id: Q96247
gene_symbol: AUX1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
description: >-
  AUX1 (AUXIN RESISTANT 1) is a multi-pass plasma membrane protein of the amino
  acid/auxin permease (AAAP) family and the founding member of the AUX1/LAX
  family of auxin influx carriers in Arabidopsis thaliana. It acts as a
  high-affinity, proton-driven secondary active transporter (an IAA-H+
  symporter) that mediates cellular uptake of the natural auxin indole-3-acetic
  acid (IAA) and synthetic auxins such as 2,4-D and 1-NAA. By importing auxin
  into specific cells, AUX1 helps establish and maintain the directional (polar)
  auxin gradients that pattern plant growth. AUX1 is expressed in root and shoot
  apical tissues; in the root apex it is found in protophloem, columella,
  lateral root cap, and epidermal cells, where it loads and unloads auxin to
  deliver the hormone to the root meristem and to the elongation zone. Through
  this transport activity AUX1 is required for root gravitropism, root hair
  development, lateral root initiation and emergence, phyllotaxis, embryonic
  root patterning, and other auxin-dependent developmental processes. AUX1
  protein traffics to the plasma membrane via a brefeldin A-insensitive,
  actin-dependent pathway distinct from PIN proteins and depends on the
  endoplasmic-reticulum accessory protein AXR4 for correct targeting. AUX1 binds
  IAA directly with a Kd of about 2.6 microM, consistent with its measured
  transport Km.
existing_annotations:
- term:
    id: GO:0003333
    label: amino acid transmembrane transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  qualifier: involved_in
  review:
    summary: >-
      This term is an inter-ontology inference from the molecular function
      GO:0015171 (amino acid transmembrane transporter activity). AUX1 belongs
      to the amino acid/auxin permease family and is sequence-similar to amino
      acid permeases, but its physiologically demonstrated substrate is the
      auxin IAA, not amino acids. No experimental evidence shows AUX1 transports
      amino acids.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation is a logical-inference IEA derived from a homology-based
      molecular function term (GO:0015171). All experimental characterization
      (heterologous transport in oocytes, direct IAA binding) demonstrates auxin
      import, not amino acid transport. The amino acid transport process is a
      family-level inference, not an established AUX1 function, so it
      over-annotates the gene.
    supported_by:
    - reference_id: PMID:16677815
      supporting_text: Upon expression of AUX1 in Xenopus oocytes, saturable,
        pH-dependent uptake of 3H-IAA was measured.
    - reference_id: PMID:8688077
      supporting_text: Polypeptide sequence similarity to amino acid permeases
        suggests that AUX1 mediates the transport of an amino acid-like
        signaling molecule.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: Direct functional evidence from heterologous expression in
        **Xenopus oocytes** demonstrates that AUX1 transports **IAA** with high
        affinity and saturable kinetics.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      AUX1 is a multi-pass integral plasma membrane protein, established by
      experimental localization in root cells. This UniProt subcellular-location
      mapping is consistent with the curated Cell membrane location.
    action: ACCEPT
    reason: >-
      Plasma membrane localization is well supported experimentally
      (PMID 11641271, PMID 16690816, PMID 17114355) and is the functional
      compartment where AUX1 imports auxin. The IEA mapping is correct.
    supported_by:
    - reference_id: PMID:11641271
      supporting_text: AUX1, asymmetrically localized to the plasma membrane of
        root protophloem cells, is proposed to promote the acropetal,
        post-phloem movement of auxin to the root apex.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: AUX1 localizes to the **plasma membrane** in heterologous
        expression (EYFP-AUX1 in oocytes), where it mediates pH-dependent,
        saturable IAA uptake.
- term:
    id: GO:0060919
    label: auxin import into cell
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  qualifier: involved_in
  review:
    summary: >-
      This biological-process term is inferred from the molecular function
      GO:0010328 (auxin influx transmembrane transporter activity) and exactly
      captures the core role of AUX1 - importing auxin (IAA) into cells. It is
      strongly supported by direct experimental transport data.
    action: ACCEPT
    reason: >-
      Auxin import into cells is the defining function of AUX1, demonstrated by
      saturable pH-dependent 3H-IAA uptake in AUX1-expressing oocytes and by
      impaired IAA accumulation in aux1 mutant root apices. The inter-ontology
      inference is biologically accurate and represents a core function.
    supported_by:
    - reference_id: PMID:16677815
      supporting_text: Upon expression of AUX1 in Xenopus oocytes, saturable,
        pH-dependent uptake of 3H-IAA was measured.
