Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0009060 aerobic respiration	IBA GO_REF:0000033	REMOVE	Summary: Aerobic respiration is a misleading over-propagation for chloroplast NDH. Reason: This protein is a plastid NDH subunit in photosynthetic electron transport, not a mitochondrial respiratory-chain component. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH FUNCTIONAL DIVERGENCE Sources checked: FB:FBgn0013679 SUPPORTS SOURCE BUT NOT TARGET PANTHER:PTN000153359 SUPPORTS SOURCE BUT NOT TARGET Donors are mitochondrial and bacterial respiratory complex I subunits; the chloroplast NDH complex functions in cyclic electron flow around photosystem I and chlororespiration, not aerobic respiration. Family-level adjudication: interpro/panther/PTHR11432/PTHR11432-review.yaml (PTN000153359 node assessment). UniProtKB:P03886 · human MT-ND1 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:P0AFD4 SUPPORTS SOURCE BUT NOT TARGET Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane file:POPTR/ndhA/ndhA-uniprot.txt NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain
GO:0003954 NADH dehydrogenase activity	IBA GO_REF:0000033	MODIFY	Summary: Generic NADH dehydrogenase activity is directionally correct but misses the chloroplast quinone acceptor context. Reason: Use the quinone-acceptor oxidoreductase term and retain the contributes_to relationship for this NDH subunit. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000153359 SUPPORTS SOURCE BUT NOT TARGET Donor complex I subunits are NADH-dependent; the plastid NDH-1 complex accepts electrons from ferredoxin/NAD(P)H onto plastoquinone, so the broader quinone-acceptor oxidoreductase term is the safe transfer. Family-level adjudication: interpro/panther/PTHR11432/PTHR11432-review.yaml (PTN000153359 node assessment). UniProtKB:P0AFD4 SUPPORTS SOURCE BUT NOT TARGET Proposed replacements: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n H(+)(out).
GO:0009535 chloroplast thylakoid membrane	IEA GO_REF:0000120	ACCEPT	Summary: Chloroplast thylakoid membrane is the correct localization for this plastid NDH subunit. Reason: The reviewed entry places the NDH subunit in the chloroplast thylakoid membrane. Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
GO:0016020 membrane	IEA GO_REF:0000002	MODIFY	Summary: Generic membrane is correct but less specific than chloroplast thylakoid membrane. Reason: Use the specific thylakoid membrane location supported by UniProt. Proposed replacements: chloroplast thylakoid membrane Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	IEA GO_REF:0000104	ACCEPT	Summary: This oxidoreductase term matches the chloroplast NAD(P)H-plastoquinone NDH reaction. Reason: It captures the redox chemistry without imposing an incorrect ubiquinone acceptor. Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n H(+)(out).
GO:0019684 photosynthesis, light reaction	IEA GO_REF:0000104	MODIFY	Summary: Photosynthesis, light reaction is correct context but less specific than cyclic photosynthetic phosphorylation. Reason: The chloroplast NDH complex operates in cyclic electron flow around photosystem I; GO:0009778 cyclic photosynthetic phosphorylation is the specific process for every subunit of this complex, matching the ndhB1/ndhB2/ndhH reviews. Proposed replacements: cyclic photosynthetic phosphorylation Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain file:POPTR/ndhA/ndhA-uniprot.txt Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient.
GO:0015990 electron transport coupled proton transport	IEA file:POPTR/ndhA/ndhA-uniprot.txt	NEW	Summary: Electron transport coupled proton transport is the direct process for chloroplast NDH. Reason: The existing GOA rows lack this direct process term even though UniProt states that the NDH redox reaction is coupled to proton translocation. Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. file:POPTR/ndhA/ndhA-uniprot.txt Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n H(+)(out).
GO:0010598 NAD(P)H dehydrogenase complex (plastoquinone)	IEA file:POPTR/ndhA/ndhA-uniprot.txt	NEW	Summary: ndhA is part of the chloroplast NDH complex. Reason: The existing GOA rows lack a complex annotation even though UniProt describes NDH as a multi-subunit complex; GO:0010598 NAD(P)H dehydrogenase complex (plastoquinone) names the plastid complex exactly (verified against QuickGO), matching the ndhH review. Supporting Evidence: file:POPTR/ndhA/ndhA-uniprot.txt NDH is composed of at least 16 different subunits

Core Functions

Contributes subunit 1 to chloroplast NDH, supporting NAD(P)H-plastoquinone electron transfer coupled to proton translocation.

Directly Involved In:

electron transport coupled proton transport cyclic photosynthetic phosphorylation

Cellular Locations:

chloroplast thylakoid membrane

In Complex:

NAD(P)H dehydrogenase complex (plastoquinone)

Supporting Evidence:

file:POPTR/ndhA/ndhA-uniprot.txt
Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n H(+)(out).
file:POPTR/ndhA/ndhA-uniprot.txt
Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient.
file:POPTR/ndhA/ndhA-uniprot.txt
SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane

References

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Suggested Experiments

Experiment: Measure NDH-dependent post-illumination chlorophyll fluorescence rise and P700 redox kinetics in ndhA perturbation lines.

Type: targeted functional assay

📚 Additional Documentation

Notes

(ndhA-notes.md)

ndhA notes

Reviewed ndhA as chloroplast NDH subunit 1. UniProt describes NAD(P)H:plastoquinone electron transfer and coupling of the redox reaction to proton translocation [file:POPTR/ndhA/ndhA-uniprot.txt].
Treated aerobic respiration and ubiquinone/NADH-dehydrogenase-specific transfers cautiously; the chloroplast reaction uses plastoquinone and fits the broader quinone-acceptor oxidoreductase term [file:POPTR/ndhA/ndhA-goa.tsv].

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