ABRAXAS1 (Q6UWZ7) — Evaluation of "microtubule binding" (GO:0008017, IBA)
Focus: function-assignment hypothesis — ABRAXAS1 directly has microtubule binding (GO:0008017)
Source: genes/human/ABRAXAS1/ABRAXAS1-ai-review.yaml → existing_annotations[2].function_hypothesis
Evidence type under review: IBA (GO_REF:0000033, PAINT phylogenetic inference)
Executive Judgment
Verdict: REFUTED / OVER-ANNOTATED (paralog carry-over).
The IBA "microtubule binding" annotation on ABRAXAS1 is not supported by any primary experimental evidence for ABRAXAS1 itself. Programmatic provenance tracing shows the term was propagated by PAINT from a shared PANTHER ancestral node (PTN001272083) whose experimental support comes from the paralog ABRAXAS2 (ABRO1 / FAM175B, UniProt Q15018) — the scaffold of the cytoplasmic BRISC complex, which genuinely localizes to the spindle pole and has direct (IDA/IMP) microtubule and spindle annotations. ABRAXAS1, by contrast, is an exclusively nuclear scaffold of the BRCA1-A complex whose experimentally supported molecular function is polyubiquitin-modification-dependent protein binding (GO:0031593, IDA).
Two co-propagated terms from the same node/source — GO:0008608 (spindle-microtubule attachment to kinetochore) and GO:0090307 (mitotic spindle assembly) — are part of the same over-annotation cluster and share the fate of GO:0008017.
Most important caveat: This is a decision about direct annotation carry-over, not a claim that ABRAXAS1 has zero mitotic role. ABRAXAS1 does participate in mitotic G2/M DNA damage checkpoint signalling (properly annotated IMP/NAS), but that is checkpoint regulation, not physical microtubule binding, and does not rescue GO:0008017.
Evidence Matrix
| # | Citation | Evidence type | Supports/Refutes | Claim tested | Key finding | Context | Confidence / limitations |
|---|---|---|---|---|---|---|---|
| 1 | QuickGO provenance (GO_REF:0000033) | computational / database | Refutes (as direct) | Is GO:0008017 experimental for ABRAXAS1? | GO:0008017 on Q6UWZ7 is IBA, assignedBy GO_Central, withFrom = PANTHER PTN001272083 + UniProtKB:Q15018 |
GO annotation record | High; definitively an inferred, not experimental, term |
| 2 | UniProt Q15018 (ABRAXAS2/ABRO1) | direct assay + localization | Competing source | Which protein actually binds microtubules? | ABRAXAS2 has GO:0008017 IDA, GO:0008608 IMP, GO:0090307 IMP; localizes to spindle pole / cytoskeleton | Human, BRISC complex | High; ABRAXAS2 is the true experimental source of the propagated cluster |
| 3 | Computed NW alignment (this run) | structural / evolutionary | Qualifies | Are ABRAXAS1 & ABRAXAS2 paralogs sharing a PANTHER family? | Global identity ~40.8% (shorter-seq) / ~45.4% (aligned core); both = MPN domain (7–160) + coiled-coil scaffold | Sequence computation | High; explains why IBA co-clusters them |
| 4 | UniProt Q6UWZ7 features/comments | database + localization | Refutes | What is ABRAXAS1's function/location? | Function = BRCA1-A scaffold recognizing K63-Ub histones; Loc: Nucleus only; MF IDA = GO:0031593 (polyUb-dependent binding) | Human | High |
| 5 | PMID 31253574 (Rabl et al., 2019, Mol Cell) | structural / review-level synthesis | Refutes | Are ABRAXAS & ABRO1 distinct scaffolds? | "…BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively" — nuclear BRCA1-A vs cytoplasmic BRISC | Human, cryo-EM/biochem | High; clarifies paralog division of labour |
| 6 | PMID 28009280 (Kyrieleis et al., 2016) | structural | Refutes | Where does ABRAXAS1 act? | Recruited to damaged chromatin; cleaves K63-Ub on histones H2A/H2AX | Human, negative-stain EM | High; nuclear/chromatin, not spindle |
| 7 | PMIDs 17525340, 19261746, 19261748, 19261749 | direct assay (IDA) | Refutes (context) | ABRAXAS1's real MF/CC | Foundational BRCA1-A papers; basis for GO:0070531 (IDA nucleus) and GO:0031593 (IDA polyUb binding) | Human cells | High |
| 8 | 34272385 / 37198153 / 31630195 | mutant phenotype / patient cells | Qualifies | ABRAXAS1 loss-of-function phenotypes | Genome-stability/HR pathway-choice, BRCA1 mislocalization, breast-cancer predisposition — all nuclear DNA-repair | Human patient cells | High; no spindle phenotype reported |
GO Curation Implications
Lead (requires curator verification):
- GO:0008017 microtubule binding (MF, IBA) → REMOVE / do not accept for ABRAXAS1. It is an IBA carry-over whose only experimental support lies in the paralog ABRAXAS2 (Q15018). No ABRAXAS1-specific experimental evidence exists.
- Co-propagated from the same node/source — treat identically:
- GO:0008608 attachment of spindle microtubules to kinetochore (BP, IBA) → remove/flag.
- GO:0090307 mitotic spindle assembly (BP, IBA) → remove/flag.
