LCYB (lycopene beta cyclase, chloroplastic; EC 5.5.1.19; also LCY1, LYC and SZL1) is the single major nuclear-encoded, plastid-targeted lycopene beta-cyclase of Arabidopsis. It is a flavoprotein (FAD/NAD(P)-binding fold) of the lycopene cyclase family that folds the psi end groups of all-trans-lycopene into six-membered beta-ionone rings. Two successive beta-cyclizations convert lycopene, via gamma-carotene, to beta-carotene; acting on the monocyclic delta-carotene made by lycopene epsilon cyclase (LCYE), LCYB adds the beta ring that completes alpha-carotene. The enzyme thus sits at the first committed branch point of cyclic-carotenoid biosynthesis, partitioning flux between the beta,beta-carotenoid branch (beta-carotene and the beta,beta-xanthophylls zeaxanthin, violaxanthin and neoxanthin) and the beta,epsilon branch (alpha-carotene and lutein). Ring formation is redox-neutral: the reduced FAD cofactor assists catalysis rather than being consumed, so LCYB is an intramolecular lyase/isomerase, not an oxidoreductase. The protein carries an N-terminal chloroplast transit peptide and functions as a membrane-associated enzyme of the chloroplast. Cyclic carotenoids made downstream of LCYB are essential structural and photoprotective pigments of the photosynthetic apparatus, and altered LCYB flux changes the carotenoid pigment composition of the plant.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | REMOVE | Summary: PAINT propagation of a mitochondrial location to LCYB from node PTN000350182, whose donors are COQ6-type mitochondrial ubiquinone monooxygenases (yeast COQ6 SGD:S000003487, human COQ6 UniProtKB:Q9Y2Z9, mouse MGI:1924408, PomBase SPBC146.12). Reason: LCYB is a chloroplast/plastid enzyme, not a mitochondrial protein. This IBA derives from PANTHER's HMM placement of Q38933 in the COQ6 family clade (PTHR43876) on the basis of a shared FAD/NAD fold; the plant lycopene cyclase has functionally and compartmentally diverged from the ancestral COQ6 monooxygenase. The target is outside the clade that inherited the mitochondrial ubiquinone function, and there is strong target-specific evidence of a plastid location (transit peptide, curated UniProt subcellular location, and all experimental studies). Over-propagated IBA removed on biological grounds; the correct location is already annotated as chloroplast. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000350182 · COQ6-type monooxygenase ancestral node SUPPORTS SOURCE BUT NOT TARGET Node seeded by COQ6 mitochondrial ubiquinone monooxygenases; the mitochondrial location is correct for those donors but not for the diverged plant lycopene cyclase that PANTHER's per-organism HMM swept into this family (PTHR43876:SF15). Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast |
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: PAINT propagation of ubiquinone biosynthesis to LCYB from the same COQ6-type node PTN000350182 (donors are COQ6/coq6 orthologs, which hydroxylate the ubiquinone ring in mitochondria). Reason: LCYB does not participate in ubiquinone biosynthesis. It is a plastid lycopene beta-cyclase (EC 5.5.1.19) with direct experimental evidence for its actual function. This annotation is the ancestral COQ6 monooxygenase role, inherited by the donors but not by LCYB, which has functionally diverged; the FAD/NAD fold shared with COQ6 caused PANTHER to place LCYB in the COQ6 family. Over-propagated IBA removed on biological grounds. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000350182 · COQ6-type monooxygenase ancestral node SUPPORTS SOURCE BUT NOT TARGET Ubiquinone biosynthesis is the ancestral function of the COQ6 donors at this node; LCYB is a lycopene cyclase and does not inherit it. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt converts lycopene to beta-carotene and |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB/Swiss-Prot subcellular-location vocabulary (SL-0049, chloroplast), mapping the curated UniProt plastid location to GO. Reason: Correct organelle. Consistent with the N-terminal chloroplast transit peptide and the curated UniProt subcellular location; carotenoid cyclization is a plastid function. Core location. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-based (AtSubP) prediction of chloroplast localization. Reason: The prediction agrees with the curated UniProt plastid location and the transit peptide; no conflict. Same core location as the SubCell and TAS annotations. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast |
| GO:0009507 chloroplast | TAS PMID:8837512 Functional analysis of the beta and epsilon lycopene cyclase... | ACCEPT | Summary: Traceable author statement of chloroplast localization from the primary functional characterization of the Arabidopsis beta and epsilon cyclases. Reason: Consistent with all other localization evidence and with the transit peptide. The cached abstract frames lycopene cyclization within the plant plastid photosynthetic membranes; deferring to the curated TAS. Core location. Supporting Evidence: PMID:8837512 Carotenoids with cyclic end groups are essential components of the file:ARATH/LCYB/LCYB-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast |
