Ndi1 (YML120C) is the internal, rotenone-insensitive NADH:ubiquinone oxidoreductase of Saccharomyces cerevisiae mitochondria, a type II NADH dehydrogenase (NDH-2; EC 1.6.5.9). It is a nuclear-encoded, single-subunit flavoprotein of about 53 kDa that carries non-covalently bound FAD and no iron-sulfur clusters. After import via an N-terminal presequence, it associates as a monotopic, peripheral protein with the matrix face of the inner membrane, where it oxidizes intramitochondrial NADH and passes the electrons via FAD to ubiquinone in the membrane. Unlike complex I it pumps no protons and is insensitive to rotenone and piericidin, but is inhibited by flavone. S. cerevisiae lacks complex I, so Ndi1 is the main entry point for matrix NADH into the respiratory chain; the external enzymes Nde1 and Nde2 and the glycerol-3-phosphate shuttle handle cytosolic NADH. Crystal structures show a homodimer whose dimer interface forms the amphipathic membrane anchor, with overlapping NADH and quinone binding sites; dimerization is needed for activity and membrane targeting. Null mutants grow on glucose and ethanol but are impaired on lactate, pyruvate and acetate. Expressed in mammalian cells, Ndi1 reaches the mitochondrial matrix side and restores rotenone-insensitive NADH oxidation in complex I-deficient cells. Overexpression raises mitochondrial reactive oxygen species and causes apoptosis-like death, and deletion lowers ROS and extends chronological lifespan. NDH-2 is ancestral in mitochondria and has been lost from the human lineage.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003954 NADH dehydrogenase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro-based assignment of the general NADH dehydrogenase activity term. Correct but general parent of the precise non-electrogenic NADH:ubiquinone oxidoreductase term. Reason: GO:0003954 is defined generically (NADH + H+ + acceptor = NAD+ + reduced acceptor) and is the parent of both the proton-pumping complex I term GO:0008137 and the non-electrogenic GO:0050136/GO:0120555 branch. Using the generic parent is correct for an NDH-2 enzyme; it does not imply complex I-type proton pumping. The more specific GO:0120555 is captured by the IDA row. Supporting Evidence: PMID:3138118 is specific for NADH with apparent Km = 31 microM |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Detected in the high-coverage yeast mitochondrial proteome (PROMITO). Reason: Consistent with the mitochondrial presequence and all targeted localization data. General but correct; the inner membrane matrix side is the precise location. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Detected in quantitative proteomics of isolated mitochondria grown on different carbon sources. Reason: Correct, consistent with all other localization evidence. General term. Supporting Evidence: PMID:24769239 isolated mitochondria extracted from yeast grown on fermentative (glucose or |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic propagation of mitochondrial localization within the eukaryotic NDH-2 clade (plant NDA/NDB, yeast NDI1/NDE1/NDE2, trypanosome and Plasmodium NDH2). Reason: The node groups eukaryotic mitochondrial NDH-2 enzymes, and NDI1 sits squarely inside it. NDI1 (SGD:S000004589) appearing among the sources is expected because it has its own experimental mitochondrial localization. Consistent with the ancestral (LOCA/LECA) origin of mitochondrial NDH2 proposed by comparative proteomics. Supporting Evidence: PMID:9733747 dehydrogenase, the catalytic side of which projects to the matrix side of the PMID:42822426 mitochondria inherited NDH2, amino acid and cofactor biosynthetic pathways |
| GO:0005739 mitochondrion | IDA PMID:11502169 Yeast mitochondrial dehydrogenases are associated in a supra... | ACCEPT | Summary: Ndi1 identified in a native-gel supramolecular NADH dehydrogenase assembly from isolated yeast mitochondria. Reason: Direct biochemical identification in mitochondria. The paper describes Ndi1 as the matrix-facing NADH dehydrogenase. Supporting Evidence: PMID:11502169 exhibiting NADH-dehydrogenase activity |
