ADAMTSL3, also called punctin-2, is a large secreted glycoprotein of the extracellular matrix. Despite the family name it is not a proteinase: it is built from two arrays of thrombospondin type-1 repeats flanking three immunoglobulin-like C2-type domains, with an ADAMTS-type cysteine-rich region and a C-terminal PLAC domain, and it lacks both the catalytic metalloprotease domain and the disintegrin-like domain that define the ADAMTS proteinases. It carries a cleaved signal peptide and extensive N-linked glycosylation, and is deposited into the matrix as a roughly 210-kDa glycoprotein. Its molecular role is that of a matricellular adaptor within the fibrillin microfibril network. It binds the N-terminal, assembly-competent half of fibrillin-1 at a site deleted in Weill-Marchesani syndrome, binds the non-catalytic C-terminal region of the proteinase ADAMTS10 with nanomolar affinity, and binds the C-terminal domains of latent TGF-beta binding protein 1 - the two matrix proteins that between them sequester the large latent TGF-beta complex. Consistent with that placement, ADAMTSL3 restrains TGF-beta signalling: its loss in mice raises active TGF-beta and SMAD2 phosphorylation in the pressure-overloaded heart, while raising it in human cardiac fibroblasts lowers SMAD2 phosphorylation, myofibroblast differentiation and collagen synthesis. In the nervous system it acts through the receptor DCC to set hippocampal synapse density and GABAergic synapse function, and parvalbumin interneurons require it cell-autonomously to build and maintain perineuronal nets, a role conserved to the nematode orthologue Ce-Punctin/MADD-4, which specifies cholinergic versus GABAergic postsynaptic identity through UNC-40/DCC. The protein is broadly expressed - in epithelia of colon, skin, breast, prostate, liver and pancreas, and in endothelium, smooth muscle, fibroblasts, cortical and ganglionic neurons and cardiac myocytes. Common variants at the ADAMTSL3 locus are among the reproducible genome-wide association signals for adult height and lean body mass, and the gene has been proposed as a candidate at schizophrenia.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0031012 extracellular matrix | IBA GO_REF:0000033 | ACCEPT | Summary: Correct, well founded, and the best-supported statement in this gene's record. Accepted as core. Resolving the WITH/FROM field settles it rather than merely making it plausible. The seventeen tokens are sixteen protein donors plus the PANTHER node PTN000347317, and every one of the sixteen resolves: Drosophila papilin and lonely heart, C. elegans mig-6/papilin, mouse Adamts1, Adamts2, Adamts7, Adamtsl2, Adamtsl4, Adamtsl5, Papln and Thsd4, rat Adamts1, and human ADAMTS9, ADAMTS10, ADAMTS17 and ADAMTSL5. Asking what each donor carries for this term in its own right, rather than assuming, returns sixteen out of sixteen with their own IDA or HDA to GO:0031012 or a descendant. There is no self-referential token, so none of the support is circular. Two of the sixteen (Drosophila loh and mouse Adamtsl5) are unreviewed TrEMBL entries, which weakens their names as evidence but not their curated annotations. The donors are not, however, in the same place. Their experimental annotations are spread across GO:0005604 basement membrane (both papilins, mouse Adamts1), GO:0005614 interstitial matrix (mouse Adamtsl4), GO:0001527 microfibril (mouse Thsd4) and GO:0031012 itself. So the general term is the genuine least common ancestor of a heterogeneous donor set, and refining it downward would mean picking one donor's compartment over another's. No specificity upgrade is warranted, and the row is not less precise than its donors. ADAMTSL3 also has its own direct evidence for this location, which the propagation happens to agree with: punctin-2 expressed in COS-7 cells is deposited in the extracellular matrix, and UniProt records the subcellular location with ECO:0000269 against that paper. That experimental annotation has never been transferred into GOA, so the IBA is currently doing work that an IDA should be doing alongside it. Reason: Sixteen of sixteen protein donors carry their own experimental annotation to this term or a descendant, with no self-referential token; the donor set is heterogeneous across basement membrane, interstitial matrix and microfibril, so GO:0031012 is the correct LCA rather than an under-specified term; and the target has independent direct evidence for the same location from PMID:14667842. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000347317 · PTHR13723 root node (ADAMTS and ADAMTS-like) SUPPORTS TRANSFER An internal tree node, not a protein. It carries four IBD annotations in PANTHER's IBD.gaf: this term, GO:0030198, GO:0004222 metalloendopeptidase activity and GO:0006508 proteolysis. Only this one reaches ADAMTSL3; see the suggested question about where the catalytic-loss NOT is attached. FB:FBgn0003137 · Drosophila Ppn, papilin (Q868Z9, Swiss-Prot) SUPPORTS TRANSFER Two independent IDA annotations to GO:0005604 basement membrane (PMID:11076767, PMID:3320045). Ambiguous cross-reference: two TrEMBL/Swiss-Prot candidates, the reviewed one taken. FB:FBgn0032252 · Drosophila loh, lonely heart (Q9VKV3, TrEMBL) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:23874219). Unreviewed entry, so its protein name is an automatic label; the curated annotation is nonetheless experimental. Four candidate accessions for this gene. MGI:MGI:109249 · mouse Adamts1 (P97857, Swiss-Prot) SUPPORTS TRANSFER Three IDA annotations across GO:0005604 and GO:0031012. Resolved via the bare numeric