Men-b (CG5889, also called dME3) encodes a Drosophila melanogaster malic enzyme paralogous to the cytosolic Men. It has the malic enzyme N-terminal and NAD(P)-binding domains and an N-terminal extension rich in basic and hydroxylated residues typical of a mitochondrial presequence, and it is most similar to the mitochondrial NADP+-dependent malic enzyme ME3 of mammals. By homology it is expected to oxidatively decarboxylate (S)-malate to pyruvate and CO2 with reduction of NADP+ to NADPH in the mitochondrial matrix. Its catalytic properties, cofactor preference and localization have not been determined experimentally in flies. Knockdown of Men-b in flight muscle impairs assembly of mitochondrial respiratory complex I, as does loss of the mitochondrial NADP-isocitrate dehydrogenase, suggesting that matrix NADPH supply supports complex I biogenesis; Men-b knockdown also causes early adult lethality and, in a genome-scale RNAi screen, altered circulating sugar levels.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004470 malic enzyme activity | IEA GO_REF:0000120 | MODIFY | Summary: Malic enzyme activity from ARBA/InterPro. Reason: Correct but general; the NADP-specific activity GO:0004473 is already annotated (IBA, ISS). Proposed replacements: malate dehydrogenase (decarboxylating) (NADP+) activity |
| GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: NADP-malic enzyme activity by phylogenetic inference (donors include fly Men, mouse Me1/Me2/Me3, Arabidopsis NADP-MEs). Reason: Men-b sits in the animal malic enzyme clade with experimentally characterized NADP-dependent enzymes and retains the catalytic and dinucleotide-binding domains. Accepted as the predicted core activity; not assayed for the fly protein. Support is family membership (PIRSF000106 malic enzyme, Pfam malic and Malic_M domains, PIRSR-predicted proton-donor active site) plus the statement that Men-b is the fly ortholog of ME3, an NADP+-using malic enzyme (PMID:35544578); the NADP+ specificity rests on the mammalian ortholog. Propagation Review Root cause: NO FAILURE CORE Supporting Evidence: file:DROME/Men-b/Men-b-uniprot.txt PIRSF; PIRSF000106; ME; 1. file:DROME/Men-b/Men-b-uniprot.txt Pfam; PF00390; malic; 1. PMID:35544578 CG5889 (Men-b) is the Drosophila ortholog of ME3. PMID:35544578 ME1 and ME3 use NADP+ as a cofactor, while ME2 can use either NADP+ or NAD+. |
| GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity | ISS GO_REF:0000024 | ACCEPT | Summary: NADP-malic enzyme activity transferred from human ME3 (Q16798). Reason: Orthology-based transfer consistent with the IBA call; predicted core activity. Supporting Evidence: PMID:35544578 CG5889 (Men-b) is the Drosophila ortholog of ME3. PMID:35544578 ME1 and ME3 use NADP+ as a cofactor, while ME2 can use either NADP+ or NAD+. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | MODIFY | Summary: Mitochondrial localization by phylogenetic inference (PTN001157886; donors mouse Me2/Me3, rat, human ME2). Reason: Plausible for Men-b, which has a presequence-like N-terminus and is most similar to mitochondrial ME3. The compartment of mitochondrial malic enzymes is the matrix, already annotated to Men-b by ISS from mouse Me3, so mitochondrial matrix is the more specific term. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001157886 SUPPORTS TRANSFER Mitochondrial ME2/ME3 node; consistent with Men-b's presequence-like N-terminus. Proposed replacements: mitochondrial matrix |
| GO:0005759 mitochondrial matrix | ISS GO_REF:0000024 | ACCEPT | Summary: Mitochondrial matrix localization transferred from mouse Me3 (Q8BMF3). Reason: Consistent with the presequence-like N-terminus of Men-b (MFSRPSLCGTVGKLCRCG...) and its similarity to ME3; not tested in flies. Supporting Evidence: PMID:35544578 ME1 is localized to the cytosol, while ME2 and ME3 are located in the mitochondrion. |
| GO:0006108 malate metabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: Malate metabolic process transferred from human ME3. Reason: Malate is the substrate of the predicted activity; same treatment as for Men. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000120 | MODIFY | Summary: Generic CH-OH oxidoreductase (NAD or NADP acceptor) activity from ARBA/InterPro. Reason: Correct but uninformative; replace with GO:0004473, already annotated. Proposed replacements: malate dehydrogenase (decarboxylating) (NADP+) activity |
| GO:0042593 glucose homeostasis | IMP PMID:25994086 Drosophila glucome screening identifies Ck1alpha as a regula... | KEEP AS NON CORE | Summary: RNAi knockdown in the glucome screen altered circulating glucose. Reason: Abstract-only screen result (about 160 hyperglycaemia candidates among about 1000 genes); a systemic phenotype that is likely an indirect metabolic consequence. Kept as non-core in deference to the curator. Supporting Evidence: PMID:25994086 Partial genomic screens of ∼1,000 genes yield ∼160 hyperglycaemia 'flyabetes' candidates |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | MODIFY | Summary: NAD binding from the malic enzyme NAD-binding domain signature (IPR012302). Reason: The InterPro domain covers both NAD- and NADP-dependent malic enzymes; by orthology to ME3 (and as annotated by ISS) Men-b is NADP-dependent, so NADP binding is the appropriate cofactor term. Cofactor preference has not been measured for the fly protein. Proposed replacements: NADP binding Supporting Evidence: PMID:35544578 ME1 and ME3 use NADP+ as a cofactor, while ME2 can use either NADP+ or NAD+. |
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Download this section (compressed HTML)Q: Is Men-b NADP- or NAD-dependent (ME3-like or ME2-like), is it imported into mitochondria, and in which tissues is it expressed relative to Men?
Q: Is the complex I assembly defect after Men-b knockdown caused by loss of matrix NADPH (as proposed for IDH2), and can it be rescued by an NADPH-generating enzyme targeted to mitochondria?
Experiment: Express Men-b recombinantly and measure kinetics with NAD+ and NADP+; tag endogenous Men-b and image co-localization with a mitochondrial matrix marker.
Hypothesis: Men-b is a mitochondrial NADP-malic enzyme.
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Download this section (compressed HTML)Malic enzyme b (Men-b) encodes a mitochondrial enzyme that catalyzes the oxidation of malate to pyruvate, with the concomitant reduction of NADP[+] to NADPH. It is involved in NADPH regeneration.
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