PSY (PSY1, At5g17230) is the single phytoene synthase of Arabidopsis thaliana, a nuclear-encoded, plastid-imported enzyme of the phytoene/squalene synthase family (EC 2.5.1.32). It catalyses the first committed step of carotenoid biosynthesis, the head-to-head condensation of two molecules of the C20 isoprenoid geranylgeranyl diphosphate via prephytoene diphosphate to give the C40 carotene 15-cis-phytoene and two diphosphate. Phytoene is then desaturated, isomerised and cyclised by PDS, Z-ISO, ZDS, CRTISO and the lycopene cyclases to the carotenes and xanthophylls that serve as photosynthetic accessory pigments and photoprotectants and as precursors of abscisic acid and strigolactones. PSY is synthesised as a 422-residue precursor with an N-terminal chloroplast transit peptide and functions as a peripheral membrane protein of the chloroplast; active PSY is membrane associated and its in vitro activity depends on a supply of GGPP from a separate GGPP synthase. PSY is the main flux-controlling enzyme of the pathway: seed- or tissue-specific overexpression drives massive carotenoid accumulation in non-photosynthetic tissues, whereas leaf carotenoid content is buffered. The amount and activity of PSY protein are regulated post-transcriptionally: the ORANGE proteins OR and OR-like bind PSY directly and are required to maintain active PSY protein levels, and FIBRILLIN6 binds PSY and stimulates its catalytic activity in chloroplasts, especially during de-etiolation and high-light acclimation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004311 geranylgeranyl diphosphate synthase activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO transfer from IPR044843 (trans-isoprenyl diphosphate synthases, bacterial-type), a superfamily-level entry whose GO mapping describes the head-to-tail prenyl elongation (FPP + IPP -> GGPP) carried out by GGPP synthases. PSY is a head-to-head condensing enzyme that consumes GGPP as its substrate; it does not synthesise GGPP. Reason: The mapped activity is that of a different enzyme class within the isoprenoid synthase fold. The Rhea reaction curated for P37271 (RHEA:34475, 2 GGPP = 15-cis-phytoene + 2 diphosphate) has GGPP as substrate, not product, and the direct Arabidopsis assay in PMID:25675505 had to add recombinant GGPP synthase because PSY in chloroplast membranes cannot make GGPP itself. This is an over-broad InterPro family mapping assigning a paralogous activity the protein does not have. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG GRANULARITY MISMATCH Sources checked: InterPro:IPR044843 Β· Trans-isoprenyl diphosphate synthases, bacterial-type SUPPORTS SOURCE BUT NOT TARGET The entry spans head-to-tail prenyltransferases (true GGPP synthases) and head-to-head synthases (squalene/phytoene synthases); the GO:0004311 mapping is correct for the former and wrong for PSY. Supporting Evidence: PMID:25675505 Here PSY activity was exclusively found membrane bound and required addition of active GGPP synthase for in vitro assay. PMID:26224804 The first committed step in the carotenoid biosynthesis pathway is the condensation of two geranylgeranyl diphosphate molecules to phytoene catalyzed by phytoene synthase (PSY). file:ARATH/PSY/PSY-uniprot.txt Xref=Rhea:RHEA:34475, ChEBI:CHEBI:27787, |
| GO:0005515 protein binding | IPI PMID:25675505 Arabidopsis OR proteins are the major posttranscriptional re... | REMOVE | Summary: Direct physical interaction of PSY with the ORANGE protein AtOR (At5g61670, UniProtKB:Q8VYD8) shown by co-IP/MS, split-ubiquitin yeast two-hybrid, co-IP in N. benthamiana and BiFC in chloroplasts. OR and OR-like act as post-transcriptional regulators that maintain the level of enzymatically active PSY. Reason: The interaction is real and biologically important, but a bare protein binding term carries no functional information about PSY. On the PSY side the interaction represents PSY being stabilised/regulated; the paper explicitly states that OR proteins are not molecular chaperones, so no more informative molecular-function term (e.g. chaperone binding) is licensed for PSY from this evidence. The informative annotation belongs on OR (the regulator). Removal does not deny the interaction. Supporting Evidence: PMID:25675505 Both Arabidopsis OR proteins interacted directly with PSY ( Fig. 1 A ). PMID:25675505 Although the OR proteins carry a DnaJ cysteine-rich zinc figure domain, they are not molecular chaperones due to the lack of the DnaJ-like defining J domain. |