| GO:0005739 mitochondrion | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning prediction of mitochondrial localization. Reason: Correct and consistent with experimental data. Supporting Evidence: PMID:9689052 catalyzed electron transfer from NADH in the matrix to ubiquinone-10 in the inner mitochondrial membranes |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (inner membrane, peripheral, matrix side). Reason: Ndi1 is a monotopic/peripheral protein bound to the matrix face of the inner membrane, which is where it reduces membrane ubiquinone. The inner membrane term is correct; the more precise GO:0099617 matrix side of mitochondrial inner membrane is proposed as NEW. Supporting Evidence: PMID:22949654 The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, PMID:22949654 structures reveal that Ndi1 is a peripheral membrane |
| GO:0005759 mitochondrial matrix | IDA PMID:1900238 Isolation and inactivation of the nuclear gene encoding the ... | ACCEPT | Summary: Oxygen-uptake experiments with mitochondria from null mutants showed that Ndi1 oxidizes NADH generated inside the mitochondrion, i.e. its active site is on the matrix side. Reason: Ndi1 is a peripheral protein on the matrix face of the inner membrane; its catalytic domain is in the matrix compartment. The matrix term is a defensible curator call (PomBase uses the same term for S. pombe ndi1 in GO-CAM). The more precise term GO:0099617 matrix side of mitochondrial inner membrane is proposed as NEW rather than replacing this curator annotation, whose full text was not available to us. Supporting Evidence: PMID:1900238 that this NADH dehydrogenase catalyzes the oxidation of NADH generated inside PMID:23086143 yeast NDH-2 (Ndi1) oxidizes NADH on the matrix side and reduces ubiquinone to |
| GO:0005759 mitochondrial matrix | IMP PMID:1900238 Isolation and inactivation of the nuclear gene encoding the ... | ACCEPT | Summary: Same localization inferred from the substrate-sidedness phenotype of ndi1 null mitochondria (loss of oxidation of internally generated NADH). Reason: Same reasoning as the IDA row from this paper. The mutant phenotype (loss of oxidation of intramitochondrial but not external NADH) does indicate matrix-side action. Supporting Evidence: PMID:1900238 that this NADH dehydrogenase catalyzes the oxidation of NADH generated inside |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: Cytosolic activity location generated by the YeastPathways (PWY3O-188, aerobic respiration electron transport chain) to GO-CAM conversion. Reason: Ndi1 is a mitochondrial protein with a cleaved presequence, bound to the matrix face of the inner membrane, and oxidizes intramitochondrial NADH, not cytosolic NADH. The cached GO-CAM row for this pathway (gomodel:RXN3O-165) places the Ndi1 activity in the cytosol, which looks like a conversion default rather than a curated location. Cytosolic NADH is oxidized by the external enzymes Nde1 and Nde2, not by Ndi1. No evidence supports cytosolic activity. Supporting Evidence: PMID:9733747 dehydrogenase, the catalytic side of which projects to the matrix side of the PMID:1900238 that this NADH dehydrogenase catalyzes the oxidation of NADH generated inside |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | IDA PMID:1900238 Isolation and inactivation of the nuclear gene encoding the ... | ACCEPT | Summary: Ndi1 directly catalyzes transfer of electrons from matrix NADH to ubiquinone in the yeast respiratory chain. Reason: Core process. Ndi1 itself performs the step (NADH oxidation and ubiquinone reduction); in S. cerevisiae, which lacks complex I, it is the main route for matrix NADH into the respiratory chain. Supporting Evidence: PMID:1900238 that this NADH dehydrogenase catalyzes the oxidation of NADH generated inside PMID:9689052 It is the main entry point into the respiratory chain in this organism, just as complex I is in mammalian mitochondria |
| GO:0015980 energy derivation by oxidation of organic compounds | IEA GO_REF:0000117 | TOO GENERAL | Summary: ARBA-predicted, very general energy metabolism process. Reason: Correct but general; it is an ancestor of the respiratory electron transport the enzyme takes part in. Acceptable for an IEA. Supporting Evidence: PMID:1900238 Inactivation of this NADH dehydrogenase does not affect |
| GO:0016491 oxidoreductase activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: Deep-node phylogenetic propagation of generic oxidoreductase activity across the bacterial and eukaryotic NDH-2 family. Reason: The node includes bacterial NDH-2 (E. coli Ndh, P00393; M. tuberculosis Ndh) and eukaryotic mitochondrial enzymes; the PAINT curator placed only the generic term at this deep node. True for NDI1, and the specific activity GO:0120555 is captured by direct evidence. Supporting Evidence: PMID:22949654 the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro FAD/NAD(P)-binding domain mapping to generic oxidoreductase activity. Reason: Correct but uninformative general parent; the specific activity is annotated separately. Supporting Evidence: PMID:3138118 The enzyme contains FAD, non-covalently linked, as the sole |
