ADPRS (ARH3, formerly ADPRHL2) is the human ADP-ribosyl-acceptor hydrolase that erases serine-linked ADP-ribosylation. It is a 363-residue, all-alpha-helical enzyme of the ADP-ribosylglycohydrolase family with a binuclear Mg2+ catalytic centre and a mobile Glu41 'flap' that gates substrate entry, and it cleaves the alpha-O-glycosidic bond at the anomeric C1'' of ADP-ribose. Its principal substrate is the mono-ADP-ribose that PARP1/2 in complex with HPF1 installs on serine residues of histones and other chromatin proteins after DNA damage; ADPRS is the only known enzyme that removes this mark, and it also reverses the rarer threonine- and tyrosine-linked ADP-ribosylation. The same active site hydrolyses protein-free poly(ADP-ribose), for which ADPRS is the dominant activity of the mitochondrial matrix because the mitochondrial PARG splice form is catalytically dead, and it hydrolyses 1''-O-acetyl-ADP-ribose, the product of sirtuin-catalysed histone deacetylation, faster than it hydrolyses poly(ADP-ribose). The protein is distributed between the nucleus (including chromatin and sites of DNA damage, to which it is recruited through ADP-ribose recognition), the cytosol and the mitochondrial matrix. By clearing ADP-ribose signals it limits the accumulation of free poly(ADP-ribose) that triggers apoptosis-inducing-factor release from mitochondria and parthanatic cell death, and it prevents persistent mono-ADP-ribose 'scars' on chromatin after single-strand break repair. Biallelic loss-of-function variants cause CONDSIAS (MIM 618170), a childhood-onset, stress-induced neurodegeneration with ataxia and seizures. ADPRS is distinct in specificity from its paralogues ADPRH/ARH1, which hydrolyses ADP-ribosyl-arginine, and the catalytically inactive ADPRHL1/ARH2.
Definition: Catalysis of the reaction: O-(ADP-D-ribosyl)-L-threonyl-[protein] + H2O = ADP-D-ribose + L-threonyl-[protein].
Justification: GO has terms for the arginine (GO:0003875), serine (GO:0140292) and glutamate (GO:0140293) ADP-ribosyl hydrolases but none for threonine, so a measured activity has nowhere to go. Voorneveld et al. synthesised a Thr-ADP-ribosylated peptide and showed that wild-type ARH3, but not the D77N or D78N catalytic mutants, hydrolyses it, more slowly than the Ser analogue. UniProt records the activity in its FUNCTION line ('proteins ADP-ribosylated on serine and threonine'). The linkage is biologically real, not only synthetic: bacterial effectors such as CteC ADP-ribosylate Thr66 of human ubiquitin. Filed as an ontology gap rather than forced onto GO:0140292, which is serine-specific by definition - a threonine hydrolase cannot be_a serine hydrolase, they are siblings, the same distinction that makes GO:0071451 wrong rather than merely general in this review's first finding. Parented instead on the shared immediate parent that GO currently gives the arginine, serine and glutamate terms, GO:0016799; if the branch-placement question raised in suggested_questions is resolved in favour of GO:0004553, this term should move with its three siblings.
Parent term: hydrolase activity, hydrolyzing N-glycosyl compounds
Supporting Evidence:
Definition: The chemical reactions and pathways resulting in the breakdown of protein-free poly(ADP-ribose).
Justification: GO has the molecular function GO:0004649 poly(ADP-ribose) glycohydrolase activity and the process GO:0051725 protein de-ADP-ribosylation, but no process term for degrading PROTEIN-FREE poly(ADP-ribose) - which is a distinct species with its own signalling role, since free PAR is the death signal that releases apoptosis-inducing factor from mitochondria. GO:0051725's definition ('removing one or more ADP-ribose residues from a protein') cannot cover a polymer that is no longer attached to a protein, and the mitochondrial matrix activity of ADPRS acts on exactly that species. Searched QuickGO and OLS for 'poly(ADP-ribose) catabolic', 'ADP-ribose catabolic' and 'ADP-ribose metabolic process': no such term exists; the searches do return GO:1990966 'ATP generation from poly-ADP-D-ribose', so the queries were working.
Parent term: catabolic process
Supporting Evidence:
Definition: A programmed necrotic cell death process initiated by hyperactivation of poly(ADP-ribose) polymerase 1, in which protein-free poly(ADP-ribose) triggers release of apoptosis-inducing factor from mitochondria and its translocation to the nucleus, where it initiates large-scale DNA fragmentation. The process is caspase-independent and does not require RIPK1, RIPK3 or MLKL.
Justification: GO has no parthanatos term. The gap has a measurable annotation cost: it is why mouse Adprs, and by transfer human ADPRS, carry GO:0060546 negative regulation of NECROPTOTIC process, a term whose target GO:0070266 is defined by RIPK1/3 activation and MLKL dependence that parthanatos does not use. GO already acknowledges the problem in the comment on GO:0097527: PARP-dependent cell death 'is sometimes referred to as PARP-dependent cell death or parthanatos; it is still being debated if it constitutes an independent cell death modality'. Adding the term (with a 'negative regulation of parthanatos' child) would let ADPRS, PARP1, AIFM1 and PARG be annotated precisely instead of being forced onto necroptosis.
Parent term: programmed necrotic cell death
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006281 DNA repair | IMP PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | ACCEPT | Summary: Catalytic-pocket mutants are defective in DNA damage repair. Reason: Site-directed mutagenesis of the catalytic pocket impaired both Ser-ADPr hydrolysis and DNA damage repair, so the BP term rests on a perturbation of this gene product. GO:0006281 is also the correct level: ARH3 acts on the ADP-ribose signal that accompanies single-strand break repair rather than performing a specific repair step - which is precisely why the more specific GO:0006287 row below does not stand. Supporting Evidence: PMID:30045870 we used site-directed mutagenesis to examine the functional roles of key residues in the catalytic pocket of ARH3 in mediating the hydrolysis of ADP-ribosyl from serine and DNA damage repair |
| GO:0006287 base-excision repair, gap-filling | TAS Reactome:R-HSA-110373 | MARK AS OVER ANNOTATED | Summary: A mitochondrial-matrix reaction inheriting a nucleoplasmic gap-filling term by pathway containment. ARH3 neither excises a base nor fills a gap. Reason: Traced end to end in Reactome's own data. ADPRS has exactly one Reactome reaction, R-HSA-8952903 'ADPRHL2 hydrolyses poly(ADP-ribose)', whose compartment is 'mitochondrial matrix' and whose input and output are both '[mitochondrial matrix]'. Reactome nests that reaction under R-HSA-110362 'POLB-Dependent Long Patch Base Excision Repair' and then R-HSA-110373 'Resolution of AP sites via the multiple-nucleotide patch replacement pathway', both of which carry compartment 'nucleoplasm'. R-HSA-110373's own goBiologicalProcess field IS GO:0006287, which is where this row comes from. The GO definition of GO:0006287 requires an apurinic endonuclease degrading bases and a polymerase synthesising a patch - ARH3 does neither. Reference-projection test, fully paginated: R-HSA-110373 gives GO:0006287 to exactly 5 entities - POLB, LIG1, FEN1, PARG and ADPRS - of which the first three are the actual gap-filling machinery. Not REMOVE: ARH3 genuinely participates in the ADP-ribose signalling that accompanies single-strand-break repair, and GO:0006281 DNA repair (IMP, human experimental) already carries that at the right granularity. REMOVE was considered and declined on a specific ground rather than from caution: what the compartment argument demonstrates is that the ROUTE is invalid (a mitochondrial reaction cannot inherit a nucleoplasmic pathway's GO term), not that the biology is false. ADPRS is genuinely recruited to nuclear DNA lesions and erases the ADP-ribose marks laid down during single-strand break repair, and PARG - the other non-gap-filling recipient of this same Reactome term - is likewise a real participant in that pathway. So the term is imprecise rather than fabricated, which is exactly what MARK_AS_OVER_ANNOTATED encodes; a REMOVE would need a positive demonstration that ADPRS is absent from base-excision repair, and no such demonstration exists. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH GRANULARITY MISMATCH Sources checked: Reactome:R-HSA-110373 · Resolution of AP sites via the multiple-nucleotide patch replacement pathway SUPPORTS SOURCE BUT NOT TARGET nucleoplasm pathway; its GO:0006287 mapping is right for POLB/LIG1/FEN1 and wrong for a mitochondrial-matrix PAR hydrolase Supporting Evidence: PMID:22433848 ADP-ribosylhydrolase 3 (ARH3), not poly(ADP-ribose) glycohydrolase (PARG) isoforms, is responsible for degradation of mitochondrial matrix-associated poly(ADP-ribose). |
