ndhB1

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

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.

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.

Proposed replacements: NAD(P)H dehydrogenase complex (plastoquinone)

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

Summary: Chloroplast thylakoid membrane is the correct localization for this NDH subunit.

Reason: The reviewed entry places this multi-pass NDH subunit in the chloroplast thylakoid membrane.

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

Summary: Photosynthesis light reaction is correct but less specific than cyclic photosynthetic phosphorylation for chloroplast NDH.

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

Summary: NDH directly performs ATP-synthesis-coupled electron transport.

Reason: The term covers electron transfer that conserves energy ultimately used for ATP synthesis. NDH transfers electrons and pumps protons; these are actual steps of that process, not a remote perturbation effect. Higher-plant NDH proton pumping directly increases the ATP yield of cyclic electron flow.

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.