| GO:0005515 protein binding | IPI PMID:25675505 Arabidopsis OR proteins are the major posttranscriptional re... | REMOVE | Summary: Direct physical interaction of PSY with AtOR-like (At5g06130, UniProtKB:Q9FKF4) shown by split-ubiquitin yeast two-hybrid and BiFC in chloroplasts; OR and OR-like are redundantly required to maintain PSY protein levels in vivo. Reason: Same reasoning as for the OR interaction: the binding is genuine but the generic term is uninformative for PSY, and the paper supports no more specific molecular function on the PSY side. The regulatory function is properly captured on OR-like. Removal does not deny the interaction. Supporting Evidence: PMID:25675505 Both Arabidopsis OR proteins interacted directly with PSY ( Fig. 1 A ). PMID:25675505 The results indicated that AtOR and AtOR-like were sufficient and required to regulate PSY protein levels in vivo, and that AtOR and AtOR-like were functionally redundant. |
| GO:0005515 protein binding | IPI PMID:37966976 Arabidopsis FIBRILLIN6 influences carotenoid biosynthesis by... | REMOVE | Summary: Direct physical interaction of PSY with FIBRILLIN6 (FBN6, At5g19940) shown by co-immunoprecipitation and co-localisation in chloroplasts. FBN6 binding stimulates PSY catalytic activity in E. coli and in planta without changing PSY protein abundance or folding. Reason: The interaction is well supported, but the generic protein binding term carries no functional information about PSY. The functionally informative side of this pair is FBN6 (an activator of PSY); there is no GO molecular function for an enzyme being activated by a partner, so no MODIFY target exists for PSY. Removal does not deny the interaction. Supporting Evidence: PMID:37966976 Arabidopsis FBN6 was found to be among the proteins co-immunoprecipitated with a GFP-tagged version of phytoene synthase (PSY), the first and main rate-determining enzyme of the carotenoid pathway (Welsch et al. 2018). PMID:37966976 our data support the conclusion that FBN6 plays a physiologically relevant role in carotenoid biosynthesis in Arabidopsis chloroplasts by physically binding to PSY to promote its enzymatic activity. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: High-throughput chloroplast proteomics of Arabidopsis rosette chloroplasts (1325 proteins identified unambiguously). The cached main text does not name At5g17230 individually (identifications are in supplementary tables), but chloroplast localisation of PSY is independently established by fluorescence microscopy and by the chloroplast transit peptide. Reason: Consistent with all direct evidence: PSY carries a chloroplast transit peptide, PSY-GFP and PSY-YFP fusions localise to chloroplasts, and PSY activity is recovered from isolated chloroplast membranes. The proteomic detection is deferred to the curator who read the supplementary data. Supporting Evidence: PMID:18431481 which unambiguously identified 1325 proteins PMID:25675505 Among these proteins, PSY was the only one exclusively localized in chloroplasts as shown in a previous report ( 27 ) and the current study ( SI Appendix , Fig. S1 ). |
| GO:0009507 chloroplast | IDA PMID:25675505 Arabidopsis OR proteins are the major posttranscriptional re... | ACCEPT | Summary: PSY-GFP localises exclusively to chloroplasts, and the BiFC signal for the PSY-OR interaction is confined to chloroplasts. Reason: Direct microscopy evidence in the paper for the chloroplast location, matching the transit peptide and the membrane-bound PSY activity recovered from chloroplast preparations. Supporting Evidence: PMID:25675505 Among these proteins, PSY was the only one exclusively localized in chloroplasts as shown in a previous report ( 27 ) and the current study ( SI Appendix , Fig. S1 ). PMID:25675505 Such interactions occurred in chloroplasts, which was in good agreement with the plastid localization of these proteins ( 27 ) ( SI Appendix , Fig. S1 ). |
