Idh encodes the NADP+-dependent isocitrate dehydrogenase of Drosophila melanogaster, a homodimeric Mg2+/Mn2+-dependent enzyme that oxidatively decarboxylates isocitrate to 2-oxoglutarate and CO2 while reducing NADP+ to NADPH. Unlike mammals, which use separate genes for the cytosolic/peroxisomal (IDH1) and mitochondrial (IDH2) enzymes, flies make both forms from a single gene: alternative transcripts encode mitochondrial isoforms with an N-terminal targeting sequence (IDHm) and a cytosolic isoform lacking it (IDHc). The enzyme is a major source of NADPH for glutathione- and thioredoxin-based antioxidant defence and for lipid synthesis. Idh mutant flies have reduced IDH activity and NADPH/NADP+ ratio, accumulate reactive oxygen species and are hypersensitive to rotenone, and Idh overexpression protects DJ-1-deficient dopaminergic neurons from oxidative stress. In flight muscle, Idh knockdown raises the NADP+:NADPH ratio and impairs assembly of respiratory complex I, linking matrix NADPH supply to oxidative phosphorylation biogenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Magnesium ion binding from InterPro IPR019818. Reason: NADP-IDH requires a divalent cation (Mg2+ or Mn2+) bound to the isocitrate in the active site. The term is specific and correct but describes a cofactor, not the core function. Supporting Evidence: file:DROME/Idh/Idh-uniprot.txt Binds 1 Mg(2+) or Mn(2+) ion per subunit. |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: NADP+-isocitrate dehydrogenase activity by phylogenetic inference (PTN008982454; donors include fly Idh itself, mouse Idh1/Idh2, yeast IDP1-3). Reason: Core catalytic activity, supported in flies by direct enzyme assays and mutant analysis. Fly Idh appearing among the donors reflects its own experimental annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008982454 SUPPORTS TRANSFER Supporting Evidence: PMID:28827794 IDHP flies successfully developed into adults (Fig 1C), but they showed decreased IDH mRNA expression, IDH enzyme activity, and NADPH/NADP+ ratio compared to wild type controls (Fig 1Dβ1F). |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IDA DOI:10.1016/0305-0491(80)90023-1 | ACCEPT | Summary: NADP+-isocitrate dehydrogenase activity of the purified Drosophila enzyme (Williamson 1980). Reason: Direct biochemical characterization of the fly enzyme; full text not available but consistent with all other evidence. |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IDA PMID:38739777 Alpha-ketoglutarate supplementation in long-lived Drosophila... | ACCEPT | Summary: NADPH-producing enzyme activities (including NADP-IDH) measured in fly extracts in an alpha-ketoglutarate supplementation study. Reason: Abstract-only access; the abstract reports measurement of NADPH-producing enzyme activities. The activity is well established for this gene, so the curator's annotation is accepted. Supporting Evidence: PMID:38739777 NADPH-producing enzymes, glutamate dehydrogenase, oxygen consumption, and levels |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: NADP+-isocitrate dehydrogenase activity from ARBA, InterPro, Rhea RHEA:19629 and EC 1.1.1.42. Reason: Correct core activity, consistent with fly experimental data. Supporting Evidence: file:DROME/Idh/Idh-uniprot.txt Reaction=D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH; |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IMP PMID:28827794 Isocitrate protects DJ-1 null dopaminergic cells from oxidat... | ACCEPT | Summary: Idh P-element mutants have reduced IDH enzyme activity and NADPH/NADP+ ratio. Reason: Direct genetic evidence that the gene encodes the NADP-IDH activity in flies. Supporting Evidence: PMID:28827794 IDHP flies successfully developed into adults (Fig 1C), but they showed decreased IDH mRNA expression, IDH enzyme activity, and NADPH/NADP+ ratio compared to wild type controls (Fig 1Dβ1F). |
| GO:0005739 mitochondrion | HDA PMID:16212416 Characterization of the Drosophila melanogaster mitochondria... | MODIFY | Summary: Identified in the larval mitochondrial proteome (Alonso et al. 2005). Reason: Proteomic detection in purified larval mitochondria, consistent with the IDHm isoforms. The term is correct but general; mitochondrial NADP-IDH is a matrix enzyme and mitochondrial matrix (GO:0005759) is already annotated to Idh (IC, from this localization plus the activity), so the more specific term is preferred, as for the IBA row. Proposed replacements: mitochondrial matrix |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | MODIFY | Summary: Mitochondrial localization by phylogenetic inference (PTN000214284; donors include fly Idh, mouse Idh1, yeast IDP1). Reason: Correct (the IDHm isoforms are mitochondrial) but the specific compartment of mitochondrial NADP-IDH is the matrix, already annotated to Idh (IC). Replace with mitochondrial matrix. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000214284 SUPPORTS TRANSFER Proposed replacements: mitochondrial matrix |