| GO:0060546 negative regulation of necroptotic process | IEA GO_REF:0000107 | MODIFY | Summary: Ensembl Compara reflection of the same mouse row, inheriting the same wrong death modality. Reason: The cell death ARH3 restrains is PARTHANATOS, not necroptosis. GO:0060546 regulates GO:0070266, whose definition requires 'activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3 ...) and ... critical dependence on mixed lineage kinase domain-like (MLKL)'. Parthanatos uses none of these: it runs PARP1 -> free PAR -> AIF release from mitochondria -> AIF nuclear translocation -> DNA cleavage, and is caspase- and RIPK-independent. The source annotation is mouse Adprs GO:0060546 IDA from PMID:30830864 (confirmed by QuickGO on Q8CG72), and both that paper and its predecessor PMID:24191052 describe the AIF/parthanatos axis explicitly. GO itself records the ambiguity rather than asserting the identity: the comment on GO:0097527 says PARP-dependent cell death 'is sometimes referred to as PARP-dependent cell death or parthanatos; it is still being debated if it constitutes an independent cell death modality'. The right move is therefore to step up one level to GO:0062099 negative regulation of programmed necrotic cell death - verified to be an ancestor of GO:0060546, so nothing is asserted that was not already implied - which drops the RIPK/MLKL commitment while keeping the regulated-necrosis claim. A GO request for an explicit parthanatos term is filed under proposed_new_terms. This row adds no independent evidence; it is the Compara mirror of the ISS row and must move with it. Propagation Review Root cause: EVIDENCE CIRCULAR OR REDUNDANT Failure modes: ROLE CONFLATION CIRCULAR PROPAGATION Sources checked: UniProtKB:Q8CG72 · mouse Adprs (reviewed) CIRCULAR OR REDUNDANT same mouse annotation as the ISS row, transferred a second time by a different pipeline Proposed replacements: negative regulation of programmed necrotic cell death Supporting Evidence: PMID:24191052 A protective effect of ARH3 results from its lowering of PAR levels in the nucleus and the cytoplasm, thereby preventing release of AIF from mitochondria and its accumulation in the nucleus |
| GO:0060546 negative regulation of necroptotic process | ISS GO_REF:0000024 | MODIFY | Summary: Right biology, wrong death modality: ARH3 restrains parthanatos, and GO:0060546's target term is defined by RIPK1/3 and MLKL. Reason: The cell death ARH3 restrains is PARTHANATOS, not necroptosis. GO:0060546 regulates GO:0070266, whose definition requires 'activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3 ...) and ... critical dependence on mixed lineage kinase domain-like (MLKL)'. Parthanatos uses none of these: it runs PARP1 -> free PAR -> AIF release from mitochondria -> AIF nuclear translocation -> DNA cleavage, and is caspase- and RIPK-independent. The source annotation is mouse Adprs GO:0060546 IDA from PMID:30830864 (confirmed by QuickGO on Q8CG72), and both that paper and its predecessor PMID:24191052 describe the AIF/parthanatos axis explicitly. GO itself records the ambiguity rather than asserting the identity: the comment on GO:0097527 says PARP-dependent cell death 'is sometimes referred to as PARP-dependent cell death or parthanatos; it is still being debated if it constitutes an independent cell death modality'. The right move is therefore to step up one level to GO:0062099 negative regulation of programmed necrotic cell death - verified to be an ancestor of GO:0060546, so nothing is asserted that was not already implied - which drops the RIPK/MLKL commitment while keeping the regulated-necrosis claim. A GO request for an explicit parthanatos term is filed under proposed_new_terms. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:Q8CG72 · mouse Adprs (reviewed) SUPPORTS SOURCE BUT NOT TARGET true ortholog with a real IDA (PMID:30830864); the defect is the term chosen for the mouse row, which transfers unchanged Proposed replacements: negative regulation of programmed necrotic cell death Supporting Evidence: PMID:24191052 A protective effect of ARH3 results from its lowering of PAR levels in the nucleus and the cytoplasm, thereby preventing release of AIF from mitochondria and its accumulation in the nucleus PMID:34479984 removal of PAR prevents excessive PAR accumulation which can lead to free PAR formation, release of apoptosis inducing factor (AIF) from mitochondria, and induction of cell death via the parthanatos pathway |
| GO:0071451 cellular response to superoxide | IBA GO_REF:0000033 | MODIFY | Summary: The clade-wide propagation of a wrong ROS species: 33 gene products now carry 'cellular response to superoxide' from a mouse H2O2 experiment. Reason: The term names the wrong reactive oxygen species. Every experiment behind this term used HYDROGEN PEROXIDE, not superoxide. GO:0070301 cellular response to hydrogen peroxide and GO:0071451 cellular response to superoxide are SIBLINGS under GO:0034614 cellular response to reactive oxygen species - verified by fetching both ancestor closures, neither contains the other - so this is not a too-general parent that quietly covers the data, it is a different chemical species. The defect originates upstream at the mouse MGI IMP (PMID:24191052) and has propagated to all 33 gene products under PANTHER:PTN008564042. The donor chain is traceable in full: mouse Adprs carries GO:0071451 by IMP from PMID:24191052 (Mashimo, Kato & Moss), whose abstract says PARG and ARH3 'regulate nuclear and cytoplasmic PAR degradation following hydrogen peroxide (H2O2) exposure'. The donor is the correct ortholog and its experiment is sound; only its term is wrong, and the IBA has copied it faithfully to the whole clade. Fixing the mouse MGI row would retract the error from all 33 gene products at once. Propagation Review Root cause: SOURCE BAD Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008564042 · ARH3/ADPRS orthologue node SUPPORTS TRANSFER fully paginated QuickGO query: 132 annotations over 33 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER 1:1 ortholog; carries its own IDA/IMP evidence for the ARH3 activity terms UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Proposed replacements: cellular response to hydrogen peroxide Supporting Evidence: PMID:24191052 PARG and ARH3, acting in tandem, regulate nuclear and cytoplasmic PAR degradation following hydrogen peroxide (H2O2) exposure |
| GO:0071451 cellular response to superoxide | IEA GO_REF:0000117 | MODIFY | Summary: ARBA rule reproducing the same wrong ROS species with no independent evidence. Reason: The term names the wrong reactive oxygen species. Every experiment behind this term used HYDROGEN PEROXIDE, not superoxide. GO:0070301 cellular response to hydrogen peroxide and GO:0071451 cellular response to superoxide are SIBLINGS under GO:0034614 cellular response to reactive oxygen species - verified by fetching both ancestor closures, neither contains the other - so this is not a too-general parent that quietly covers the data, it is a different chemical species. The defect originates upstream at the mouse MGI IMP (PMID:24191052) and has propagated to all 33 gene products under PANTHER:PTN008564042. ARBA:ARBA00043602 is a machine-learned rule trained on the existing annotation set, so it inherits rather than corroborates the error. It should follow the IMP and IBA rows to GO:0070301. Propagation Review Root cause: EVIDENCE CIRCULAR OR REDUNDANT Failure modes: CIRCULAR PROPAGATION GRANULARITY MISMATCH Sources checked: ARBA:ARBA00043602 · ARBA machine-learned rule CIRCULAR OR REDUNDANT learned from the same GO:0071451 rows it now reproduces Proposed replacements: cellular response to hydrogen peroxide Supporting Evidence: PMID:30401461 cell viability was reduced upon hydrogen peroxide exposure, although it was rescued by expression of wild-type ADPRHL2 mRNA as well as treatment with a PARP1 inhibitor |