MGI id; the doubled MGI:MGI: form returns HTTP 400. MGI:MGI:1347346 · mouse Adamts7 (Q68SA9, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:15192113). MGI:MGI:1347356 · mouse Adamts2 (Q8C9W3, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:16556917). MGI:MGI:1913798 · mouse Adamtsl5 (D3Z689, TrEMBL) SUPPORTS TRANSFER HDA and IDA to GO:0031012 (PMID:22159717, PMID:23010571). Unreviewed entry. MGI:MGI:1925044 · mouse Adamtsl2 (Q7TSK7, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:17509843). This is the one family member for which PAINT has curated the loss of catalytic activity. MGI:MGI:2386139 · mouse Papln, papilin (Q9EPX2, Swiss-Prot) SUPPORTS TRANSFER HDA to GO:0031012 and IDA to GO:0005604 basement membrane (PMID:18757743). MGI:MGI:2389008 · mouse Adamtsl4 (Q80T21, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0005614 interstitial matrix and to GO:0031012 (PMID:18757743). MGI:MGI:2672033 · mouse Thsd4 / ADAMTSL6 (Q3UTY6, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0001527 microfibril and to GO:0031012 (PMID:19940141). The most specific compartment in the donor set. RGD:621241 · rat Adamts1 (Q9WUQ1, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:15777654). UniProtKB:Q6ZMM2 · human ADAMTSL5 (Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:23010571). UniProtKB:Q8TE56 · human ADAMTS17 (Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:28176809). UniProtKB:Q9H324 · human ADAMTS10 (Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:21402694). Also a direct high-affinity binding partner of ADAMTSL3 (KD 2 nM, PMID:22242013), so this donor is functionally as well as phylogenetically connected. UniProtKB:Q9P2N4 · human ADAMTS9 (Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0031012 (PMID:12514189). WB:WBGene00003242 · C. elegans mig-6, papilin (O76840, Swiss-Prot) SUPPORTS TRANSFER IDA to GO:0005604 basement membrane (PMID:19297413). Worth flagging for anyone re-deriving this row: this token does not resolve through UniProt's xref:wormbase- index, which is keyed on transcript ids, and it is NOT madd-4 (WBGene00009958) even though madd-4 is the worm orthologue that dominates this gene's neural literature. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **16 of 16** carry their own experimental annotation to GO:0031012 or a descendant. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md the donor set is heterogeneous in *which* matrix compartment it occupies, so the general parent is the least common ancestor rather than a curator failing to be specific. PMID:14667842 Using these and a monoclonal antibody to a C-terminal myc tag, we show that in transfected COS-7 cells, punctin-2 is expressed as a 210-kDa glycoprotein that is located in the extracellular matrix. Knowledge gap: UniProt records ADAMTSL3's extracellular matrix localisation with ECO:0000269|PubMed:14667842, but no corresponding IDA row exists in GOA, so the only localisation annotation this gene carries for its best-established compartment is a phylogenetic inference. OPEN CURATION Resolve: Transfer the UniProt ECO:0000269 subcellular location to GOA as an IDA row. "CC -!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular" — file:human/ADAMTSL3/ADAMTSL3-uniprot.txt |
| GO:0030198 extracellular matrix organization | IEA GO_REF:0000002 | ACCEPT | Summary: Accepted, and it is better founded than its provenance suggests. As delivered this is a family-level signature mapping: IPR013273 is the ADAMTS/ADAMTS-like PRINTS signature, which matches catalytic ADAMTS proteinases and non-catalytic ADAMTS-like proteins alike, so on its own it says only that ADAMTSL3 belongs to a family that remodels matrix. For a protein with no catalytic domain that would be a thin argument, since the family's best-known route to matrix organisation is proteolysis, which ADAMTSL3 cannot perform. Three independent lines of evidence nonetheless support the term for this protein specifically. It binds the N-terminal, assembly-competent half of fibrillin-1 by surface plasmon resonance, and the Weill-Marchesani three-domain deletion in fibrillin-1 abolishes that binding, so the interaction maps to a defined region of a microfibril scaffold protein. Adamtsl3 knock-out mice show altered matrix output and TGF-beta activity in the pressure-overloaded heart, and ADAMTSL3 overexpression in human cardiac fibroblasts lowers collagen synthesis and myofibroblast differentiation. And in the brain, loss of Adamtsl3 reduces perineuronal nets, which are a specialised extracellular matrix, in a cell-autonomous manner in parvalbumin interneurons. So the term is right, and the interesting point is that the reasoning behind the automatic assignment is not the reasoning that justifies it. Kept general rather than refined: the three lines of evidence point at three different matrices (microfibril, cardiac interstitium, perineuronal net), which is exactly the situation in which the parent term is the correct call. Reason: A family-level InterPro signature term that independent gene-specific evidence happens to support: fibrillin-1 binding by SPR with a mapped binding site, altered cardiac matrix output in Adamtsl3-null mice with a human-cell gain-of-function counterpart, and cell-autonomous loss of perineuronal nets in Adamtsl3-null parvalbumin interneurons. Left general because those three lines implicate three different matrices. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-uniprot.txt DR InterPro; IPR013273; ADAMTS/ADAMTS-like. PMID:22242013 ADAMTSL-2, -3, and -6 and papilin polypeptides did not bind to recombinant fibrillin-1 polypeptides with the WMS three-domain deletion (Figure 5a and Table S1). PMID:42277231 Here, we identify the schizophrenia-associated glycoprotein Adamtsl3 as a PV+ cell-autonomous regulator of PNN integrity. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP2-3 (P0C7H8, 128 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HI-II-14, the CCSB proteome-scale binary interactome map (PMID:25416956), and KRTAP2-3 has 10 distinct partners in IntAct - the one partner in this set that is not a high-degree prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP2-3 is a cysteine-rich hair-cortex keratin-associated protein and carries 10 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP10-8 (P60410, 259 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HI-II-14, the CCSB proteome-scale binary interactome map (PMID:25416956), and KRTAP10-8 has 415 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP10-8 is a cysteine-rich hair-cortex keratin-associated protein and carries 415 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Seen in both HI-II-14 and HuRI, but those two maps share the CCSB ORFeome and search space, so the repeat is not independent replication - and KRTAP10-8 is one of the highest-degree preys in the set. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRT40 (Q6A162, 431 aa) is a type I hair-follicle intermediate-filament keratin. The pair was reported only in HI-II-14, the CCSB proteome-scale binary interactome map (PMID:25416956), and KRT40 has 448 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRT40 is a type I hair-follicle intermediate-filament keratin and carries 448 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Over-annotated. NOTCH2NLA (Q7Z3S9, 236 aa) is a hominid-specific partial NOTCH2 duplicate acting on NOTCH2 in the secretory pathway. The pair was reported only in HI-II-14, the CCSB proteome-scale binary interactome map (PMID:25416956), and NOTCH2NLA has 276 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. NOTCH2NLA is a hominid-specific partial NOTCH2 duplicate acting on NOTCH2 in the secretory pathway and carries 276 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Over-annotated. MDFI (Q99750, 246 aa) is a nuclear and cytoplasmic inhibitor of MyoD-family bHLH transcription factors. The pair was reported only in HI-II-14, the CCSB proteome-scale binary interactome map (PMID:25416956), and MDFI has 483 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. MDFI is a nuclear and cytoplasmic inhibitor of MyoD-family bHLH transcription factors and carries 483 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Seen in both HI-II-14 and HuRI, but those two maps share the CCSB ORFeome and search space, so the repeat is not independent replication - and MDFI is one of the highest-degree preys in the set. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. CYSRT1 (A8MQ03, 144 aa) is a cornified-envelope protein of the keratin/KRTAP interaction network. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and CYSRT1 has 516 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. CYSRT1 is a cornified-envelope protein of the keratin/KRTAP interaction network and carries 516 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. GLRX3 (O76003, 335 aa) is a cytosolic monothiol glutaredoxin and cytosolic iron-sulfur assembly factor. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and GLRX3 has 190 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. GLRX3 is a cytosolic monothiol glutaredoxin and cytosolic iron-sulfur assembly factor and carries 190 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP12-3 (P60328, 96 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP12-3 has 141 distinct partners in IntAct - a moderately connected prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP12-3 is a cysteine-rich hair-cortex keratin-associated protein and carries 141 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP10-6 (P60371, 365 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP10-6 has 77 distinct partners in IntAct - a moderately connected prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP10-6 is a cysteine-rich hair-cortex keratin-associated protein and carries 77 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP10-8 (P60410, 259 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP10-8 has 415 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP10-8 is a cysteine-rich hair-cortex keratin-associated protein and carries 415 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Seen in both HI-II-14 and HuRI, but those two maps share the CCSB ORFeome and search space, so the repeat is not independent replication - and KRTAP10-8 is one of the highest-degree preys in the set. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP1-1 (Q07627, 177 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP1-1 has 188 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP1-1 is a cysteine-rich hair-cortex keratin-associated protein and carries 188 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP5-7 (Q6L8G8, 165 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP5-7 has 61 distinct partners in IntAct - a moderately connected prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP5-7 is a cysteine-rich hair-cortex keratin-associated protein and carries 61 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. MDFI (Q99750, 246 aa) is a nuclear and cytoplasmic inhibitor of MyoD-family bHLH transcription factors. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and MDFI has 483 distinct partners in IntAct - an extreme interactome hub. