NdhK iron-sulfur subunit in Populus trichocarpa. It forms part of the thylakoid NADH dehydrogenase-like complex, which transfers electrons from reduced ferredoxin to plastoquinone and couples this reaction to proton translocation during cyclic electron flow around photosystem I. NdhK contributes a 4Fe–4S center and lines the plastoquinone-binding pocket. The resulting proton gradient supports ATP synthesis and photosynthetic energy balance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009060 aerobic respiration | IBA GO_REF:0000033 | UNDECIDED | Summary: Chlororespiration prevents categorical rejection from chloroplast localization alone. Reason: The GO definition does not restrict this process to mitochondria. Tobacco ndhJK/ndhCJK mutants and PTOX inhibition support NDH participation in chlororespiratory electron flow, while independent work demonstrates energy-conserving proton pumping. Whether the full GO process is sufficiently supported for this inherited Populus assertion, including oxygen-coupled energy conservation where required, is under shared adjudication. Current target descent from the positive ancestral node is verified; photosynthetic specialization alone is not evidence of loss. Propagation Review Root cause: UNRESOLVED Sources checked: FB:FBgn0030718 UNRESOLVED PANTHER:PTN000242188 UNRESOLVED Current exact target leaf descends from PTN000242188. The prior localization-only respiratory exclusion is withdrawn; evaluate demonstrated chlororespiratory capacity separately from the resolved NADH-donor mismatch. UniProtKB:O75251 · human NDUFS7 UNRESOLVED UniProtKB:P0AFC7 UNRESOLVED Supporting Evidence: PMID:27066014 chlororespiratory pathway was suppressed when NDH was inactivated. PMID:28559282 pumps approximately two protons |
| GO:0045271 respiratory chain complex I | IBA GO_REF:0000033 | MODIFY | Summary: Use the chloroplast NDH complex rather than NADH-oxidizing respiratory complex I. Reason: The chloroplast complex has a ferredoxin-input architecture and a plastoquinone-reduction site, distinct from the NADH-entry complex specified by GO:0045271. GO:0010598 explicitly allows ferredoxin as the possible donor despite its historical NAD(P)H label. This structural and reaction-level distinction does not rule out chlororespiration. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH LINEAGE OR TAXON MISMATCH Sources checked: FB:FBgn0030718 SUPPORTS SOURCE BUT NOT TARGET FB:FBgn0039669 SUPPORTS SOURCE BUT NOT TARGET MGI:MGI:1922656 SUPPORTS SOURCE BUT NOT TARGET PANTHER:PTN000242188 SUPPORTS SOURCE BUT NOT TARGET Exact target descent from PTN000242188 is verified. Complex identity and absence of the NADH-oxidizing module support the replacement; no general exclusion of respiratory processes is asserted. UniProtKB:O75251 · human NDUFS7 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:P0AFC7 SUPPORTS SOURCE BUT NOT TARGET UniProtKB:P42026 SUPPORTS SOURCE BUT NOT TARGET Proposed replacements: NAD(P)H dehydrogenase complex (plastoquinone) Supporting Evidence: PMID:21505067 CRR31 was essential for the efficient operation of Fd-dependent plastoquinone reduction in vitro. file:POPTR/ndhK/ndhK-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | IBA GO_REF:0000033 | MODIFY | Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction. Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000242188 SUPPORTS SOURCE BUT NOT TARGET The exact target leaf lies beneath PTN000242188 in the retrieved tree. Challenge the retained NADH-donor assertion on demonstrated chloroplast complex architecture and donor chemistry, not donor count or absence of target assays. Ferredoxin-dependent activity is retained. UniProtKB:O75251 · human NDUFS7 SUPPORTS SOURCE BUT NOT TARGET Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors Supporting Evidence: PMID:21505067 CRR31 was essential for the efficient operation of Fd-dependent plastoquinone reduction in vitro. PMID:28559282 pumps approximately two protons |
| GO:0015990 electron transport coupled proton transport | IBA GO_REF:0000033 | ACCEPT | Summary: Coupled electron transfer and proton transport are core NDH functions. Reason: Higher-plant NDH conserves ferredoxin-to-plastoquinone redox energy by proton pumping. This subunit contributes to the electron-transfer/proton-pumping complex and therefore directly participates in the process. Supporting Evidence: PMID:28559282 pumps approximately two protons |
