LCYE (lycopene epsilon cyclase, also LUT2/LUTEIN DEFICIENT 2; EC 5.5.1.18) is a nuclear-encoded, plastid-targeted, membrane-associated flavoenzyme of the lycopene cyclase family that acts at the central branch point of carotenoid biosynthesis. It forms a single epsilon ring at one psi-end of all-trans-lycopene, converting the symmetrical linear lycopene into the monocyclic delta-carotene (and, correspondingly, neurosporene into alpha-zeacarotene). Together with the related lycopene beta cyclase (LCYB), which forms beta rings, LCYE commits carotenoid flux into the beta,epsilon (alpha-carotene) branch: delta-carotene is beta-cyclized by LCYB to alpha-carotene, which is then hydroxylated on both rings to give zeinoxanthin and ultimately lutein, the most abundant xanthophyll of the photosynthetic light-harvesting antenna. Unlike the bicyclic beta cyclase, plant LCYE normally adds only one ring; a single residue (Arabidopsis Leu-448) acts as a molecular switch, and its substitution to His or Arg converts the enzyme into a bi-epsilon-cyclase. The mature protein carries an N-terminal chloroplast transit peptide and functions as a multi-pass membrane protein of the plastid (chloroplast) membrane, where its hydrophobic carotenoid substrates reside. Loss of LCYE (the lut2 mutant) abolishes lutein, redirecting flux to beta,beta xanthophylls (violaxanthin, antheraxanthin), and impairs the rapid induction of nonphotochemical quenching, though single mutants remain viable with near-wild-type photosynthesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-based (AtSubP) prediction of chloroplast localization. Consistent with the N-terminal chloroplast transit peptide and the plastid location of carotenoid biosynthesis. Reason: Correct organelle for a plastid-targeted carotenoid biosynthetic enzyme; agrees with the curated UniProt subcellular location and the TAS annotation. Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt Plastid, chloroplast membrane |
| GO:0009507 chloroplast | TAS PMID:8837512 Functional analysis of the beta and epsilon lycopene cyclase... | ACCEPT | Summary: Traceable-author-statement chloroplast localization from the paper that first identified and functionally analysed the Arabidopsis beta and epsilon lycopene cyclases. Carotenoid cyclization occurs in the plastid. Reason: Correct location, consistent with the transit peptide, the membrane sub-location and the ISM prediction. Retained as a core location (parent of chloroplast membrane). Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt Plastid, chloroplast membrane |
| GO:0009975 cyclase activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning electronic annotation to the generic parent 'cyclase activity'. GO:0009975 is a verified is_a ancestor of the specific lycopene epsilon cyclase activity, so the term is correct but uninformatively broad. Reason: The gene has a precise, experimentally established molecular function, lycopene epsilon cyclase activity (GO:0045435, EC 5.5.1.18), which is the appropriate specific replacement for the generic 'cyclase activity'. Proposed replacements: lycopene epsilon cyclase activity Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt EC=5.5.1.18 file:ARATH/LCYE/LCYE-uniprot.txt epsilon-cyclization reaction which converts lycopene to delta-carotene |
| GO:0016117 carotenoid biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR010108 (lycopene cyclase beta/epsilon family) to the carotenoid biosynthetic process. LCYE performs a committed cyclization step of carotenoid biosynthesis, so the process term is correct and appropriately specific. Reason: Correct domain-level inference that agrees with the experimental IMP annotation and the mutant pigment phenotypes. Core biological process. Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt Involved in carotenoid biosynthesis. Catalyzes the single |
