LONRF2 is a RING-type ubiquitin E3 ligase that recognizes abnormally structured and misfolded proteins and promotes their ubiquitination as part of protein quality control. Directly studied substrates include abnormal TDP-43 and hnRNP M as well as artificial misfolded proteins. LONRF2 is predominantly expressed in neurons under unperturbed conditions; loss in mouse and motor-neuron models causes pathological protein accumulation, reduced neuronal survival, shortened neurites, motor-neuron degeneration, and cerebellar ataxia. In endometrial-cancer cells, LONRF2 also ubiquitinates and promotes degradation of ALDOA, with context-specific effects on glycolysis and malignant phenotypes. LONRF2 contains TPR repeats, a RING region, and a Lon N-terminal substrate-binding-domain homolog, but lacks the AAA+ ATPase and proteolytic domains that define Lon peptidases. Two isoforms are annotated; isoform 2 lacks the N-terminal 243 residues, but the isoforms have not been functionally compared.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006515 protein quality control for misfolded or incompletely synthesized proteins | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference assigns LONRF2 to protein quality control for misfolded proteins. Reason: This is a core biological role of LONRF2 and is independently supported by direct LONRF2 evidence: the protein binds and ubiquitylates abnormally structured TDP-43, hnRNP M1, and artificial misfolded proteins. The direct evidence validates the mammalian/PANTHER transfer rather than merely relying on family naming. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1920209 · mouse Lonrf2 SUPPORTS TRANSFER Mouse Lonrf2 has direct experimental protein-quality-control evidence from PMID:37474791, and the same study directly characterizes LONRF2. PANTHER:PTN002762616 · LONRF2 mammalian subfamily node SUPPORTS TRANSFER The subfamily-level inference is independently corroborated by direct LONRF2 binding and ubiquitination of abnormally structured proteins. Supporting Evidence: PMID:37474791 Here, we show that LONRF2 is a bona fide protein quality control ubiquitin ligase induced in post-mitotic senescent cells. |
| GO:0031175 neuron projection development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference links LONRF2 to neuron projection development. Reason: The mouse donor is supported by reduced neurite length in Lonrf2-deficient motor neurons, and ectopic LONRF2 rescued shortened neurites in ALS-patient-derived motor neurons. This supports a neuronal projection phenotype, but it is a contextual consequence of the protein-quality-control activity rather than the core molecular function and does not establish a universal developmental role in every neuron type. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: MGI:MGI:1920209 · mouse Lonrf2 SUPPORTS TRANSFER The mouse loss-of-function neurite phenotype supports transfer while defining the neuronal and long-term-culture context. PANTHER:PTN002762616 · LONRF2 mammalian subfamily node SUPPORTS TRANSFER The subfamily node is consistent with direct mammalian LONRF2 neuronal phenotypes, although the process remains non-core. Supporting Evidence: PMID:37474791 Mouse induced pluripotent stem cell-derived MNs lacking LONRF2 showed reduced survival, shortening of neurites and accumulation of pTDP-43 and G3BP1 after long-term culture. |
| GO:0051402 neuron apoptotic process | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic inference links LONRF2 to neuronal apoptosis, but the reported loss-of-function phenotypes support a protective rather than pro-apoptotic role. Reason: Reduced motor-neuron survival and age-dependent degeneration after Lonrf2 loss indicate that LONRF2 protects neurons from apoptotic death; they do not show that LONRF2 executes neuronal apoptosis. The directionally explicit negative-regulation term therefore better represents the source biology while remaining a contextual, downstream consequence of protein quality control. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: REGULATORY SIGN INVERSION Sources checked: MGI:MGI:1920209 · mouse Lonrf2 SUPPORTS TRANSFER The source is a current MGI IMP annotation from PMID:37474791, but the reported loss-of-function phenotypes support negative regulation of neuronal apoptosis. PANTHER:PTN002762616 · LONRF2 mammalian subfamily node SUPPORTS TRANSFER The node transfers a secondary neuronal outcome within the conserved mammalian LONRF2 subfamily, but the unsigned parent obscures the protective direction. Proposed replacements: negative regulation of neuron apoptotic process Supporting Evidence: PMID:37474791 Lonrf2-/- mice exhibit age-dependent TDP-43-mediated motor neuron (MN) degeneration and cerebellar ataxia. |