| GO:0071451 cellular response to superoxide | IMP PMID:30401461 Bi-allelic ADPRHL2 Mutations Cause Neurodegeneration with De... | MODIFY | Summary: The human experiment used hydrogen peroxide, not superoxide. Reason: The term names the wrong reactive oxygen species. Every experiment behind this term used HYDROGEN PEROXIDE, not superoxide. GO:0070301 cellular response to hydrogen peroxide and GO:0071451 cellular response to superoxide are SIBLINGS under GO:0034614 cellular response to reactive oxygen species - verified by fetching both ancestor closures, neither contains the other - so this is not a too-general parent that quietly covers the data, it is a different chemical species. The defect originates upstream at the mouse MGI IMP (PMID:24191052) and has propagated to all 33 gene products under PANTHER:PTN008564042. In this human row specifically, Danhauser et al. state that patient fibroblast viability 'was reduced upon hydrogen peroxide exposure'. Superoxide is never used. GO:0070301 cellular response to hydrogen peroxide is the term the experiment supports. Proposed replacements: cellular response to hydrogen peroxide Supporting Evidence: PMID:30401461 cell viability was reduced upon hydrogen peroxide exposure, although it was rescued by expression of wild-type ADPRHL2 mRNA as well as treatment with a PARP1 inhibitor |
| GO:0140290 peptidyl-serine ADP-deribosylation | IBA GO_REF:0000033 | ACCEPT | Summary: The process counterpart of GO:0140292, propagated across a clade that is exactly the ADPRS orthologues. Reason: The WITH/FROM set is the PANTHER node plus mouse Adprs (MGI:MGI:2140364 = Q8CG72, the true 1:1 ortholog, reviewed Swiss-Prot) plus ADPRS itself (UniProtKB:Q9NX46). A self-referential IBA records a PAINT curator judging the function core for this gene, which is correct here. PANTHER:PTN008564042 was fully paginated through QuickGO: 132 annotations over 33 gene products, every one an ADPRS ortholog (adprs/ADPRHL2/ADPRS symbols across vertebrates, Nematostella, Trichoplax, Daphnia, Aspergillus). It reaches neither ADPRH nor ADPRHL1, so the paralog-specificity leak this family invites has not occurred. The mouse donor carries its own IDA (PMID:29234005). Direction is correct: the term is DE-ribosylation, the removal reaction, not the installation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008564042 · ARH3/ADPRS orthologue node SUPPORTS TRANSFER fully paginated QuickGO query: 132 annotations over 33 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER 1:1 ortholog; carries its own IDA/IMP evidence for the ARH3 activity terms UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Supporting Evidence: PMID:29234005 ARH3-deficient mouse embryonic fibroblasts are characterized by a specific increase in serine-ADP-ribosylation in vivo under untreated conditions as well as following hydrogen peroxide stress |
| GO:0140290 peptidyl-serine ADP-deribosylation | IDA PMID:28650317 Serine ADP-ribosylation reversal by the hydrolase ARH3. | ACCEPT | Summary: Serine ADP-ribosylation is reversed in cells, and the reversal requires ARH3. Reason: Quantitative proteomics during the DNA damage response showed histone Ser-ADPr is reversible and that the reversal depends on ARH3. Supporting Evidence: PMID:28650317 we identified ARH3/ADPRHL2 as capable of efficiently and specifically removing Ser-ADPr of histones and other proteins |
| GO:0140290 peptidyl-serine ADP-deribosylation | IDA PMID:29234005 Proteomic analyses identify ARH3 as a serine mono-ADP-ribosy... | ACCEPT | Summary: ARH3-null cells accumulate serine-ADP-ribosylation in vivo. Reason: The cellular phenotype is the process-level readout of the molecular function; both basal and H2O2-stressed conditions show the accumulation. Supporting Evidence: PMID:29234005 ARH3-deficient mouse embryonic fibroblasts are characterized by a specific increase in serine-ADP-ribosylation in vivo under untreated conditions as well as following hydrogen peroxide stress |
| GO:0140290 peptidyl-serine ADP-deribosylation | IDA PMID:33186521 An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ... | ACCEPT | Summary: Site-level mono-ADPr proteomics shows the mark's turnover depends on ARH3. Reason: An orthogonal, chemical-biology route to the same process claim. Same scope caveat as the matching GO:0140292 row: the cached copy is abstract-only and names mono-ADPr without naming serine, so the residue specificity cannot be quoted from it. Supporting Evidence: PMID:33186521 Mono-ADPr proteomics and poly-to-mono comparisons at the modification site level have revealed the prevalence of mono-ADPr upon DNA damage and illustrated its dependence on PARG and ARH3. |
| GO:0140290 peptidyl-serine ADP-deribosylation | IEA GO_REF:0000120 | ACCEPT | Summary: Automatic annotation agreeing with three human IDAs and the mouse ortholog. Reason: Redundant with the experimental rows but correct; the WITH/FROM names the reviewed mouse ortholog. Supporting Evidence: PMID:34625544 We find that HPF1 and ARH3 inversely and homogenously regulate the serine ADP-ribosylome on a proteome-wide scale |
| GO:0005634 nucleus | EXP PMID:17991898 Functional localization of two poly(ADP-ribose)-degrading en... | ACCEPT | Summary: Nuclear pool of ARH3, from a paper whose abstract reports only the mitochondrial work. Reason: ARH3 is genuinely multi-compartment and the nuclear pool is where it erases chromatin Ser-ADPr, so the term is right. But the citation cannot be quoted for it: the cached copy of PMID:17991898 is abstract-only and the abstract is entirely about the mitochondrial matrix, with no nuclear statement. UniProt nonetheless records 'Nucleus {ECO:0000269|PubMed:17991898}', i.e. a curator's reading of the full text. Marked full-text-unavailable rather than propped up with a verbatim quote about mitochondria, and the nuclear claim is anchored on PMID:34479984, which states it directly. Same pattern as the GO:0005739 HTP row. Supporting Evidence: PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localisation propagated across the orthologue clade; the human gene already holds it by EXP and IDA. Reason: The WITH/FROM set is the PANTHER node plus mouse Adprs (MGI:MGI:2140364 = Q8CG72, the true 1:1 ortholog, reviewed Swiss-Prot) plus ADPRS itself (UniProtKB:Q9NX46). A self-referential IBA records a PAINT curator judging the function core for this gene, which is correct here. PANTHER:PTN001045209 was fully paginated: 128 annotations over 64 gene products, all ADPRS orthologs, each receiving exactly GO:0005634 and GO:0005739. It too reaches neither ADPRH nor ADPRHL1. Mouse Adprs holds GO:0005634 by its own IDA (PMID:24191052) and EXP (PMID:16278211). is_active_in is the right qualifier - nuclear Ser-ADPr removal is catalysis, not passive residence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001045209 · ARH3/ADPRS orthologue node (localisation) SUPPORTS TRANSFER fully paginated QuickGO query: 128 annotations over 64 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER carries its own IDA for nucleus, mitochondrion and EXP for mitochondrial matrix (PMID:24191052) UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Supporting Evidence: PMID:24191052 A protective effect of ARH3 results from its lowering of PAR levels in the nucleus and the cytoplasm, thereby preventing release of AIF from mitochondria and its accumulation in the nucleus |