    - reference_id: PMID:11641271
      supporting_text: MS analysis shows that IAA accumulation in aux1 mutant root
        apices is impaired, consistent with an AUX1 phloem unloading function.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: the dominant **regulated cellular uptake** is via **influx
        carriers** such as AUX1/LAX proteins. Reviews emphasize that AUX1/LAX
        transporters are **major auxin influx carriers** required to establish
        auxin gradients that drive development.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32612234
  qualifier: enables
  review:
    summary: >-
      This generic protein binding annotation derives from a large-scale
      phytohormone interactome screen; the WITH/FROM partner is UniProtKB:Q9FZ33
      (AXR4), the ER accessory protein required for AUX1 trafficking to the
      plasma membrane. The term protein binding is uninformative about molecular
      function.
    action: REMOVE
    reason: >-
      GO:0005515 protein binding is too generic to convey a meaningful molecular
      function and is discouraged as a core annotation. The biologically
      relevant interaction (AUX1 with AXR4) reflects a chaperone/trafficking
      relationship rather than the activity of AUX1 itself, and is better
      represented by the trafficking biology described in PMID:16690816 than by
      a bare binding term.
    supported_by:
    - reference_id: PMID:32612234
      supporting_text: we experimentally generated a systems-level map of the
        Arabidopsis phytohormone signalling network, consisting of more than
        2,000 binary protein-protein interactions.
    - reference_id: PMID:16690816
      supporting_text: AXR4 is a previously unidentified accessory protein of the
        endoplasmic reticulum (ER) that regulates localization of AUX1 but not of
        PIN proteins.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: The 2024 study provides biochemical evidence that AXR4
        **physically interacts** with AUX1 and **reduces AUX1 aggregation in a
        dose-dependent fashion**, supporting a model in which AXR4 functions as
        an **ER accessory/chaperone-like factor** enabling proper folding/ER exit
        and plasma-membrane targeting of AUX1.
- term:
    id: GO:0010262
    label: somatic embryogenesis
  evidence_type: IEP
  original_reference_id: PMID:36345646
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      AUX1 (as part of the AUX1/LAX influx carrier system together with PIN
      efflux carriers) contributes to polar auxin transport required for somatic
      embryo development. This is an auxin-transport-dependent developmental
      process, peripheral to the core transport function of AUX1 and involving
      redundancy with LAX/PIN family members.
    action: KEEP_AS_NON_CORE
    reason: >-
      The paper shows that polar auxin transport, with AUX1/LAX influx and PIN1
      efflux carriers as drivers, is required for the transition of embryonic
      cells to proembryos and later differentiation. This is a legitimate
      downstream developmental role but is a pleiotropic consequence of AUX1
      transport activity rather than a core molecular function, and is shared
      redundantly across the family.
    supported_by:
    - reference_id: PMID:36345646
      supporting_text: polar auxin transport, with AUXIN/LIKE-AUX influx and
        PIN-FORMED1 efflux carriers as important drivers, is required for the
        transition of embryonic cells to proembryos and, later, for correct cell
        fate specification and differentiation.
- term:
    id: GO:0010262
    label: somatic embryogenesis
  evidence_type: IMP
  original_reference_id: PMID:36345646
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      Duplicate of the somatic embryogenesis annotation from the same study,
      here with mutant-phenotype evidence. AUX1/LAX-mediated auxin import
      contributes to somatic embryo development as part of polar auxin transport.
    action: KEEP_AS_NON_CORE
    reason: >-
      Same rationale as the IEP annotation from the same study (PMID:36345646),
      a genuine but peripheral, redundantly shared developmental role downstream
      of AUX1 auxin transport activity. Retained as non-core. Duplicate terms
      with different evidence codes are acceptable.