| GO:0009507 chloroplast | IDA PMID:37966976 Arabidopsis FIBRILLIN6 influences carotenoid biosynthesis by... | ACCEPT | Summary: PSY-GFP concentrates in fluorescent dots within chloroplasts and co-localises with FBN6-RFP in chloroplasts. Reason: Direct confocal evidence for chloroplast localisation; consistent with the other IDA/HDA rows and with the transit peptide. Supporting Evidence: PMID:37966976 When analyzing the co-immunoprecipitation assays, we noticed that the PSY-GFP protein concentrated in fluorescent dots within chloroplasts (Fig. 2A). PMID:37966976 indicating that FBN6 and PSY co-localize within chloroplasts, as expected for interacting proteins. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of chloroplast localisation, consistent with the predicted N-terminal chloroplast transit peptide (residues 1-70) and with the experimental chloroplast annotations. Reason: Correct prediction corroborated by three experimental rows and by the UniProt transit-peptide feature. Supporting Evidence: file:ARATH/PSY/PSY-uniprot.txt /note="Chloroplast" PMID:25675505 Among these proteins, PSY was the only one exclusively localized in chloroplasts as shown in a previous report ( 27 ) and the current study ( SI Appendix , Fig. S1 ). |
| GO:0010287 plastoglobule | IDA PMID:23023170 Plastid localization of the key carotenoid enzyme phytoene s... | KEEP AS NON CORE | Summary: Transiently expressed At-PSY-RFP in cowpea leaf protoplasts localised to fixed speckles attached to thylakoid/prolamellar-body regions; the speckles were identified as plastoglobules by co-localisation with a maize fibrillin (shown directly for maize PSY2/PSY3 and extended to the Arabidopsis protein). The authors note that PSY had not been detected in any sub-plastid proteome at the time. Reason: A genuine direct observation, but from an overexpressed fluorescent fusion in a heterologous protoplast, and the assignment of the puncta to plastoglobules rests on co-localisation with a fibrillin marker. Later work shows that PSY-GFP forms identical puncta together with FBN6, a protein that proteomics places in thylakoid and envelope membranes rather than plastoglobules, and envelope proteome studies detect PSY. The membrane-associated pool (chloroplast membrane, peripheral) is the functionally characterised location; plastoglobule association is plausible but unresolved, so the row is retained as a non-core, uncertain sub-plastid location rather than accepted as the core site of activity. Supporting Evidence: PMID:23023170 Arabidopsis PSY localized to plastoglobules (as did maize PSY2 and 3 and rice PSY1, 2, and 3). PMID:23023170 Merging of both signals confirmed colocalization of PSYs with Zm-PG2; thus, we consider the speckles to be plastoglobuli. PMID:37966976 FBN6 is the only FBN enriched in purified envelope fractions where PSY is also found (Ferro et al. 2010; Bouchnak et al. 2019). Knowledge gap: The sub-plastid compartment in which Arabidopsis PSY is catalytically active (plastoglobule, envelope membrane, or thylakoid-associated membrane) has not been resolved by fractionation of native, untagged protein. "Chloroplast suborganellar localization of the key pathway enzyme, PSY , has yet to be detected by proteomic analysis." β PMID:23023170 "Here PSY activity was exclusively found membrane bound and required addition of active GGPP synthase for in vitro assay." β PMID:25675505 |
