PIN1 (PIN-FORMED 1, AtPIN1) — Arabidopsis thaliana — curation notes

UniProt: Q9C6B8 (PINI_ARATH); locus AT1G73590; TCDB 2.A.69.1.1 (auxin efflux carrier / AEC family).

Core identity and molecular function

PIN1 is a plasma-membrane, polytopic (10-TM) secondary transporter that mediates
cellular auxin efflux. Its polar (asymmetric) localization at the plasma membrane
sets the direction of intercellular (polar) auxin transport, generating the local auxin
gradients/maxima that drive organogenesis, vascular patterning, embryo axis formation
and phyllotaxis.

• Founding identification as auxin efflux carrier component, basal localization in vascular
  cells, polar auxin transport: PMID:9856939. Disruption phenotype: naked, pin-shaped inflorescences.
• Direct demonstration of active auxin efflux and structural mechanism: PIN1 expressed in
  HEK293F cells mediates active IAA efflux (enhanced by D6PK), inhibited by NPA
  PMID:35917925.
• Substrate recognition: binds IAA (and IBA, IPA, 4-Cl-IAA) at an intracellular pocket;
  residues V51, N112, N478, I582 coordinate IAA PMID:35917925.
• Fold: 10-TM NhaA fold, TM1–TM5 / TM6–TM10 inverted repeats; inward-facing conformation
  PMID:35917925.
• Homodimer: cryo-EM shows a dimeric PIN1 (TM1, TM2, TM7 dimer interface)
  PMID:35917925. This supports the GOA
  IDA annotations GO:0042802 identical protein binding and GO:0042803 protein
  homodimerization activity.

So the appropriate, informative MF terms are:
- GO:0010329 auxin efflux transmembrane transporter activity (IDA + IMP) — ACCEPT, core.
- GO:0042803 protein homodimerization activity / GO:0042802 identical protein binding — ACCEPT (homodimer is structurally established), non-core.

Localization

• Plasma membrane is the functional site (multiple IDA/EXP): PMID:9856939, PMID:20439545,
  PMID:33705718.
• Polar PM domains: apical vs basal localization is phosphorylation-dependent
  PMID:20407025.
  Basal PM localization in vascular cells PMID:9856939. Apical/basal domains:
  GO:0016324 apical plasma membrane, GO:0009925 basal plasma membrane, GO:0045177 apical
  part of cell — all reflect the polar PM domain (cell periphery GO:0071944).
• GO:0005737 cytoplasm (HDA, PMID:15610358): PIN1 cycles between PM and endosomal
  compartments via GNOM-dependent recycling (UniProt FUNCTION). Cytoplasmic/endosomal
  signal is real (trafficking intermediates) but not the functional compartment; keep as
  non-core.
• GO:0009506 plasmodesma (HDA, PMID:21533090, proteomics): high-throughput proteome; PIN1
  is a PM protein and plasmodesmal PM is continuous with PM; weak/peripheral, keep non-core.
• GO:0009505 plant-type cell wall (IDA, PMID:18539115): PIN1 is an integral membrane
  protein; cell-wall assignment is not biologically meaningful for an auxin efflux carrier
  and likely reflects PM/apoplast-adjacent signal; mark as over-annotated.
• GO:0010168 ER body (IDA, PMID:36398993): PMID:36398993 is a tomato BIG/rosette paper
  about calcium and wound-induced rooting; it concerns ER localization of BIG, not PIN1
  ER-body localization. ER bodies are ER-derived structures found in Brassicaceae; there is
  no strong support that PIN1 is an ER-body resident. The long PINs (incl. PIN1) are PM
  proteins; only short PINs (PIN5/PIN8) are ER PMID:35917925. Treat ER body as a dubious annotation -> REMOVE/over-annotated. Marked UNDECIDED-leaning-REMOVE; chose MARK_AS_OVER_ANNOTATED conservatively is not appropriate since it appears to be a mis-assignment; chose REMOVE with rationale.

Regulation / interactors (the "protein binding" GO:0005515 IPI rows)

All GO:0005515 rows are uninformative bare "protein binding"; replace with specific
interactor context in reason, action MARK_AS_OVER_ANNOTATED (interaction is real but term
uninformative; per project guidance avoid bare protein binding as core).