    supported_by:
    - reference_id: PMID:36345646
      supporting_text: the stronger embryo defects observed after combining
        mutations in influx and efflux carriers indicate a cooperative function
        between auxin influx and efflux carriers in controlling embryo
        development
- term:
    id: GO:0009624
    label: response to nematode
  evidence_type: HEP
  original_reference_id: PMID:16478044
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      This annotation is based on a microarray survey reporting that AUX1 (among
      50 transporter genes) showed altered expression upon root-knot nematode
      infestation. It reflects transcriptional regulation of AUX1 in response to
      nematodes, not a demonstrated functional role of AUX1 in the response.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The evidence is expression-pattern (HEP) data from a transcriptomic screen
      of nematode-induced galls; the study did not test whether AUX1 is required
      for the nematode response. An expression change does not establish
      involvement in the biological process, so this is an over-annotation of a
      correlative observation.
    supported_by:
    - reference_id: PMID:16478044
      supporting_text: Expression of 50 transporter genes from 18 different gene
        families was significantly changed upon nematode infestation.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: ISM
  original_reference_id: GO_REF:0000122
  qualifier: located_in
  review:
    summary: >-
      Computational (AtSubP) prediction of plasma membrane localization,
      consistent with the experimentally established multi-pass plasma membrane
      location of AUX1.
    action: ACCEPT
    reason: >-
      Although the evidence is a sequence-based prediction (ISM), it agrees with
      direct experimental localization data (PMID:11641271, PMID:16690816) and
      with the multi-pass transmembrane topology of the protein. Correct, if
      redundant with the experimental plasma membrane annotations.
    supported_by:
    - reference_id: PMID:16690816
      supporting_text: Loss of AXR4 resulted in abnormal accumulation of AUX1 in
        the ER of epidermal cells, indicating that the axr4 agravitropic
        phenotype is caused by defective AUX1 trafficking in the root epidermis.
- term:
    id: GO:0048829
    label: root cap development
  evidence_type: IMP
  original_reference_id: PMID:19952011
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      aux1 lax mutants have enlarged radicle root caps with altered columella
      cell number, size and organization, indicating that AUX1/LAX auxin influx
      carriers act redundantly in establishing embryonic root cap cell pattern.
      AUX1 contributes within this auxin-transport-dependent developmental
      process.
    action: KEEP_AS_NON_CORE
    reason: >-
      Mutant phenotype evidence supports a role in root cap / embryonic root
      organization, but the effect is largely redundant within the AUX1/LAX
      family (strong defects require quadruple mutants) and is a developmental
      consequence of AUX1 auxin import activity rather than a distinct core
      function.
    supported_by:
    - reference_id: PMID:19952011
      supporting_text: aux1 lax mutants have a larger radicle root cap than the
        wild type and this is associated with a significant increase in the
        root-cap cell number, average cell size, or both.
- term:
    id: GO:0010011
    label: auxin binding
  evidence_type: IDA
  original_reference_id: PMID:18614710
  qualifier: enables
  review:
    summary: >-
      AUX1 expressed in baculovirus-infected insect cell membranes binds IAA
      directly with a Kd of about 2.6 microM, comparable to its transport Km.
      Auxin analogues and influx inhibitors specifically displace IAA,
      confirming direct, specific binding of the auxin substrate.
    action: ACCEPT
    reason: >-
      Direct assay evidence demonstrates specific binding of the transport
      substrate IAA to AUX1. This is a genuine molecular function reflecting the
      initial substrate-recognition event of the transport cycle and supports the
      transporter activity annotation.
    supported_by:
    - reference_id: PMID:18614710
      supporting_text: These membranes proved suitable for determination of the
        binding of IAA to AUX1 and enabled us to determine a K(d) of 2.6 mum,
        comparable with estimates for the K(m) for IAA transport.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: Binding assays yielded a reported **Kd ≈ 2.6 µM** and **Bmax
        ≈ 11,800 fmol IAA/mg membrane protein**, with **maximal specific binding
        around pH 5–6**.