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. MDFI is a nuclear and cytoplasmic inhibitor of MyoD-family bHLH transcription factors and carries 483 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Seen in both HI-II-14 and HuRI, but those two maps share the CCSB ORFeome and search space, so the repeat is not independent replication - and MDFI is one of the highest-degree preys in the set. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP3-2 (Q9BYR7, 98 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP3-2 has 84 distinct partners in IntAct - a moderately connected prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP3-2 is a cysteine-rich hair-cortex keratin-associated protein and carries 84 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Over-annotated. KRTAP2-4 (Q9BYR9, 128 aa) is a cysteine-rich hair-cortex keratin-associated protein. The pair was reported only in HuRI, the CCSB human reference binary interactome map (PMID:32296183), and KRTAP2-4 has 89 distinct partners in IntAct - a moderately connected prey. All fifteen GO:0005515 rows on this gene come from two systematic yeast two-hybrid interactome maps and nothing else. Querying IntAct directly for P82987 returns the same pairs logged under three method names - two hybrid array, two hybrid prey pooling approach and validated two hybrid - which are sub-methods of one Y2H pipeline rather than three independent assays, so the NbExp values in the UniProt INTERACTION block count Y2H variants and not orthogonal confirmation. Disaggregating IntAct by pair rather than by gene - which is the only way the question can be answered, because ADAMTSL3's gene-level record also covers 17 partners that are not in GOA - shows that 0 of these 13 pairs carries any non-Y2H detection method. The anti-tag co-immunoprecipitation and BioID methods present in ADAMTSL3's IntAct record belong entirely to those other 17 partners, from separate publications that are not the source of any GOA row reviewed here. The partner set behaves like screen background rather than like biology. Nine of the thirteen partners are hair keratins or keratin-associated proteins and a tenth, CYSRT1, is a cornified-envelope protein embedded in the same interaction network; the remaining three are cytosolic or nuclear. The median number of distinct IntAct partners across the thirteen is 188 against 30 for ADAMTSL3 itself, and six of them exceed 180, so most of this set consists of high-degree promiscuous preys. There is also a compartment problem that the assay cannot see. ADAMTSL3 has a cleaved signal peptide and is secreted into the extracellular matrix; hair keratin-associated proteins are intracellular constituents of the hair cortex, GLRX3 is cytosolic and MDFI is nuclear and cytoplasmic. In a two-hybrid assay both proteins are expressed in the yeast nucleus, where a signal peptide is inert, so the pairing is never tested in a compartment where it could occur. Marked over-annotated rather than removed. These are real observations recorded correctly by IntAct curators from published screens, and a screen hit can turn out to matter; what it does not do is license a functional claim, and bare protein binding conveys none in any case. Reason: Unreplicated systematic yeast two-hybrid hit. KRTAP2-4 is a cysteine-rich hair-cortex keratin-associated protein and carries 89 distinct IntAct partners against ADAMTSL3's 30. Disaggregating IntAct per pair rather than per gene shows this pair, like all 13, carries no non-Y2H detection method; it has no orthogonal assay, no follow-up in the ADAMTSL3 literature, and ADAMTSL3 is a secreted matrix protein that does not share a compartment with it in vivo. Bare protein binding conveys no function even where the pairing is real. Supporting Evidence: file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md ADAMTSL3 itself has 30 distinct IntAct partners; the median for its 13 annotated partners is 188. file:human/ADAMTSL3/ADAMTSL3-bioinformatics/RESULTS.md **GOA partners with any non-Y2H detection method: 0 of 13** - every one of these pairs rests on yeast two-hybrid sub-methods alone, with no orthogonal assay. file:human/ADAMTSL3/ADAMTSL3-uniprot.txt FT SIGNAL 1..26 |
| GO:0071953 elastic fiber | TAS PMID:23962539 Elastic fibres in health and disease. | KEEP AS NON CORE | Summary: Kept, but as a non-core location, because no one has ever localised ADAMTSL3 protein to an elastic fibre. The source is a specialist review of elastic-fibre biology, not primary data, and the cached record is abstract-only. Its abstract does not mention ADAMTSL3, so the supporting statement is in text I cannot read. I therefore tested whether this is a bulk projection. Querying QuickGO by reference returns 66 annotations over 62 distinct entities, all TAS and all from GO_Central, split across four terms - so it is indeed a reference-driven curation of an elastic-fibre proteome. But it is not an indiscriminate family sweep, and that is what decides the action: the GO:0071953 set takes ADAMTSL3, ADAMTSL4, ADAMTSL5 and THSD4 with their mouse orthologues while leaving out ADAMTSL1, ADAMTSL2 and PAPLN. A curator applying the term by family membership would have taken all seven. The selection therefore tracks the review's content, which makes this a genuine traceable author statement rather than an artefact. Against that, the biochemistry stops short of a location. ADAMTSL3 binds the N-terminal half of fibrillin-1 and the C-terminal domains of LTBP-1, which is why the association is plausible - but the paper that established