• PMID:17237354 WITH UniProtKB:Q9LJX0 = ABCB19/PGP19 — PIN–P-glycoprotein co-action in auxin transport.
• PMID:17889649 / PMID:20080776 WITH O64682 = PID (PINOID kinase) — phosphorylates PIN1 HL, controls polarity.
• PMID:33705718 WITH Q0WL52 = NPY5/MEL1 (MAB4/MEL family) — recruited to PM by PIN1, maintains polarity.
• PMID:22715043 WITH Q9LHE7 (FYPP1) and Q9SX52 (FYPP3) — PP6 phosphatase, dephosphorylates PIN.
• PMID:36226797 WITH AT3G55880 = SUE4 — PIN1-interacting membrane protein, acropetal transport under S deficiency.
• PMID:17586653 WITH Q9LY87 — K63 ubiquitin ligase context (apical dominance).

UniProt SUBUNIT: "Homodimer. Interacts with TOPP4 ... Interacts with FYPP1 and FYPP3 ...
Component of a complex made of PINs, MAB4/MELs and AGC kinases at the plasma membrane.
Binds directly to NPY5/MEL1."

Biological processes (mostly IMP / acts_upstream_of_or_within)

Core BP:
- GO:0009926 auxin polar transport (IMP, PMID:16601150) — CORE.
- GO:0060918 auxin transport (IEA/IMP) — CORE (parent of polar transport).
- GO:0010315 auxin export across the plasma membrane (IDA, PMID:35917925) — CORE, most precise BP for the efflux event.
- GO:0055085 transmembrane transport (IEA) — accept as broad-but-correct parent.

Downstream developmental processes (pleiotropic; PIN1 acts upstream-of-or-within via auxin
gradients) — keep as non-core:
- GO:0009908 flower development; GO:0010229 inflorescence development (PMID:20407025; pin1 = pin-shaped naked inflorescence).
- GO:0048825 cotyledon development (IGI PMID:15371311); GO:0048826 cotyledon morphogenesis; GO:0009793 embryo development (PMID:20407025).
- GO:0010358 leaf shaping (PMID:16971475); GO:0010051 xylem and phloem pattern formation (PMID:16943276).
- GO:0009630 gravitropism (PMID:16601150); GO:0009640 photomorphogenesis (TAS PMID:16141452).
- GO:0048364 root development; GO:0048367 shoot system development (PMID:9856939/PMID:11060241).
- GO:0010262 somatic embryogenesis (IMP PMID:36345646); GO:0048830 adventitious root development (IMP PMID:36398993 — tomato ro/big paper; PIN1 accumulation Ca-sensitive). The adventitious-root annotation rests on an indirect tomato study; keep as non-core but flagged.

Deep research synthesis (Falcon / Edison Scientific, 2026-06-06)

The Falcon deep-research report (file:ARATH/PIN1/PIN1-deep-research-falcon.md) corroborates
the existing review and adds no contradicting evidence. Key points used to strengthen the
review:

• Disambiguation: the target is the Arabidopsis PIN-FORMED1 auxin transporter (Q9C6B8,
  At1g73590), not the animal PIN1 prolyl isomerase; the 2022 cryo-EM study explicitly
  references Q9C6B8 ["demonstrates PIN1-mediated auxin (IAA) efflux and inhibitor (NPA)
  binding, matching the UniProt record provided"].
• Core MF: PIN1 "exports auxin from the cytosol toward the apoplast" via "a defined
  intracellular binding pocket that coordinates IAA" (apo/IAA-bound/NPA-bound inward-facing
  states); IAA Kd = 83 ± 10 µM vs NPA Kd = 0.15 ± 0.08 µM (ITC, pH 7.0), NPA a competitive
  inhibitor of the same site. Supports GO:0010329 (auxin efflux transmembrane transporter
  activity) and GO:0010315 (auxin export across the PM).
• Polar transport: polar PM distribution "determines the direction of auxin flow between
  neighboring cells"; PIN1 "frequently described as basally localized" in vascular tissue
  and root stele. Supports GO:0009926 (auxin polar transport) and GO:0009925 (basal PM).
• Transport mechanism: elevator-like alternating-access; energetics consistent with a
  uniport-like mechanism, though the in vivo energy source remains unresolved (no GO change
  warranted).
• Developmental output: "pin1 mutants exhibit severe organ initiation failures, producing
  'pin-like' stems with reduced or absent flowers/organs" — supports the non-core
  inflorescence/flower-development annotations.
• Regulation context (2023–2024): D6PK activates PIN1 transport; PID/WAG bias apical sorting;
  GNOM-dependent recycling and K63-ubiquitin/vacuolar turnover; phosphoinositide/CLE-peptide
  hubs and ENHANCER OF PINOID modulate PIN1 patterning. These reinforce (but do not change)
  the MARK_AS_OVER_ANNOTATED decisions on the bare protein-binding (GO:0005515) interactor rows.

