Functional annotation report: Arabidopsis **PDS/PDS3** (At4g14210; UniProt Q07356) Falcon Edison Scientific Literature 52 citations 1 artifacts 2026-09-26T22:20:43.676695

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Functional annotation report: Arabidopsis PDS/PDS3 (At4g14210; UniProt Q07356)

Executive conclusion

The requested identity is verified. PDS, also called PDS3, is the single-copy Arabidopsis thaliana locus At4g14210, encoding the plastid-targeted 15-cis-phytoene desaturase (EC 1.3.5.5). The literature reports a 566-amino-acid precursor, a 75-residue plastid-targeting peptide, and a 491-residue mature protein. This agrees with UniProt Q07356 and excludes unrelated proteins that share the acronym PDS. Its reported NAD/FAD-binding and amine-oxidase-like oxidoreductase architecture is consistent with the supplied Amino_oxidase, FAD/NAD-binding, Phytoene_desaturase, and carotenoid/retinoid oxidoreductase annotations. (ruizsola2012carotenoidbiosynthesisin pages 7-8, mcquinn2018atpdsoverexpressionin pages 4-7, ruizsola2012carotenoidbiosynthesisin pages 3-4)

Primary annotation: AtPDS is an FAD-dependent, plastoquinone-coupled oxidoreductase that catalyzes the first two desaturations of the plant poly-cis carotenoid pathway:

15-cis-phytoene → 9,15-di-cis-phytofluene → 9,15,9′-tri-cis-ζ-carotene.

It introduces symmetric double bonds at C11–C12 and C11′–C12′. The enzyme acts at plastid membranes, principally the chloroplast envelope and also thylakoids. Loss of activity interrupts carotenoid production, causing phytoene accumulation, defective plastid development, photobleaching/albinism, and dwarfism. (koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 7-8, gupta2022thegeneticcomponents pages 4-5, ruizsola2012carotenoidbiosynthesisin pages 7-8, chen2010isolationandcharacterization pages 1-2)