| GO:0061630 ubiquitin protein ligase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference supports LONRF2 as a RING-type ubiquitin E3 ligase. Reason: Ubiquitin protein ligase activity is the core molecular function and is directly corroborated for LONRF2 by its ubiquitination of abnormally structured proteins. The mammalian donor and PANTHER node are especially relevant; the distant fission- yeast donor supports only the broadly conserved RING-E3 activity and is not used to transfer LONRF2 substrate specificity or neuronal biology. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1920209 · mouse Lonrf2 SUPPORTS TRANSFER Direct mammalian LONRF2 ubiquitination evidence strongly supports transfer of the broad ligase activity. PANTHER:PTN009070514 · LONRF-family RING E3 node SUPPORTS TRANSFER The family node supports the conserved RING-E3 activity and is independently validated in LONRF2. PomBase:SPAC6B12.07c · fission-yeast LONRF-family protein SUPPORTS TRANSFER This distant donor is relevant only to the broad conserved ubiquitin ligase activity, not mammalian substrates or neuronal processes. Supporting Evidence: PMID:37474791 LONRF2 binds and ubiquitylates abnormally structured TDP-43 and hnRNP M1 and artificially misfolded proteins. |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | MARK AS OVER ANNOTATED | Summary: A neurodegenerative-disease interactome screen reported 17 candidate binary partners for LONRF2. Reason: The source is a systematic yeast two-hybrid map connecting roughly 5,000 proteins through approximately 30,000 candidate interactions. The individual edges may be useful hypotheses, but pooling them under generic protein binding neither defines a specific LONRF2 activity nor establishes that these proteins are endogenous substrates, cofactors, or members of one stable complex. The TARDBP/Q13148 edge is independently corroborated by PMID:37474791, but that does not make the pooled generic term informative. Supporting Evidence: PMID:32814053 Here, we report on an interactome map that focuses on neurodegenerative disease (ND), connects ∼5,000 human proteins via ∼30,000 candidate interactions and is generated by systematic yeast two-hybrid interaction screening of ∼500 ND-related proteins and integration of literature interactions. |
| GO:0043021 ribonucleoprotein complex binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl transfers ribonucleoprotein-complex binding from mouse Lonrf2. Reason: The transferred source is mouse Lonrf2, and PMID:37474791 reports LONRF2 binding to abnormally structured TDP-43 and hnRNP M1. Recognition of aberrant ribonucleoprotein-associated substrates is therefore defensible, but this term captures one substrate context and should not imply broad binding to normal ribonucleoprotein complexes or replace the core misfolded-protein recognition and E3 activities. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:F6ZE64 · mouse Lonrf2 protein SUPPORTS TRANSFER The mouse source record supports the substrate-context binding term, while PMID:37474791 independently reports binding to abnormal RNA-binding proteins. ensembl:ENSMUSP00000117600 · mouse Lonrf2 Ensembl protein SUPPORTS TRANSFER The Ensembl ortholog is the mouse Lonrf2 product used for the automatic one-to-one mammalian transfer. Supporting Evidence: PMID:37474791 LONRF2 binds and ubiquitylates abnormally structured TDP-43 and hnRNP M1 and artificially misfolded proteins. |
| GO:0051787 misfolded protein binding | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl transfers misfolded protein binding from mouse Lonrf2. Reason: The mouse donor supports this term, and PMID:37474791 directly reports that LONRF2 binds abnormally structured and artificially misfolded proteins. This substrate-recognition activity is a core component of the LONRF2 protein-quality-control E3 mechanism and is not based solely on orthology. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:F6ZE64 · mouse Lonrf2 protein SUPPORTS TRANSFER The mouse source record carries the transferred misfolded-protein-binding assertion, independently corroborated by PMID:37474791. ensembl:ENSMUSP00000117600 · mouse Lonrf2 Ensembl protein SUPPORTS TRANSFER The one-to-one mouse ortholog supports transfer, independently corroborated by direct LONRF2 evidence in the same study. Supporting Evidence: PMID:37474791 LONRF2 binds and ubiquitylates abnormally structured TDP-43 and hnRNP M1 and artificially misfolded proteins. |
