ZDS (zeta-carotene desaturase, EC 1.3.5.6; also ZDS1, CLB5, SPC1, PDE181) is a nuclear-encoded, plastid-targeted flavoenzyme that performs the third of the four backbone steps of the plant/cyanobacterial poly-cis carotene-desaturation route (PDS -> Z-ISO -> ZDS -> CRTISO) leading from 15-cis-phytoene to lycopene. ZDS introduces two double bonds at the C-7 and C-7' positions of 9,9'-di-cis-zeta-carotene, proceeding through the intermediate 7,9,9'-tri-cis-neurosporene, to yield 7,7',9,9'-tetra-cis-lycopene (pro-lycopene); the two desaturations are coupled to the reduction of two molecules of a lipophilic quinone (plastoquinone), so the enzyme is an oxidoreductase acting on the CH-CH group with a quinone acceptor. Because its substrate must first have its central 15-cis bond isomerised (by Z-ISO), ZDS acts on the di-cis-zeta-carotene rather than on the PDS product directly, and its own poly-cis product is subsequently isomerised to all-trans-lycopene by CRTISO before ring cyclisation. The protein carries an N-terminal transit peptide and functions as a membrane-associated enzyme of plastids, localising to the chloroplast (including the chloroplast envelope) and chromoplast. ZDS is essential for carotenoid biosynthesis: loss-of-function alleles are seedling-lethal albinos with growth arrest, and carotenoid deficiency additionally causes photoprotection loss, ABA deficiency, altered leaf development and disrupted plastid-to-nucleus retrograde signalling, the latter mediated by an apocarotenoid signal formed by cleavage of the phytoene/zeta-carotene intermediates that accumulate when ZDS is absent.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: High-throughput mass-spectrometry identification of ZDS among the Arabidopsis chloroplast proteome. Consistent with the N-terminal chloroplast transit peptide and with UniProt's plastid/chloroplast assignment for this carotenoid biosynthetic enzyme. Reason: Correct organelle for a plastid-localised carotenoid biosynthetic enzyme. The cached proteomics paper does not name ZDS in the abstract body, but the curated HDA hit is fully consistent with the transit peptide and with the mutant phenotypes, which are entirely plastidial; deferring to the curator and retaining as a core location. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast PMID:18431481 916 nuclear-encoded proteins were assigned with high confidence to the plastid |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB/Swiss-Prot subcellular-location vocabulary (SL-0049, chloroplast). Matches the manually curated UniProt subcellular location and the HDA proteomics evidence. Reason: Correct and consistent with all other localization evidence; a valid mapping of the curated plastid location to GO. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-based (AtSubP) prediction of chloroplast localization. Consistent with the experimentally supported chloroplast/chromoplast location and the N-terminal transit peptide. Reason: Prediction agrees with the curated location and with the HDA proteomics; no conflict. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009509 chromoplast | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB subcellular-location vocabulary (SL-0063, chromoplast). ZDS functions in carotenoid-accumulating chromoplasts as well as chloroplasts; the poly-cis desaturation stereochemistry was originally characterised in chromoplast membranes. Reason: Correct: UniProt curates chromoplast as a location for ZDS, and carotenoid biosynthesis is a defining chromoplast function. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | ACCEPT | Summary: Identification of ZDS in the Arabidopsis chloroplast-envelope-membrane proteome. As a membrane-associated, quinone-dependent enzyme, ZDS is expected to reside in plastid membranes, and envelope association is a plausible sub-plastidial location. Reason: A curated HDA sub-plastidial localization consistent with the enzyme's membrane-association requirement. Retained as a more specific location within the chloroplast; the cached abstract describes the envelope proteomics method rather than naming ZDS, so deferring to the curator. Supporting Evidence: PMID:12938931 identify and characterize membrane proteins localized to the Arabidopsis thaliana chloroplastic envelope membrane file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009941 chloroplast envelope | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: AT_CHLORO proteomics assignment of ZDS to the chloroplast envelope fraction using semiquantitative spectral counting across stroma, thylakoid and envelope subfractions. Corroborates the envelope sub-localization from PMID:12938931. Reason: Second independent curated envelope-proteomics hit; consistent with the enzyme's membrane association. Kept as a specific location. Supporting Evidence: PMID:20061580 accurate subplastidial localization of previously known and newly identified proteins file:ARATH/ZDS/ZDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0016117 carotenoid biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR014103 (zeta-carotene desaturase family). ZDS performs a committed desaturation step of the carotene backbone, so the biosynthetic-process term is correct. Reason: Correct and appropriately specific domain-level inference; agrees with the experimental IMP annotations and the mutant pigment phenotypes. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt PATHWAY: Carotenoid biosynthesis; lycopene biosynthesis. |