No UNDECIDED actions were present and none were created; no new GO term with a verifiable ID
emerged from the report (the regulatory/interactor findings remain best captured by specific
interactor context rather than bare protein binding, consistent with existing decisions).
Status remains DRAFT.

Summary of decisions

• ACCEPT (core MF/BP/CC): auxin efflux transmembrane transporter activity (x2), auxin export across PM, auxin polar transport, auxin transport (x2), plasma membrane (multiple), transmembrane transport.
• ACCEPT non-core / homodimer: identical protein binding, protein homodimerization activity.
• KEEP_AS_NON_CORE: polar PM subdomains (apical/basal PM, apical part of cell, cell periphery), cytoplasm, plasmodesma, and all developmental BPs.
• MARK_AS_OVER_ANNOTATED: bare protein binding rows; plant-type cell wall.
• REMOVE: ER body (mis-assignment / wrong paper context).

PR #1417 review fix: bare-title supporting_text (2026-06-06)

Reviewer (ai4c-agent) flagged ~12 supporting_text entries that were merely the
publication TITLE rather than evidentiary excerpts. Each cited PMID was opened and
checked against the specific GO term claim.

Replaced title with a real verbatim quote (publication substantiates the claim):
- PMID:17237354 (GO:0005515, ABCB19/PGP19 interaction) — Y2H + coIP statement.
- PMID:20439545 (GO:0005886 plasma membrane) — "those PINs were localized in the plasma membrane...".
- PMID:36226797 (GO:0005515, SUE4 interaction) — "SUE4...interacts with the polar auxin transporter PIN1".
- PMID:22715043 (GO:0005515, FYPP1/3 interaction) — "FyPP1 and FyPP3 interact with a subset of PIN proteins...".
- PMID:17586653 (GO:0005515, RGLG2 interaction) — "RGLG2 and PIN1 can interact in the yeast two-hybrid system".
- PMID:15371311 (GO:0048825 cotyledon development) — pin1/pid disrupt cotyledon symmetry.
- PMID:16107478 (GO:0045177 apical part of cell) — PIN1 polarity in the apex.
- PMID:11060241 (GO:0048367 shoot system development) — pin1 organ-initiation/naked inflorescence.
- PMID:16601150 (GO:0009926 auxin polar transport, + same in core_functions[1]) — PINs mediate efflux in heterologous cells.
- PMID:36345646 (GO:0010262 somatic embryogenesis) — PIN-FORMED1 efflux drives PAT required for proembryo transition (full text).

Set to UNDECIDED (cited paper does NOT substantiate the claim / no usable PIN1-specific text):
- PMID:17889649 (GO:0005515, PID) — abstract reports PP2A/PINOID colocalization, not a PIN1-PID binding assay.
- PMID:20080776 (GO:0005515, PID) — states in vitro results do NOT support the site as a PID target; no PIN1-PID binding assay.
- PMID:15610358 (GO:0005737 cytoplasm) — generic GFP-fusion methods paper; no PIN1-specific localization.
- PMID:21533090 (GO:0009506 plasmodesma) — plasmodesmal proteome text does not mention PIN1 at all.
- PMID:18337510 (GO:0005886 plasma membrane) — ATI/actin/vesicle study; no PIN1 PM localization data in available text.
- PMID:19825598 (GO:0005886 plasma membrane) — about SCAR complex (BRK1/SCAR1) PM localization; PIN1 not mentioned.
- PMID:18539115 (GO:0005886 plasma membrane) — WOX2/WOX8 paper; PIN1 only as a reporter for auxin response, no PM localization.
- PMID:16971475 (GO:0010358 leaf shaping) — AS1/KNOX paper; PIN1 not mentioned.
- PMID:16943276 (GO:0010051 xylem/phloem patterning) — HVE/CAND1 paper explicitly states pathway involves "...but not...PIN1...".
- PMID:16141452 (GO:0009640 photomorphogenesis) — BR/PAT/tropism via PIN2 protein; no PIN1-specific photomorphogenesis evidence.
- PMID:16601150 (GO:0009630 gravitropism) — rate-limiting efflux paper; does not mention gravitropism.