Annotation aspect Best-supported conclusion Evidence type/species Key quantitative detail Principal source
Identity and precursor PDS/PDS3 is the single-copy Arabidopsis locus At4g14210, consistent with UniProt Q07356, encoding plastid-targeted phytoene desaturase. The protein is synthesized as a precursor and processed after plastid import. Direct Arabidopsis thaliana annotation and chloroplast-proteomics synthesis 566-aa precursor; 75-aa targeting peptide; 491-aa mature protein Ruiz-Sola & Rodríguez-Concepción, 2012, DOI (ruizsola2012carotenoidbiosynthesisin pages 7-8, ruizsola2012carotenoidbiosynthesisin pages 3-4)
Family and domains The literature describes plant PDS as an oxidoreductase with NAD/FAD-binding and amine-oxidase-like domains, agreeing with the supplied Amino_oxidase, FAD/NAD-binding, Phytoene_desaturase, and carotenoid/retinoid oxidoreductase annotations. Sequence/domain inference for AtPDS; family-level structural support from plant PDS homologs AtPDS and tomato PDS coding sequences share about 72% identity McQuinn et al., 2018, DOI (mcquinn2018atpdsoverexpressionin pages 4-7)
Reaction, substrate, and product PDS performs two symmetric dehydrogenations of 15-cis-phytoene, introducing double bonds at C11–C12 and C11′–C12′. The reaction proceeds through 9,15-di-cis-phytofluene to 9,15,9′-tri-cis-ζ-carotene. Arabidopsis pathway evidence plus direct biochemical characterization of rice plant PDS Two new conjugated double bonds; the central 15-cis geometry contributes to regioselective substrate positioning Chen et al., 2010, DOI; Koschmieder et al., 2017, DOI (koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 7-8, koschmieder2017planttypephytoenedesaturase pages 20-22, chen2010isolationandcharacterization pages 1-2)
FAD and plastoquinone Enzyme-bound FAD accepts reducing equivalents during phytoene dehydrogenation; oxidized plastoquinone is the physiological electron acceptor and becomes plastoquinol. Molecular oxygen does not directly substitute for quinone in the characterized plant enzyme. Direct rice PDS biochemistry; Arabidopsis genetic evidence establishes plastoquinone dependence FAD is the sole detected protein-bound redox cofactor in recombinant rice PDS Norris et al., 1995, DOI; Gemmecker et al., 2015, DOI (gemmecker2015phytoenedesaturasefrom pages 17-18, gemmecker2015phytoenedesaturasefrom pages 1-2, koschmieder2017planttypephytoenedesaturase pages 24-25)
Pathway position PDS initiates the plant poly-cis desaturation sequence downstream of phytoene synthase. Its ζ-carotene product is processed in the order Z-ISO → ZDS → CRTISO, ultimately yielding all-trans-lycopene; plastoquinol is reoxidized through photosynthetic electron transport or PTOX-dependent routes. Direct Arabidopsis pathway genetics and plant-pathway synthesis PDS is the first of two carotene desaturases responsible for four total desaturation steps between phytoene and lycopene Ruiz-Sola & Rodríguez-Concepción, 2012, DOI; Chen et al., 2010, DOI (ruizsola2012carotenoidbiosynthesisin pages 7-8, chen2010isolationandcharacterization pages 1-2, ruizsola2012carotenoidbiosynthesisin pages 5-7)
Subcellular localization AtPDS is imported into plastids and acts at internal lipid–aqueous interfaces. Arabidopsis chloroplast proteomics places it predominantly at the envelope and secondarily in thylakoids; catalytically active plant PDS is membrane associated. Direct Arabidopsis chloroplast proteomics; plant-homolog biochemical support Reported distribution: 84% envelope and 16% thylakoid; 75-aa targeting peptide Ruiz-Sola & Rodríguez-Concepción, 2012, DOI (ruizsola2012carotenoidbiosynthesisin pages 7-8, ruizsola2012carotenoidbiosynthesisin pages 3-4)
Oligomer and structure Plant PDS has an FAD-containing oxidoreductase fold and associates monotopically with membranes. The active rice homolog is proposed to be a homotetramer organized as a dimer of dimers, with hydrophobic channels serving phytoene and plastoquinone and possible channeling of phytofluene between subunits. Direct rice PDS crystallography, cross-linking, chromatography, EM, and kinetic modeling; inference for AtPDS Approximate 43-Å carotene-binding cavity; mutations at the cavity end retained only about 5% of wild-type activity Gemmecker et al., 2015, DOI; Brausemann et al., 2017, DOI; Koschmieder et al., 2017, DOI (brausemann2017structureofphytoene pages 1-3, gemmecker2015phytoenedesaturasefrom pages 17-18, koschmieder2017planttypephytoenedesaturase pages 20-22)
Loss-of-function phenotype Arabidopsis pds3 loss of function causes albinism and dwarfism, consistent with failure to synthesize photoprotective carotenoids and consequent disruption of chloroplast development. PDS silencing similarly produces an easily scored bleaching phenotype. Direct Arabidopsis T-DNA, CRISPR, and gene-silencing evidence Visible albino/null phenotype can occur in the CRISPR T1 generation Gupta & Hirschberg, 2022, DOI (gupta2022thegeneticcomponents pages 4-5)
2024 root and retinal findings Arabidopsis pds3-1 has short primary roots and fewer lateral roots. Acute PDS inhibition by fluridone transiently increases root IAA/auxin signaling, suppresses primary-root growth, and alters lateral-root positioning; retinal partially rescues the pds3-1 and fluridone phenotypes. These data implicate a carotenoid-derived retinal signal, although the exact endogenous mechanism remains interpretive. Direct Arabidopsis mutant, pharmacological, hormone, and reporter experiments Retinal tested at 20 µM; fluridone at 800 nM or 12.8 µM depending on experiment; rescue weakened after more than 60 h Xu et al., 2024, DOI (xu2024exogenousapplicationof pages 2-4, xu2024exogenousapplicationof pages 8-9, xu2024exogenousapplicationof pages 1-2, xu2024exogenousapplicationof pages 9-10)
Herbicide inhibition Norflurazon and fluridone inhibit PDS, causing phytoene accumulation, carotenoid depletion, and bleaching. Structural and kinetic evidence indicates that norflurazon occupies or perturbs the plastoquinone-binding region and stabilizes reduced FAD; resistance substitutions can impair inhibitor binding but usually reduce catalytic fitness. Arabidopsis pharmacology/phenotype plus direct rice structural and kinetic evidence Tested resistant rice-PDS variants retained less than 5% activity in one structure–function study Brausemann et al., 2017, DOI; Koschmieder et al., 2017, DOI (brausemann2017structureofphytoene pages 1-3, koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 20-22, gupta2022thegeneticcomponents pages 4-5)
AtPDS biofortification Constitutive heterologous AtPDS expression in tomato depleted upstream phytoene/phytofluene and increased downstream ζ-carotene, lycopene, and β-carotene, demonstrating that PDS can be a flux-control point in ripening fruit. Direct transgenic tomato application using Arabidopsis AtPDS Four lines tested; phytoene fell to 28.5–35.3% and phytofluene to 24.9–30.7% of control; ζ-carotene rose to 213.2–262.6%, lycopene up to 131.1%, β-carotene up to 142.8%, and total carotenoids up to 128.5% McQuinn et al., 2018, DOI (mcquinn2018atpdsoverexpressionin pages 7-11, mcquinn2018atpdsoverexpressionin pages 26-29)

