Regulation of COPII Vesicle Coating — Obsoletion & Replacement

Overview

A GO obsoletion proposal will retire GO:0003400 regulation of COPII vesicle
coating (BP) and merge its annotations into GO:0048208 COPII vesicle
coating (BP). The rationale, captured in the upstream ontology ticket, is
that the proteins currently annotated to GO:0003400 act part_of the COPII
vesicle coating pathway (they are components of the coating machinery —
SAR1, SEC12, SEC23, SEC16, SED4, PEF1, PREB) rather than upstream regulators
of that pathway, so the "regulation of …" parent does not describe their
biology accurately. One UniProt entry on the upstream list (human MAPK15,
Q8TD08) is being disputed and is slated for removal rather than transfer.

The replacement term GO:0048208 is also being renamed at the same time:

GO:0048208 COPII vesicle coating → COPII vesicle coat assembly
GO:0006901 vesicle coating → vesicle coat assembly

(both labels were rebranded to clearer "coat assembly" wording in the
go-ontology PR opened in response to the obsoletion request).

This project tracks the impact on AI Gene Review and queues affected genes
for review, since none of the directly annotated genes are currently in this
repository.

Upstream tickets

Annotation tracker: geneontology/go-annotation#6389
Ontology ticket: geneontology/go-ontology#31945 (CLOSED — obsoletion + rename applied via PR #32013)

Obsoletion plan (per upstream)

Obsoleted term	ID	Replacement
regulation of COPII vesicle coating	GO:0003400	GO:0048208 COPII vesicle coat assembly (renamed from "COPII vesicle coating")

Term labels were verified in OLS on 2026-05-24. Both GO:0003400 and
GO:0048208 are still live in OLS at the time of this check (the obsoletion
will become visible after the next GO release ingests PR #32013).

Affected experimental annotations (from upstream spreadsheet)

11 EXP annotations across two groups (SGD 8, UniProt 3). Pulled from the
upstream Google Sheet on 2026-05-24:

#	Group	Gene	Species	ID	PMID	Evidence	PANTHER	Status
1	SGD	SAR1	S. cerevisiae	SGD:S000006139	PMID:14627716	IDA	PTHR45684	move to GO:0048208
2	SGD	SAR1	S. cerevisiae	SGD:S000006139	PMID:15665868	IDA	PTHR45684	move to GO:0048208
3	SGD	SED4	S. cerevisiae	SGD:S000000663	PMID:21291503	IDA	PTHR23284	move to GO:0048208
4	SGD	PEF1	S. cerevisiae	SGD:S000003290	PMID:22792405	IDA	PTHR46212	move to GO:0048208
5	SGD	PEF1	S. cerevisiae	SGD:S000003290	PMID:22792405	IMP	PTHR46212	move to GO:0048208
6	SGD	PEF1	S. cerevisiae	SGD:S000003290	PMID:22792405	IPI (with SGD:S000002354)	PTHR46212	move to GO:0048208
7	SGD	SEC12	S. cerevisiae	SGD:S000005309	PMID:8377826	IDA	PTHR23284	move to GO:0048208
8	SGD	SEC23	S. cerevisiae	SGD:S000006385	PMID:8451644	IDA	PTHR11141	move to GO:0048208
9	UniProt	SEC16A	H. sapiens	UniProtKB:O15027	PMID:17005010	IMP	PTHR13402	move to GO:0048208
10	UniProt	MAPK15	H. sapiens	UniProtKB:Q8TD08	PMID:24618899	IMP	PTHR24055	DISPUTED — to be removed (ValWood, per upstream issue body)
11	UniProt	PREB	H. sapiens	UniProtKB:Q9HCU5	PMID:32358066	IDA	PTHR23284	move to GO:0048208

Mappings flagged for redirection

unirule2go: UniRule:UR001628761 → GO:0003400. Verified live via
UniProt REST on 2026-05-24. Condition set: PANTHER PTHR23284 AND
taxon ∈ {Mammalia (40674), Arabidopsis (3701), Ascomycota (4890)}. This
is the SEC12/PREB/SED4 family (matches affected SGD SEC12 + SED4 and
human PREB entries above), so a clean redirect to GO:0048208 (COPII
vesicle coat assembly) is appropriate once the obsoletion lands. The
human MAPK15 PTHR24055 entry is outside this rule's family condition and
is independently handled by the disputed-annotation removal.