| GO:0061630 ubiquitin protein ligase activity | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl transfers ubiquitin protein ligase activity from mouse Lonrf2. Reason: The mouse donor supports this term, and PMID:37474791 directly demonstrates LONRF2-dependent ubiquitination of abnormal protein substrates. The transfer is therefore sound and duplicates, rather than conflicts with, the independently reviewed IBA annotation for the same core activity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:F6ZE64 · mouse Lonrf2 protein SUPPORTS TRANSFER The mouse source record carries the transferred ligase assertion, independently corroborated by PMID:37474791. ensembl:ENSMUSP00000117600 · mouse Lonrf2 Ensembl protein SUPPORTS TRANSFER The one-to-one mouse ortholog transfer is independently corroborated by direct LONRF2 ubiquitination evidence. Supporting Evidence: PMID:37474791 Here, we show that LONRF2 is a bona fide protein quality control ubiquitin ligase induced in post-mitotic senescent cells. |
| GO:0016567 protein ubiquitination | IDA PMID:42442502 The ubiquitin ligase LONRF2 inhibits glycolysis and malignan... | NEW | Summary: In endometrial-cancer cells, LONRF2 interacts with ALDOA and promotes its ubiquitination and degradation. Reason: The direct substrate result supports protein ubiquitination with ALDOA recorded as the input. GO:0016567 is deliberately used instead of a polyubiquitination or linkage-specific child because the abstract does not state the ubiquitin-chain number or topology. The associated glycolysis and cancer phenotypes are context-specific and are not used to define the core LONRF2 process. Supporting Evidence: PMID:42442502 LONRF2 interacted with ALDOA and induced its ubiquitination and degradation. |
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Download this section (compressed HTML)Q: Which E2 enzymes, ubiquitin-chain linkages, and degradation pathways are used by LONRF2 for abnormal TDP-43, hnRNP M, artificial misfolded proteins, and ALDOA?
Q: Which endogenous neuronal substrates account for pathological protein accumulation, neurite shortening, and motor-neuron degeneration after LONRF2 loss?
Q: Is ALDOA a physiological LONRF2 substrate outside endometrial-cancer cells, and are the glycolytic and tumor phenotypes specific to that disease context?
Q: Do isoforms 1 and 2 differ because isoform 2 lacks the N-terminal TPR-repeat region, and which isoform was used in the published functional experiments?
Q: Is the N-terminal RING-like region at residues 143-193 an intact zinc-binding catalytic module, an atypical regulatory element, or a degenerate remnant?
Experiment: Reconstitute sequence-verified full-length LONRF2 with an E1, ubiquitin, and a panel of human E2 enzymes, using abnormal TDP-43, hnRNP M, and ALDOA as substrates. Compare wild type with RING-disrupting variants and identify substrate sites and chain linkages by quantitative mass spectrometry.
Hypothesis: LONRF2 uses a restricted set of E2 enzymes to ubiquitinate abnormal protein substrates with defined chain topologies.
Type: reconstituted ubiquitination assay
Experiment: Acutely degrade endogenous LONRF2 in human iPSC-derived motor neurons, then integrate diGly ubiquitin-remnant proteomics, insoluble-proteome profiling, pulse-chase turnover, and longitudinal neurite and survival measurements. Rescue with wild-type but not RING-disrupted LONRF2 and biochemically validate prioritized direct substrates.
Hypothesis: A limited endogenous substrate set connects LONRF2 ligase activity to neuronal protein homeostasis and survival.
Type: acute neuronal perturbation and ubiquitin proteomics
Experiment: Compare endogenous LONRF2 knockout and rescue across endometrial-cancer cells, nontransformed endometrial cells, and neurons, measuring ALDOA ubiquitination, half-life, glycolytic flux, and abundance. Include ALDOA mutants at mapped ubiquitination sites to test causality without assuming a particular chain linkage.
Hypothesis: LONRF2-dependent ALDOA ubiquitination is context-dependent rather than a universal determinant of glycolysis.
Type: comparative substrate-validation study
Experiment: Express sequence-verified isoforms from the same genomic landing site at matched levels and compare localization, proximity interactomes, misfolded-protein binding, E2 engagement, ubiquitination of validated substrates, and rescue of neuronal LONRF2-loss phenotypes.
Hypothesis: The N-terminal truncation in isoform 2 changes substrate selection or localization while retaining RING-dependent ligase capacity.
Type: isoform-comparative functional analysis
Experiment: Measure zinc stoichiometry and determine the structure of residues 143-193, then introduce ligand-disrupting variants into full-length LONRF2 and compare them with C-terminal RING variants in reconstituted ubiquitination, substrate binding, and cellular turnover assays.