Table: Evidence matrix for Arabidopsis PDS/PDS3 that separates direct Arabidopsis findings from mechanistic inference based on other plant PDS homologs. It summarizes molecular function, localization, phenotypes, recent developmental findings, and biotechnology applications.

1. Identity verification and nomenclature

The authoritative Arabidopsis pathway synthesis identifies PDS3/At4g14210 as the gene encoding phytoene desaturase. It is reported as a single-copy Arabidopsis gene, distinct from ZDS/At3g04870, the downstream ζ-carotene desaturase. Thus, literature using PDS for human pyruvate dehydrogenase phosphatases, microbial enzymes, or unrelated same-symbol genes is not relevant to Q07356 and was excluded. (ruizsola2012carotenoidbiosynthesisin pages 7-8, ruizsola2012carotenoidbiosynthesisin pages 3-4)

The domain assignments are coherent with the biochemistry. PDS is a flavoprotein oxidoreductase; sequence analyses describe plant PDS/ZDS proteins as containing NAD-binding and amine-oxidase-like regions, while plant-PDS structures reveal an FAD-containing oxidoreductase fold. These observations support, rather than conflict with, the supplied InterPro/Pfam annotations. The “NAD-binding” fold designation should not be mistaken for evidence that NAD(P) is the physiological electron acceptor: biochemical evidence instead supports enzyme-bound FAD and diffusible plastoquinone. (brausemann2017structureofphytoene pages 1-3, mcquinn2018atpdsoverexpressionin pages 4-7, gemmecker2015phytoenedesaturasefrom pages 1-2)

2. Primary biochemical function

Reaction and substrate specificity

PDS acts on the highly hydrophobic C40 carotene 15-cis-phytoene. Two sequential, symmetric dehydrogenations extend the phytoene chromophore:

  1. 15-cis-phytoene is desaturated at one C11–C12 position to form 9,15-di-cis-phytofluene.
  2. The opposite C11′–C12′ bond is desaturated to produce 9,15,9′-tri-cis-ζ-carotene.

The chemistry both removes hydrogen and establishes the characteristic poly-cis product geometry. Direct plant-PDS assays identified phytofluene as the intermediate and the tri-cis ζ-carotene as the final PDS product. Experiments with shortened phytoene analogues indicate that the central 15-cis configuration is an important positional determinant of regioselectivity. (koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 7-8, koschmieder2017planttypephytoenedesaturase pages 20-22, chen2010isolationandcharacterization pages 1-2)

The best current kinetic model, developed with purified rice PDS, is an ordered ping-pong bi-bi mechanism: carotene reduction of enzyme-bound FAD and subsequent FAD reoxidation by quinone occur sequentially, apparently using overlapping regions of the catalytic cavity. Intermediate channeling between subunits may increase the efficiency of the two-step conversion. Because these detailed assays used rice PDS, the catalytic chemistry is strong plant-homolog evidence for AtPDS rather than a direct kinetic determination of recombinant Q07356. (brausemann2017structureofphytoene pages 1-3, koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 7-8)

Cofactor and electron acceptor

FAD is the protein-bound redox cofactor. During carotene dehydrogenation it is reduced to FADH₂/FADred; oxidized plastoquinone then accepts the reducing equivalents and becomes plastoquinol. Purified plant PDS did not use molecular oxygen as an effective substitute for quinone, supporting classification as a 15-cis-phytoene:plastoquinone oxidoreductase, rather than a conventional oxygen-dependent oxidase. Arabidopsis mutants deficient in plastoquinone synthesis fail in phytoene desaturation, providing genetic evidence that this electron carrier is essential in vivo. (gemmecker2015phytoenedesaturasefrom pages 17-18, gemmecker2015phytoenedesaturasefrom pages 1-2, koschmieder2017planttypephytoenedesaturase pages 24-25)