| GO:0005634 nucleus | IDA PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | ACCEPT | Summary: Nuclear ARH3, evidenced in the cached record by its recruitment to DNA lesions. Reason: Recruitment to DNA lesions is necessarily nuclear, and that is what the cached record of PMID:30045870 supports. The cached copy is abstract-only (pdf_partial extraction) and contains no sentence naming the nucleus as such, so the localisation term cannot be quoted directly from it; the explicit statement is anchored on PMID:34479984 instead. UniProt cites PMID:30045870 for Chromosome rather than Nucleus, which is consistent with what the abstract actually says. Supporting Evidence: PMID:30045870 ADPR recognition is essential for the recruitment of ARH3 to DNA lesions PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005634 nucleus | IDA PMID:34479984 Biallelic ADPRHL2 mutations in complex neuropathy affect ADP... | ACCEPT | Summary: Nuclear localisation, and the CONDSIAS V335G variant that selectively loses it. Reason: Beijer et al. show V335G keeps mitochondrial localisation but loses cytosolic/nuclear localisation - a variant that dissociates the compartments and therefore confirms the wild-type nuclear pool is real and functionally required. Supporting Evidence: PMID:34479984 Although the V335G mutation retains its mitochondrial localization, it has altered cytosolic/nuclear localization. PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location keyword mapping that agrees with the experimental rows. Reason: UniProt's SUBCELLULAR LOCATION lists Nucleus with ECO:0000269 from PubMed:17991898 and PubMed:34479984, so the SL-0191 mapping reflects curated experimental evidence rather than a fold guess. Supporting Evidence: PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: HPA immunofluorescence places ARH3 in the nucleoplasm, consistent with four independent nuclear rows. Reason: A single antibody IF experiment would be weak alone, but it refines an independently established nuclear localisation and matches where the chromatin Ser-ADPr substrate is. Note what supports what: the nuclear pool is documented in the literature (PMID:34479984, quoted), while the nucleoplasm refinement rests on the HPA immunofluorescence image itself - GO_REF:0000052 has no PMID, so there is no paper to quote for the sub-compartment, and that is stated rather than papered over with a quote about something else. Supporting Evidence: PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. PMID:34479984 Strikingly, ARH3(V335G)-GFP showed a substantial reduction in the nuclear signal compared with ARH3(WT)-GFP |
| GO:0005694 chromosome | EXP PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | ACCEPT | Summary: Chromatin association, driven by ADP-ribose recognition at DNA lesions. Reason: ARH3 is recruited to DNA lesions and its substrate is ADP-ribosylated histone; chromosome is the compartment in which the serine-ADPr eraser function is exercised. Supporting Evidence: PMID:30045870 ADPR recognition is essential for the recruitment of ARH3 to DNA lesions |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: Keyword mapping backed by the same experimental observation. Reason: UniProt's SUBCELLULAR LOCATION lists Chromosome with ECO:0000269|PubMed:30045870, the row immediately above. Supporting Evidence: PMID:30045870 ADPR recognition is essential for the recruitment of ARH3 to DNA lesions |
| GO:0005737 cytoplasm | EXP PMID:16278211 Identification and characterization of a mammalian 39-kDa po... | ACCEPT | Summary: Cytoplasmic pool, from a paper whose cached abstract makes no localisation statement. Reason: The cytoplasmic pool is real - ARH3 lowers cytosolic as well as nuclear PAR - and UniProt records 'Cytoplasm {ECO:0000269|PubMed:16278211}'. But the cached copy of PMID:16278211 is abstract-only and its abstract is purely biochemical: it contains no localisation sentence at all, so nothing in it can be quoted for this row. Marked full-text-unavailable and anchored on PMID:34479984 instead. Supporting Evidence: PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005737 cytoplasm | IDA PMID:34479984 Biallelic ADPRHL2 mutations in complex neuropathy affect ADP... | ACCEPT | Summary: Cytosolic localisation, and the V335G variant that specifically loses it. Reason: The variant evidence is the strongest form: a point mutation that removes the cytosolic/nuclear pools while sparing the mitochondrial one. Supporting Evidence: PMID:34479984 Although the V335G mutation retains its mitochondrial localization, it has altered cytosolic/nuclear localization. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Keyword mapping consistent with two experimental rows. Reason: UniProt's SUBCELLULAR LOCATION lists Cytoplasm with ECO:0000269 from PubMed:16278211 and PubMed:34479984. Supporting Evidence: PMID:34479984 ARH3 protein has been shown to reside in the cytosol, the nucleus and in mitochondria. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: MitoCoP high-confidence mitochondrial proteome; corroborates, and is corroborated by, three independent low-throughput rows. Reason: A reference-projection test shows PMID:34800366 carries 1235 annotations, i.e. it is a bulk proteome import - exactly the shape that is suspicious when it stands alone. Here it does not: mitochondrial matrix localisation of ARH3 was established by targeted imaging and fractionation (PMID:17991898) and by the functional demonstration that Arh3-null mitochondria lose PAR-degrading activity (PMID:22433848). Note the assigner is FlyBase and the gene-level MitoCoP call lives in the study's supplementary inventory, not in the article text, so no gene-level quote from this paper is available - stated rather than papered over. Supporting Evidence: PMID:34800366 it is crucial to establish a high-confidence inventory of the human mitochondrial proteome PMID:22433848 embryonic fibroblasts from ARH3(-/-) mice lack most of the mitochondrial PAR degrading activity detected in wild-type cells |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial localisation propagated across the orthologue clade. Reason: The WITH/FROM set is the PANTHER node plus mouse Adprs (MGI:MGI:2140364 = Q8CG72, the true 1:1 ortholog, reviewed Swiss-Prot) plus ADPRS itself (UniProtKB:Q9NX46). A self-referential IBA records a PAINT curator judging the function core for this gene, which is correct here. PANTHER:PTN001045209 was fully paginated: 128 annotations over 64 gene products, all ADPRS orthologs, each receiving exactly GO:0005634 and GO:0005739. It too reaches neither ADPRH nor ADPRHL1. One observation worth recording rather than acting on: the mouse donor holds the more specific GO:0005759 mitochondrial matrix by EXP (PMID:24191052), so this IBA lands one level ABOVE its donor. Human ADPRS already holds GO:0005759 by two EXP rows of its own, so no information is lost and no downward MODIFY is warranted; the generalisation reflects PAN-GO's restricted term set. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001045209 · ARH3/ADPRS orthologue node (localisation) SUPPORTS TRANSFER fully paginated QuickGO query: 128 annotations over 64 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER carries its own IDA for nucleus, mitochondrion and EXP for mitochondrial matrix (PMID:24191052) UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Supporting Evidence: PMID:22433848 embryonic fibroblasts from ARH3(-/-) mice lack most of the mitochondrial PAR degrading activity detected in wild-type cells |
| GO:0005739 mitochondrion | IDA PMID:34479984 Biallelic ADPRHL2 mutations in complex neuropathy affect ADP... | ACCEPT | Summary: Mitochondrial localisation retained even by the V335G variant that loses the other compartments. Reason: Direct imaging in patient-derived and transfected cells. Supporting Evidence: PMID:34479984 Although the V335G mutation retains its mitochondrial localization, it has altered cytosolic/nuclear localization. |
| GO:0005759 mitochondrial matrix | EXP PMID:17991898 Functional localization of two poly(ADP-ribose)-degrading en... | ACCEPT | Summary: Functional localisation of ARH3 to the mitochondrial matrix. Reason: Niere et al. targeted PARP1 catalytic domain to the matrix to generate PAR there and showed that full-length ARH3 localises to, and degrades PAR within, the matrix. This is the specific compartment, not just 'mitochondrion'. Supporting Evidence: PMID:17991898 Both full-length ARH3 and a PARG isoform, which arises from alternative splicing, localized to the mitochondrial matrix. |