| GO:0019646 aerobic electron transport chain | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways aerobic respiration electron transport chain, with Ndi1 as an entry dehydrogenase. Reason: Ndi1 feeds electrons from matrix NADH to ubiquinone, which are then carried through complexes III and IV to oxygen; that chain generates the gradient even though Ndi1 itself pumps no protons. Parent of the more specific GO:0006120. Supporting Evidence: PMID:11479321 rotenone-insensitive, flavone-sensitive, and antimycin A-sensitive. Thus the |
| GO:0042802 identical protein binding | IPI PMID:22949654 The structure of the yeast NADH dehydrogenase (Ndi1) reveals... | MODIFY | Summary: Crystal structure shows Ndi1 forms an intimate homodimer whose packing forms the membrane anchor. Reason: The self-interaction is a functional homodimer, not a generic binding event; protein homodimerization activity is more informative. Dimerization creates the amphipathic membrane anchor and, per Feng et al., is needed for activity and membrane targeting. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:22949654 protein forming an intimate dimer, in which packing of the monomeric units |
| GO:0042802 identical protein binding | IPI PMID:23086143 Structural insight into the type-II mitochondrial NADH dehyd... | MODIFY | Summary: Structural and mutational evidence that Ndi1 homodimerizes through its C-terminal domain, which is required for catalysis and membrane targeting. Reason: Same as the Iwata et al. row; the evidence specifically supports protein homodimerization activity. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:23086143 We find that Ndi1 homodimerization PMID:23086143 through its carboxy-terminal domain is critical for its catalytic activity and |
| GO:0043065 positive regulation of apoptotic process | IMP PMID:16436509 Yeast AMID homologue Ndi1p displays respiration-restricted a... | MARK AS OVER ANNOTATED | Summary: Overexpression of NDI1 (but not NDE1) causes apoptosis-like death associated with mitochondrial ROS; deletion lowers ROS and extends chronological lifespan. Reason: The phenotypes come mainly from overexpression and depend on respiratory state and on downstream ETC components, which points to excess electron flux and ROS from an NADH-oxidizing flavoenzyme rather than a dedicated role in apoptotic signaling. Interrupting downstream ETC components suppresses the toxicity, consistent with an indirect bioenergetic effect. The annotation is experimental and the full text was not cached, so it is not removed, but it does not represent a function Ndi1 performs. Supporting Evidence: PMID:16436509 The apoptotic effect of NDI1 overexpression is associated with PMID:16436509 electron transport chain can suppress the growth inhibition from Ndi1p |
| GO:0050136 NADH dehydrogenase (quinone) (non-electrogenic) activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 1.6.5.9 / Rhea mapping to non-electrogenic NADH:quinone oxidoreductase activity. Reason: Correct; Ndi1 reduces several quinones (ubiquinones and menaquinone) without proton pumping. Parent of the more specific GO:0120555. Supporting Evidence: PMID:3138118 enzyme can use ubiquinone-2, -6 or -10, menaquinone, dichloroindophenol or PMID:22949654 transfer of an electron from NADH via FAD to quinone, without proton pumping. |
| GO:0120555 NADH dehydrogenase (ubiquinone) (non-electrogenic) activity | IDA PMID:3138118 Purification and characterization of a rotenone-insensitive ... | ACCEPT | Summary: Purified single-subunit FAD enzyme catalyzing rotenone-insensitive NADH:ubiquinone (Q6) oxidoreduction. Reason: Core molecular function. The 1988 paper suggested the purified enzyme was the external dehydrogenase, but the 1991 gene isolation and disruption by the same group showed it is the internal enzyme encoded by NDI1, so the annotation correctly attaches to NDI1. The non-electrogenic term is correct (no proton pumping). Supporting Evidence: PMID:3138118 by flavone (I50 = 95 microM), but not by rotenone or piericidin PMID:1900238 isolation of the nuclear gene encoding this single-subunit enzyme PMID:11479321 wild-type 143B.TK(-) cells, as expected from the lack of proton pumping activity |