| GO:0009975 cyclase activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning annotation of the generic parent term 'cyclase activity' (catalysis of a ring-closure reaction). Reason: Correct but uninformatively broad. GO:0009975 is a verified is_a ancestor of the specific, experimentally supported molecular function GO:0045436 lycopene beta cyclase activity (EC 5.5.1.19), which is the appropriate replacement. Proposed replacements: lycopene beta cyclase activity Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt EC=5.5.1.19 file:ARATH/LCYB/LCYB-uniprot.txt Reaction=a carotenoid psi-end derivative = a carotenoid beta-end |
| GO:0016117 carotenoid biosynthetic process | IDA PMID:8837512 Functional analysis of the beta and epsilon lycopene cyclase... | ACCEPT | Summary: Direct assay: heterologous expression of the Arabidopsis beta cyclase in lycopene-accumulating E. coli showed it introduces beta rings at both ends of lycopene to form beta-carotene, establishing participation in carotenoid biosynthesis. Reason: Strong experimental support for participation in carotenoid biosynthesis; LCYB performs a committed cyclization step of the pathway. Core biological process. Supporting Evidence: PMID:8837512 introduces a ring at both ends of lycopene to form the bicyclic PMID:8837512 both enzymes use the linear, symmetrical |
| GO:0016117 carotenoid biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR010108 (Lycopene_cyclase_b/e family) to carotenoid biosynthetic process. Reason: Correct domain-level inference: IPR010108 is the lycopene cyclase family and its members act in carotenoid biosynthesis. Consistent with the IDA annotation and with the mutant pigment phenotypes. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt Belongs to the lycopene cyclase family |
| GO:0016123 xanthophyll biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT propagation of xanthophyll biosynthetic process to the plant lycopene beta-cyclase clade (node PTN001789479, donor plant LCYB UniProtKB:K4C9E2). LCYB forms the beta rings that are subsequently hydroxylated/epoxidized to the beta,beta-xanthophylls. Reason: Real but downstream involvement. LCYB supplies the committed beta-ring precursor of the beta,beta-xanthophyll branch: the hypomorphic szl1 allele has reduced violaxanthin, antheraxanthin and neoxanthin, showing LCYB is required for beta,beta-xanthophyll accumulation. The final xanthophyll chemistry (hydroxylation/epoxidation) is performed by other enzymes, so this is kept as a non-core process; the core molecular function is the cyclase activity itself. Supporting Evidence: PMID:19549928 have low levels of violaxanthin, antheraxanthin, and neoxanthin. |
| GO:0016491 oxidoreductase activity | IBA GO_REF:0000033 | REMOVE | Summary: PAINT propagation of oxidoreductase activity to LCYB from the COQ6-type node PTN000350182 (donors are COQ6 flavin monooxygenases). Reason: LCYB is not an oxidoreductase. Its reaction (lycopene cyclization, EC 5.5.1.19) is redox-neutral: the reduced FAD cofactor assists catalysis but is not consumed, and there is no net change in oxidation state. GO:0016491 is not an is_a ancestor of the true function GO:0045436 (lycopene cyclase sits under the isomerase branch via intramolecular oxidoreductase activity, not under EC 1 oxidoreductase). This IBA is the ancestral COQ6 monooxygenase activity inherited by the donors but not by the diverged plant cyclase; over-propagated IBA removed on biological grounds. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000350182 · COQ6-type monooxygenase ancestral node SUPPORTS SOURCE BUT NOT TARGET Oxidoreductase (monooxygenase) activity is correct for the COQ6 donors; LCYB catalyzes a redox-neutral cyclization and does not inherit it. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt EC=5.5.1.19 |
| GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping assigning a monooxygenase-type activity (incorporation or reduction of molecular oxygen) to the lycopene cyclase domain IPR010108. Reason: Incorrect activity for LCYB. Lycopene beta cyclase (EC 5.5.1.19) is an intramolecular lyase that closes beta-ionone rings; it does not incorporate or reduce molecular oxygen and performs no monooxygenase reaction. GO:0016705 is not an is_a ancestor of the true molecular function. This InterPro2GO mapping assigns an activity the protein does not have; removed on biological grounds. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt Reaction=a carotenoid psi-end derivative = a carotenoid beta-end |
| GO:0016860 intramolecular oxidoreductase activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning annotation of 'intramolecular oxidoreductase activity', a subclass of isomerase activity. Reason: Correct but uninformatively broad. GO:0016860 is a verified is_a ancestor of the specific molecular function GO:0045436 lycopene beta cyclase activity (the lycopene cyclase belongs to the isomerase/intramolecular-lyase branch). Replace with the specific, experimentally supported term. Proposed replacements: lycopene beta cyclase activity Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt EC=5.5.1.19 |