| GO:0016117 carotenoid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the CrtB/PSY family node PTN000770577 that phytoene synthases act in carotenoid biosynthesis; descendant evidence includes plant, cyanobacterial and fungal (Neurospora al-2) phytoene synthases, and the Arabidopsis gene itself (its IDA is one of the evidences used to place the node, so its presence in WITH/FROM is expected). Reason: Phytoene synthesis is the committed step of carotenoid biosynthesis and the ancestral function of this family; the node placement is sound and the Arabidopsis experimental data agree. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000770577 Β· PTN000770577 SUPPORTS TRANSFER Family node for CrtB/PSY phytoene synthases; the function is ancestral to the whole family and is experimentally confirmed in the target. Supporting Evidence: PMID:25675505 Phytoene synthase (PSY) catalyzes the first committed step in carotenoid biosynthesis and controls carbon flux into the carotenoid biosynthetic pathway PMID:12805607 In the present paper, we show that seed-specific overexpression of an endogenous Arabidopsis phytoene synthase gene results in significant increases of the levels of Ξ²-carotene, luteins, and violaxanthin. |
| GO:0016117 carotenoid biosynthetic process | IDA PMID:25675505 Arabidopsis OR proteins are the major posttranscriptional re... | ACCEPT | Summary: Direct in vitro PSY activity from Arabidopsis chloroplast membranes and in vivo phytoene accumulation in norflurazon-treated PSY-GFP overexpressors; PSY protein level set by OR determines carotenoid content in roots and seedlings. Reason: PSY performs the committed catalytic step of the pathway; this is the core biological process of the gene. Supporting Evidence: PMID:25675505 Overexpression of PSY β GFP led to about a twofold increase of phytoene in NFZ-treated etiolated seedlings ( Fig. 4 C ), indicating that PSY β GFP functioned properly in the transgenic lines. PMID:25675505 Phytoene synthase (PSY) catalyzes the first committed step in carotenoid biosynthesis and controls carbon flux into the carotenoid biosynthetic pathway |
| GO:0016117 carotenoid biosynthetic process | IMP PMID:12805607 Seed-specific overexpression of an endogenous Arabidopsis ph... | ACCEPT | Summary: Seed-specific (napA promoter) overexpression of the endogenous Arabidopsis PSY gene gave a 43-fold increase in seed beta-carotene with increased lutein, violaxanthin, lycopene, alpha-carotene and chlorophyll, showing that PSY flux limits carotenoid synthesis in seeds. Reason: Gain-of-function genetic evidence in Arabidopsis for the gene's role in carotenoid biosynthesis; the cloned gene is the At5g17230 cDNA of Scolnik and Bartley. Downstream germination/ABA effects are consequences of increased xanthophyll supply and are not annotated to PSY. Supporting Evidence: PMID:12805607 In the present paper, we show that seed-specific overexpression of an endogenous Arabidopsis phytoene synthase gene results in significant increases of the levels of Ξ²-carotene, luteins, and violaxanthin. PMID:12805607 An endogenous phytoene synthase was sequenced and cloned by RT-PCR from Arabidopsis homologous to the gene cloned by Scolnik and Bartley ( 1994 ). |
| GO:0016120 carotene biosynthetic process | IEA GO_REF:0000108 | ACCEPT | Summary: Inter-ontology inference from 15-cis-phytoene synthase activity. Phytoene is a C40 hydrocarbon carotene, so the enzyme that forms it participates in carotene biosynthesis. (In the current ontology GO:0016120 is not a descendant of GO:0016117; the two terms are complementary here.) Reason: Logically correct inference. The more precise child GO:1901174 phytoene biosynthetic process is a descendant of this carried term and is therefore not proposed as a redundant new annotation. Supporting Evidence: PMID:26224804 The first committed step in the carotenoid biosynthesis pathway is the condensation of two geranylgeranyl diphosphate molecules to phytoene catalyzed by phytoene synthase (PSY). file:ARATH/PSY/PSY-uniprot.txt Xref=Rhea:RHEA:34475, ChEBI:CHEBI:27787, |
| GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO transfer from the squalene/phytoene synthase conserved-site signature to the EC 2.5.1 parent class. Phytoene synthase (EC 2.5.1.32) is indeed an alkyl-transferring transferase, so the term is correct but is a generic grandparent of GO:0046905. Reason: Correct but uninformative parent term; the specific activity 15-cis-phytoene synthase activity is annotated with IDA, IBA and IEA and represents the core function. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR019845 Β· Squalene/phytoene synthase, conserved site SUPPORTS TRANSFER The conserved site is present in PSY and the EC 2.5.1 parent class is correct; the mapping is simply coarse. Supporting Evidence: PMID:12805607 Phytoene synthase catalyzes the dimerization of two molecules of geranylgeranyl pyrophosphate to phytoene and has been shown to be rate limiting for the synthesis of carotenoids. |