| GO:0016117 carotenoid biosynthetic process | IMP PMID:8837513 Arabidopsis carotenoid mutants demonstrate that lutein is no... | ACCEPT | Summary: Mutant-phenotype (IMP) evidence from the lut2 carotenoid mutants: loss of epsilon-ring cyclization eliminates lutein and reroutes carotenoid flux to beta,beta-carotenoids, establishing participation of the epsilon cyclase in carotenoid biosynthesis in planta. Reason: Strong experimental support for participation in carotenoid biosynthesis; the lut2 locus cosegregates with the epsilon cyclase gene and its biochemical phenotype is a block in epsilon ring cyclization. Core biological process. Supporting Evidence: PMID:8837513 phenotype is consistent with a disruption of epsilon ring cyclization. PMID:8837513 locus cosegregates with the recently isolated epsilon cyclase gene |
| GO:0016123 xanthophyll biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT phylogenetic propagation of xanthophyll biosynthetic process to the plant lycopene epsilon-cyclase clade at node PTN008674247. LCYE forms the epsilon ring that is the defining structural feature of the beta,epsilon-xanthophyll lutein, committing flux into the branch that yields it. The Arabidopsis locus appearing in its own WITH/FROM marks that experimental grounding exists on the target and is not circular. Reason: Sound node placement: the epsilon cyclase is required for and structurally contributes to the beta,epsilon-xanthophyll branch (lutein), and the target carries direct experimental evidence for the cyclase activity. The acts_upstream_of_or_within-style relationship is appropriate for an enzyme that acts just before the dedicated ring-hydroxylation steps of xanthophyll formation. Supporting Evidence: PMID:8837513 lutein biosynthesis but not for the biosynthesis of beta, beta-carotenoids. file:ARATH/LCYE/LCYE-uniprot.txt Required for lutein biosynthesis (PubMed:9789087). |
| GO:0016123 xanthophyll biosynthetic process | IGI PMID:16890225 Elucidation of the beta-carotene hydroxylation pathway in Ar... | ACCEPT | Summary: Genetic-interaction (IGI) evidence from combinatorial mutants of the carotenoid ring hydroxylases (CHY1/AT4G25700, CHY2/AT5G52570) with LUT2 and LUT5. Building chy1chy2lut2 and related combinations to dissect the xanthophyll (hydroxylation) pathway places LUT2 (the epsilon cyclase) within xanthophyll biosynthesis. Reason: Experimental genetic-interaction annotation from a paper that explicitly used the lut2 lycopene epsilon-cyclase mutant to elucidate the beta,epsilon-xanthophyll hydroxylation pathway; the cyclase supplies the epsilon-ring substrate for the lutein-forming hydroxylations. Deferring to the curator's IGI. Core process. Supporting Evidence: PMID:16890225 constructed double and triple mutant combinations in CHY1, CHY2, LUT1, LUT5 and |
| GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from IPR010108 to a monooxygenase-type activity. This is a wrong molecular function for LCYE: the enzyme is an intramolecular cyclase/isomerase (EC 5.5.1.18) whose reaction (a carotenoid psi-end derivative = a carotenoid epsilon-end derivative) incorporates no molecular oxygen and involves no net redox. Reason: GO:0016705 is not an is_a ancestor of lycopene epsilon cyclase activity (GO:0045435); verified ancestry places the specific term under cyclase activity and intramolecular oxidoreductase/isomerase activity, not under this paired-donor oxygenase. The lycopene cyclase family shares a FAD/NAD-binding fold with FAD-dependent oxygenases, which led InterPro2GO to assign an oxygenase activity the protein does not have. The correct molecular function is captured by the GO:0045435 annotation and by the MODIFY of GO:0009975 and GO:0016860. Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt a carotenoid psi-end derivative = a carotenoid epsilon-end file:ARATH/LCYE/LCYE-uniprot.txt EC=5.5.1.18 |
| GO:0016860 intramolecular oxidoreductase activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA electronic annotation to 'intramolecular oxidoreductase activity'. Verified GO ancestry shows this is a true is_a parent of lycopene epsilon cyclase activity (GO places the plant lycopene cyclases under intramolecular oxidoreductase / isomerase activity), so the term is correct but uninformatively broad. Reason: Correct branch but too general. The specific, experimentally supported molecular function is lycopene epsilon cyclase activity (GO:0045435, EC 5.5.1.18), which is the appropriate replacement. Not removed, because GO:0016860 genuinely subsumes the specific term in the current ontology. Proposed replacements: lycopene epsilon cyclase activity Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt EC=5.5.1.18 file:ARATH/LCYE/LCYE-uniprot.txt epsilon-cyclization reaction which converts lycopene to delta-carotene |
