Echs1 (Q0E987, Drosophila melanogaster) research notes

Drosophila melanogaster Echs1 / CG6543 (FlyBase FBgn0033879; UniProt Q0E987, unreviewed TrEMBL). Ortholog of human ECHS1 (P30084), short-chain enoyl-CoA hydratase 1 / mitochondrial "crotonase"; EC 4.2.1.17. Gene on chromosome 2R. Encodes two isoforms (A = AAF58326.1, B = AAF58327.1).

Identity / orthology

• UniProt entry name Q0E987_DROME, SubName "Enoyl-CoA hydratase, short chain 1, isoform A/B", with EC=4.2.1.17 and EC=4.2.1.116 assigned from EMBL records [Echs1-uniprot.txt: "EC=4.2.1.17 {ECO:0000313|EMBL:AAF58326.1, ECO:0000313|EMBL:AAF58327.1}"].
• Gene symbol Echs1 and ORF name CG6543, FlyBase FBgn0033879 [Echs1-uniprot.txt GN lines]. AGR/CTD cross-reference to human gene CTD:1892 (ECHS1) [Echs1-uniprot.txt: "DR CTD; 1892; -."].
• Domain architecture: crotonase-like fold — CDD cd06558 "crotonase-like"; Pfam PF00378 ECH_1; InterPro IPR001753 Enoyl-CoA_hydra/iso, IPR014748 Enoyl-CoA_hydra_C, IPR018376 Enoyl-CoA_hyd/isom_CS; PROSITE PS00166 ENOYL_COA_HYDRATASE; PANTHER PTHR11941:SF54 "ENOYL-COA HYDRATASE, MITOCHONDRIAL"; SUPFAM SSF52096 ClpP/crotonase [Echs1-uniprot.txt DR lines]. This is the canonical short-chain enoyl-CoA hydratase (crotonase) signature.
• The fly protein is 295 aa with an N-terminal region rich in Arg/Ser resembling a mitochondrial targeting presequence (MANIAKIFAS RAQCVLQAAA RQPQVATRFS SSS...) [Echs1-uniprot.txt SQ]. Consistent with a matrix enzyme, though the transit peptide is not experimentally annotated in this TrEMBL entry.

Core enzymatic function (by orthology to human ECHS1)

Human ECHS1 catalyses the second step of the mitochondrial beta-oxidation spiral: reversible hydration of a 2-trans-enoyl-CoA to the corresponding (3S)-3-hydroxyacyl-CoA (EC 4.2.1.17), acting on short/medium-chain substrates (C4-C16) with highest efficiency toward crotonyl-CoA. It also hydrates branched-chain amino acid pathway intermediates (methacrylyl-CoA/acryloyl-CoA from valine; 3-methylcrotonyl-CoA from leucine; tiglyl-CoA from isoleucine).

• PMID:26251176.
• PMID:26251176.

The fly UniProt DR block records the corresponding GO/pathway assignments: enoyl-CoA hydratase activity (GO:0004300, ISS), 3-hydroxypropionyl-CoA dehydratase activity (GO:0043956, ISS), fatty acid beta-oxidation (GO:0006635, ISS), L-valine catabolic process (GO:0006574, IMP), and mitochondrion (GO:0005739, IDA) [Echs1-uniprot.txt DR GO lines]. Reactome links the fly gene to "Branched-chain amino acid catabolism" (R-DME-70895) and to the beta-oxidation spiral steps (R-DME-77310/77346/77348/77350/77352) [Echs1-uniprot.txt DR Reactome lines].

GOA annotations under review (Echs1-goa.tsv)

Only two GOA annotations, both IEA:

1. GO:0003824 catalytic activity — IEA, GO_REF:0000002 (InterPro IPR018376). Root-level MF placeholder; correct but uninformative, subsumed by enoyl-CoA hydratase activity. Action: MARK_AS_OVER_ANNOTATED (matches human ECHS1 review handling of the same InterPro-derived term).
2. GO:0004300 enoyl-CoA hydratase activity — IEA, GO_REF:0000120 (ARBA:ARBA00086629 | EC:4.2.1.17). This is the defining/core molecular function, assigned from the EC number. Action: ACCEPT. Supported by ortholog biochemistry (PMID:26251176) and by functional rescue of the fly mutant by a human ECHS1 transgene (Mele et al. 2025).

(Note: the UniProt DR block lists further FlyBase GO annotations — GO:0005739 mitochondrion IDA, GO:0006574 L-valine catabolic process IMP, GO:0006635 fatty acid beta-oxidation ISS, GO:0043956 3-hydroxypropionyl-CoA dehydratase ISS — but these are NOT present in the QuickGO GOA export (Echs1-goa.tsv), so per instructions they are not added as existing_annotations. They inform the description and core_functions.)

Drosophila functional evidence (ortholog grounding)

• PMID:40056416 (Li et al., Cell Rep 2025; abstract-only, full_text_available: false): HIBCH and ECHS1 are "two Leigh syndrome genes"; their loss in cultured cells causes "abnormal mitochondrial morphology and respiratory defects." Directly in Drosophila: "Fly eyes lacking either protein exhibit age-dependent degeneration." "Elevated lysine methacrylation (Kmea) is observed in both HIBCH- and ECHS1-deficient cells and fly tissues." Mechanistically, loss of ECHS1 lets the valine-pathway intermediate methacrylyl-CoA accumulate and drive ectopic protein lysine methacrylation. This paper is the basis for the FlyBase IMP annotation to L-valine catabolic process and is a strong, organism-matched support for the fly gene's role in valine catabolism.
• Mele et al. 2025, J Inherit Metab Dis (doi:10.1002/jimd.12840; biorxiv 2024.08.15.608013) — NOT cached, cited from notes only: a Drosophila model of Echs1 (CG6543) deficiency; "Echs1 null larvae recapitulated human ECHS1D phenotypes including poor motor behaviour and early mortality and could be rescued by the expression of a human ECHS1 transgene," and valine dietary restriction extends survival. This establishes functional orthology (human ECHS1 rescues fly Echs1 loss) and confirms the valine-catabolism connection in the fly. Because it is not in the publications/ cache, it is used only as background here, not as verbatim supporting_text for annotations.

Decisions summary

• Enzyme is the fly crotonase (EC 4.2.1.17); core MF = enoyl-CoA hydratase activity (GO:0004300). ACCEPT the GOA IEA for it.
• Root "catalytic activity" (GO:0003824) is over-annotated relative to the specific hydratase term. MARK_AS_OVER_ANNOTATED.
• Core BP = fatty acid beta-oxidation (GO:0006635) and L-valine catabolic process (GO:0006574) by orthology + fly genetic evidence (PMID:40056416; Mele 2025). These are captured in core_functions but NOT added to existing_annotations because they are absent from the GOA export.
• Localization: mitochondrion (matrix, by orthology); not in GOA export, so not an existing_annotation, but noted for description.