Contractile Vacuole Tethering — Obsoletion & Replacement (GO:0140025)

IN_PROGRESS OBSOLETION

Contractile Vacuole Tethering — Obsoletion & Replacement (GO:0140025)

Overview

A GO obsoletion proposal retires GO:0140025 contractile vacuole tethering
involved in discharge (a BP term). The rationale mirrors the parallel
membrane-tether obsoletions in this batch (ER–PM, mito–ER,
peroxisome–chloroplast): the activity is more appropriately captured at the
molecular function level. The new MF term
GO:7770067 contractile vacuole-plasma membrane tether activity has been
added upstream as the replacement, with parent
GO:0140177 membrane-membrane adaptor activity.

This project tracks the impact on AI Gene Review and queues the two affected
Dictyostelium discoideum genes (rab8A and p2xA) for review.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement
contractile vacuole tethering involved in discharge GO:0140025 MF: GO:7770067 contractile vacuole-plasma membrane tether activity

The new MF term definition (per upstream PR #31942):

The binding activity of a molecule that brings together the contractile
vacuolar membrane and the plasma membrane, either via membrane lipid binding
or by interacting with a membrane protein, to establish or maintain the
localization of the contractile vacuole at a specific plasma membrane
discharge site. [PMID:22323285]

Synonyms: "contractile vacuole-plasma membrane tethering activity" (EXACT),
"plasma membrane-contractile vacuole tether activity" (EXACT).

Affected upstream groups (from issue body)

Group Annotations Status
dictyBase 2 pending — "May be automatically transferred" per upstream

The two annotations are:

Gene Locus UniProt Reference Evidence
rab8A DDB_G0280043 P20790 PMID:22323285 IMP
p2xA DDB_G0272004 Q86JM7 PMID:24335649 IMP

Mappings to be reviewed

None. The issue body explicitly lists no InterPro2GO, UniProt-Keywords, or
UniRule mappings for GO:0140025.

Impact on this repo

Neither rab8A nor p2xA is currently reviewed in this repository
(genes/DICDI/ contains tlcd4b, mlcD, and nip7 — none of the contractile
vacuole tether annotations). This means no existing reviews need refresh
for the obsoletion itself, but the two affected genes represent a coherent
small candidate set for proactive review now that the replacement MF term
is in place.

Scope

Candidate genes for initial review

Verify each with just fetch-gene DICDI <gene> before starting; confirm the
UniProt accession from the UniProt API.

  1. rab8A (D. discoideum, UniProt P20790, locus DDB_G0280043) — Rab8a
    small GTPase. PMID:22323285 (Essid et al. 2012, Mol Biol Cell) is the
    anchor publication for the new MF term itself: "Rab8a regulates the
    exocyst-mediated kiss-and-run discharge of the Dictyostelium
    contractile vacuole". This is the cleanest review target — the underlying
    experiment characterised the molecular tethering activity of Rab8a at the
    contractile vacuole / plasma membrane discharge site.

  2. p2xA (D. discoideum, UniProt Q86JM7, locus DDB_G0272004) — P2X
    receptor A (DdP2X). PMID:24335649. The IMP annotation should be evaluated
    carefully: P2X receptors are normally Ca²⁺/cation channels, so the
    tether-activity assignment should be verified against the paper's actual
    loss-of-function phenotype before accepting GO:7770067 as a core function.
    This is the more interpretation-sensitive review.

Proposed approach and priority

  1. Wait for the dictyBase migration. The issue body notes that the two
    annotations "may be automatically transferred". If dictyBase has not yet
    migrated them at the time of review, the new rows should appear under
    GO:7770067; the review can then ACCEPT (rab8A) or assess (p2xA) the
    migrated MF annotations directly.

  2. Anchor on rab8A. rab8A is the direct PMID:22323285 case that motivated
    the new MF term, so it is the natural anchor review. ACCEPT GO:7770067
    as a core function, capture the exocyst interaction
    (rab8A → Sec3/Sec5 etc.) as a related binding activity, and propose
    contractile vacuole discharge (GO:0070177) as the process context.

  3. Review p2xA second. Use the rab8A review template, but verify that
    the PMID:24335649 evidence really supports a tether activity rather than a
    channel-mediated regulatory role. If the evidence is weak,
    MARK_AS_OVER_ANNOTATED rather than mechanically ACCEPTing the migrated
    row.

  4. Use the pair as a coherent batch — these are the only two annotations
    to the obsoleted term, so completing both closes the loop for the entire
    GO:0140025 → GO:7770067 migration as far as the literature is concerned.

Priority

Low–medium. Only 2 affected annotations, both in a non-priority organism
for this repository (D. discoideum has only 3 existing reviews — tlcd4b,
mlcD, nip7), and the upstream migration is likely to be handled directly by
dictyBase. The review value is mainly in (a) anchoring the new GO:7770067
term with a high-quality core_function entry for rab8A, and (b) sanity-checking
the p2xA tether call before it propagates further.

Status