AUX1 (AUXIN RESISTANT 1) — curation notes

UniProt: Q96247 (AUX1_ARATH); locus AT2G38120; synonyms AUX, PIR1, WAV5.
Family: amino acid/polyamine transporter 2 family; amino acid/auxin permease
(AAAP) subfamily (TC 2.A.18.1). 485 aa, multi-pass (≈11 TM helices) integral
membrane protein. Founding member of the AUX1/LAX auxin influx carrier family
(AUX1, LAX1, LAX2, LAX3).

Core molecular function: auxin influx transporter

• Heterologous expression in Xenopus oocytes confers saturable, pH-dependent
  high-affinity uptake of 3H-IAA; reduced by 2,4-D and 1-NOA; function-abrogating
  mutations reduce uptake PMID:16677815
  PMID:16677815
• Direct binding of IAA to AUX1 (baculovirus/insect cell membranes), Kd ≈ 2.6 µM,
  matching transport Km; auxin analogues/influx inhibitors displace IAA
  PMID:18614710
• Mechanism: IAA-H+ symporter (proton-driven), pH optimum 5.0–6.0
  PMID:18614710 UniProt KW "Symport" maps to GO:0015293 symporter activity (DR
  line in uniprot.txt).
• UniProt FUNCTION: "Carrier protein involved in proton-driven auxin influx."

GO terms (verified in GOA / UniProt entry)

• GO:0010328 auxin influx transmembrane transporter activity (IDA, PMID:16677815) — CORE MF
• GO:0010011 auxin binding (IDA, PMID:18614710) — ACCEPT
• GO:0060919 auxin import into cell (IEA inferred from GO:0010328) — ACCEPT, core BP
• GO:0009926 auxin polar transport (TAS, PMID:16839804) — ACCEPT, core BP
• GO:0015293 symporter activity — added as NEW (mechanism), from UniProt KW DR line

Substrate specificity caveat (amino acid transport)

AUX1 is homologous to amino acid permeases, which seeded amino-acid-transport
annotations, but the only demonstrated physiological substrate is auxin (IAA).
PMID:8688077
No experimental amino acid transport demonstrated. Therefore:
- GO:0015171 amino acid transmembrane transporter activity (ISS, PMID:9484486) — MARK_AS_OVER_ANNOTATED. NB the cited PMID:9484486 is actually a study of aux1 mRNA processing / nonsense-mediated decay, not amino acid transport.
- GO:0003333 amino acid transmembrane transport (IEA, inferred from GO:0015171) — MARK_AS_OVER_ANNOTATED.

Subcellular localization

• Functional site = plasma membrane (multi-pass), asymmetric/polar in protophloem
  PMID:11641271; IDA PM also in PMID:16690816.
  GO:0005886 plasma membrane — ACCEPT (IEA, ISM, IDA copies).
• GO:0009986 cell surface (IDA, PMID:11641271) — MODIFY → GO:0005886 (data support
  plasma membrane; cell surface is the less precise/external term).
• Endosome (GO:0005768) and Golgi (GO:0005794), IDA PMID:17114355 — KEEP_AS_NON_CORE:
  these are trafficking-itinerary pools, not the functional transport site.
  AUX1 trafficking is BFA-insensitive, actin-dependent, GNOM-independent, distinct
  from PIN PMID:17114355
• Trafficking to PM requires ER protein AXR4 PMID:16690816

Protein interaction

GO:0005515 protein binding (IPI, PMID:32612234), WITH/FROM UniProtKB:Q9FZ33 = AXR4.
PMID:32612234 is a large-scale phytohormone interactome (>2000 binary PPIs). Bare
"protein binding" is uninformative; the biology (AXR4 = ER chaperone for AUX1
trafficking) is captured elsewhere. Action: REMOVE.

Developmental / physiological roles (downstream of transport; KEEP_AS_NON_CORE except gravitropism)

• GO:0009958 positive gravitropism (IMP, PMID:8688077) — ACCEPT, core process.
  Gene named for agravitropic aux1 root phenotype PMID:8688077 PMID:11641271
• GO:0010311 lateral root formation (IGI PMID:18622388; IMP PMID:17215297) —
  KEEP_AS_NON_CORE; LAX3 redundancy and lateral root positioning correlate with
  gravitropic waving PMID:17215297
• GO:0001736 establishment of planar polarity & GO:0048765 root hair cell
  differentiation (IGI PMID:17084699) — KEEP_AS_NON_CORE; combinatorial AUX1+EIN2+
  GNOM shape auxin gradient for root hair positioning PMID:17084699
• GO:0048829 root cap development (IMP PMID:19952011) — KEEP_AS_NON_CORE; AUX1/LAX
  redundant in embryonic root cap patterning PMID:19952011
• GO:0010262 somatic embryogenesis (IEP + IMP, PMID:36345646) — KEEP_AS_NON_CORE;
  AUX1/LAX influx + PIN1 efflux drive polar auxin transport in SE PMID:36345646
• GO:0009624 response to nematode (HEP, PMID:16478044) — MARK_AS_OVER_ANNOTATED;
  AUX1 only shows altered expression in nematode galls, no functional requirement
  shown PMID:16478044

Action summary

ACCEPT: 6 (GO:0005886 IEA, GO:0060919, GO:0010011, GO:0010328, GO:0009958,
GO:0009926, GO:0005886 ISM, GO:0005886 IDA) — note 3 PM copies + gravitropism +
transporter MF + auxin import + auxin binding + polar transport.
KEEP_AS_NON_CORE: somatic embryogenesis x2, root cap development, lateral root x2,
planar polarity, root hair, endosome, Golgi.
MARK_AS_OVER_ANNOTATED: amino acid transport (BP), amino acid transporter (MF),
response to nematode.
MODIFY: cell surface → plasma membrane.
REMOVE: protein binding.
NEW: symporter activity (GO:0015293, mechanism).

