id: A4GYX1
gene_symbol: ndhA
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3694
  label: Populus trichocarpa
description: 'Chloroplast NDH subunit 1 membrane protein that contributes to NAD(P)H-plastoquinone electron
  transfer coupled to proton translocation in the thylakoid membrane.'
existing_annotations:
- term:
    id: GO:0009060
    label: aerobic respiration
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Aerobic respiration is a misleading over-propagation for chloroplast NDH.
    action: REMOVE
    reason: This protein is a plastid NDH subunit in photosynthetic electron transport, not a
      mitochondrial respiratory-chain component.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane'
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur
        (Fe-S) centers, to quinones in the photosynthetic chain
- term:
    id: GO:0003954
    label: NADH dehydrogenase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    summary: Generic NADH dehydrogenase activity is directionally correct but misses the chloroplast
      quinone acceptor context.
    action: MODIFY
    reason: Use the quinone-acceptor oxidoreductase term and retain the contributes_to relationship
      for this NDH subunit.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) +
        n H(+)(out).
    proposed_replacement_terms:
    - &id001
      id: GO:0016655
      label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
- term:
    id: GO:0009535
    label: chloroplast thylakoid membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Chloroplast thylakoid membrane is the correct localization for this plastid NDH
      subunit.
    action: ACCEPT
    reason: The reviewed entry places the NDH subunit in the chloroplast thylakoid membrane.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane'
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Generic membrane is correct but less specific than chloroplast thylakoid membrane.
    action: MODIFY
    reason: Use the specific thylakoid membrane location supported by UniProt.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane'
    proposed_replacement_terms:
    - &id002
      id: GO:0009535
      label: chloroplast thylakoid membrane
- term:
    id: GO:0016655
    label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: This oxidoreductase term matches the chloroplast NAD(P)H-plastoquinone NDH reaction.
    action: ACCEPT
    reason: It captures the redox chemistry without imposing an incorrect ubiquinone acceptor.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) +
        n H(+)(out).
- term:
    id: GO:0019684
    label: photosynthesis, light reaction
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: Photosynthesis, light reaction is appropriate for chloroplast NDH electron flow.
    action: ACCEPT
    reason: NDH transfers electrons to quinones in the photosynthetic chain and contributes to
      thylakoid proton gradients.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur
        (Fe-S) centers, to quinones in the photosynthetic chain
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: Couples the redox reaction to proton translocation, and thus conserves the
        redox energy in a proton gradient.
- term:
    id: GO:0015990
    label: electron transport coupled proton transport
  evidence_type: IEA
  original_reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
  review:
    summary: Electron transport coupled proton transport is the direct process for chloroplast NDH.
    action: NEW
    reason: The existing GOA rows lack this direct process term even though UniProt states that the
      NDH redox reaction is coupled to proton translocation.
    supported_by:
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: Couples the redox reaction to proton translocation, and thus conserves the
        redox energy in a proton gradient.
    - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) +
        n H(+)(out).
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings:
  - statement: GO_REF:0000002 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: GO_REF:0000033 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between
    related proteins based on shared sequence features
  findings:
  - statement: GO_REF:0000104 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: GO_REF:0000120 supplied one or more source GOA annotations reviewed in this file.
- id: file:POPTR/ndhA/ndhA-uniprot.txt
  title: UniProtKB reviewed entry for ndhA
  findings:
  - statement: UniProt identifies ndhA as chloroplast NAD(P)H-quinone oxidoreductase subunit 1,
      using plastoquinone as electron acceptor and coupling redox chemistry to proton translocation.
- id: file:POPTR/ndhA/ndhA-goa.tsv
  title: QuickGO GOA annotations for ndhA
  findings:
  - statement: GOA rows supplied the existing_annotations reviewed in this file.
core_functions:
- description: Contributes subunit 1 to chloroplast NDH, supporting NAD(P)H-plastoquinone electron
    transfer coupled to proton translocation.
  contributes_to_molecular_function: *id001
  directly_involved_in:
  - id: GO:0015990
    label: electron transport coupled proton transport
  locations:
  - *id002
  supported_by:
  - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
    supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n
      H(+)(out).
  - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
    supporting_text: Couples the redox reaction to proton translocation, and thus conserves the
      redox energy in a proton gradient.
  - reference_id: file:POPTR/ndhA/ndhA-uniprot.txt
    supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane'
proposed_new_terms: []
suggested_questions:
- question: Does Populus ndhA contribute most strongly to cyclic electron flow, chlororespiration,
    or stress-specific photosynthetic balancing?
suggested_experiments:
- description: Measure NDH-dependent post-illumination chlorophyll fluorescence rise and P700 redox
    kinetics in ndhA perturbation lines.
  experiment_type: targeted functional assay