| GO:0005759 mitochondrial matrix | EXP PMID:34479984 Biallelic ADPRHL2 mutations in complex neuropathy affect ADP... | ACCEPT | Summary: Second experimental source for the mitochondrial pool - but this paper measures the organelle, not the matrix. Reason: Beijer et al. localise ARH3 to mitochondria by live-cell imaging against MitoID and by subcellular fractionation. The sub-compartment is where the citation stops short: the word 'matrix' does not occur anywhere in the cached full text (checked; 0 occurrences, against 89 for 'mitochondri'). UniProt nevertheless lists this reference under 'Mitochondrion matrix', so the curator's call may rest on imaging detail the text does not spell out, and per CLAUDE.md an experimental call is not overruled from incomplete evidence. ACCEPT with the limitation stated, and the specific compartment anchored on PMID:17991898, which demonstrates PAR-degrading activity inside the matrix directly. Supporting Evidence: PMID:34479984 Most importantly, these results clearly show that after cellular stress, nuclear ADPr is increased in patient cells compared with control cells but remained unchanged in cytosolic and mitochondrial fractions PMID:17991898 Both full-length ARH3 and a PARG isoform, which arises from alternative splicing, localized to the mitochondrial matrix. PMID:17991898 This conclusion was based on the direct demonstration of their PAR-degrading activity within mitochondria of living cells. |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Keyword mapping backed by three ECO:0000269 references in UniProt. Reason: UniProt's SUBCELLULAR LOCATION gives Mitochondrion matrix with evidence from PubMed:17991898, PubMed:34479984 and PubMed:22433848. Supporting Evidence: PMID:17991898 Both full-length ARH3 and a PARG isoform, which arises from alternative splicing, localized to the mitochondrial matrix. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-8952903 | ACCEPT | Summary: Reactome places its ADPRHL2 PAR-hydrolysis reaction in the mitochondrial matrix, matching the experimental rows. Reason: The Reactome reaction R-HSA-8952903 is annotated with compartment 'mitochondrial matrix' and both its input and output species are '[mitochondrial matrix]'. That compartment assignment is correct and independently supported; it is the reaction's PLACEMENT inside a nucleoplasmic BER pathway that generates the separate GO:0006287 problem. Supporting Evidence: PMID:22433848 ADP-ribosylhydrolase 3 (ARH3), not poly(ADP-ribose) glycohydrolase (PARG) isoforms, is responsible for degradation of mitochondrial matrix-associated poly(ADP-ribose). |
| GO:0090734 site of DNA damage | IDA PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | ACCEPT | Summary: ARH3 accumulates at DNA lesions, and the recruitment requires ADP-ribose recognition. Reason: A specific, well-supported location term: the paper shows both the accumulation and its molecular determinant, which also explains why catalytic-pocket variants are pathogenic. Supporting Evidence: PMID:30045870 ADPR recognition is essential for the recruitment of ARH3 to DNA lesions |
| GO:0000287 magnesium ion binding | IDA PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | ACCEPT | Summary: Two catalytic Mg2+ ions resolved in the ARH3:ADP-ribose structure. Reason: A cofactor, not a substrate: UniProt records 'Binds 2 magnesium ions per subunit' with six ECO:0000269 references, and the metal-coordinating residues (Glu41, Thr76, Asp77, Asp78) are the mutagenesis targets that abolish activity. Supporting Evidence: PMID:30045870 Our analyses revealed a group of acidic residues in ARH3 that keep two Mg2+ ions at the catalytic center |
| GO:0000287 magnesium ion binding | IDA PMID:33894202 Structural and biochemical analysis of human ADP-ribosyl-acc... | ACCEPT | Summary: The two magnesium ions have distinct, separable roles, established by structure plus mutagenesis. Reason: Pourfarjam et al. show MgA positions the substrate for catalysis while MgB contributes to substrate binding, and that Ca2+ substitution suppresses activity - metal binding is specific, not incidental. Supporting Evidence: PMID:33894202 MgA is crucial for optimal substrate positioning for catalysis, whereas MgB plays a key role in substrate binding |
| GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds | IDA PMID:30045870 Structure-function analyses reveal the mechanism of the ARH3... | MODIFY | Summary: Uninformative parent standing in for the activity the paper actually measured; replace with GO:0140292. Reason: PMID:30045870 is entirely about hydrolysis of the SERINE-linked ADP-ribosyl group: the ARH3:ADP-ribose structure, the two catalytic magnesium ions, the Glu41 flap, and mutagenesis of the catalytic pocket 'in mediating the hydrolysis of ADP-ribosyl from serine'. No poly(ADP-ribose) or general O-glycoside was assayed. GO:0004553 is true of the gene only because GO:0004649 is its child, and GO:0004649 is separately and abundantly annotated - so as written the row is both too general and attributed to a paper that did not measure it. Note an ontology wrinkle that this MODIFY exposes: GO:0140292 is NOT a descendant of GO:0004553; GO places it under GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, although the Ser-ADPr bond is an O-glycoside. That is raised as a question for GO rather than curated around. Proposed replacements: ADP-ribosylserine-[protein] hydrolase activity Supporting Evidence: PMID:30045870 we used site-directed mutagenesis to examine the functional roles of key residues in the catalytic pocket of ARH3 in mediating the hydrolysis of ADP-ribosyl from serine and DNA damage repair PMID:29907568 ARH3 preferentially hydrolyzes O-linkages attached to the anomeric C1″ of ADP-ribose |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | EXP PMID:16278211 Identification and characterization of a mammalian 39-kDa po... | ACCEPT | Summary: The original identification of ARH3 as a 39-kDa poly(ADP-ribose) glycohydrolase. Reason: ARH3 is a genuine, EC-numbered poly(ADP-ribose) glycohydrolase (EC 3.2.1.143, RHEA:52216) and is the dominant PAR-degrading activity of the mitochondrial matrix, where the catalytic PARG isoform is absent. Its PAR activity is real but kinetically minor against nuclear PAR relative to PARG; that is a rate statement, not a reason to reject the term. Oka et al. state the activity and its substrate scope in one sentence, including the negatives that distinguish ARH3 from ARH1. Supporting Evidence: PMID:16278211 We report here the identification of an ARH1-like protein, termed poly(ADP-ribose) hydrolase or ARH3, which exhibited PARG activity, generating ADP-ribose from poly-(ADP-ribose), but did not hydrolyze ADP-ribose-arginine, -cysteine, -diphthamide, or -asparagine bonds. PMID:16278211 ARH3 activity, like that of ARH1, was enhanced by Mg(2+). |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | EXP PMID:22433848 ADP-ribosylhydrolase 3 (ARH3), not poly(ADP-ribose) glycohyd... | ACCEPT | Summary: ARH3, not PARG, carries the mitochondrial matrix PAR-degrading activity. Reason: Arh3-knockout MEFs lose most mitochondrial PAR-degrading activity, which is the strongest cellular evidence that this activity is physiological rather than an in vitro curiosity. Supporting Evidence: PMID:22433848 embryonic fibroblasts from ARH3(-/-) mice lack most of the mitochondrial PAR degrading activity detected in wild-type cells |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic propagation of the PARG activity across the ADPRS orthologue clade; donor carries its own IDA. Reason: The WITH/FROM set is the PANTHER node plus mouse Adprs (MGI:MGI:2140364 = Q8CG72, the true 1:1 ortholog, reviewed Swiss-Prot) plus ADPRS itself (UniProtKB:Q9NX46). A self-referential IBA records a PAINT curator judging the function core for this gene, which is correct here. PANTHER:PTN008564042 was fully paginated through QuickGO: 132 annotations over 33 gene products, every one an ADPRS ortholog (adprs/ADPRHL2/ADPRS symbols across vertebrates, Nematostella, Trichoplax, Daphnia, Aspergillus). It reaches neither ADPRH nor ADPRHL1, so the paralog-specificity leak this family invites has not occurred. Mouse Adprs holds GO:0004649 by two independent IDAs (PMID:24191052, PMID:30830864), so the donor is not itself a transfer. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008564042 · ARH3/ADPRS orthologue node SUPPORTS TRANSFER fully paginated QuickGO query: 132 annotations over 33 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER 1:1 ortholog; carries its own IDA/IMP evidence for the ARH3 activity terms UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Supporting Evidence: PMID:24191052 PARG and ARH3, acting in tandem, regulate nuclear and cytoplasmic PAR degradation following hydrogen peroxide (H2O2) exposure |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IDA PMID:17075046 The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 hydrolyzes O... | ACCEPT | Summary: PAR glycohydrolase activity measured alongside the much faster O-acetyl-ADP-ribose reaction. Reason: Ono et al. assayed both substrates on the same preparation; the PAR activity is real and Mg(2+)-dependent, and the vicinal aspartates D77/D78 are required for both. Supporting Evidence: PMID:17075046 the poly(ADP-ribose) glycohydrolase ARH3 hydrolyzed O-acetyl-ADP-ribose to produce ADP-ribose in a time- and Mg(2+)-dependent reaction |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IDA PMID:30830864 PARP1 inhibition alleviates injury in ARH3-deficient mice an... | ACCEPT | Summary: PAR-degrading activity assayed in the context of ARH3-deficient patient cells and knockout mice. Reason: Mashimo et al. attribute the protective effect of ARH3 to lowering cytosolic and nuclear PAR, which requires the PAR glycohydrolase activity. Supporting Evidence: PMID:30830864 PAR degradation is mainly controlled by poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribose-acceptor hydrolase 3 (ARH3). PMID:30830864 Our previous results demonstrated that ARH3 confers protection against hydrogen peroxide (H2O2) exposure, by lowering cytosolic and nuclear PAR levels and preventing apoptosis-inducing factor (AIF) nuclear translocation. |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IDA PMID:33894202 Structural and biochemical analysis of human ADP-ribosyl-acc... | ACCEPT | Summary: Structural and kinetic dissection of PAR hydrolysis and its two magnesium ions. Reason: Pourfarjam et al. measure PAR hydrolysis directly and dissect the metal requirement. Supporting Evidence: PMID:33894202 ARH3 has a unique ARH fold and a di-Mg2+-containing catalytic center (21, 22, 23) and can efficiently reverse not only PARylation but also mono(ADP-ribosyl)ation (MARylation) at serine |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IDA PMID:34019811 Unrestrained poly-ADP-ribosylation provides insights into ch... | ACCEPT | Summary: PAR activity measured in the same study that establishes ARH3 as the serine-MAR eraser. Reason: Prokhorova et al. state directly that ARH3 acts on PAR chains in vitro, though less efficiently than PARG. The quantitative caveat is part of the annotation's meaning, not an objection to it. Supporting Evidence: PMID:34019811 ARH3 is the only hydrolase able to remove serine-linked mono(ADP-ribose) (MAR) but is much less efficient than PARG against poly(ADP-ribose) (PAR) chains in vitro. |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IDA PMID:34479984 Biallelic ADPRHL2 mutations in complex neuropathy affect ADP... | ACCEPT | Summary: Patient-variant study that assays PAR hydrolysis by wild-type and mutant ARH3. Reason: Beijer et al. characterise CONDSIAS variants for catalytic activity against both MARylated and PARylated substrates, which requires assaying the wild-type PAR activity as the reference. Supporting Evidence: PMID:34479984 The (ADP-ribosyl)hydrolase activity of ARH3 WT and mutants was assessed using H3 and poly(ADP-ribose)polymerase (PARP)1 MARylated and PARylated, respectively, in presence of 32P-NAD+ as substrates. |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automatic annotation anchored on RHEA:52216 and EC 3.2.1.143, both of which UniProt assigns with experimental evidence. Reason: The WITH/FROM names the exact RHEA reaction and EC number; UniProt carries EC=3.2.1.143 with ECO:0000269 from PubMed:16278211, 17075046 and 22433848. Anchor checked rather than assumed. Supporting Evidence: PMID:22433848 ADP-ribosylhydrolase 3 (ARH3), not poly(ADP-ribose) glycohydrolase (PARG) isoforms, is responsible for degradation of mitochondrial matrix-associated poly(ADP-ribose). |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IMP PMID:33769608 Molecular Tools for the Study of ADP-Ribosylation: A Unified... | MODIFY | Summary: Wrong substrate class: this paper contains no poly(ADP-ribose) experiment at all. It assays MONO-ADP-ribosylated Ser/Thr/Cys peptides, so the row belongs on GO:0140292. Reason: Read in full, PMID:33769608 is a peptide-chemistry paper: it synthesises MARylated peptides and asks which hydrolase reverses each linkage. The only ARH3 result is that wild-type ARH3, but not the D77N or D78N catalytic mutants, hydrolyses the Ser-linked (peptide 24) and Thr-linked (peptide 27) MONO-ADP-ribose, while the Cys-linked analogue resists. No polymer is used anywhere in the study, so nothing in it supports poly(ADP-ribose) glycohydrolase activity. GO:0004649 is correct for this gene from eleven other rows; this particular citation does not substantiate it, and the same experiment substantiates GO:0140292 exactly. This produces a deliberate same-term/different-action divergence with the eleven ACCEPT rows: the divergence is per-reference, not per-term, and suppressing it would have meant discarding the finding. The threonine half of the same figure has no GO term at all and is filed under proposed_new_terms. Proposed replacements: ADP-ribosylserine-[protein] hydrolase activity Supporting Evidence: PMID:33769608 We found that ARH3, but not its catalytic mutants D77 N or D78 N, is capable of hydrolysing the glycosidic linkage in 24 (Ser) and 27 (Thr) |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | IMP PMID:34321462 Mechanistic insights into the three steps of poly(ADP-ribosy... | ACCEPT | Summary: Mechanistic dissection of the three steps of poly(ADP-ribosylation) reversal, using ARH3 catalytic mutants. Reason: Rack et al. resolve ARH3 with dimeric ADP-ribose and an ADP-ribosylated peptide and explain, structurally, why its activity on long PAR is low. Genuinely a poly(ADP-ribose) study, unlike PMID:33769608. Supporting Evidence: PMID:34321462 Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages PMID:34321462 Yet PAR binding fails to efficiently induce these structural in ARH3, thus providing a structural explanation for the observed low hydrolytic activity towards this substrate. |