No InterPro2GO or UniProt-Keywords mappings to GO:0003400 were listed in the
upstream issue.

Impact on this repo

No genes directly annotated to GO:0003400 are currently reviewed here.
Searches under genes/ for SAR1, SED4, PEF1, SEC12, SEC23, SEC16A, MAPK15,
and PREB (and the UniProt accessions O15027, Q8TD08, Q9HCU5) returned no
matches on 2026-05-24. This means no existing reviews need refresh for
the obsoletion itself; the project is a queueing exercise that lines up
COPII machinery components for prospective review.

The repo currently has a related COPII track in
projects/ only via the parallel vesicle-targeting / vesicle-tethering
obsoletions (VESICLE_TARGETING_OBSOLETION.md,
SYNAPTIC_VESICLE_DOCKING_OBSOLETION.md,
ER_PM_TETHERING_OBSOLETION.md,
MITO_ER_TETHERING_OBSOLETION.md,
CILIARY_BASAL_BODY_DOCKING_OBSOLETION.md), and via the yeast ERV14 review
(tracked separately in #402
against #6406
for COPII cargo receptor activity). Adding canonical COPII coating
components (SAR1, SEC23, SEC16) here would substantially strengthen the
ER-to-Golgi early-secretory-pathway coverage.

Scope

Organisms: S. cerevisiae (SAR1, SED4, PEF1, SEC12, SEC23) and human
(SEC16A, PREB; MAPK15 is dispute-only). All 11 EXP rows are mammalian or
fungal — no plant or invertebrate direct annotations are on the upstream
list.
GO branches: BP only. The replacement is in the same branch (parent
GO:0006901 vesicle coat assembly / GO:0048193 Golgi vesicle transport),
so existing parent classifications are preserved. No MF or CC overlap.
Type of fix: terminological — annotated proteins genuinely participate
in COPII coat formation (they are coat components or coat regulators
that act as part of the pathway), and the obsoletion simply removes a
spurious "regulation of …" framing. Most reviews can ACCEPT the
replacement GO:0048208 as core function for the SAR1/SEC23/SEC16 family
and KEEP_AS_NON_CORE for accessory regulators (SED4, PEF1).
Special case: human MAPK15 (Q8TD08) annotation is disputed by the
upstream curator and should be REMOVED rather than transferred. A MAPK15
review here would need to evaluate PMID:24618899 directly and either
confirm the removal or push back.

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> before starting. None
are currently in the repo.

Tier 1 — canonical COPII coat GTPase + scaffold

SAR1A (human, UniProt Q9NR31) — small Ras-family GTPase that
nucleates COPII coat assembly on the ER membrane after activation by
SEC12 (the cognate GEF). The yeast SAR1 entry on the upstream list
(SGD:S000006139, PMID:14627716 and PMID:15665868) reflects the same
biology; reviewing the human SAR1A is the highest-value anchor here
because SAR1A is well-studied, has clear core function (GTPase activity
driving COPII coat assembly), and serves a similar didactic role to
CEP290 in the parallel cilia-obsoletion project.
SEC23A (human, UniProt Q15436) — inner-layer COPII coat subunit
and SAR1 GAP. The yeast SEC23 entry (SGD:S000006385, PMID:8451644)
captures the canonical biochemistry. SEC23A loss-of-function causes
cranio-lenticulo-sutural dysplasia, so the gene is also clinically
well-characterised — a good complement to SAR1A.