the binding says in as many words that the colocalisation experiment could not be done for want of antibodies, and no later work has done it. The gap is therefore not an oversight in this review; it is the state of the field. Kept as non-core rather than removed: overruling a specialist curator's traceable statement on the strength of a full text I have not read would be exactly the wrong call, and the term is consistent with everything that is known. Not accepted as core because a location for which no localisation experiment exists should not be presented as established. Reason: A traceable author statement from a specialist elastic-fibre review, applied selectively within the ADAMTSL family rather than by family membership, and consistent with ADAMTSL3's demonstrated binding to fibrillin-1 and LTBP-1. But no published experiment localises ADAMTSL3 protein to an elastic fibre or a microfibril - the study that established the fibrillin-1 binding states that the colocalisation could not be attempted because antibodies did not exist - so it is retained without being treated as an established core location. Supporting Evidence: PMID:23962539 They are laid down during development, and comprise a cross-linked elastin core within a template of fibrillin-based microfibrils. PMID:22242013 Since antibodies specific for ADAMTSL-2 and -3 are not yet available, we were unable to determine whether these proteins also colocalize with fibrillin-1 in skin and whether these are also reduced in WMΔ mutant mice. Knowledge gap: ADAMTSL3 has never been localised in tissue. There is no published immunolocalisation of the endogenous protein to microfibrils, elastic fibres, or any other defined matrix structure. OPEN BIOLOGY CC_DARK Resolve: Raise ADAMTSL3-specific antibodies and perform immunofluorescence and immunoelectron microscopy on skin, aorta and myocardium, with fibrillin-1 co-staining and an Adamtsl3-null control for specificity. "Since antibodies specific for ADAMTSL-2 and -3 are not yet available, we were unable to determine whether these proteins also colocalize with fibrillin-1 in skin" — PMID:22242013 |
| GO:0050840 extracellular matrix binding | ISS PMID:22242013 Microenvironmental regulation by fibrillin-1. | NEW | Summary: Proposed. This is the gene's best-characterised molecular activity and it is entirely absent from GOA, which currently gives ADAMTSL3 no molecular function beyond bare protein binding to a set of two-hybrid preys. Surface plasmon resonance shows that the C-terminal end of ADAMTSL-3 binds the N-terminal half of fibrillin-1, that the Weill-Marchesani three-domain deletion in fibrillin-1 abolishes that binding, that the same ADAMTSL-3 fragment binds the non-catalytic C-terminal region of ADAMTS-10 with a KD of 2 nM, and that it binds the C-terminal domains of LTBP-1. Two negative controls in the same panel show the binding is selective rather than sticky: ADAMTSL-1 does not bind fibrillin-1 or ADAMTS-10, and ADAMTSL-3 does not bind LTBP-4. Fibrillin-1 and LTBP-1 are both extracellular matrix components, so GO:0050840 states what was measured. The same term was chosen independently for the same biology in this repository's ADAMTSL4 review, which keeps the two paralogues consistent. Deliberately not the child term GO:0050436 microfibril binding, which is defined as binding to a microfibril - a supramolecular assembly. What was assayed was binding to soluble recombinant fibrillin-1 polypeptides, which is binding to a microfibril component, not to a microfibril; and the two other measured partners, LTBP-1 and ADAMTS-10, are not microfibrils at all, so the child term would cover only part of the evidence while asserting more than any of it. Whether ADAMTSL3 engages assembled microfibrils is precisely the untested question recorded against the elastic-fiber row. Coded ISS rather than IPI because the species of the ADAMTSL-3 reagent is not resolvable from the paper. The Results describe the panel as recombinant human ADAMTSL-1, -2 and -3, but the Methods say the ADAMTSL3 constructs were made from a RIKEN clone and mouse lung cDNA - and say the same, explicitly, for ADAMTSL2, which the Results sentence also calls human. Only ADAMTSL1 is unambiguously human in the Methods. A curator should upgrade this to IPI, with UniProtKB:P35555 (human FBN1) as the WITH/FROM interactor, if the authors confirm the construct was human; until then the conservative code is the honest one. Note the WITH/FROM here carries only UniProtKB:G3UXC7, the mouse orthologue: for ISS the field must hold the sequence-similar entity from which the inference is drawn, and the binding partner belongs there only under IPI. Reason: ADAMTSL3 binds fibrillin-1 and LTBP-1, both extracellular matrix proteins, by surface plasmon resonance with mapped sites and selective negative controls, yet GOA records no molecular function for this gene other than bare protein binding to two-hybrid preys. ISS rather than IPI because the paper contradicts itself about whether the ADAMTSL-3 polypeptide was human or mouse. Supporting Evidence: PMID:22242013 Similar to ADAMTSL-6 [24], ADAMTSL-2, -3, and papilin polypeptides interacted with the N-terminal half of fibrillin-1, while ADAMTSL-1 did not. PMID:22242013 SPR also showed that the C-terminal end of ADAMTS-10 interacted with the C-terminal end of ADAMTSL-3 with high binding affinity (KD = 2 nM) (Figure 5c). PMID:22242013 Binding between ADAMTSL-3 and the C-terminal domains of LTBP-1 was also detected, but neither ADAMTSL-2 nor -3 interacted with LTBP-4. PMID:22242013 Constructs for ADAMTSL3 were made using a clone (RIKEN) and mouse lung cDNA. |
| GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway | IMP PMID:36539599 ADAMTSL3 knock-out mice develop cardiac dysfunction and dila... | NEW | Summary: Proposed. Loss-of-function and gain-of-function agree in sign, and the gain-of-function half was done on human cells with the human protein. Adenoviral overexpression of full-length ADAMTSL3 in cultured human foetal cardiac fibroblasts reduced phospho-SMAD2 and active TGF-beta, and reduced the large latent complex components LAP and LTBP1 in both cell and matrix lysates; a 84-gene TGF-beta pathway array showed TGFB1, TGFB2, SMAD3, SMAD4 and TGFBR1 down and the inhibitory SMAD6 up. In the reciprocal direction, Adamtsl3-null mouse hearts show raised active TGF-beta and phospho-SMAD2 after aortic banding. Coded IMP because adenoviral overexpression is a perturbation, not an assay of the protein at native levels. The mechanism is consistent with the binding data: LTBP-1 and fibrillin-1 are the two proteins that hold the large latent TGF-beta complex in the matrix, and ADAMTSL3 binds both. What is not yet shown is whether the reduction in signalling follows from sequestering latent complex or from the transcriptional changes, so the term is proposed at the level of the pathway rather than as a specific molecular mechanism. The cardiac phenotypes themselves are deliberately not proposed as GO terms. They are mouse, and they are responses to experimental pressure overload rather than normal physiology; the reviewable claim is the regulation of the signalling pathway, which has human-cell support. Reason: Human ADAMTSL3 overexpressed in human cardiac fibroblasts reduces phospho-SMAD2, active TGF-beta and large-latent-complex components, and Adamtsl3-null mouse hearts show the reciprocal increase after pressure overload. GOA carries no biological-process annotation for this gene beyond a family-level InterPro term, and this is the best-supported process claim in its literature. Supporting Evidence: PMID:36539599 For further mechanistic insights, we overexpressed full-length ADAMTSL3 (L3) and a vehicle control adenovirus (veh) in cultures of human foetal CFBs (hfCFBs) PMID:36539599 Immunoblotting revealed reduced pSMAD (Fig. 4h) and reduced active TGFβ (Fig. 4i), indicating reduced TGFβ signalling. PMID:36539599 Taken together, the loss-of-function and gain-of-function studies suggest ADAMTSL3 as an inhibitor of TGFβ signalling in the heart in vivo and in cardiac fibroblasts in vitro. |
| GO:0050808 synapse organization | ISS PMID:37572323 Adamtsl3 mediates DCC signaling to selectively promote GABAe... | NEW | Summary: Proposed, on mouse conditional knockouts, and coded ISS for that reason. Early post-natal neuronal deletion of Adamtsl3 in mouse reduces DCC protein and the density of both glutamatergic and GABAergic synapses; adult deletion in GABAergic or glutamatergic neurons leaves DCC-Netrin-1 function at glutamatergic synapses intact but controls DCC signalling at GABAergic synapses, and the Adamtsl3-DCC unit is required for activity-dependent adaptation there. A second mouse study finds Adamtsl3 is required cell-autonomously in parvalbumin interneurons for perineuronal net formation and maintenance, with adult deletion reactivating juvenile ocular-dominance plasticity. The orthology behind the inference is unusually good for a mouse-to-human transfer. The C. elegans orthologue Ce-Punctin/MADD-4 is itself a secreted synaptic organiser that specifies whether a postsynaptic domain is cholinergic or GABAergic, and it acts through UNC-40/DCC - the same receptor as in the mouse hippocampus. So the receptor and the synaptic role are conserved from nematode to mouse, which is a stronger basis than sequence similarity alone. Human ADAMTSL3 protein is present in cortical and ganglionic neurons. One caveat is recorded rather than glossed: MADD-4 is the orthologue of both ADAMTSL1 and ADAMTSL3, so the worm data are shared between the two human paralogues and cannot be assigned to ADAMTSL3 alone. The mouse conditional knockouts can, and they are what the annotation rests on; the worm work is cited as evidence that the DCC-dependent synaptic role is ancestral, not as evidence about the human gene. Held as non-core, and deliberately not carried into core_functions: the direct evidence is entirely non-human and the molecular activity underlying the effect on DCC is unknown, which is recorded below as an MF_DARK knowledge gap. An earlier draft of this review listed the neuronal role among the core functions while this row called it non-core; the two passages rested on the same premise and reached opposite conclusions, so the core_functions entry has been removed and this row is the single statement of the position. The biology is not lost: it is described in the gene description, set out in full here, and its matrix component is carried by GO:0030198 in core function 1. Reason: Mouse conditional knockouts show Adamtsl3 is required for hippocampal synapse density and for DCC signalling at GABAergic synapses, and a second mouse study shows a cell-autonomous requirement in parvalbumin interneurons for perineuronal nets. The DCC-dependent synaptic role is conserved to the C. elegans orthologue, and human ADAMTSL3 is expressed in cortical and ganglionic neurons. Coded ISS because no human experiment exists, and proposed as non-core for the same reason. Supporting Evidence: PMID:37572323 We demonstrate that early post-natal deletion of Adamtsl3 in neurons impairs DCC protein expression, causing reduced density of both