PDS (15-cis-phytoene desaturase, EC 1.3.5.5; also PDS3, locus At4g14210) is a nuclear-encoded, plastid-targeted FAD-containing flavoenzyme that performs the first of the two desaturation steps of the plant/cyanobacterial poly-cis carotene-desaturation route (PDS -> Z-ISO -> ZDS -> CRTISO) that converts 15-cis-phytoene into lycopene. PDS introduces two double bonds symmetrically at the C-11 and C-11' positions of 15-cis-phytoene, proceeding through the intermediate phytofluene, and with concomitant trans-to-cis isomerization of the neighbouring C-9 and C-9' double bonds, to yield 9,15,9'-tri-cis-zeta-carotene; the two desaturations are coupled to the reduction of two molecules of the lipophilic quinone plastoquinone, so the enzyme is a quinone-dependent oxidoreductase acting on the CH-CH group. Its tri-cis-zeta-carotene product is subsequently isomerized by Z-ISO and further desaturated by ZDS, and the resulting poly-cis-lycopene is isomerized to all-trans-lycopene by CRTISO before ring cyclization. The protein carries an N-terminal transit peptide and functions as a peripheral-membrane enzyme of plastid membranes, localizing to the chloroplast (including the chloroplast envelope and thylakoid) and to the chromoplast, and it forms a homotetramer. PDS catalyses one of the earliest and rate-influencing steps of carotenoid biosynthesis and is the molecular target of the bleaching herbicides norflurazon and fluridone, which compete at its quinone-binding site.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | KEEP AS NON CORE | Summary: High-throughput protein-correlation-profiling (size-exclusion chromatography plus LC/MS) of Arabidopsis leaf fractions detected PDS in the cytosolic pool. The same study explicitly reports that many proteins are dual-localized and partition between cytosolic and membrane-associated pools. Reason: PDS is a nuclear-encoded plastid enzyme with an N-terminal transit peptide; the cytosolic signal in a whole-cell fractionation most plausibly reflects the newly translated pre-import precursor and/or the dual-pool detection reported by this method, not a functional cytosolic activity. Retained as an experimentally observed but non-core (non-functional) location rather than removed, since it is a valid HDA hit. Supporting Evidence: PMID:28887381 were clearly partitioned between cytosolic and membrane-associated pools file:ARATH/PDS/PDS-uniprot.txt TRANSIT 1..86 |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: Large-scale mass-spectrometry identification of PDS among the Arabidopsis chloroplast proteome; the study assigned ~916 nuclear-encoded proteins with high confidence to the plastid. Consistent with the N-terminal chloroplast transit peptide and UniProt's plastid/chloroplast assignment. Reason: Correct organelle for a plastid-localized carotenoid biosynthetic enzyme; agrees with the transit peptide and with all other localization evidence. Core location. Supporting Evidence: PMID:18431481 916 nuclear-encoded proteins were assigned with high confidence to the plastid file:ARATH/PDS/PDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| 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 plastid location to GO. Reason: Correct and consistent with the HDA proteomics, the ISM prediction and the curated UniProt location. Supporting Evidence: file:ARATH/PDS/PDS-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 location and the N-terminal transit peptide. Reason: Prediction agrees with the curated location and the HDA proteomics; no conflict. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009507 chloroplast | TAS PMID:9700076 Regulation of phytoene desaturase expression is independent ... | ACCEPT | Summary: Traceable author statement from a study of PDS expression in Arabidopsis, which states that carotenoid synthesis in higher plants occurs in the plastids and that PDS is nuclear-encoded and post-translationally imported into the plastid compartment. Reason: Consistent with the plastid/chloroplast location of PDS; an author-asserted location corroborated by the proteomics and prediction evidence. Supporting Evidence: PMID:9700076 Synthesis of carotenoids in higher plants occurs in the plastids |
| GO:0009509 chromoplast | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB subcellular-location vocabulary (SL-0063, chromoplast). PDS functions in carotenoid-accumulating chromoplasts as well as chloroplasts; UniProt records "Ripening fruit" as a developmental stage and the original poly-cis desaturation stereochemistry was characterized in chromoplast membranes. Reason: Correct: UniProt curates chromoplast as a location for PDS, and carotenoid biosynthesis is a defining chromoplast function. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast file:ARATH/PDS/PDS-uniprot.txt DEVELOPMENTAL STAGE: Ripening fruit. |
| GO:0009509 chromoplast | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity transfer of the chromoplast location from an ortholog (Q40406). Consistent with the UniProt chromoplast assignment and with the ripening-fruit developmental expression. Reason: A valid ortholog-based location that matches the curated chromoplast assignment; carotenoid biosynthesis is a core chromoplast function. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast. Plastid, chromoplast |