- term:
    id: GO:0010311
    label: lateral root formation
  evidence_type: IGI
  original_reference_id: PMID:18622388
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      AUX1 functions with its paralog LAX3 in auxin influx that promotes lateral
      root development; LAX3 acts in cortical/epidermal cells overlaying
      primordia to promote emergence, while AUX1 contributes to lateral root
      formation through auxin distribution. Genetic interaction within the
      AUX1/LAX family.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supported by genetic-interaction evidence within the auxin influx carrier
      family. Lateral root formation is a real developmental output of
      AUX1-mediated auxin transport but is a downstream, partly redundant role
      rather than the core molecular function of AUX1.
    supported_by:
    - reference_id: PMID:18622388
      supporting_text: Auxin induces the expression of a previously
        uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells
        directly overlaying new primordia.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: '**aux1 mutants show ~50% reduction in emerged lateral
        roots**, supporting AUX1-mediated auxin uptake as a quantitative
        determinant of LR development.'
- term:
    id: GO:0001736
    label: establishment of planar polarity
  evidence_type: IGI
  original_reference_id: PMID:17084699
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      Combinatorial action of AUX1, EIN2 and GNOM provides vectorial information
      for planar polarity of root hair positioning; the auxin gradient is
      abolished in aux1 ein2 gnom triple mutants. AUX1 contributes by shaping the
      auxin gradient through its import activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genetic-interaction evidence supports a role in coordinating root
      epidermal planar polarity via auxin gradient formation. This is a
      developmental consequence of AUX1 auxin transport acting together with
      other genes, not a distinct core function of AUX1.
    supported_by:
    - reference_id: PMID:17084699
      supporting_text: combinatorial action of the auxin influx carrier AUX1,
        ETHYLENE-INSENSITIVE2 (EIN2), and GNOM genes mediates the vector for
        coordinate hair positioning.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: aux1 mutants have **shorter root hairs** (rescuable by
        exogenous auxin) and show **~30-fold higher frequency of double-hair
        formation**, indicating disrupted epidermal patterning/polarity.
- term:
    id: GO:0048765
    label: root hair cell differentiation
  evidence_type: IGI
  original_reference_id: PMID:17084699
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      In aux1 ein2 gnom mutants, root hair positioning switches from polar to
      axial and the auxin gradient is lost, indicating AUX1 acts with EIN2 and
      GNOM in patterning root hair cells. The annotation captures the role of
      AUX1 in root hair development via auxin gradient formation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supported by genetic interaction data showing AUX1 contributes to root
      hair cell polarity/positioning. This is a developmental output of AUX1
      auxin import, peripheral to its core transport function. (UniProt also
      notes AUX1 involvement in trichoblast polarization and root hair
      elongation.)
    supported_by:
    - reference_id: PMID:17084699
      supporting_text: In aux1;ein2;gnom eb triple mutant roots, hairs display
        axial (apical or basal) instead of coordinate polar (basal) position
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: The AUX/LAX overview reports AUX1 expression in **epidermal
        non-hair cells** and links AUX1 to root hair development and planar
        polarity.
- term:
    id: GO:0010328
    label: auxin influx transmembrane transporter activity
  evidence_type: IDA
  original_reference_id: PMID:16677815
  qualifier: enables
  review:
    summary: >-
      Heterologous expression of AUX1 in Xenopus oocytes confers saturable,
      pH-dependent high-affinity 3H-IAA uptake that is reduced by 2,4-D and
      1-NOA and by mutations that abrogate AUX1 function in planta. This directly
      demonstrates that AUX1 is an auxin influx transmembrane transporter and is
      the core molecular function.
    action: ACCEPT
    reason: >-
      This is the central, experimentally validated molecular function of AUX1.
      Direct transport assays in a heterologous system, plus the
      genotype-phenotype concordance of transport-abrogating mutations, provide
      strong IDA support. Represents the core function of the gene.
    supported_by:
    - reference_id: PMID:16677815
      supporting_text: Mutations in AUX1 that abrogate physiological responses to
        IAA in planta resulted in loss or reduction of 3H-IAA uptake in
        AUX1-expressing oocytes.