| GO:0031969 chloroplast membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB/Swiss-Prot subcellular-location vocabulary (SL-0053, chloroplast membrane). LCYE is a multi-pass membrane protein of the plastid membrane, where its hydrophobic carotenoid substrates reside. Reason: Correct and more specific than the parent 'chloroplast' location; consistent with the two predicted transmembrane helices and the curated UniProt membrane sub-location. Core location. Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt Plastid, chloroplast membrane file:ARATH/LCYE/LCYE-uniprot.txt Multi-pass membrane protein |
| GO:0045435 lycopene epsilon cyclase activity | TAS PMID:8837513 Arabidopsis carotenoid mutants demonstrate that lutein is no... | ACCEPT | Summary: Traceable-author-statement annotation of the defining molecular function: cyclization of one psi-end of all-trans-lycopene to an epsilon ring, giving monocyclic delta-carotene (EC 5.5.1.18). The activity was demonstrated by heterologous expression of the Arabidopsis epsilon cyclase and further dissected by single-residue mutagenesis. Reason: The precise, experimentally established core molecular function of the gene. Directly supported by functional analysis in E. coli and by the lut2 loss-of-function pigment phenotype. Core molecular function. Supporting Evidence: file:ARATH/LCYE/LCYE-uniprot.txt epsilon-cyclization reaction which converts lycopene to delta-carotene PMID:11226339 adds one epsilon-ring to the symmetrical linear substrate lycopene PMID:8837512 forming the monocyclic delta-carotene (epsilon, psi-carotene) |
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Download this section (compressed HTML)Q: Where within the chloroplast does LCYE act (envelope versus thylakoid membrane), and does it function as a monomer or an oligomer? The single-residue ring-number switch and the membrane orientation of lycopene suggest subunit interactions may set mono- versus bi-cyclization, but no LCYE-specific fractionation, structure, or complex has been reported.
Suggested experts: Francis X. Cunningham Jr., Barry J. Pogson
Q: Should Arabidopsis LCYE carry a more specific process annotation, alpha-carotene biosynthetic process (GO:1901824)? LCYE forms the epsilon ring of alpha-carotene, but that term is a descendant of carotenoid biosynthetic process (GO:0016117) which LCYE already carries, so it was not proposed here to avoid redundancy; a curator may wish to add the more specific term.
Suggested experts: Joseph Hirschberg
Experiment: Express and purify the mature (transit-peptide-cleaved) His-tagged Arabidopsis LCYE and the L448H/L448R variants, reconstitute in liposomes with reduced FAD, and assay against all-trans-lycopene (and neurosporene); follow delta-carotene versus epsilon-carotene product ratios and determine Km/kcat by C30 reversed-phase HPLC-PDA/MS. Complements the prior E. coli color-complementation data with quantitative in vitro kinetics.
Hypothesis: Arabidopsis LCYE is a strictly mono-epsilon-cyclase that converts all-trans-lycopene to delta-carotene using reduced FAD, and Leu-448 alone determines the single-ring outcome.
Type: in vitro enzyme assay with purified recombinant protein
Experiment: Localise a native-promoter LCYE-GFP fusion (complementing lut2) by confocal imaging and by immunoblot of purified envelope/stroma/thylakoid fractions, and test physical/functional interaction with LCYB and the LUT1/LUT5/CHY hydroxylases by co-immunoprecipitation and by carotenoid profiling of the corresponding higher-order mutants.
Hypothesis: LCYE resides in a specific plastid membrane subcompartment and channels lycopene toward the beta,epsilon branch in coordination with LCYB and the downstream ring hydroxylases.
Type: subcellular localization plus interaction and metabolite profiling
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