| GO:0009534 chloroplast thylakoid | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: AT_CHLORO subplastidial proteomics (semiquantitative spectral counting across stroma, thylakoid and envelope fractions) assigned PDS in part to the thylakoid fraction. As a membrane-associated, quinone-dependent enzyme, PDS is expected to reside in plastid membranes, and thylakoid association is a plausible sub-plastidial location. Reason: A curated HDA sub-plastidial localization consistent with the enzyme's peripheral membrane association; retained as a specific membrane site within the chloroplast. The cached full text describes the subplastidial-localization method rather than naming PDS in the abstract, so deferring to the curator. Supporting Evidence: PMID:20061580 accurate subplastidial localization of previously known and newly identified proteins file:ARATH/PDS/PDS-uniprot.txt Peripheral membrane protein |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | ACCEPT | Summary: Identification of PDS in the Arabidopsis chloroplast-envelope-membrane proteome. As a peripheral-membrane, quinone-dependent enzyme, PDS is expected to reside in plastid membranes, and envelope association is a well-documented sub-plastidial location for the carotenoid desaturases. Reason: A curated HDA sub-plastidial localization consistent with the enzyme's membrane association; retained as a more specific location within the chloroplast. The cached abstract describes the envelope-proteomics method rather than naming PDS, so deferring to the curator. Supporting Evidence: PMID:12938931 identify and characterize membrane proteins localized to the Arabidopsis thaliana chloroplastic envelope membrane file:ARATH/PDS/PDS-uniprot.txt Peripheral membrane protein |
| GO:0009941 chloroplast envelope | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: AT_CHLORO proteomics assignment of PDS to the chloroplast envelope fraction using semiquantitative spectral counting. Corroborates the envelope sub-localization from PMID:12938931. Reason: Second independent curated envelope-proteomics hit consistent with the enzyme's peripheral membrane association; kept as a specific location. Supporting Evidence: PMID:20061580 accurate subplastidial localization of previously known and newly identified proteins file:ARATH/PDS/PDS-uniprot.txt Peripheral membrane protein |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProtKB subcellular-location vocabulary (SL-0162, membrane), reflecting UniProt's curated assignment of PDS as a peripheral membrane protein. Reason: Correct but generic. PDS acts on membrane-embedded hydrophobic substrates and is a peripheral membrane protein of plastid membranes; the term is broad but not wrong, and the specific plastid membrane sites (envelope, thylakoid) are separately annotated. Retained as a correct broad location. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt Peripheral membrane protein |
| GO:0016020 membrane | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity transfer of the membrane location from the rice ortholog (A2XDA1), the source of UniProt's "Peripheral membrane protein" assignment for PDS. Reason: Correct and consistent with the curated peripheral-membrane assignment and with the IEA membrane annotation; a valid broad location. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt Peripheral membrane protein |
| GO:0016117 carotenoid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT phylogenetic propagation of carotenoid biosynthetic process to the PDS clade at node PTN000078359 in PTHR42923. The IBD was seeded by the Arabidopsis PDS locus itself (AT4G14210/Q07356) and tomato PDS; the target appearing in its own WITH/FROM (AT4G14210) is the expected marker that experimental grounding exists on the target, not circularity. Reason: Sound node placement: PDS/CrtP orthologs across plants and cyanobacteria share the same committed phytoene-desaturation step of carotenoid biosynthesis, and the target carries direct experimental evidence for the activity. Core biological process. Supporting Evidence: PMID:9914519 the two carotene desaturases phytoene desaturase and carotene zeta-carotene desaturase from Arabidopsis thaliana |
| GO:0016117 carotenoid biosynthetic process | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Direct assay of recombinant Arabidopsis PDS reconstituted with GGPP synthase and phytoene synthase (and ZDS) in E. coli, demonstrating its role in the plant poly-cis carotenoid desaturation pathway that yields pro-lycopene. Reason: Experimental demonstration that PDS participates in carotenoid biosynthesis, performing the first committed desaturation. Core biological 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. |
| GO:0016117 carotenoid biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR014102 (Phytoene_desaturase family) to carotenoid biosynthetic process. PDS performs a committed desaturation step, so the biosynthetic-process term is correct. Reason: Correct and appropriately specific domain-level inference from the phytoene-desaturase family signature; agrees with the IBA and IDA annotations. Note this is not a wrong-paralog mapping (IPR014102 is the phytoene desaturase family itself), so the InterPro2GO rows for PDS are biologically correct and retained. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt PATHWAY: Carotenoid biosynthesis; lycopene biosynthesis. |
| GO:0016120 carotene biosynthetic process | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Direct assay of the recombinant plant desaturation pathway showing formation of hydrocarbon carotenes (zeta-carotene through pro-lycopene). PDS's immediate product, tri-cis-zeta-carotene, is a carotene, and the pathway produces the carotene pro-lycopene. Reason: Experimental support for participation in carotene (hydrocarbon carotenoid) biosynthesis. Core process. Note the current ontology places GO:0016120 outside GO:0016117 (via carotene/isoprenoid 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:0016120 carotene biosynthetic process | IEA GO_REF:0000117 | ACCEPT | Summary: Automated ARBA machine-learning annotation to carotene biosynthetic process, matching the manually curated pathway and the IDA evidence. Reason: Correct: PDS produces a hydrocarbon carotene (zeta-carotene) and is part of the lycopene-forming carotene pathway; consistent with the IDA annotation. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt PATHWAY: Carotenoid biosynthesis; lycopene biosynthesis. |