| GO:0031969 chloroplast membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Mapped from the UniProt subcellular location "Plastid, chloroplast membrane; Peripheral membrane protein" (evidence PMID:25675505, PMID:26224804). Active PSY is recovered exclusively from chloroplast membrane fractions and PSY is detected in envelope proteomes. Reason: The membrane-bound pool is the catalytically active form of PSY, so chloroplast membrane is the functional location; consistent with the curated UniProt location and with the OR-dependent membrane association of PSY. Supporting Evidence: file:ARATH/PSY/PSY-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast membrane PMID:25675505 Here PSY activity was exclusively found membrane bound and required addition of active GGPP synthase for in vitro assay. PMID:37966976 FBN6 is the only FBN enriched in purified envelope fractions where PSY is also found (Ferro et al. 2010; Bouchnak et al. 2019). |
| GO:0046905 15-cis-phytoene synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of the family-defining catalytic activity at node PTN000770577; descendants with experimental phytoene synthase activity include plant PSYs, bacterial/cyanobacterial CrtB and fungal al-2. The Arabidopsis gene's own IDA contributes to the node placement. Reason: Core molecular function, ancestral to the family and directly confirmed in Arabidopsis by in vitro chloroplast-membrane assays and by complementation of a crtB-deficient E. coli carotenoid operon. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000770577 Β· PTN000770577 SUPPORTS TRANSFER Family node for CrtB/PSY phytoene synthases; the activity is the family-defining function and is experimentally confirmed in the target. Supporting Evidence: PMID:25675505 PSY activity was about 50% higher in the AtOR -overexpressing lines than in WT. PMID:37966976 Strains co-transformed with such constructs harboring Arabidopsis PSY and FBN6 sequences were found to produce significantly more Ξ²-carotene than those expressing only PSY or co-expressing PSY and FBN4 (Fig. 3, B and C), despite that PSY protein levels remained very similar in all the cases (Fig. 3D). |
| GO:0046905 15-cis-phytoene synthase activity | IDA PMID:25675505 Arabidopsis OR proteins are the major posttranscriptional re... | ACCEPT | Summary: PSY activity measured in vitro in chloroplast membranes isolated from Arabidopsis (radiolabelled IPP/DMAPP with recombinant GGPP synthase supplying GGPP), and in vivo as phytoene accumulation in norflurazon-treated tissue; PSY-GFP overexpression doubled phytoene in etiolated seedlings. Reason: Direct enzymatic evidence for the core catalytic activity of P37271; this is the basis of the UniProt EC 2.5.1.32 and Rhea assignments. Supporting Evidence: PMID:25675505 PSY activity was about 50% higher in the AtOR -overexpressing lines than in WT. PMID:25675505 Overexpression of PSY β GFP led to about a twofold increase of phytoene in NFZ-treated etiolated seedlings ( Fig. 4 C ), indicating that PSY β GFP functioned properly in the transgenic lines. |
| GO:0046905 15-cis-phytoene synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation from the UniProt catalytic activity (RHEA:34475, EC 2.5.1.32), itself curated from the direct Arabidopsis assays in PMID:25675505. Reason: Correct and specific; matches the experimentally demonstrated reaction 2 GGPP = 15-cis-phytoene + 2 diphosphate. Supporting Evidence: file:ARATH/PSY/PSY-uniprot.txt Xref=Rhea:RHEA:34475, ChEBI:CHEBI:27787, PMID:25675505 PSY activity was about 50% higher in the AtOR -overexpressing lines than in WT. |