Note: PIN1 plasma-membrane localization itself remains well supported by other rows
(PMID:33705718, PMID:35917925, PMID:20439545); the UNDECIDED PM rows reflect that those
particular citations don't substantiate localization, hence the validator's
"inconsistent review actions for GO:0005886" warning (expected/acceptable).
Status kept DRAFT; validation: ✓ Valid.

2026-10-05 update (auxin_polar_transport module curation)

• Resolved eight UNDECIDED rows. Several had been judged from abstract-only caches; per the curation policy experimental annotations are deferred to curators rather than rejected:
• leaf shaping (PMID:16971475) and xylem/phloem pattern formation (PMID:16943276): KEEP_AS_NON_CORE. The 16943276 abstract shows pin1 was among the mutants analysed PMID:16943276.
• photomorphogenesis TAS (PMID:16141452): supported by the full text PMID:16141452.
• plasmodesma HDA: KEEP_AS_NON_CORE; cytoplasm HDA: MARK_AS_OVER_ANNOTATED; gravitropism IMP (PMID:16601150, abstract-only): stays UNDECIDED.
• All GO:0005515 rows switched to REMOVE (repository policy: protein binding is uninformative; removal does not deny the interaction).
• Basal and apical plasma membrane rows upgraded to ACCEPT (core polar locations used in core_functions).
• 2026-10-06: gravitropism IMP (PMID:16601150) — Europe PMC reports no PMC/open-access full text; evidence not seen. Deferred to curator as KEEP_AS_NON_CORE (polar auxin transport is required for gravitropic responses). No UNDECIDED rows remain.

Polar auxin transport source audit — 2026-10-26

This dated audit supersedes conflicting earlier shorthand. All 45 original annotation payloads, including qualifiers and inherited NEW rows, were retained exactly. Every row was reconsidered against the target biology and cited sources. Actual Falcon and fallback provider attempts failed; the orchestration logs are preserved in .cache/module-audit-logs/auxin-polar-fetch/provider-publication-results.json. Existing provider reports, where present, served only as discovery aids. Manual primary-source inspection and normally fetched caches support the decisions below. No provider report was fabricated.

The core is direct plasma-membrane auxin efflux. PMID:35917925 resolves the transport pocket, inhibitor interaction and homodimer, but also observes monomeric particles; do not infer obligatory native dimer stoichiometry. Protein homodimerization is an integral structural property, not an automatically peripheral interaction. Polar localization is tissue/construct dependent. PMID:15514156 supports a PID-induced basal-to-apical shift, while the PIN1-GFP2 construct under the PIN2 promoter in PMID:33705718 is predominantly basal. Cellular export is distinct from the anatomical direction of transport.

Full PMID:36398993 was normally recovered from the publisher at publications/url_https___oup.silverchair-cdn.com_article-minimal_6833154.md. Its Arabidopsis pin1;2 and higher-order PIN root-regeneration genetics are real; pin1;2 has a reported 32% rooting reduction. Fig.7 ER-body localization is instead the C-terminal BIG fragment fused to mScarlet-i, compared with an ER-HDEL marker. Only the ER-body claim is rejected after target-resolved full-text inspection. The finding is not based on a tomato-focused title/abstract. Live GO:0010168 refers to the specialized ER-derived body, not the general ER organelle.

Cytoplasm HDA is retained as contextual: cytoplasm is not synonymous with soluble cytosol and PIN1 intracellular trafficking independently corroborates a cytoplasmic membrane pool. The cell-wall IDA remains UNDECIDED after the accessible abstract and unsuccessful full-PDF retrieval; plasma-membrane localization does not establish exclusion. Plasmodesmata HDA is retained non-core using the actual PMID:21533090 Table S1 raw identification: AT1G73590.1, Excel row 1345, two unique peptides, 4.34% coverage. The fraction is enriched, not pure; no exclusive plasmodesmatal residence or function is inferred. Reproducible shared analysis is in ../ABCB1/ABCB1-source-analysis/. Imported GO Table S3 is not evidence. Reversed FYPP accessions in old prose were removed; actual FYPP1/FYPP3 interaction evidence remains.

Final actions: 15 ACCEPT, 15 KEEP_AS_NON_CORE, 6 MODIFY, 8 REMOVE, 1 UNDECIDED. This panel contains no negated source rows; there are no manufactured NOT assertions. Exact-row payload proof and focused validation are recorded in .cache/module-audit-logs/auxin-polar-six-*. Reciprocal scientific consultation with the parallel annotation reviewer confirmed source-specific localization, integral binding and substrate-assay distinctions.