Plastoquinol is reoxidized by photosynthetic electron transport in green tissue and by the plastid terminal oxidase PTOX or related routes, particularly in nonphotosynthetic plastids. PTOX is therefore functionally coupled to PDS through the shared quinone pool, although it is not a stable PDS subunit and is not absolutely required for all desaturation in illuminated green tissue. (koschmieder2017planttypephytoenedesaturase pages 1-3, ruizsola2012carotenoidbiosynthesisin pages 7-8, chen2010isolationandcharacterization pages 1-2, ruizsola2012carotenoidbiosynthesisin pages 5-7)

3. Position in carotenoid metabolism

PDS acts immediately after phytoene synthase, which condenses two geranylgeranyl diphosphate molecules to produce 15-cis-phytoene. The subsequent plant poly-cis sequence is:

PSY → PDS → Z-ISO → ZDS → CRTISO → all-trans-lycopene.

PDS produces 9,15,9′-tri-cis-ζ-carotene; Z-ISO isomerizes its central 15-cis bond to create the substrate accepted by ZDS. ZDS introduces two additional double bonds, and CRTISO, assisted by photoisomerization in illuminated tissue, completes conversion of poly-cis intermediates toward all-trans-lycopene. Lycopene is then cyclized and modified to form α- and β-carotene-derived xanthophylls. (ruizsola2012carotenoidbiosynthesisin pages 7-8, chen2010isolationandcharacterization pages 1-2, ruizsola2012carotenoidbiosynthesisin pages 5-7)

This pathway explains why the primary consequences of PDS deficiency extend beyond pigmentation. Carotenoids stabilize photosynthetic pigment–protein complexes and quench chlorophyll triplets and singlet oxygen; they also supply precursors for abscisic acid, strigolactones, retinal-related compounds, and other apocarotenoid signals. Nevertheless, these downstream effects should be distinguished from PDS’s precise molecular function, which is phytoene desaturation rather than direct hormone synthesis or signaling. (gupta2022thegeneticcomponents pages 4-5, gemmecker2015phytoenedesaturasefrom pages 1-2)

4. Cellular and intraplastid localization

AtPDS is nucleus encoded and synthesized as a precursor carrying an N-terminal plastid-targeting sequence. Reported Arabidopsis annotation gives a 566-aa precursor, 75-aa targeting peptide, and 491-aa mature protein. Chloroplast proteomic assignments place approximately 84% at envelope membranes and 16% in thylakoid membranes. Independent biochemical observations indicate that catalytically active plant PDS is membrane associated, fitting the extreme hydrophobicity of phytoene, ζ-carotene, and plastoquinone. (ruizsola2012carotenoidbiosynthesisin pages 7-8, ruizsola2012carotenoidbiosynthesisin pages 3-4)

Plant PDS is best viewed as a monotopically membrane-associated enzyme, not a multipass transporter. Its active site faces the lipid–water interface and contains hydrophobic channels that permit carotene and quinone access from the membrane. Rice-PDS chromatography, cross-linking, electron microscopy, kinetics, and crystallography support an active homotetramer arranged as a dimer of dimers. A roughly 43-Å cavity accommodates extended phytoene, and the tetrameric arrangement may channel phytofluene between catalytic sites. This quaternary model is persuasive for plant PDS but remains homolog-based inference for AtPDS because an AtPDS structure has not been reported in the retrieved evidence. (brausemann2017structureofphytoene pages 1-3, gemmecker2015phytoenedesaturasefrom pages 17-18, koschmieder2017planttypephytoenedesaturase pages 20-22)

5. Genetic and physiological evidence in Arabidopsis

Arabidopsis pds3 T-DNA loss-of-function mutants are albino and dwarfed. CRISPR knockout likewise produces an easily recognized albino/null phenotype, and RNAi or virus-induced silencing causes bleached sectors. These findings are consistent with depletion of colored and photoprotective carotenoids, followed by photooxidative damage and impaired chloroplast differentiation. Because the phenotype is visually conspicuous, PDS has become a standard positive control for plant RNA-silencing and genome-editing systems. (gupta2022thegeneticcomponents pages 4-5)

The phenotype is not evidence that PDS directly synthesizes chlorophyll or gibberellin. Rather, blocking carotenoid production destabilizes developing photosynthetic systems and perturbs plastid metabolism and plastid-to-nucleus signaling; downstream hormone changes and dwarfism are consequently pleiotropic manifestations of the primary carotenoid lesion.

6. Recent research, 2023–2024

Carotenoid engineering context

A 2023 review emphasized modern carotenoid-engineering strategies—including CRISPR base editing, targeted transgene insertion, synthetic chloroplast-to-chromoplast conversion, viral expression, and microbial production. Within this framework, PDS remains both a metabolic-engineering target and a sensitive visible reporter, but PSY and carotenoid-storage capacity frequently exert stronger control over total pathway output. Thus, PDS is not universally rate limiting; its control coefficient depends on tissue, developmental state, substrate supply, and sequestration capacity.