| GO:0046905 15-cis-phytoene synthase activity | TAS PMID:12805607 Seed-specific overexpression of an endogenous Arabidopsis ph... | ACCEPT | Summary: Author statement that phytoene synthase dimerises two GGPP molecules to phytoene, in a paper overexpressing the endogenous Arabidopsis PSY gene in seeds with the expected increase in downstream carotenoids. Reason: Traceable author statement of the correct core activity, corroborated by the direct IDA evidence in PMID:25675505 and PMID:37966976. Supporting Evidence: PMID:12805607 Phytoene synthase catalyzes the dimerization of two molecules of geranylgeranyl pyrophosphate to phytoene and has been shown to be rate limiting for the synthesis of carotenoids. |
| GO:0051996 squalene synthase [NAD(P)H] activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO transfer from IPR033904 (trans-isoprenyl diphosphate synthases, head-to-head), the domain shared by squalene synthase and phytoene synthase. Squalene synthase condenses two FPP molecules and reduces the presqualene intermediate with NAD(P)H; PSY condenses two GGPP molecules to 15-cis-phytoene with no reductive step. Reason: The mapping assigns the activity of the sterol-pathway paralog to a carotenoid-pathway enzyme. PSY's substrate is C20 GGPP (not C15 FPP), its product is the C40 carotene phytoene (not the C30 triterpene squalene), and RHEA:34475 involves no NAD(P)H. The shared head-to-head fold does not imply shared substrate specificity or the reductase half-reaction. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: InterPro:IPR033904 Β· Trans-isoprenyl diphosphate synthases, head-to-head SUPPORTS SOURCE BUT NOT TARGET The domain is genuinely present in PSY, but the GO:0051996 mapping describes the squalene synthase members of the domain family, not the phytoene synthases. Supporting Evidence: PMID:12805607 Phytoene synthase catalyzes the dimerization of two molecules of geranylgeranyl pyrophosphate to phytoene and has been shown to be rate limiting for the synthesis of carotenoids. file:ARATH/PSY/PSY-uniprot.txt Xref=Rhea:RHEA:34475, ChEBI:CHEBI:27787, |
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Download this section (compressed HTML)Q: In which chloroplast sub-compartment is native Arabidopsis PSY catalytically active - the envelope membrane, thylakoid-associated membrane domains, or plastoglobules? Fluorescent fusions form puncta that co-localise with a plastoglobule fibrillin in one study and with the non-plastoglobule protein FBN6 in another, while envelope proteomics detects PSY and activity is recovered only from membrane fractions.
Suggested experts: plastid proteomics groups, carotenoid biochemistry groups
Q: Does the OR/OR-like-PSY interaction act by holding PSY in a folded, membrane-competent state (holdase-like activity), and should OR therefore carry a molecular-function term such as protein stabilisation or unfolded protein binding, rather than the interaction being recorded as bare protein binding on PSY?
Suggested experts: GO curators for plastid proteostasis, OR/Clp protease biochemists
Q: By what mechanism does FBN6 increase PSY turnover without changing PSY abundance or protease accessibility - product (phytoene) removal via its lipocalin motif, substrate channelling from GGPP synthase, or altered membrane partitioning?
Suggested experts: carotenoid enzymology groups
Experiment: Immunoblot untagged PSY across purified envelope, thylakoid, stroma and plastoglobule fractions from wild-type Arabidopsis chloroplasts (with fibrillin, TIC/TOC and LHC markers), alongside in vitro phytoene synthase assays of each fraction supplemented with recombinant GGPP synthase, to assign the catalytically active pool to a defined sub-compartment.
Hypothesis: Native PSY is enriched in the chloroplast envelope rather than in plastoglobules.
Type: subcellular fractionation with activity assay
Experiment: Reconstitute purified recombinant mature PSY with and without FBN6 in liposomes and measure steady-state kinetics (kcat, Km for GGPP) and phytoene partitioning into the lipid phase; compare with a lipocalin-motif mutant of FBN6 and with the bacterial CrtB control, which FBN6 does not stimulate.
Hypothesis: FBN6 stimulates PSY catalysis directly by relieving product inhibition or accelerating phytoene release.
Type: in vitro enzyme kinetics with reconstituted proteins
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