| GO:0004649 poly(ADP-ribose) glycohydrolase activity | TAS Reactome:R-HSA-8952903 | ACCEPT | Summary: Reactome reaction 'ADPRHL2 hydrolyses poly(ADP-ribose)' - a faithful, single-gene statement. Reason: Reference-projection test, fully paginated: Reactome:R-HSA-8952903 yields 2 annotations on 1 entity (this gene). It is a gene-specific curated reaction, not a bulk import, and its summation cites Oka et al. 2006 and Niere et al. 2008. Contrast the same gene's GO:0006287 TAS, which comes from an enclosing pathway. Supporting Evidence: PMID:16278211 We report here the identification of an ARH1-like protein, termed poly(ADP-ribose) hydrolase or ARH3, which exhibited PARG activity, generating ADP-ribose from poly-(ADP-ribose), but did not hydrolyze ADP-ribose-arginine, -cysteine, -diphthamide, or -asparagine bonds. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: TNKS (tankyrase-1) from a single HuRI yeast two-hybrid screen, with no orthogonal assay and no mechanistic fit. Reason: Both GO:0005515 rows come from PMID:32296183 (HuRI). Expanding the IntAct records shows this is ONE yeast two-hybrid screen logged under three sub-methods - 'two hybrid array', 'two hybrid prey pooling approach' and 'validated two hybrid' - which is exactly what UniProt's NbExp=3 counts; MI-score 0.56, no orthogonal assay, no co-immunoprecipitation, no structure. There is no topological objection (both partners and ADPRS are nuclear/cytoplasmic), and that check is reported as negative rather than omitted. O95271 resolves to reviewed canonical TNKS1_HUMAN (1327 aa), so this is not a TrEMBL/ORFeome substitution. The pairing is superficially attractive - an ADP-ribosyl eraser meeting a PARP writer - and that is exactly why it needs checking: tankyrase-1's UniProt catalytic activities install ADP-ribose on ASPARTATE and GLUTAMATE side chains (4-O-(ADP-D-ribosyl)-L-aspartyl and 5-O-(ADP-D-ribosyl)-L-glutamyl), a linkage class reversed by the macrodomain hydrolases (GO:0140293), not by ARH3, whose measured scope is Ser/Thr/Tyr, PAR and O-acetyl-ADP-ribose. TNKS also has 186 IntAct partners against ADPRS's 35. PubMed returns no study of an ARH3-tankyrase interaction. Not asserted to be false - unreplicated and uninformative. Supporting Evidence: PMID:32296183 Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: PRDM5 isoform 2 from the same single HuRI screen; no follow-up anywhere. Reason: Both GO:0005515 rows come from PMID:32296183 (HuRI). Expanding the IntAct records shows this is ONE yeast two-hybrid screen logged under three sub-methods - 'two hybrid array', 'two hybrid prey pooling approach' and 'validated two hybrid' - which is exactly what UniProt's NbExp=3 counts; MI-score 0.56, no orthogonal assay, no co-immunoprecipitation, no structure. There is no topological objection (both partners and ADPRS are nuclear/cytoplasmic), and that check is reported as negative rather than omitted. Q9NQX1 resolves to reviewed canonical PRDM5_HUMAN, a PR/SET zinc-finger transcriptional repressor, and the annotation is against its isoform 2. PRDM5 has 96 IntAct partners against ADPRS's 35. A PubMed query for ARH3 and PRDM5 returns zero hits. Judged per partner rather than per gene, and it lands in the same place as the TNKS row for the same reason. Supporting Evidence: PMID:32296183 Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0061463 O-acetyl-ADP-ribose deacetylase activity | IDA PMID:17075046 The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 hydrolyzes O... | ACCEPT | Summary: ARH3 hydrolyses the sirtuin product O-acetyl-ADP-ribose, the reaction it performs fastest. Reason: Directly measured, Mg(2+)-dependent, and abolished by the D77N/D78N vicinal-aspartate mutant. This links ARH3 to sirtuin signalling and is a core activity, not an in vitro artefact. Supporting Evidence: PMID:17075046 the poly(ADP-ribose) glycohydrolase ARH3 hydrolyzed O-acetyl-ADP-ribose to produce ADP-ribose in a time- and Mg(2+)-dependent reaction |
| GO:0061463 O-acetyl-ADP-ribose deacetylase activity | IDA PMID:21498885 Hydrolysis of O-acetyl-ADP-ribose isomers by ADP-ribosylhydr... | ACCEPT | Summary: Isomer-resolved follow-up: the true substrate is the 1''-O-acetyl isomer. Reason: Kasamatsu et al. reasoned that ARH3 attacks C-1'' and therefore could not be cleaving the 2''- or 3''-acetyl isomers, and demonstrated a third, 1''-O-acetyl isomer in equilibrium with them. UniProt encodes exactly this (RHEA:58112). The GO term's definition still says 'either the 2'' or 3'' position', which is the pre-2011 understanding. Supporting Evidence: PMID:21498885 we postulated the existence of a third isomer, 1″-OAADPr, in equilibrium with 2″- and 3″-isomers |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Correct and core: the defining activity of ARH3, propagated across a node whose entire reach is ADPRS orthologs. Reason: The WITH/FROM set is the PANTHER node plus mouse Adprs (MGI:MGI:2140364 = Q8CG72, the true 1:1 ortholog, reviewed Swiss-Prot) plus ADPRS itself (UniProtKB:Q9NX46). A self-referential IBA records a PAINT curator judging the function core for this gene, which is correct here. PANTHER:PTN008564042 was fully paginated through QuickGO: 132 annotations over 33 gene products, every one an ADPRS ortholog (adprs/ADPRHL2/ADPRS symbols across vertebrates, Nematostella, Trichoplax, Daphnia, Aspergillus). It reaches neither ADPRH nor ADPRHL1, so the paralog-specificity leak this family invites has not occurred. The mouse donor holds GO:0140292 by its own IMP (PMID:29234005), so the transfer is not circular. RHEA:58256 anchors the reaction in UniProt with five ECO:0000269 references. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008564042 · ARH3/ADPRS orthologue node SUPPORTS TRANSFER fully paginated QuickGO query: 132 annotations over 33 gene products, all ADPRS orthologs MGI:MGI:2140364 · mouse Adprs (UniProtKB:Q8CG72, reviewed) SUPPORTS TRANSFER 1:1 ortholog; carries its own IDA/IMP evidence for the ARH3 activity terms UniProtKB:Q9NX46 · human ADPRS (self) SUPPORTS TRANSFER self-reference: the target is its own IBD seed Supporting Evidence: PMID:29234005 Here we report that, in vitro, ARH3 specifically binds and demodifies proteins and peptides that are MARylated |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IDA PMID:28650317 Serine ADP-ribosylation reversal by the hydrolase ARH3. | ACCEPT | Summary: Direct demonstration that ARH3 is the serine-ADP-ribosyl hydrolase. Reason: Fontana et al. screened human hydrolases and identified ARH3 as the enzyme that reverses Ser-ADPr on histones and other proteins. This is the founding experiment for the term. Supporting Evidence: PMID:28650317 we identified ARH3/ADPRHL2 as capable of efficiently and specifically removing Ser-ADPr of histones and other proteins |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IDA PMID:29234005 Proteomic analyses identify ARH3 as a serine mono-ADP-ribosy... | ACCEPT | Summary: In vitro demodification of MARylated peptides and proteins, plus in vivo Ser-ADPr accumulation on ARH3 loss. Reason: Abplanalp et al. show ARH3 binds and demodifies MARylated substrates in vitro and that ARH3-deficient cells accumulate serine-ADP-ribosylation. Supporting Evidence: PMID:29234005 Here we report that, in vitro, ARH3 specifically binds and demodifies proteins and peptides that are MARylated PMID:29234005 ARH3-deficient mouse embryonic fibroblasts are characterized by a specific increase in serine-ADP-ribosylation in vivo under untreated conditions as well as following hydrogen peroxide stress |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IDA PMID:33186521 An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ... | ACCEPT | Summary: HPF1/PARP1 chemical-biology platform confirms ARH3-dependent removal of mono-ADP-ribose. Reason: Bonfiglio et al. use mono-ADPr proteomics to show that mono-ADP-ribosylation after DNA damage depends on PARG and ARH3. Scope of what can be quoted: the cached copy is abstract-only, and the abstract names mono-ADPr without naming the serine linkage, so the residue specificity that this term asserts cannot be quoted from it - UniProt cites this paper with ECO:0000269 for RHEA:58256 from the full text. The row is marked full-text-unavailable rather than given a quote that names serine from some other paper. Supporting Evidence: PMID:33186521 Mono-ADPr proteomics and poly-to-mono comparisons at the modification site level have revealed the prevalence of mono-ADPr upon DNA damage and illustrated its dependence on PARG and ARH3. |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IDA PMID:34625544 The regulatory landscape of the human HPF1- and ARH3-depende... | ACCEPT | Summary: Proteome-wide ADP-ribosylome shows ARH3 is a global regulator of serine ADPr. Reason: Hendriks et al. compare HPF1- and ARH3-depleted cells across the ADP-ribosylome and find ARH3 inversely regulates the serine ADPr proteome, i.e. it is the erasing arm of the serine mark. Supporting Evidence: PMID:34625544 We find that HPF1 and ARH3 inversely and homogenously regulate the serine ADP-ribosylome on a proteome-wide scale |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IDA PMID:37268618 Serine ADP-ribosylation in Drosophila provides insights into... | ACCEPT | Summary: FlyBase-assigned row that nonetheless rests on a direct assay of the HUMAN enzyme. Reason: The paper is titled for Drosophila, and FlyBase is the assigner, so the row invites the 'wrong organism' reflex. It is sound: hARH3 was purified and used directly as the Ser-linked-ADPr-specific human hydrolase in the assays, and UniProt cites this paper with ECO:0000269 for RHEA:58256. Reported as a check that came back negative. Supporting Evidence: PMID:37268618 we purified the modified peptide and incubated it with two human (ADP-ribosyl)hydrolases, hTARG1 and hARH3, which are specific for Glu/Asp- and Ser-linked ADPr respectively PMID:37268618 while Drosophila lacks ARH3, there is a striking evolutionary adaptation of dParg that confers functional equivalency to both human PARG and ARH3 |