    - reference_id: PMID:16677815
      supporting_text: The measured Km for AUX1-mediated uptake of 3H-IAA was at
        concentrations at which physiological responses are observed for
        exogenously added IAA and 2,4-D.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: Direct functional evidence from heterologous expression in
        **Xenopus oocytes** demonstrates that AUX1 transports **IAA** with high
        affinity and saturable kinetics.
- term:
    id: GO:0015171
    label: amino acid transmembrane transporter activity
  evidence_type: ISS
  original_reference_id: PMID:9484486
  qualifier: enables
  review:
    summary: >-
      This molecular function is assigned by sequence similarity (ISS): AUX1
      belongs to the amino acid/auxin permease (AAAP) family and resembles amino
      acid permeases. However, the demonstrated substrate is auxin (IAA), not
      amino acids; no experimental data show AUX1 transports amino acids. The
      cited reference (a study of aux1 mRNA processing) does not establish amino
      acid transport.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation rests on family-level homology to amino acid permeases, but
      all functional evidence identifies IAA as the physiological substrate. The
      substrate-specific term GO:0010328 (auxin influx transmembrane transporter
      activity) is the accurate molecular function. Retained but flagged as an
      over-annotation, since the broad permease relationship is real while amino
      acid transport activity has not been demonstrated.
    supported_by:
    - reference_id: PMID:8688077
      supporting_text: Indole-3-acetic acid, the major form of auxin in higher
        plants, is structurally similar to tryptophan and is a likely substrate
        for the AUX1 gene product.
    - reference_id: PMID:16677815
      supporting_text: Upon expression of AUX1 in Xenopus oocytes, saturable,
        pH-dependent uptake of 3H-IAA was measured.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: as an **auxin influx carrier** (auxin transporter protein
        1) in the **AUX/LAX family** within the **AAAP (amino acid/auxin
        permease) superfamily**
- term:
    id: GO:0009958
    label: positive gravitropism
  evidence_type: IMP
  original_reference_id: PMID:8688077
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      aux1 mutations abolish root gravitropic curvature and confer
      auxin-resistant root growth; AUX1 is expressed in root apical tissues that
      regulate gravitropic curvature. AUX1-facilitated auxin uptake into distal
      elongation zone tissues is required for the differential growth underlying
      root gravitropism.
    action: ACCEPT
    reason: >-
      Strong mutant-phenotype evidence establishes that AUX1 is required for root
      (positive) gravitropism, the phenotype for which the gene was named. This
      is a well-characterized, biologically central output of AUX1 auxin
      transport and is appropriately retained as a core process annotation.
    supported_by:
    - reference_id: PMID:8688077
      supporting_text: Mutations within the AUX1 gene confer an auxin-resistant
        root growth phenotype and abolish root gravitropic curvature.
    - reference_id: PMID:11641271
      supporting_text: AUX1 is necessary for root gravitropism by facilitating
        basipetal auxin transport to distal elongation zone tissues.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: AUX1 is essential for gravitropism and mediates auxin
        movement from the **lateral root cap to the epidermis of the elongation
        zone**, enabling differential growth during bending
- term:
    id: GO:0010311
    label: lateral root formation
  evidence_type: IMP
  original_reference_id: PMID:17215297
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      Lateral roots are spaced along the primary root in a regular pattern that
      correlates with gravity-induced waving and depends on AUX1; AUX1
      contributes to auxin-dependent priming of pericycle cells for lateral root
      initiation. Mutant-phenotype evidence links AUX1 to lateral root
      positioning/formation.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a duplicate lateral root formation term (here IMP from a
      positioning study) supporting a real developmental role of AUX1 downstream
      of its auxin transport activity. Retained as non-core, consistent with the
      IGI lateral-root annotation.
    supported_by:
    - reference_id: PMID:17215297
      supporting_text: lateral roots are spaced along the main axis in a regular
        left-right alternating pattern that correlates with gravity-induced
        waving and depends on AUX1, an auxin influx carrier essential for
        gravitropic response.