| GO:0045436 lycopene beta cyclase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of lycopene beta cyclase activity to the LCYB clade at node PTN001789482, seeded by the Arabidopsis LCYB locus itself (AGI_LocusCode:AT3G10230). Reason: The correct, appropriately specific molecular function, inherited across plant lycopene beta-cyclases and directly demonstrated for this gene. The appearance of AT3G10230 (LCYB itself) in the WITH/FROM is the expected marker that experimental grounding exists on the target, not circular. Core molecular function. Supporting Evidence: file:ARATH/LCYB/LCYB-uniprot.txt Reaction=a carotenoid psi-end derivative = a carotenoid beta-end PMID:8837512 introduces a ring at both ends of lycopene to form the bicyclic |
| GO:0045436 lycopene beta cyclase activity | IDA PMID:19549928 Lutein accumulation in the absence of zeaxanthin restores no... | ACCEPT | Summary: Direct evidence: the szl1 suppressor was mapped to a point mutation in the LCYB gene, and pigment analysis established LCYB as the major lycopene beta-cyclase of Arabidopsis (the hypomorphic Gly451Glu enzyme retains reduced activity). Reason: Experimental (IDA) support for the defining molecular function of the gene. The allele-specific pigment phenotype (reduced beta,beta-xanthophylls, increased lutein/alpha-carotene) directly reflects reduced beta-cyclase activity. Core molecular function. Supporting Evidence: PMID:19549928 contains a point mutation in the lycopene beta-cyclase (LCYB) gene. PMID:19549928 LCYB appears to be the major lycopene beta-cyclase and is not |
| GO:0045436 lycopene beta cyclase activity | IDA PMID:8837512 Functional analysis of the beta and epsilon lycopene cyclase... | ACCEPT | Summary: Direct biochemical demonstration: the Arabidopsis beta cyclase expressed in lycopene-accumulating E. coli introduces beta rings at both ends of lycopene to form bicyclic beta-carotene (EC 5.5.1.19). Reason: The primary experimental establishment of the gene's molecular function. Core molecular function. Supporting Evidence: PMID:8837512 introduces a ring at both ends of lycopene to form the bicyclic file:ARATH/LCYB/LCYB-uniprot.txt EC=5.5.1.19 |
| GO:1901812 beta-carotene biosynthetic process | IDA PMID:8837512 Functional analysis of the beta and epsilon lycopene cyclase... | NEW | Summary: Proposed new annotation. LCYB catalyzes the two beta-cyclizations that convert all-trans-lycopene, via gamma-carotene, to beta-carotene, i.e. it performs the committed ring-forming chemistry of beta-carotene formation. Reason: LCYB does the actual work of beta-carotene biosynthesis (it catalyses the cyclization steps that form the two beta rings), so it participates in the process rather than merely supplying a substrate; the participation test is satisfied. beta-carotene biosynthetic process is the defining product-level term for a lycopene beta-cyclase and is not currently in the annotation set. Directly supported by the Cunningham 1996 heterologous assay and by the UniProt beta-carotene biosynthesis pathway. GO:1901812 is a descendant of GO:0016117 and is more specific than the carotenoid-level term. Supporting Evidence: PMID:8837512 introduces a ring at both ends of lycopene to form the bicyclic file:ARATH/LCYB/LCYB-uniprot.txt Carotenoid biosynthesis; beta-carotene biosynthesis. |
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Download this section (compressed HTML)Q: What is the sub-plastidial location and membrane topology of Arabidopsis LCYB in vivo, and does it act at the chloroplast envelope, the thylakoid, or both? Chloroplast localization is well supported, but the exact intraplastid site of the membrane-associated cyclase for Q38933 is unresolved.
Suggested experts: Barry J. Pogson, Manuel Rodriguez-Concepcion
Q: How is carbon partitioning at the lycopene branch point controlled between LCYB (beta,beta) and LCYE (beta,epsilon), and what determines whether LCYB adds one or two beta rings? The 1996 work established the branch point but the kinetic and regulatory basis of partitioning in planta is not quantified.
Suggested experts: Francis X. Cunningham
Experiment: Express and purify mature His-tagged Arabidopsis LCYB, reconstitute in liposomes with FAD, and assay against all-trans-lycopene and against delta-carotene (with LCYE) following gamma-carotene, beta-carotene and alpha-carotene intermediates and products by C30 reversed-phase HPLC-PDA/MS; test FAD dependence and confirm the absence of net redox change and oxygen consumption.
Hypothesis: Arabidopsis LCYB is an FAD-dependent, redox-neutral lycopene beta-cyclase that converts all-trans-lycopene to beta-carotene via gamma-carotene and adds the beta ring to delta-carotene to form alpha-carotene.
Type: in vitro enzyme assay with purified recombinant protein
Experiment: Localize a native-promoter LCYB-GFP fusion (complementing szl1) by confocal imaging and by immunoblot of purified envelope/stroma/thylakoid fractions; compare carotenoid profiles (beta-carotene, zeaxanthin, violaxanthin, neoxanthin, lutein, alpha-carotene) in wild type, szl1 and LCYB-overexpression backgrounds by HPLC.
Hypothesis: LCYB resides in a specific chloroplast membrane compartment and its loss reduces beta,beta-xanthophylls while redirecting flux to the lutein branch.
Type: subcellular localization plus metabolite profiling of mutant and overexpression lines
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