| GO:0140292 ADP-ribosylserine-[protein] hydrolase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automatic annotation whose WITH/FROM cites RHEA:58256, the exact reaction, plus the mouse ortholog. Reason: Unusually well-anchored for an IEA: the WITH/FROM names RHEA:58256 (O-(ADP-D-ribosyl)-L-seryl-[protein] + H2O = ADP-D-ribose + L-seryl-[protein]) and Q8CG72, the reviewed mouse ortholog. The same reaction is in UniProt's CATALYTIC ACTIVITY with five ECO:0000269 references. Redundant with the IDA rows but not wrong. Supporting Evidence: PMID:34321462 Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages |
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Download this section (compressed HTML)Q: GO:0140292 ADP-ribosylserine-[protein] hydrolase activity and GO:0140293 ADP-ribosylglutamate-[protein] hydrolase activity are both placed under GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds. Both linkages are O-glycosidic: the acceptor atom is the serine side-chain hydroxyl oxygen and the glutamate carboxylate oxygen respectively, and UniProt/RHEA name the substrates 'O-(ADP-D-ribosyl)-L-seryl-[protein]' (RHEA:58256) and '5-O-(ADP-D-ribosyl)-L-glutamyl-[protein]'. The internal control is their sibling GO:0003875 ADP-ribosylarginine-[protein] hydrolase activity, which IS N-glycosidic (the guanidino nitrogen) and is correctly placed. Should the serine and glutamate terms move under GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds? Note the practical consequence on this gene: GO:0004553 is currently annotated to ADPRS from a paper (PMID:30045870) that measured only serine-linked hydrolysis, and the two terms are in disjoint branches, so the generalisation a curator would expect does not hold.
Suggested experts: GO ontology editors, ADP-ribosylation biochemists
Q: GO:0071451 cellular response to superoxide is held by all 33 gene products under PANTHER node PTN008564042 (the ADPRS orthologue clade). The chain traces back to one mouse MGI IMP on PMID:24191052, in which the stressor was hydrogen peroxide, and the human IMP (PMID:30401461) also used hydrogen peroxide. GO:0070301 and GO:0071451 are siblings, not parent and child, so the current annotation is not a safe generalisation. Would MGI re-term the mouse row to GO:0070301, which would retract the error from the whole clade at once?
Suggested experts: MGI curators, GO Central PAINT curators
Q: Reactome models ADPRS's only reaction, R-HSA-8952903 'ADPRHL2 hydrolyses poly(ADP-ribose)', in the mitochondrial matrix, but nests it inside the nucleoplasmic pathways R-HSA-110362 and R-HSA-110373, whose GO mapping (GO:0006287 base-excision repair, gap-filling) is then exported to ADPRS as a TAS annotation. Should the mitochondrial reaction be moved out of the long-patch BER pathway, or the pathway-to-GO export be made compartment-aware?
Suggested experts: Reactome curators, GOA
Q: Should ADPRS carry GO:0072570 ADP-D-ribose binding? Recombinant hARH3 binds free ADP-ribose with micromolar affinity, nine PDB entries resolve ADP-ribose in the catalytic groove, and ADP-ribose recognition is required for recruitment to DNA lesions - so the binding has a consequence beyond turnover. Against it, ADP-ribose is the product of every reaction the enzyme catalyses, and GO practice discourages annotating an enzyme to binding of its own substrate or product. Raised as a question rather than proposed as an annotation, because the argument turns on a curation convention rather than on missing data.
Suggested experts: GO Central, UniProt curators
Q: UniProt's CATALYTIC ACTIVITY for ADPRS includes alpha-NAD(+) + H2O = ADP-D-ribose + nicotinamide (RHEA:68792, ECO:0000269 from PubMed:31599159 and PubMed:34321462), and ARH3 has the highest alpha-NADase specific activity of the enzymes tested, yet no GO molecular function covers it. GO:0003953 NAD+ nucleosidase activity is defined for NAD+ without an anomeric qualifier, and the measured enzymes hydrolyse alpha- but explicitly not beta-NAD+, so using it would over-claim. Is an 'alpha-NAD(+) glycohydrolase activity' term warranted, or should GO:0003953 gain an anomer-specific child?
Suggested experts: GO Central, ADP-ribosylation biochemists
Q: The 2006 ARH3 structure paper (PMID:17015823) reports that recombinant hARH3 'efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins'. That negative was overturned in 2017 when ARH3 was shown to be the serine MONO-ADP-ribosylhydrolase (PMID:28650317, PMID:29234005) - the 2006 assay used arginine-linked mono-ADP-ribosylated substrates, on which ARH3 genuinely is inactive. Recorded so the older statement is not re-imported as a NOT annotation.
Suggested experts: GOA, UniProt curators
Experiment: Compare ADPRS-null and wild-type cells side by side under (i) exogenous H2O2, (ii) a pure superoxide generator such as paraquat or KO2 with catalase present to suppress secondary H2O2, and (iii) menadione. Read out PAR accumulation, AIF nuclear translocation and viability. If only the H2O2 arm shows an ADPRS-dependent difference, the annotation should be GO:0070301 alone; if the superoxide arm also responds, both terms are warranted and the existing row is salvaged rather than corrected.
Hypothesis: ADPRS's protection against oxidative-stress-induced death is specific to hydrogen peroxide-derived signalling rather than to superoxide, as the current GO annotation implies.
Type: cell-based stress panel with ROS-species discrimination
Experiment: In an ADPRS-null background, test whether the death phenotype is rescued by PARP1 inhibition and AIFM1 knockdown (parthanatos arm) but not by RIPK1 inhibition (necrostatin-1), RIPK3 knockout or MLKL knockout (necroptosis arm). A clean dissociation would settle whether GO:0060546 or a parthanatos-specific term is the correct annotation, and would inform the GO term request filed here.
Hypothesis: ADPRS restrains parthanatos specifically and has no role in RIPK1/RIPK3/MLKL-dependent necroptosis.
Type: genetic and pharmacological epistasis
Experiment: Infect cells expressing wild-type or catalytically dead ADPRS with a CteC-secreting bacterium, or express CteC ectopically, and quantify Thr66-ADP-ribosylated ubiquitin by targeted mass spectrometry over time. Persistence of the mark in the catalytically dead background would establish an in vivo role and support the proposed ADP-ribosylthreonine-[protein] hydrolase activity term.
Hypothesis: The threonine-linked ADP-ribosylhydrolase activity of ADPRS is used in cells, not only on synthetic peptides.
Type: targeted mass spectrometry with bacterial effector
Experiment: Attempt endogenous reciprocal co-immunoprecipitation from a nuclear extract, and quantify affinity by a label-free method (ITC or SPR) with recombinant proteins. Include a proximity-labelling arm (ADPRS-TurboID) to test whether either partner is in the neighbourhood at native abundance. A negative result would justify moving both rows from MARK_AS_OVER_ANNOTATED to REMOVE; a positive would justify replacing GO:0005515 with an informative term.
Hypothesis: The two HuRI two-hybrid partners, TNKS and PRDM5, do not form physiologically relevant complexes with ADPRS.
Type: orthogonal interaction validation
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