| GO:0016117 carotenoid biosynthetic process | IMP PMID:17468780 The Arabidopsis Spontaneous Cell Death1 gene, encoding a zet... | ACCEPT | Summary: Characterisation of the allelic spc1-1/spc1-2 (zds) mutants. spc1-2 is seedling-lethal with growth arrest; the weak spc1-1 allele bleaches and has substantially reduced downstream carotenoids, and both were mapped to ZDS, establishing ZDS as essential for carotenoid biosynthesis in planta. Reason: Strong experimental (IMP) support for participation in carotenoid biosynthesis: loss of ZDS reduces the carotenoids downstream of its step. Core biological process. Supporting Evidence: PMID:17468780 SPC1 encodes a putative zeta-carotene desaturase (ZDS) in the carotenoid biosynthesis pathway PMID:17468780 several major carotenoid compounds downstream of SPC1/ZDS were substantially reduced in spc1-1, suggesting that SPC1 is a functional ZDS |
| GO:0016117 carotenoid biosynthetic process | IMP PMID:24907342 An Uncharacterized Apocarotenoid-Derived Signal Generated in... | ACCEPT | Summary: The zds/clb5/spc1/pde181 mutant alleles were used to show that carotenoid biosynthesis depends on ZDS activity; blocking upstream phytoene desaturase rescues the mutant phenotypes, confirming ZDS acts within the carotenoid biosynthetic pathway. Reason: Independent IMP support (a distinct set of ZDS mutant alleles) for the same biosynthetic process; consistent with PMID:17468780. Core biological process. Supporting Evidence: PMID:24907342 Biosynthesis of the signal depends on ΞΆ-carotene desaturase activity encoded by the ΞΆ-CAROTENE DESATURASE (ZDS)/CHLOROPLAST BIOGENESIS5 (CLB5) gene in Arabidopsis thaliana |
| GO:0016120 carotene biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT phylogenetic propagation of carotene biosynthetic process to the ZDS clade at node PTN007457606 in PTHR42923. The IBD was seeded by the Arabidopsis ZDS locus itself (AT3G04870/Q38893), so the gene appearing in its own WITH/FROM is the expected marker that experimental grounding exists on the target; this is not circular. Reason: Sound node placement: ZDS orthologs across plants and cyanobacteria share the same di-cis-zeta-carotene desaturase step in the carotene backbone, and the target carries direct experimental evidence for the activity. Retained. Supporting Evidence: PMID:9914519 the two carotene desaturases phytoene desaturase and carotene zeta-carotene desaturase from Arabidopsis thaliana |
| GO:0016120 carotene biosynthetic process | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Direct assay of recombinant Arabidopsis ZDS reconstituted with GGPP synthase, phytoene synthase and PDS in E. coli, showing formation of the carotene pro-lycopene through the plant poly-cis desaturation pathway. Reason: Experimental demonstration that ZDS participates in carotene (hydrocarbon carotenoid) biosynthesis, producing the tetra-cis-lycopene carotene. Core process. Note the current ontology places GO:0016120 outside GO:0016117 (via isoprenoid/carotene metabolic process); left as annotated, not modified. Supporting Evidence: PMID:9914519 We show that pro-lycopene (7,9,7',9'-tetra-cis)-lycopene is the main end product of the plant desaturation pathway in these cells. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR002937 (amino oxidase / FAD-binding domain) to the generic parent 'oxidoreductase activity'. ZDS is indeed an oxidoreductase (EC 1.3.5.6, a quinone-dependent desaturase), but the specific molecular function is known. Reason: Correct but uninformatively broad. The gene has a precise, experimentally supported molecular function, 9,9'-di-cis-zeta-carotene desaturase activity (GO:0016719, EC 1.3.5.6), which is the appropriate replacement. Proposed replacements: 9,9'-di-cis-zeta-carotene desaturase activity Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt EC=1.3.5.6 file:ARATH/ZDS/ZDS-uniprot.txt Reaction=9,9'-di-cis-zeta-carotene + 2 a quinone = 7,7',9,9'-tetra-cis- |