- term:
    id: GO:0009986
    label: cell surface
  evidence_type: IDA
  original_reference_id: PMID:11641271
  qualifier: located_in
  review:
    summary: >-
      AUX1 is an integral plasma membrane protein, asymmetrically localized to
      the plasma membrane of root protophloem cells. The cited study establishes
      plasma membrane localization; cell surface (GO:0009986) is a less precise
      rendering of the curated plasma membrane location.
    action: MODIFY
    reason: >-
      The experimental evidence supports plasma membrane localization rather than
      the more generic/loosely defined cell surface term. GO:0009986 (cell
      surface) refers to the external side/region of the cell surface and is not
      the most accurate description of a multi-pass integral membrane transporter.
      Replace with the plasma membrane term that the same data support.
    proposed_replacement_terms:
    - id: GO:0005886
      label: plasma membrane
    supported_by:
    - reference_id: PMID:11641271
      supporting_text: AUX1, asymmetrically localized to the plasma membrane of
        root protophloem cells, is proposed to promote the acropetal,
        post-phloem movement of auxin to the root apex.
- term:
    id: GO:0005768
    label: endosome
  evidence_type: IDA
  original_reference_id: PMID:17114355
  qualifier: located_in
  review:
    summary: >-
      Live-cell imaging shows AUX1 resides at the apical plasma membrane and at
      highly dynamic subpopulations of Golgi apparatus and endosomes in all cell
      types, with PM and intracellular pools interconnected by actin-dependent
      constitutive trafficking. The endosomal pool reflects AUX1 trafficking
      rather than its functional transport site.
    action: KEEP_AS_NON_CORE
    reason: >-
      Direct imaging evidence supports endosomal localization as part of the
      constitutive trafficking itinerary of AUX1. It is a genuine location but
      represents the trafficking route to/from the plasma membrane, not the site
      where AUX1 performs auxin import. Retained as non-core.
    supported_by:
    - reference_id: PMID:17114355
      supporting_text: AUX1 resides at the apical plasma membrane of protophloem
        cells and at highly dynamic subpopulations of Golgi apparatus and
        endosomes in all cell types.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: in **axr4** mutants AUX1 is retained/accumulates in the
        **endoplasmic reticulum (ER)** rather than reaching the plasma membrane.
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: PMID:17114355
  qualifier: located_in
  review:
    summary: >-
      Same live-cell imaging study shows AUX1 in dynamic subpopulations of the
      Golgi apparatus, interconnected with the plasma membrane pool by
      actin-dependent trafficking. The Golgi pool reflects the
      biosynthetic/trafficking route rather than the functional site of auxin
      transport.
    action: KEEP_AS_NON_CORE
    reason: >-
      Direct imaging supports a Golgi-associated pool of AUX1 as part of its
      trafficking pathway. Legitimate localization but peripheral to the
      functional plasma membrane site of auxin import; retained as non-core.
    supported_by:
    - reference_id: PMID:17114355
      supporting_text: AUX1 resides at the apical plasma membrane of protophloem
        cells and at highly dynamic subpopulations of Golgi apparatus and
        endosomes in all cell types.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: AUX1 (and LAX2) maturation and delivery to the plasma
        membrane.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:16690816
  qualifier: located_in
  review:
    summary: >-
      AUX1 normally localizes to the plasma membrane; loss of the ER accessory
      protein AXR4 causes abnormal AUX1 accumulation in the ER, demonstrating
      that correct AUX1 plasma membrane targeting is AXR4-dependent. Direct
      experimental support for plasma membrane localization.
    action: ACCEPT
    reason: >-
      Direct assay evidence (IDA) for the functional plasma membrane location of
      AUX1, the compartment where it imports auxin. Core localization; duplicate
      of the IEA/ISM plasma membrane annotations with stronger experimental
      backing.
    supported_by:
    - reference_id: PMID:16690816
      supporting_text: Loss of AXR4 resulted in abnormal accumulation of AUX1 in
        the ER of epidermal cells, indicating that the axr4 agravitropic
        phenotype is caused by defective AUX1 trafficking in the root epidermis.