| GO:0120555 NADH dehydrogenase (ubiquinone) (non-electrogenic) activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based assignment of the specific activity. Reason: Consistent with the direct biochemical evidence. Supporting Evidence: PMID:3138118 by flavone (I50 = 95 microM), but not by rotenone or piericidin |
| GO:0120555 NADH dehydrogenase (ubiquinone) (non-electrogenic) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways GO-CAM conversion assigning the specific activity. Reason: Correct activity (the location attached in the same conversion is not; see the cytosol row). Supporting Evidence: PMID:9689052 catalyzed electron transfer from NADH in the matrix to ubiquinone-10 in the inner mitochondrial membranes |
| GO:0071949 FAD binding | IDA PMID:3138118 Purification and characterization of a rotenone-insensitive ... | NEW | Summary: The purified enzyme contains non-covalently bound FAD as its sole prosthetic group, and the crystal structures show the FAD between the NADH and quinone sites. Reason: FAD is the redox cofactor Ndi1 uses to pass electrons from NADH to quinone, shown directly on the purified yeast protein. FAD binding is routinely annotated for flavoprotein oxidoreductases. Not currently in GOA for NDI1. Supporting Evidence: PMID:3138118 The enzyme contains FAD, non-covalently linked, as the sole PMID:9689052 The internal, rotenone-insensitive NADH-Q oxidoreductase of S. cerevisiae mitochondria is a single polypeptide enzyme with noncovalently bound FAD as a cofactor |
| GO:0099617 matrix side of mitochondrial inner membrane | IDA PMID:22949654 The structure of the yeast NADH dehydrogenase (Ndi1) reveals... | NEW | Summary: Ndi1 is a monotopic, peripheral membrane protein on the matrix face of the inner membrane. Reason: The definition of GO:0099617 explicitly includes peripherally associated proteins on the matrix leaflet, which is exactly the topology shown structurally and by sidedness assays. It is more precise than either mitochondrial inner membrane or mitochondrial matrix alone. Supporting Evidence: PMID:22949654 The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, PMID:9733747 dehydrogenase, the catalytic side of which projects to the matrix side of the |
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Download this section (compressed HTML)Q: Should the cytosol (GO:0005829) is_active_in row produced by the YeastPathways PWY3O-188 GO-CAM conversion be retired? Ndi1 is a matrix-facing inner membrane enzyme, and the cytosolic location looks like a pathway-level default in the conversion.
Suggested experts: SGD curators, YeastPathways curators
Q: Should the NDI1 overexpression phenotypes (apoptosis-like death and ROS) support a regulation-of-apoptosis annotation, or would an annotation to ROS production or no process annotation better reflect an indirect effect of excess NADH oxidation?
Suggested experts: SGD curators
Q: Is the native-gel supramolecular assembly of Ndi1 with external dehydrogenases and TCA enzymes a stable physiological complex that channels NADH, or a co-migration artifact of colorless native PAGE?
Suggested experts: yeast mitochondrial bioenergetics researchers
Q: Which of the two ubiquinone sites seen in the Feng et al. structure is used in the membrane, and does the Feng FAD-UQ(I) intermediate model or the Iwata overlapping-site model describe catalysis?
Suggested experts: NDH-2 structural biologists
Experiment: Protease-protection and alkaline carbonate extraction of mitochondria and mitoplasts from cells expressing untagged Ndi1, alongside cytosolic fractions, with NADH:UQ oxidoreductase assays of each fraction.
Hypothesis: Ndi1 is active only at the matrix face of the inner membrane, not in the cytosol.
Type: biochemical
Experiment: Overexpress catalytically dead (FAD-binding or NADH-site) and dimerization-defective Ndi1 mutants, measure ROS and cell death markers, and test rescue by antioxidants or by co-expression of alternative oxidase.
Hypothesis: The pro-death effect of NDI1 overexpression requires its catalytic activity and the resulting ROS, not a separate apoptotic function.
Type: genetic
NADH:ubiquinone oxidoreductase; transfers electrons from NADH to ubiquinone in respiratory chain but does not pump protons, in contrast to higher eukaryotic multisubunit respiratory complex I; upon apoptotic stress, is activated in mitochondria by N-terminal cleavage, then translocates to cytoplasm to induce apoptosis; homolog of human AIFM2; yeast NDI1 complements several phenotypes of human cell line with mutated MT-ND4, implicated in Leber hereditary optic neuropathy
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