| GO:0016719 9,9'-di-cis-zeta-carotene desaturase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of the di-cis-zeta-carotene desaturase activity to the ZDS clade at node PTN007457606 (PTHR42923), seeded by the Arabidopsis ZDS experimental annotation. The gene's presence in its own WITH/FROM marks that experimental grounding exists on the target and is not circular. Reason: The correct, appropriately specific molecular function, inherited across the ZDS/CrtQ family and directly demonstrated for this gene. Core molecular function. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt Reaction=9,9'-di-cis-zeta-carotene + 2 a quinone = 7,7',9,9'-tetra-cis- PMID:9914519 zeta-Carotene then meets the stereospecific requirements of zeta-carotene desaturase and pro-lycopene is formed. |
| GO:0016719 9,9'-di-cis-zeta-carotene desaturase activity | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Direct biochemical demonstration: recombinant Arabidopsis ZDS expressed in E. coli converts zeta-carotene to pro-lycopene (7,9,7',9'-tetra-cis-lycopene) via neurosporene, with the stereoselectivity of the plant poly-cis pathway (UniProt EC 1.3.5.6, ECO:0000269|PubMed:9914519). Reason: The defining, experimentally established molecular function of the gene. Core function. Supporting Evidence: PMID:9914519 We show that pro-lycopene (7,9,7',9'-tetra-cis)-lycopene is the main end product of the plant desaturation pathway in these cells. file:ARATH/ZDS/ZDS-uniprot.txt The main product is 7,9,7',9'-tetra-cis-lycopene |
| GO:0016719 9,9'-di-cis-zeta-carotene desaturase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation combining InterPro (IPR014103), Rhea (RHEA:30955) and EC (1.3.5.6) evidence for the di-cis-zeta-carotene desaturase reaction. Matches the curated catalytic activity exactly. Reason: Correct and precise; the same molecular function supported by IDA and IBA and by the curated Rhea reaction. Core function. Supporting Evidence: file:ARATH/ZDS/ZDS-uniprot.txt Reaction=9,9'-di-cis-zeta-carotene + 2 a quinone = 7,7',9,9'-tetra-cis- file:ARATH/ZDS/ZDS-uniprot.txt EC=1.3.5.6 |
| GO:1901177 lycopene biosynthetic process | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Reconstitution of the plant desaturation pathway showed pro-lycopene as the main end product, placing ZDS directly in lycopene biosynthesis (UniProt pathway: carotenoid biosynthesis; lycopene biosynthesis). Reason: ZDS performs a committed desaturation step whose product is the (poly-cis) lycopene that CRTISO then isomerises to all-trans-lycopene; direct experimental support for participation in lycopene biosynthesis. Core process. Supporting Evidence: PMID:9914519 We show that pro-lycopene (7,9,7',9'-tetra-cis)-lycopene is the main end product of the plant desaturation pathway in these cells. file:ARATH/ZDS/ZDS-uniprot.txt PATHWAY: Carotenoid biosynthesis; lycopene biosynthesis. |
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Download this section (compressed HTML)Q: What is the physiological electron acceptor and the sub-plastidial membrane environment of Arabidopsis ZDS in vivo? The reaction uses a lipophilic quinone (plastoquinone) in vitro, but whether ZDS feeds electrons into the photosynthetic plastoquinone pool and whether it works from the envelope, thylakoid or both is not resolved.
Suggested experts: Peter Beyer, Barry J. Pogson
Q: Which apocarotenoid, produced by CCD4 cleavage of the phytoene/zeta-carotene that accumulates when ZDS is absent, is the retrograde/leaf-development signal, and how does it act? This would separate ZDS's catalytic role from the indirect signalling phenotypes of zds/clb5 mutants.
Suggested experts: Patricia LeΓ³n, Manuel RodrΓguez-ConcepciΓ³n
Experiment: Express and purify mature His-tagged Arabidopsis ZDS, reconstitute in plastoquinone- loaded liposomes, and assay against 9,15,9'-tri-cis-zeta-carotene versus 9,9'-di-cis-zeta-carotene (with/without Z-ISO), following intermediates and products by C30 reversed-phase HPLC-PDA/MS; test decyl-plastoquinone versus decyl-ubiquinone as acceptor.
Hypothesis: Arabidopsis ZDS is a quinone-dependent desaturase that acts specifically on 9,9'-di-cis-zeta-carotene (requiring prior Z-ISO isomerization) and produces 7,7',9,9'-tetra-cis-lycopene via 7,9,9'-tri-cis-neurosporene.
Type: in vitro enzyme assay with purified recombinant protein
Experiment: Localise a native-promoter ZDS-GFP fusion (complementing spc1/clb5) by confocal imaging and by immunoblot of purified envelope/stroma/thylakoid fractions; then compare carotenoid profiles, retrograde marker-gene expression and leaf morphology in zds, zds ziso and zds ccd4 backgrounds to test the substrate-cleavage signal model.
Hypothesis: ZDS resides in the chloroplast envelope/plastid membranes and its loss, not the loss of all-trans carotenoids per se, drives the retrograde-signalling phenotype through substrate-derived apocarotenoids.
Type: subcellular localization plus genetic epistasis with metabolite and transcript profiling
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