- term:
    id: GO:0009926
    label: auxin polar transport
  evidence_type: TAS
  original_reference_id: PMID:16839804
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      AUX1 is one of the carrier proteins that mediate carrier-based polar auxin
      transport, contributing the influx (uptake) component alongside PIN efflux
      carriers. The review (TAS) places AUX1 within the polar auxin transport
      system that establishes directional auxin fluxes in the root apex.
    action: ACCEPT
    reason: >-
      The auxin import activity of AUX1 is an integral part of carrier-mediated
      polar auxin transport; this process annotation accurately reflects its
      contribution to directional auxin movement. Well supported by the transport
      literature and represents a core biological process for AUX1.
    supported_by:
    - reference_id: PMID:16839804
      supporting_text: Auxin moves between plant cells through a combination of
        membrane diffusion and carrier-mediated transport. Several classes of
        membrane proteins that facilitate auxin uptake and efflux have recently
        been identified in Arabidopsis.
    - reference_id: PMID:11641271
      supporting_text: AUX1, asymmetrically localized to the plasma membrane of
        root protophloem cells, is proposed to promote the acropetal,
        post-phloem movement of auxin to the root apex.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: AUX1/LAX transporters are **major auxin influx carriers**
        required to establish auxin gradients that drive development.
- term:
    id: GO:0015293
    label: symporter activity
  evidence_type: IEA
  original_reference_id: PMID:18614710
  qualifier: enables
  review:
    summary: >-
      AUX1 is an IAA-H+ symporter; its auxin uptake is proton-driven and
      pH-dependent, with a binding/transport pH optimum consistent with
      co-transport of protons with the dissociated IAA anion. UniProt assigns the
      Symport keyword and GO:0015293 (symporter activity). This mechanistic
      molecular function complements the substrate-specific auxin influx
      transporter term and is not present among the curated GOA annotations.
    action: NEW
    reason: >-
      The proton-coupled symport mechanism is well established for AUX1 (pH
      dependence of transport and binding; AUX/LAX proteins act as IAA-H+
      symporters) and is reflected in the UniProt Symport keyword (GO:0015293 via
      UniProtKB-KW in the UniProt entry). Adding it makes the co-transport
      mechanism explicit. GO ID taken from the UniProt GO cross-reference lines
      for this entry.
    supported_by:
    - reference_id: PMID:18614710
      supporting_text: Members of the AUX/LAX family of membrane transporters,
        conserved in all higher plant species, are believed to act as IAA-H +
        symporters.
    - reference_id: PMID:18614710
      supporting_text: The pH optimum for specific binding was observed between pH
        5.0 and 6.0, where IAA would be expected to be 60% to 95% in the
        dissociated state.
    - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
      supporting_text: Mechanistic synthesis indicates AUX1 operates as a
        **proton-coupled symporter** (H+:IAA−), energized by the plasma-membrane
        proton motive force.
references:
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: GO_REF:0000122
  title: AtSubP analysis
  findings: []
- id: PMID:11641271
  title: Localization of the auxin permease AUX1 suggests two functionally distinct
    hormone transport pathways operate in the Arabidopsis root apex.
  findings: []
- id: PMID:16478044
  title: Nematode-induced changes of transporter gene expression in Arabidopsis roots.
  findings: []
- id: PMID:16677815
  title: High-affinity auxin transport by the AUX1 influx carrier protein.
  findings: []
- id: PMID:16690816
  title: AXR4 is required for localization of the auxin influx facilitator AUX1.
  findings: []
- id: PMID:16839804
  title: 'Auxin transport: a field in flux.'
  findings: []
- id: PMID:17084699
  title: Vectorial information for Arabidopsis planar polarity is mediated by combined
    AUX1, EIN2, and GNOM activity.
  findings: []
- id: PMID:17114355
  title: Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses
    a novel pathway distinct from PIN1.
  findings: []
- id: PMID:17215297
  title: Auxin-dependent regulation of lateral root positioning in the basal meristem
    of Arabidopsis.
  findings: []
- id: PMID:18614710
  title: The binding of auxin to the Arabidopsis auxin influx transporter AUX1.
  findings: []
- id: PMID:18622388
  title: The auxin influx carrier LAX3 promotes lateral root emergence.
  findings: []
- id: PMID:19952011
  title: The AUX1 LAX family of auxin influx carriers is required for the establishment
    of embryonic root cell organization in Arabidopsis thaliana.
