutants arrest at L3 and exhibit splicing defects
supporting_text: ubl-5 null mutants arrest at L3, and ubl-5 expression is
elevated at L3, aligning with a critical developmental window for its
splicing function
- statement: UBL-5 lacks C-terminal di-Gly motif for covalent conjugation
supporting_text: UBL-5/Hub1 is a ubiquitin-like protein that, unlike many
UBLs, lacks the C-terminal di-Gly motif for covalent conjugation
- statement: UBL-5 functions via non-covalent protein-protein interactions
supporting_text: Not a covalent modifier... UBL-5 does not act through
E1-E2-E3 conjugation but via direct protein-protein interactions in the
splicing machinery
- id: file:worm/ubl-5/ubl-5-uniprot.txt
title: UniProtKB entry for UBL-5 C. elegans
findings:
- statement: 73 amino acid ubiquitin-like protein
supporting_text: 73 AA
- statement: Contains Hub1/Ubl5 domain (IPR039732)
supporting_text: InterPro; IPR039732; Hub1/Ubl5
- statement: Cytoplasmic localization by sequence similarity
supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}'
- statement: Interacts with DVE-1 in stress-dependent manner
supporting_text: Interacts with dve-1; the interaction occurs in a
mitochondrial stress-dependent manner
- id: file:worm/ubl-5/ubl-5-hypotheses/function-hypothesis-go-0031386/openscientist.md
title: OpenScientist hypothesis report for ubl-5 GO:0031386
publication_type: DEEP_RESEARCH
findings:
- statement: OpenScientist refutes protein tag activity for ubl-5.
supporting_text: is **not supported** and should be treated as an over-annotation.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Focused OpenScientist report confirms that GO:0031386 requires
covalent conjugation, while ubl-5/Hub1 lacks the di-glycine motif and functions
through non-covalent spliceosome-factor binding.
core_functions:
- description: UBL-5 is an essential spliceosome-associated cofactor. Kolathur
et al. (2023) demonstrated that UBL-5 binds HIND-containing spliceosomal
proteins SART-1 and PRP-38, co-IPs with spliceosomal components, and loss of
function causes accumulation of unspliced transcripts and L3 larval arrest.
This is now considered the primary molecular function of UBL-5.
molecular_function:
id: GO:1990935
label: splicing factor binding
directly_involved_in:
- id: GO:0000398
label: mRNA splicing, via spliceosome
locations:
- id: GO:0005634
label: nucleus
supported_by:
- reference_id: file:worm/ubl-5/ubl-5-deep-research-falcon.md
supporting_text: UBL-5 binds HIND-containing spliceosomal proteins SART-1
and PRP-38... Loss of ubl-5 causes selective splicing defects (intron
retention and trans-/cis-splicing defects) and developmental arrest (L3
lethality)
- description: UBL-5 is a positive regulator of UPR-mt. Multiple independent
studies (PMID:16816413, PMID:17925224, PMID:23870130) demonstrate that UBL-5
is required for activation of mitochondrial chaperone genes (hsp-6, hsp-60)
during mitochondrial stress. UBL-5 forms a complex with the transcription
factor DVE-1 to activate UPR-mt target gene expression.
molecular_function:
id: GO:0003713
label: transcription coactivator activity
directly_involved_in:
- id: GO:0034514
label: mitochondrial unfolded protein response
in_complex:
id: GO:0005667
label: transcription regulator complex
locations:
- id: GO:0005634
label: nucleus
supported_by:
- reference_id: PMID:17925224
supporting_text: 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)
- reference_id: PMID:16816413
supporting_text: 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
proposed_new_terms: []
suggested_questions:
- question: 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.
suggested_experiments:
- description: 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.
tags:
- caeel-upr-stress