| GO:0005506 iron ion binding | IEA GO_REF:0000104 | MODIFY | Summary: Generic iron ion binding is less informative than the specific 4Fe-4S cluster binding annotation. Reason: NdhK coordinates one 4Fe–4S cluster in the primary spinach structure, independently supporting the homologous Populus cofactor annotation. The specific 4 iron, 4 sulfur cluster binding term captures the cofactor more precisely. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: PMID:39856350 NdhI coordinates two 4Fe–4S clusters and NdhK coordinates one |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | IEA GO_REF:0000002 | MODIFY | Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction. Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here. Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors Supporting Evidence: PMID:21505067 CRR31 was essential for the efficient operation of Fd-dependent plastoquinone reduction in vitro. PMID:28559282 pumps approximately two protons |
| GO:0009535 chloroplast thylakoid membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Chloroplast thylakoid membrane is the correct localization for ndhK. Reason: The UniProt entry places the protein on the chloroplast thylakoid membrane. Supporting Evidence: file:POPTR/ndhK/ndhK-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane |
| GO:0009536 plastid | IEA GO_REF:0000117 | MODIFY | Summary: Plastid is correct but too broad for this thylakoid membrane NDH subunit. Reason: Use the more specific chloroplast thylakoid membrane term. Proposed replacements: chloroplast thylakoid membrane Supporting Evidence: file:POPTR/ndhK/ndhK-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 | MODIFY | Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction. Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here. Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors Supporting Evidence: PMID:21505067 CRR31 was essential for the efficient operation of Fd-dependent plastoquinone reduction in vitro. PMID:28559282 pumps approximately two protons |
| 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: Higher-plant NDH contributes directly to the light reactions through ferredoxin-dependent cyclic electron flow and proton pumping. The existing cyclic photosynthetic phosphorylation replacement provides useful specificity without asserting loss of the broader process. Proposed replacements: cyclic photosynthetic phosphorylation Supporting Evidence: PMID:28559282 pumps approximately two protons |
| GO:0048038 quinone binding | IEA GO_REF:0000002 | ACCEPT | Summary: NdhK physically contributes to the plastoquinone pocket. Reason: The spinach structure places NdhK helices and loops along the plastoquinone-binding cavity with NdhA and NdhH. This provides subunit-specific structural support for the conserved NdhK binding role, beyond merely observing that the whole complex uses quinone. Supporting Evidence: PMID:39856350 The PQ-binding pocket is formed by subunits NdhA, NdhH and NdhK |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: Iron-sulfur cluster binding is correct but less specific than the curated 4Fe-4S cluster binding. Reason: NdhK coordinates one 4Fe–4S cluster in the primary spinach structure, independently supporting the homologous Populus cofactor annotation. The specific 4 iron, 4 sulfur cluster binding term captures the cofactor more precisely. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: PMID:39856350 NdhI coordinates two 4Fe–4S clusters and NdhK coordinates one |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: The specific 4Fe-4S cluster binding annotation is supported by the HAMAP-curated UniProt entry. Reason: NdhK coordinates one 4Fe–4S cluster in the primary spinach structure, independently supporting the homologous Populus cofactor annotation. The specific 4 iron, 4 sulfur cluster binding term captures the cofactor more precisely. Supporting Evidence: PMID:39856350 NdhI coordinates two 4Fe–4S clusters and NdhK coordinates one |
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Download this section (compressed HTML)Q: Does Populus ndhK loss specifically affect cyclic electron flow or chlororespiratory NDH activity under stress?
Q: Does conserved NDH-dependent chlororespiration support the inherited respiratory process term in Populus? The shared ndhD OpenScientist request distinguishes demonstrated electron flow and proton pumping from proposed oxygen-coupled ATP production.
Experiment: Measure chlorophyll fluorescence and P700 redox kinetics in ndhK perturbation lines under fluctuating light.
Type: targeted functional assay
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