| GO:0005739 mitochondrion | IDA PMID:28827794 Isocitrate protects DJ-1 null dopaminergic cells from oxidat... | MODIFY | Summary: Mitochondrial localization of IDHm isoforms shown in Drosophila (Kim et al. 2017). Reason: Experimental localization of the IDHm isoforms to mitochondria. The term is correct but general; mitochondrial NADP-IDH is a matrix enzyme and mitochondrial matrix (GO:0005759) is already annotated to Idh (IC, from this localization plus the activity), so the more specific term is preferred, as for the IBA row. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:28827794 (B) Cytosolic and mitochondrial localization of IDH isoforms. |
| GO:0005759 mitochondrial matrix | IC PMID:28827794 Isocitrate protects DJ-1 null dopaminergic cells from oxidat... | ACCEPT | Summary: Mitochondrial matrix inferred by the FlyBase curator from the NADP-IDH activity and mitochondrial localization. Reason: Mitochondrial NADP-IDH is a matrix enzyme; reasonable curator inference. Supporting Evidence: PMID:28827794 (B) Cytosolic and mitochondrial localization of IDH isoforms. |
| GO:0005777 peroxisome | IBA GO_REF:0000033 | REMOVE | Summary: Peroxisome localization by phylogenetic inference (PTN002483519; donors human IDH1 O75874, mouse Idh1, rat Idh1, yeast IDP3, Aspergillus C8VIX5). Reason: Peroxisomal targeting of the donor enzymes (human IDH1, yeast IDP3) depends on a C-terminal PTS1 signal. All Drosophila Idh isoforms in UniProt (B7Z0E0, Q7KUB1, Q8IQA7, Q7KUB0, Q9VSI6) end in ...AVAAK, which lacks a PTS1, and fly Idh isoforms are described as cytosolic or mitochondrial. There is no fly evidence for peroxisomal Idh; the transfer is not supported for this gene. Murari et al. note that CG7176 "could function in the cytosol, peroxisome, and/or mitochondrion" because it is the sole IDH1/IDH2 ortholog, but that is a possibility raised from orthology, not an observation, and it does not overcome the absence of a PTS1. This automated IBA row is removed, whereas the curator-made ISS row is only marked as over-annotated, in deference to the curator. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN002483519 SUPPORTS SOURCE BUT NOT TARGET Donors carry a C-terminal PTS1; fly Idh isoforms end in AVAAK and lack it. Supporting Evidence: PMID:28827794 However, in Drosophila, a cytosolic isoform (IDHc) and mitochondrial isoforms (IDHm1 and IDHm2) are expressed from the single gene IDH PMID:35544578 CG7176 (dIDH2) is the sole Drosophila ortholog of both IDH1 and IDH2, suggesting that it could function in the cytosol, peroxisome, and/or mitochondrion. |
| GO:0005777 peroxisome | ISS PMID:22758915 An inventory of peroxisomal proteins and pathways in Drosoph... | MARK AS OVER ANNOTATED | Summary: Peroxisome localization by sequence similarity to human IDH1 (O75874), from the Faust et al. 2012 peroxisome inventory. Reason: Human IDH1 is peroxisomal through a C-terminal PTS1, but all fly Idh isoforms end in ...AVAAK and lack a PTS1; fly Idh isoforms are described as cytosolic or mitochondrial. The inventory is abstract-only here and gives no fly localization data for Idh, so the similarity-based peroxisomal assignment is likely an over-annotation. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Cytosol localization by phylogenetic inference (PTN000930158; donors fly Idh, mouse Idh1, human IDH1). Reason: The IDHc isoform is cytosolic, as shown experimentally in flies (IDA). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000930158 SUPPORTS TRANSFER Supporting Evidence: PMID:28827794 However, in Drosophila, a cytosolic isoform (IDHc) and mitochondrial isoforms (IDHm1 and IDHm2) are expressed from the single gene IDH |
| GO:0005829 cytosol | IDA PMID:28827794 Isocitrate protects DJ-1 null dopaminergic cells from oxidat... | ACCEPT | Summary: Cytosolic localization of the IDHc isoform in Drosophila. Reason: Experimental localization of the cytosolic isoform. Supporting Evidence: PMID:28827794 (B) Cytosolic and mitochondrial localization of IDH isoforms. |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Tricarboxylic acid cycle by phylogenetic inference (PTN008982454; donor Mycobacterium tuberculosis Icd P9WKL1). Reason: The only experimental donor is a bacterial NADP-IDH, which is the TCA-cycle isocitrate dehydrogenase in bacteria. In animals the TCA-cycle step is catalysed by the NAD+-dependent isocitrate dehydrogenase complex (Idh3 subunits in flies), and the NADP+-dependent enzymes are regarded as NADPH-producing enzymes. Fly evidence links Idh to NADPH supply and redox balance, not to TCA-cycle flux; the term is therefore an over-annotation for this gene. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: UniProtKB:P9WKL1 SUPPORTS SOURCE BUT NOT TARGET Bacterial Icd is the TCA-cycle IDH; in animals that role is taken by NAD-IDH. |