glutamatergic and GABAergic synapses. PMID:22014523 MADD-4's activity is dependent on UNC-40/DCC, a netrin receptor, which functions cell-autonomously to direct membrane extension. PMID:17597111 ADAMTSL3 is expressed in epithelial cells of the colon, fallopian tube, skin, breast, prostate, epididymis, liver, pancreatic islets and bile ducts, as well as by vascular endothelial cells, smooth muscle cells, fibroblasts, cortical and ganglionic neurons and cardiac myocytes. file:human/ADAMTSL3/ADAMTSL3-deep-research-affinage.md The biochemical mechanism by which this non-catalytic ECM protein controls DCC receptor levels has not been characterized in the available corpus. Knowledge gap: No molecular activity is known for ADAMTSL3 in the nervous system. How a secreted matrix glycoprotein raises DCC protein levels, and whether it does so by binding DCC, by binding something that presents DCC, or by altering the matrix in which DCC sits, is unestablished. OPEN BIOLOGY MF_DARK Resolve: Test direct ADAMTSL3-DCC binding by SPR with purified ectodomains, and ask whether the fibrillin-1-binding C-terminal region is sufficient for the synaptic effect in a rescue experiment. "The biochemical mechanism by which this non-catalytic ECM protein controls DCC receptor levels has not been characterized in the available corpus." — file:human/ADAMTSL3/ADAMTSL3-deep-research-affinage.md |
| GO:0002020 protease binding | ISS PMID:22242013 Microenvironmental regulation by fibrillin-1. | NEW | Summary: Proposed. The tightest measured interaction this protein has is with a protease, and no term currently records it. Surface plasmon resonance gives a KD of 2 nM between the C-terminal end of ADAMTSL-3 and the C-terminal end of ADAMTS-10, a secreted metalloproteinase mutated in recessive Weill-Marchesani syndrome. GO:0002020 is defined as binding to a protease or a peptidase, so the term states exactly that. It is selective within the family in the same experiment: neither ADAMTSL-1 nor ADAMTSL-2 bound ADAMTS-10, which the authors read as ADAMTS enzymes partnering with specific ADAMTSL proteins. Worth being clear about what this does and does not claim. The region of ADAMTS-10 involved is its non-catalytic C-terminal Tsp1-repeat region, not the catalytic domain, so this is not evidence of protease inhibition, and no inhibitor term is proposed. Whether ADAMTSL3 modulates ADAMTS-10 activity or merely co-occupies fibrillin-1 with it is untested, and is one of the suggested experiments. Coded ISS for the same reason as the GO:0050840 row: the paper's Results call the ADAMTSL-3 reagent human while its Methods describe a RIKEN clone and mouse lung cDNA. On an IPI upgrade the WITH/FROM interactor would be UniProtKB:Q9H324 (human ADAMTS10). This row is part of the same matricellular adaptor function as GO:0050840 rather than a separate one, which is why core function 1 describes the ADAMTS-10 binding but carries GO:0050840 as its single molecular_function term. Family precedent: this repository's merged ADAMTSL4 review also carries GO:0002020, so the two paralogues stay consistent. Reason: ADAMTSL3 binds the non-catalytic C-terminal region of the metalloproteinase ADAMTS10 with a KD of 2 nM by SPR, selectively within the family, and no GO term currently records the tightest measured interaction this protein has. ISS rather than IPI because the source paper contradicts itself about whether the ADAMTSL-3 polypeptide was human or mouse. No inhibitor term is proposed: the contact is with the Tsp1 region, not the catalytic domain. Supporting Evidence: PMID:22242013 SPR also showed that the C-terminal end of ADAMTS-10 interacted with the C-terminal end of ADAMTSL-3 with high binding affinity (KD = 2 nM) (Figure 5c). PMID:22242013 However, neither ADAMTSL-2 nor -1 bound to ADAMTS-10, indicating that ADAMTS enzymes may partner only with specific ADAMTSL proteins. PMID:22242013 The C-terminal recombinant ADAMTS-10 polypeptide used in the SPR studies represents the noncatalytic region of ADAMTS-10, a region composed primarily of Tsp1 repeats (Figure S3). |
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Download this section (compressed HTML)Q: PAINT has already made the key-residue judgement that the ADAMTS catalytic domain is lost in this family, but has attached it to the wrong node. In PTHR13723, the root node PTN000347317 carries GO:0004222 metalloendopeptidase activity and GO:0006508 proteolysis as IBD, seeded exclusively by genuine ADAMTS proteinases; node PTN002673039 carries NOT GO:0004222 by IKR and NOT GO:0006508 by IRD. Streaming the PANTHER leaf GAF shows PTN002673039 projects onto exactly 22 leaves, every one an ADAMTSL2 orthologue. The identical loss of the metalloprotease and disintegrin domains is shared by ADAMTSL1, ADAMTSL3, ADAMTSL4, ADAMTSL5, PAPLN, THSD4 and the invertebrate members madd-4, loh and papilin, none of which carries the NOT. Could the IKR be moved or duplicated to the ancestral node of the non-catalytic ADAMTSL clade? That single edit would state the catalytic loss for six further human genes. I have not proposed a gene-level NOT GO:0004222 row for ADAMTSL3 alone, because the defect is clade-wide and fixing one leaf would leave the other five untouched while duplicating machinery PAINT already has in the right form - but a leaf-level NOT, inferred from the absent metalloprotease and disintegrin domains, would be the correct fallback if the node cannot be re-annotated. Related observation for the same curators: the NOT GO:0006508 IRD row at PTN002673039 produces no leaf annotation at all, not even on ADAMTSL2.