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

A Falcon deep-research report (AUX1-deep-research-falcon.md) was generated and
used to augment the review with file:ARATH/AUX1/AUX1-deep-research-falcon.md
supporting_text entries. Key corroborations (no decisions weakened):

• Core MF / auxin import / polar transport: "Direct functional evidence from
  heterologous expression in Xenopus oocytes demonstrates that AUX1 transports
  IAA with high affinity and saturable kinetics" (Yang 2006); AUX1/LAX are
  "major auxin influx carriers required to establish auxin gradients that drive
  development."
• Symporter (NEW GO:0015293) mechanism reinforced: AUX1 "operates as a
  proton-coupled symporter (H+:IAA−)"; commonly cited stoichiometry 2 H+ per IAA−
  (Singh 2018 review). Supports the NEW symporter annotation and the proposed
  auxin:proton symporter term.
• Auxin binding (GO:0010011): Kd ≈ 2.6 µM, Bmax ≈ 11,800 fmol/mg, binding optimum
  pH 5–6 (Carrier 2008), matching transport Km.
• Plasma membrane localization confirmed (EYFP-AUX1).
• AXR4 = ER accessory/chaperone-like factor; in axr4, AUX1 accumulates in the ER
  rather than reaching the PM; AXR4 physically interacts with AUX1 and reduces
  AUX1 aggregation dose-dependently (Tidy et al. 2024, Plant Physiol,
  doi:10.1093/plphys/kiad506). This 2024 mechanistic study reinforces REMOVE of
  the bare protein binding term (AXR4 interaction reflects trafficking/chaperone
  biology, not AUX1's own MF) and the KEEP_AS_NON_CORE Golgi/endosome trafficking
  pools.
• Gravitropism (core): AUX1 moves auxin from lateral root cap to elongation-zone
  epidermis (Tang 2024 review).
• Lateral root: aux1 mutants ~50% reduction in emerged lateral roots; root hair:
  ~30-fold higher double-hair frequency, shorter root hairs (Swarup & Péret 2012)
  — corroborate KEEP_AS_NON_CORE developmental roles.

No new GO IDs were introduced from the deep research (the only NEW term,
GO:0015293, was already present from the UniProt KW DR line). The amino-acid
transport annotations remain MARK_AS_OVER_ANNOTATED: the report consistently
identifies IAA (not amino acids) as the demonstrated substrate while placing AUX1
in the AAAP superfamily, supporting the over-annotation call. No UNDECIDED
actions were present to resolve. status kept DRAFT.

Notes on resources

All 15 cited PMIDs are cached under publications/. A Falcon deep-research report
is now available (AUX1-deep-research-falcon.md + ..._artifacts/artifact-00.md).
Recent cryo-EM structures of AUX1 exist (PDB 9JDR, 9M2H) per the UniProt entry but
the structure papers were not in the cached set, so not cited.

Polar auxin transport source audit — 2026-10-26

This dated audit supersedes conflicting earlier shorthand. All 23 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 directly supported core remains auxin influx, with pH-dependent uptake and proton-coupling mechanism separated from a measured integer stoichiometry. PMID:16677815 reports “saturable, pH-dependent uptake of 3H-IAA”. New target structural studies PMID:40378849 and PMID:40579814 were available as abstracts; PMID:40720658 was read in full. The latter states “These results confirm AUX1 as a direct mediator of active auxin influx.” His249 protonation/deprotonation supports a coupling model, not an experimentally determined H+:IAA ratio. Structural constructs and their assays are distinguished from native root physiology; no family-wide stoichiometry is asserted.

Amino-acid transport MF/BP remain UNDECIDED: AAAP membership is not enough to assign a substrate, but positive IAA assays do not exclude an additional amino-acid capacity. The recovered sources did not provide an exact-target amino-acid negative assay. This corrects the prior categorical overpropagation rationale without fabricating an ancestral loss.

The nematode response is a contextual, redundant transport contribution supported independently by PMID:21156858: “We observed no decrease in H. schachtii infectivity in aux1 and lax3 single mutants.” The double and quadruple carrier mutants are affected. The effector-binding experiment in that source concerns LAX3, not AUX1. Golgi residence is retained separately from plasma-membrane transport; root-organelle claims were not narrowed merely to the dominant membrane location. The inherited proton-symport NEW is retained, not newly manufactured by this audit.

Final actions: 8 ACCEPT, 10 KEEP_AS_NON_CORE, 1 MODIFY, 1 NEW, 1 REMOVE, 2 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.