Tier 2 — coat-recruiting / scaffolding regulators with direct annotations

SEC16A (human, UniProt O15027) — the human direct-annotation
target on the upstream list (PMID:17005010, IMP). SEC16A organises
transitional-ER exit sites and recruits the SAR1/SEC23/SEC24 complex.
Confirming GO:0048208 as core function and reviewing the broader
ER-exit-site machinery annotations would be useful.
PREB / SEC12 (human, UniProt Q9HCU5) — the human direct-annotation
target on the upstream list (PMID:32358066, IDA). PREB is the mammalian
SEC12 ortholog, a guanine nucleotide exchange factor for SAR1. Pairs
naturally with the SAR1A review.

Tier 3 — yeast-only entries (lower repo priority)

Yeast SAR1, SEC12, SEC23, SED4, PEF1 (SGD) — the 8 SGD direct
annotations cover the same biology as the human Tier 1/2 entries. A
single human-anchored review per family is more efficient than separate
yeast reviews, but the SED4 and PEF1 entries describe accessory
regulators (SED4 = SEC12 paralog without measurable GEF activity in
vitro; PEF1 = penta-EF-hand calcium-binding protein with a non-canonical
regulatory role) that have no direct human equivalent in this repo yet,
so a yeast PEF1 review would be worth adding once the canonical entries
are in.

Special case — disputed annotation

MAPK15 / ERK7 (human, UniProt Q8TD08) — the disputed
PMID:24618899 IMP annotation. Worth a focused review only if there is
independent interest in MAPK15; for the obsoletion-tracking purpose, the
simpler action is to wait for the upstream removal and not start a
ground-up MAPK15 review here.

Proposed approach

Wait for the obsoletion to land before bulk-rewriting. The upstream
ontology ticket #31945 is CLOSED and the corresponding PR (#32013) was
opened on 2026-04-22; the obsoletion + rename will be visible once a
GO release ingests it. Reviews can proceed on the underlying biology
now using the live GO:0048208 term ID (action codes ACCEPT / MODIFY /
REMOVE are independent of the obsoletion timing).
Begin with SAR1A (human) as the anchor review. The COPII coat GTPase
is the canonical example for the replacement term and has substantial
biochemistry / cryo-EM literature for core_functions synthesis.
Follow with SEC23A (human) to cover the inner coat layer and the
SAR1-GAP relationship — gives a paired review that exercises the
GTPase / GAP partnership in one of the field's textbook examples.
Add SEC16A and PREB if the project expands beyond the GTPase /
GAP pair, since they are the human entries actually on the upstream list.
Defer the yeast-only entries (SAR1, SEC12, SEC23, SED4, PEF1) and
the disputed MAPK15 unless interest develops; the human Tier 1/2 reviews
cover the biology more efficiently for this repo's audience.
Cross-reference with the ERV14 COPII cargo receptor project
(#402,
tracking go-annotation#6406)
— that project covers the cargo-recognition side of COPII budding,
which sits immediately downstream of the coat-assembly biology covered
here.
Flag the disputed MAPK15 annotation upstream if interest develops in
reviewing it locally; otherwise the upstream removal stands on its own.

Priority

Medium-low. The biology is canonical and well-established, and no
existing reviews are blocked by the obsoletion (no SAR1 / SEC23 / SEC16 /
PREB reviews exist here yet). This is opportunistic — SAR1A and SEC23A in
particular are major unreviewed components of the early secretory pathway,
so the obsoletion is a reasonable trigger to start that coverage.

Status

2026-05-24 — Project file created. Tracking upstream issue #6389 (opened
2026-04-22). Upstream ontology ticket #31945 is CLOSED and PR #32013 has
been opened to obsolete GO:0003400 + rename GO:0048208 and GO:0006901.
Verified GO:0003400 and GO:0048208 still live in OLS on 2026-05-24;
verified UniRule UR001628761 (PTHR23284, mammalian/Arabidopsis/Ascomycota
scope) live in UniProt REST on 2026-05-24. No gene reviews started yet
in this repo; none of the 11 affected genes are present under genes/.