Suggested experts: GO Central / PAINT curators, PANTHER
Q: Within PTHR13723, why does GO:0030198 extracellular matrix organization reach ADAMTSL2, ADAMTSL4 and THSD4 from node PTN000347317 but not ADAMTSL3 or ADAMTSL5, and why do human ADAMTSL1 and PAPLN receive no PAINT annotation at all when their mouse and fly orthologues do? The split does not track any biological criterion I can find - ADAMTSL3 has direct fibrillin-1 binding data and a matrix phenotype in two independent mouse knockouts, which is more than several of the members that do receive the term.
Suggested experts: GO Central / PAINT curators
Q: PMID:22242013 contradicts itself about the species of the ADAMTSL-3 reagent. The Results describe recombinant human ADAMTSL-1, -2 and -3, while the Methods state that the ADAMTSL3 constructs were made from a RIKEN clone and mouse lung cDNA, and say the same explicitly for ADAMTSL2. Which is correct? The answer decides whether the fibrillin-1, ADAMTS-10 and LTBP-1 interactions should be annotated to human ADAMTSL3 as IPI or as ISS from the mouse orthologue.
Suggested experts: Authors of PMID:22242013 (Sakai / Apte laboratories)
Q: UniProt records ADAMTSL3's extracellular matrix localisation with ECO:0000269|PubMed:14667842, but GOA has no corresponding IDA row, so the only localisation annotation the gene carries is a phylogenetic inference. Can the UniProt experimental localisation be propagated into GOA?
Suggested experts: UniProt-GOA
Q: ADAMTSL3 binds fibrillin-1 and LTBP-1 and restrains TGF-beta signalling, and the ADAMTSL2 and ADAMTS10 mutations that cause geleophysic dysplasia and Weill-Marchesani syndrome act on the same microfibril axis - yet no Mendelian disorder has been attributed to ADAMTSL3, only common-variant associations with height and lean mass. Is that because loss of ADAMTSL3 is tolerated, or because the phenotype has not been looked for? Are there biallelic loss-of-function carriers in large sequencing cohorts, and what are their stature and cardiac phenotypes?
Suggested experts: Human genetics of the fibrillinopathies, gnomAD / large cohort sequencing
Experiment: Raise and validate ADAMTSL3-specific antibodies against a region absent from the other ADAMTSLs, using Adamtsl3-null tissue as the specificity control - the reagent gap has blocked this question since 2012. Then perform immunofluorescence and immunoelectron microscopy on skin, aorta and myocardium with fibrillin-1 co-staining, and test whether ADAMTSL3 co-fractionates with microfibrils extracted by bacterial collagenase digestion.
Hypothesis: ADAMTSL3 is a component of fibrillin microfibrils rather than a soluble matrix protein that binds fibrillin-1 transiently.
Type: immunolocalisation and biochemical fractionation
Experiment: Separate the two mechanisms in the human cardiac fibroblast system. Compare full-length ADAMTSL3 with a C-terminal fragment carrying the fibrillin-1 and LTBP-1 binding activity but nothing else, and with a construct in which those binding surfaces are disrupted; read out phospho-SMAD2 and active TGF-beta against matrix-bound versus soluble LTBP1 and LAP. If sequestration is the mechanism, the binding-competent fragment should suffice and the effect should require an assembled fibrillin scaffold - testable by repeating in FBN1-null fibroblasts.
Hypothesis: ADAMTSL3 restrains TGF-beta signalling by retaining the large latent complex on microfibrils, not by altering transcription of the pathway.
Type: structure-function and epistasis in human cells
Experiment: Test whether ADAMTSL3 modulates ADAMTS10's activity or its microfibril association: reconstitute fibrillin-1 microfibril assembly in vitro and in cell culture with and without ADAMTSL3, and ask whether ADAMTSL3 alters ADAMTS10 binding to fibrillin-1, its zymogen processing, or its proteolytic activity. A non-catalytic family member that binds a proteinase of the same family at nanomolar affinity is a candidate regulator of that proteinase, which no GO term currently records.
Hypothesis: ADAMTSL3 and ADAMTS10 act as a complex on fibrillin-1, as the 2 nM binding affinity suggests.
Type: in vitro reconstitution
Experiment: Do the experiment that would license an experimental rather than an inferred annotation for the human gene: delete or knock down ADAMTSL3 in human iPSC-derived cortical neuron and parvalbumin-interneuron cultures and assay DCC protein levels, synapse density and perineuronal net formation, with rescue by wild-type human ADAMTSL3. Include the reported schizophrenia-associated variant rs950169 in the rescue panel.
Hypothesis: The mouse Adamtsl3 neuronal phenotypes reflect a function conserved in human ADAMTSL3.
Type: human iPSC neuronal model
Experiment: Measure growth-plate architecture, chondrocyte proliferation and phospho-SMAD2 in Adamtsl3-null mice against littermate controls, and test whether long-bone growth retardation is rescued by TGF-beta pathway inhibition. The Weill-Marchesani fibrillin-1 mouse, which loses the ADAMTSL binding site, already shows retardation of long bone growth, so the axis is testable genetically.
Hypothesis: The height and lean-mass association at the ADAMTSL3 locus acts through TGF-beta availability in the growth plate.
Type: mouse skeletal phenotyping
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