| GO:0016166 phytoene dehydrogenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of phytoene dehydrogenase activity to the PDS clade at node PTN000078359 (PTHR42923), seeded by Arabidopsis PDS (AT4G14210/Q07356) and tomato PDS (P28554). 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 PDS/CrtP family and directly demonstrated for this gene. Core molecular function. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt EC=1.3.5.5 PMID:9914519 the two carotene desaturases phytoene desaturase and carotene zeta-carotene desaturase from Arabidopsis thaliana |
| GO:0016166 phytoene dehydrogenase activity | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | ACCEPT | Summary: Direct biochemical demonstration: recombinant Arabidopsis PDS expressed in E. coli converts 15-cis-phytoene to zeta-carotene (via phytofluene) in the plant poly-cis desaturation pathway (UniProt EC 1.3.5.5, ECO:0000269|PubMed:9914519). Reason: The defining, experimentally established molecular function of the gene. Core function. Supporting Evidence: PMID:9914519 Whereas in the dark mainly zeta-carotene, the phytoene desaturase product, accumulates file:ARATH/PDS/PDS-uniprot.txt Converts phytoene into zeta-carotene via the intermediary of |
| GO:0016166 phytoene dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation combining InterPro (IPR014102, Phytoene_desaturase) and ARBA evidence for phytoene dehydrogenase activity. Matches the curated catalytic activity. Reason: Correct and precise; the same molecular function supported by IDA and IBA. Core function. Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt EC=1.3.5.5 |
| 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'. PDS is indeed an oxidoreductase (EC 1.3.5.5, a plastoquinone-dependent desaturase), but the specific molecular function is known. Reason: Correct but uninformatively broad. The gene has a precise, experimentally supported molecular function, phytoene dehydrogenase activity (GO:0016166, EC 1.3.5.5), which is already annotated by IDA/IBA/IEA and is the appropriate specific replacement for this generic parent. Proposed replacements: phytoene dehydrogenase activity Supporting Evidence: file:ARATH/PDS/PDS-uniprot.txt EC=1.3.5.5 file:ARATH/PDS/PDS-uniprot.txt Converts phytoene into zeta-carotene via the intermediary of |
| GO:1901177 lycopene biosynthetic process | IDA PMID:9914519 Two Arabidopsis thaliana carotene desaturases, phytoene desa... | NEW | Summary: Proposed new annotation. Reconstitution of the plant poly-cis desaturation pathway in E. coli (GGPP synthase, phytoene synthase, PDS and ZDS) yields pro-lycopene as the main end product; PDS performs the first two of the four desaturations required to convert phytoene to lycopene, and UniProt curates PDS in the "lycopene biosynthesis" pathway. Reason: PDS does part of the work of lycopene biosynthesis (it catalyses two committed desaturations of the phytoene-to-lycopene route), so it participates in the process rather than merely being required for it. Comparator check: its sibling desaturase ZDS, standing in the same role in the same pathway and characterized in the same paper, carries GO:1901177 (IDA); PDS is not annotated to it, which is a genuine gap. Both the participation and comparator tests are satisfied. Proposed conservatively as a well-grounded process term already curated for the downstream partner. 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/PDS/PDS-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 PDS in vivo? The reaction uses plastoquinone in vitro, but whether PDS feeds electrons into the photosynthetic plastoquinone pool (via the plastid terminal oxidase to reoxidize plastoquinol) and whether it acts predominantly at the envelope or the thylakoid is not resolved.
Suggested experts: Peter Beyer, Barry J. Pogson
Q: Does Arabidopsis PDS3 have functions or phenotypes beyond its catalytic step - for example in plastid development or apocarotenoid-mediated retrograde signalling - that are separable from the loss of downstream carotenoids, and are these attributable to accumulated phytoene/phytofluene substrates rather than to the enzyme itself?
Suggested experts: Manuel Rodríguez-Concepción
Experiment: Express and purify mature His-tagged Arabidopsis PDS, reconstitute in plastoquinone-loaded liposomes, and assay against 15-cis-phytoene, following intermediates (phytofluene) and product (tri-cis-zeta-carotene) by C30 reversed-phase HPLC-PDA/MS; test decyl-plastoquinone versus decyl-ubiquinone as acceptor and measure competitive inhibition by norflurazon and fluridone at the quinone-binding region.
Hypothesis: Arabidopsis PDS is a plastoquinone-dependent desaturase that acts on 15-cis-phytoene and produces 9,15,9'-tri-cis-zeta-carotene via phytofluene, and is inhibited at its quinone site by norflurazon/fluridone.
Type: in vitro enzyme assay with purified recombinant protein
Experiment: Localize a native-promoter PDS-GFP fusion (complementing a pds3 mutant) by confocal imaging and by immunoblot of purified envelope/stroma/thylakoid fractions; combine with pulse-chase import assays into isolated chloroplasts to test whether the cytosolic signal corresponds to unprocessed precursor.
Hypothesis: PDS resides in the chloroplast envelope/thylakoid membranes and its cytosolic detection reflects the pre-import precursor rather than a functional cytosolic pool.
Type: subcellular localization plus in vitro chloroplast import assay
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