Hypothesis: The N-terminal RING-like region is structurally and functionally distinct from the conserved C-terminal RING.
Type: structural and comparative domain-function analysis
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The E2 enzyme requirements, ubiquitin-chain architecture, and immediate degradation machinery used by LONRF2 remain unresolved in the locally available evidence.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: LONRF2 directly binds and ubiquitinates abnormal TDP-43, hnRNP M, artificial misfolded proteins, and ALDOA, but both direct studies are cached as abstracts and neither abstract specifies chain linkage, E2 choice, or a reconstituted reaction.
Significance: These mechanistic details determine how LONRF2 selects ubiquitination outcomes and whether different substrate classes use the same reaction pathway.
What would resolve it: Reconstitute full-length LONRF2 with a panel of human E2 enzymes and defined substrates, quantify ubiquitin transfer and chain topology by mass spectrometry, and test proteasome and autophagy dependencies in matched cellular assays.
Provenance (the field's own admissions):
Gap: Whether the N-terminal InterPro RING-like region at residues 143-193 is an intact zinc-coordinating RING or an atypical or degenerate remnant is unresolved.
OPEN BIOLOGY MF_DARK
What is known: The C-terminal RING at residues 448-487 has conserved-site support and strong family conservation, whereas the N-terminal call lacks an IPR017907 conserved-site overlap and has low identity to the RNF4 control. Sequence analysis alone cannot determine metal occupancy, fold integrity, or catalytic contribution.
Significance: Resolving the first region will establish whether LONRF2 contains one functional RING module or a second structurally distinct zinc-binding element.
What would resolve it: Determine the structure and zinc stoichiometry of the isolated N-terminal region, then compare full-length wild type and ligand-disrupting variants in reconstituted ubiquitin-transfer and cellular substrate-turnover assays.
Provenance (the field's own admissions):
Gap: The physiological substrate spectrum of LONRF2 and the extent to which the ALDOA axis operates outside endometrial-cancer models are unknown.
OPEN BIOLOGY BP_DARK
What is known: Abnormally structured RNA-binding proteins are direct protein-quality-control substrates, whereas ALDOA ubiquitination and its glycolytic consequences were demonstrated in an endometrial-cancer setting; high-throughput binary interactors are not validated substrates.
Significance: Defining endogenous substrates across tissues is necessary to connect the core E3 reaction to neuronal homeostasis and to determine whether the cancer result reflects a broader metabolic function.
What would resolve it: Use acute endogenous LONRF2 depletion with diGly ubiquitin-remnant proteomics and quantitative protein turnover in neurons and non-neuronal cells, followed by wild-type rescue and direct biochemical validation of prioritized substrates.
Provenance (the field's own admissions):
Gap: The native subcellular site of LONRF2 activity and any regulated cofactor assembly are not established.
OPEN BIOLOGY CC_DARK
What is known: The literature establishes substrates and neuronal expression, but the current GOA set contains no direct cellular-component annotation, and the large binary-interaction screen does not define a physiological stable complex.
Significance: Compartment and transient cofactors constrain which abnormal proteins LONRF2 can recognize and where ubiquitination occurs.
What would resolve it: Endogenously tag LONRF2 and combine quantitative live-cell imaging, biochemical fractionation, and proximity labeling under basal and proteotoxic-stress conditions, validating candidate cofactors by reciprocal endogenous assays.
Provenance (the field's own admissions):
Gap: Whether isoforms 1 and 2 differ in substrate recognition, ubiquitin-ligase activity, localization, or neuronal function is unknown, and the isoform tested in each direct study is not identified in the cached abstracts.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Isoform 2 lacks residues 1-243, removing most of the annotated N-terminal TPR-repeat region while retaining the RING and Lon N-terminal-domain homolog; no isoform-specific GO annotation or functional comparison is available.
Significance: Loss of the N-terminal interaction architecture could alter substrate selection without abolishing the retained RING module, so results from unspecified constructs cannot safely be assumed to apply equally to both isoforms.
What would resolve it: Compare sequence-verified isoforms expressed at matched endogenous levels for misfolded-protein binding, E2 engagement, substrate ubiquitination, stability, localization, and rescue of LONRF2-loss phenotypes.
Provenance (the field's own admissions):
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