- Retain the informative, experimentally grounded MF: GO:0031593 polyubiquitin modification-dependent protein binding (IDA) — this is the appropriate, more-specific molecular function and should be the annotation curators keep. (Do not fall back to bare "protein binding".)
- Retain CC: GO:0070531 BRCA1-A complex (IDA), GO:0005634 nucleus (IDA).
This is an MF-term removal driven by paralog-based IBA over-annotation, with a better-supported MF already in place.
Mechanistic Scope
- Immediate molecular activity actually tested/supported for ABRAXAS1: a scaffold/adaptor that reads K63-linked polyubiquitin (via associated RAP80/BRCC36) and physically tethers BRCA1–BARD1 to ubiquitinated H2A/H2AX at DNA double-strand breaks. Molecular function = polyubiquitin-dependent protein binding; cellular component = nuclear BRCA1-A complex.
- Microtubule binding is a molecular activity of a different gene product (ABRAXAS2), not a downstream phenotype of ABRAXAS1. There is no direct-binding, localization, or mutant evidence placing ABRAXAS1 on microtubules or the spindle.
- ABRAXAS1's only mitosis-adjacent role is G2/M DNA-damage checkpoint signalling — a regulatory/pathway consequence, distinct from GO:0008017.
Conflicts and Alternatives
- Paralog confusion (primary explanation): ABRAXAS1 (Q6UWZ7, nuclear BRCA1-A) vs
ABRAXAS2 (Q15018, cytoplasmic BRISC, spindle pole). ~41% identical; same PANTHER
family → PAINT propagated ABRAXAS2's experimental spindle/microtubule terms to
ABRAXAS1. The
withFromfield explicitly names Q15018 as the source. - Node separation is telling: the genuine ubiquitin-binding term (GO:0031593) propagated from a different ancestral node (PTN001272081) and is independently IDA on ABRAXAS1; the microtubule cluster propagated from PTN001272083 and is IDA/IMP only on ABRAXAS2. The annotations that are real are internally corroborated; the microtubule ones are not.
- No isoform/organism rescue found: UniProt lists ABRAXAS1 localization as Nucleus only; no spindle/cytoskeletal isoform is annotated.
Knowledge Gaps
| Gap | What was checked | Why it matters | What would resolve it |
|---|---|---|---|
| Any direct ABRAXAS1–tubulin/microtubule interaction | Literature search (multiple queries) + UniProt + QuickGO | If a real interaction existed, removal would be wrong | An in vitro microtubule co-sedimentation/pelleting assay with purified ABRAXAS1; IF co-localization with tubulin in mitosis |
| Whether ABRAXAS1 ever localizes to spindle/centrosome | UniProt subcellular location (Nucleus only); HPA nuclear body | Localization would be a prerequisite for the term | High-resolution mitotic IF / live imaging of endogenous ABRAXAS1 |
| PAINT node review status | Traced node PTN001272083 + Q15018 | Curators may already have flagged the node | Inspect the PANTHER family tree annotation and whether a NOT/qualifier was applied |
Discriminating Tests
- Microtubule co-sedimentation assay with purified recombinant ABRAXAS1 ± taxol-stabilized microtubules — direct test of GO:0008017; ABRAXAS2 as positive control.
- Mitotic immunofluorescence / live imaging of endogenous ABRAXAS1 vs ABRAXAS2 to test spindle-pole localization (expected: ABRAXAS2 yes, ABRAXAS1 no).
- Depletion phenotype comparison: siABRAXAS1 vs siABRAXAS2 spindle-assembly / chromosome mis-attachment scoring — the spindle phenotype should segregate to ABRAXAS2.
- PANTHER tree audit of PTN001272083 to confirm the experimental basis is exclusively ABRAXAS2-lineage and apply an experimental-evidence-based override for ABRAXAS1.
Curation Leads (require curator verification)
- Action change: Remove/reject IBA GO:0008017 (and co-clustered GO:0008608, GO:0090307) on ABRAXAS1 as paralog over-annotation; keep GO:0031593 (IDA) as the informative MF.
- Candidate reference to cite for the over-annotation source (verify snippet): PMID 31253574 — "…the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively."
- Candidate reference for ABRAXAS1's true nuclear function (verify snippet): PMID 28009280 — "It is recruited to damaged chromatin as a component of the BRCA1-A deubiquitinase, which cleaves K63-linked ubiquitin chains attached to histone H2A and H2AX."
- Suggested curator question: Does GO_Central want to add a
NOTqualifier or experimental-override for ABRAXAS1 at node PTN001272083, given that Q15018 (ABRAXAS2) is the sole experimental source and ABRAXAS1 is nucleus-restricted? - Suggested experiment: microtubule co-pelleting of purified ABRAXAS1 (definitive).
Provenance (computed this run)
- UniProt Q6UWZ7: 409 aa; MPN domain 7–160; coiled-coil 206–260; Loc = Nucleus; MF IDA = GO:0031593.
- QuickGO: GO:0008017 = IBA / GO_REF:0000033 / assignedBy GO_Central / withFrom PANTHER:PTN001272083 + UniProtKB:Q15018.
- UniProt Q15018 (ABRAXAS2): microtubule binding IDA; spindle attachment IMP; spindle assembly IMP; Loc = spindle pole/cytoskeleton.
- Needleman–Wunsch ABRAXAS1 vs ABRAXAS2: ~40.8% identity (shorter seq) / ~45.4% (aligned core) → true paralogs in one PANTHER family.