| GO:0006102 isocitrate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Isocitrate metabolic process by phylogenetic inference (PTN008982454). Reason: Isocitrate is the substrate of the enzyme; the process is directly performed by Idh. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008982454 SUPPORTS TRANSFER |
| GO:0006102 isocitrate metabolic process | IDA DOI:10.1016/0305-0491(80)90023-1 | ACCEPT | Summary: Isocitrate metabolism shown with purified Drosophila NADP-IDH (Williamson 1980). Reason: Purification and characterization of fly NADP-IDH; full text not available here, but the annotation is consistent with the enzyme's established activity. |
| GO:0006102 isocitrate metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: Isocitrate metabolic process from InterPro IPR004790. Reason: Isocitrate is the enzyme's substrate; consistent with the IBA and IDA annotations. |
| GO:0006739 NADP+ metabolic process | IBA GO_REF:0000033 | MODIFY | Summary: NADP+ metabolic process by phylogenetic inference (PTN000214284; donors Arabidopsis cICDH, mouse Idh1). Reason: Correct but general. The specific role of the enzyme in NADP metabolism is reduction of NADP+ to NADPH, i.e. NADPH regeneration (GO:0006740, a child of this term), supported in flies by the reduced NADPH/NADP+ ratio of Idh mutants. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000214284 SUPPORTS TRANSFER Proposed replacements: NADPH regeneration Supporting Evidence: PMID:28827794 IDH catalyzes decarboxylation of isocitrate into Ξ±-ketoglutarate and CO2, and also produces NADPH, which provides a reducing power to antioxidant processes scavenging ROS [29]. PMID:35544578 (C to G) NADP:NADPH ratio (C), relative ROS levels (D), relative caspase 3 activity levels (E), relative mitochondrial free ferrous iron levels (F), and extent of lipid peroxidation (G) of dIDH2-KD1, dIDH2-KD2, and wild-type flies 4 days after eclosure. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: Generic CH-OH oxidoreductase (NAD or NADP acceptor) activity from InterPro. Reason: Correct but uninformative parent of the specific activity GO:0004450, which is already annotated. Proposed replacements: isocitrate dehydrogenase (NADP+) activity |
| GO:0034599 cellular response to oxidative stress | IMP PMID:28827794 Isocitrate protects DJ-1 null dopaminergic cells from oxidat... | KEEP AS NON CORE | Summary: Idh mutants accumulate ROS and are hypersensitive to rotenone; Idh overexpression protects DJ-1 mutants. Reason: Supported by fly genetics; the role follows from NADPH supply for antioxidant systems rather than a dedicated stress-response function, so it is kept as non-core. Supporting Evidence: PMID:28827794 Consistently, the survival rate of IDHP flies radically declined under rotenone treatments showing that IDH is indispensable for sustaining resistance to oxidative stress (Fig 1I). |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | MODIFY | Summary: NAD binding from InterPro IPR019818 (isocitrate/isopropylmalate dehydrogenase conserved site). Reason: The InterPro signature covers both NAD- and NADP-dependent members of the family. This enzyme uses NADP+, not NAD+, as its coenzyme, so the appropriate cofactor term is NADP binding. Proposed replacements: NADP binding Supporting Evidence: file:DROME/Idh/Idh-uniprot.txt Reaction=D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH; |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: What fraction of cytosolic NADPH in fly fat body comes from IDHc compared with G6pd/Pgd and Men, and does this change with diet (sugar versus lipid)?
Q: Do the mitochondrial IDHm isoforms contribute to TCA-cycle isocitrate oxidation in flies, or only to matrix NADPH supply?
Q: Is the complex I assembly defect of Idh knockdown muscle caused by loss of matrix NADPH specifically (IDHm isoforms), and is it shared with Men-b knockdown?
Experiment: Isoform-specific knockouts (IDHc versus IDHm) followed by compartment-resolved NADPH/NADP+ sensors and 13C-isotope tracing of isocitrate/2-oxoglutarate flux.
Hypothesis: IDHc and IDHm supply NADPH to separate compartments and are not functionally redundant.
Loading supporting contentβ¦
Download this section (compressed HTML)Isocitrate dehydrogenase (Idh) encodes a cytosolic enzyme that catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate, with the concomitant reduction of NADP[+] to NADPH. It functions, along with Men, G6pd, and Pgd, in a small network of NADP reducing enzymes. Idh also participates in NADPH regeneration in the mitochondrion and the peroxisome.
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)