  findings: []
- id: PMID:32612234
  title: Extensive signal integration by the phytohormone protein network.
  findings: []
- id: PMID:36345646
  title: Endogenous auxin maintains embryonic cell identity and promotes somatic embryo
    development in Arabidopsis.
  findings: []
- id: PMID:8688077
  title: 'Arabidopsis AUX1 gene: a permease-like regulator of root gravitropism.'
  findings: []
- id: PMID:9484486
  title: 'The Arabidopsis AUX1 gene: a model system to study mRNA processing in plants.'
  findings: []
- id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report for AUX1
  findings: []
core_functions:
- description: >-
    High-affinity, proton-coupled auxin (IAA) influx transporter that imports the
    auxin hormone across the plasma membrane, the founding biochemical activity
    of the AUX1/LAX family.
  molecular_function:
    id: GO:0010328
    label: auxin influx transmembrane transporter activity
  directly_involved_in:
  - id: GO:0060919
    label: auxin import into cell
  - id: GO:0009926
    label: auxin polar transport
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:16677815
    supporting_text: Upon expression of AUX1 in Xenopus oocytes, saturable,
      pH-dependent uptake of 3H-IAA was measured.
  - reference_id: PMID:18614710
    supporting_text: >-
      These membranes proved suitable for determination of the binding of IAA to AUX1 and
      enabled us to determine a K(d) of 2.6 mum, comparable with estimates for the K(m) for
      IAA transport.
  - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
    supporting_text: Direct functional evidence from heterologous expression in
      **Xenopus oocytes** demonstrates that AUX1 transports **IAA** with high
      affinity and saturable kinetics.
  - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
    supporting_text: Mechanistic synthesis indicates AUX1 operates as a
      **proton-coupled symporter** (H+:IAA−), energized by the plasma-membrane
      proton motive force.
- description: >-
    By importing auxin into specific root apical cells (protophloem, columella,
    lateral root cap, epidermis), AUX1 establishes the auxin gradients that drive
    root gravitropism; aux1 mutants are agravitropic and auxin-resistant.
  molecular_function:
    id: GO:0010328
    label: auxin influx transmembrane transporter activity
  directly_involved_in:
  - id: GO:0009958
    label: positive gravitropism
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:8688077
    supporting_text: Mutations within the AUX1 gene confer an auxin-resistant root
      growth phenotype and abolish root gravitropic curvature.
  - reference_id: PMID:11641271
    supporting_text: AUX1 is necessary for root gravitropism by facilitating
      basipetal auxin transport to distal elongation zone tissues.
  - reference_id: file:ARATH/AUX1/AUX1-deep-research-falcon.md
    supporting_text: AUX1 is essential for gravitropism and mediates auxin
      movement from the **lateral root cap to the epidermis of the elongation
      zone**, enabling differential growth during bending
proposed_new_terms:
- proposed_name: auxin:proton symporter activity
  proposed_definition: Enables the transfer of auxin (indole-3-acetic acid) from
    one side of a membrane to the other, coupled to the transport of a proton in
    the same direction, driven by the transmembrane proton-motive force.
  proposed_parent:
    id: GO:0015293
    label: symporter activity
  justification: AUX1 mediates proton-driven, pH-dependent auxin uptake and AUX/LAX
    proteins act as IAA-H+ symporters; a substrate-specific symporter term would
    capture both the mechanism (proton coupling) and the substrate (auxin), which
    neither GO:0010328 (substrate-specific, mechanism-agnostic) nor GO:0015293
    (mechanism only) fully expresses.
  supported_by:
  - reference_id: PMID:18614710
    supporting_text: Members of the AUX/LAX family of membrane transporters,
      conserved in all higher plant species, are believed to act as IAA-H +
      symporters.
suggested_questions:
- question: Does AUX1 transport any amino acids or other AAAP-family substrates
    in addition to IAA, or is its substrate specificity restricted to auxins in
    planta?
- question: What structural features (from the recent cryo-EM structures)
    determine proton coupling and the asymmetric (polar) plasma membrane
    localization of AUX1 in protophloem cells?