2024 retinal–auxin findings

Xu and colleagues reported in August 2024 that Arabidopsis pds3-1 has short primary roots and reduced lateral-root formation. Acute pharmacological inhibition with fluridone suppressed wild-type primary-root growth, increased lateral-root density while redistributing lateral roots between pre-existing and newly grown root regions, increased root IAA after 8 and 24 hours, and transiently activated the DR5:LUC auxin reporter. These responses were absent or attenuated in material carrying a fluridone-insensitive PDS transgene, strengthening target attribution. (xu2024exogenousapplicationof pages 2-4, xu2024exogenousapplicationof pages 1-2, xu2024exogenousapplicationof pages 9-10)

Exogenous retinal at 20 µM partially rescued pds3-1 short roots and initially rescued fluridone-treated wild-type roots; rescue weakened after more than 60 hours. Retinal did not simply normalize every phenotype—it did not consistently restore lateral-root density or directly impose a reproducible change in free IAA—so the authors’ model that a retinal-derived signal promotes auxin homeostasis is biologically plausible but not yet a complete molecular mechanism. The most secure conclusion is that PDS-dependent carotenoid metabolism influences root auxin dynamics and architecture through one or more downstream apocarotenoids, with retinal able to compensate for part of the defect. [Xu et al., Plant Physiology 196:1659–1673, published August 2024; https://doi.org/10.1093/plphys/kiae405]. (xu2024exogenousapplicationof pages 2-4, xu2024exogenousapplicationof pages 8-9, xu2024exogenousapplicationof pages 1-2, xu2024exogenousapplicationof pages 11-12)

7. Inhibitors, herbicide mechanism, and resistance

PDS is the molecular target of bleaching herbicides including norflurazon and fluridone. Inhibition blocks FAD reoxidation by plastoquinone, causing phytoene accumulation and depletion of downstream carotenoids. Without carotenoid photoprotection, chlorophyll and membranes undergo photooxidative injury, producing the characteristic white phenotype. Structural evidence indicates that norflurazon binds in or near the plastoquinone region and stabilizes reduced FAD; excess quinone can relieve inhibition in vitro, consistent with competition. (brausemann2017structureofphytoene pages 1-3, gemmecker2015phytoenedesaturasefrom pages 17-18, gemmecker2015phytoenedesaturasefrom pages 1-2)

Resistance substitutions can reduce herbicide affinity, but there is a substantial catalytic trade-off. In rice-PDS structure–function experiments, several norflurazon-resistant variants retained less than 5% of wild-type activity; substitutions at the distal end of the carotene cavity similarly left only about 5% activity while preserving product identity. Accordingly, target-site resistance is chemically feasible but may carry a strong fitness or flux penalty. (koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 20-22, gupta2022thegeneticcomponents pages 4-5)

8. Applications and real-world implementations

Functional-genomics reporter

PDS is among the most widely used visible marker genes in plant CRISPR, RNAi, and virus-induced gene-silencing experiments. Successful disruption produces albino or mosaic white tissue without requiring specialized analytical equipment. In Arabidopsis, efficient CRISPR systems have generated visible PDS3-null phenotypes as early as the T1 generation. This use is technically valuable, although the severe phenotype means PDS is generally a method-validation target rather than a desirable agronomic knockout. (gupta2022thegeneticcomponents pages 4-5)

Herbicide discovery and selectable markers

The phytoene/plastoquinone/FAD cavity is an established site for bleaching-herbicide development. Conversely, engineered inhibitor-resistant PDS variants can serve as selectable markers or herbicide-tolerance traits. Structure-guided design must balance inhibitor resistance against the frequently observed loss of catalytic activity. (brausemann2017structureofphytoene pages 1-3, koschmieder2017planttypephytoenedesaturase pages 1-3, koschmieder2017planttypephytoenedesaturase pages 20-22)

Carotenoid biofortification

Heterologous AtPDS overexpression in four stable tomato lines demonstrated that PDS can be a flux-control point in ripening fruit. Phytoene fell to 28.5–35.3% and phytofluene to 24.9–30.7% of control, whereas ζ-carotene rose to 213.2–262.6%, lycopene to as much as 131.1%, β-carotene to 142.8%, and total carotenoids to as much as 128.5%. Expressed differently, the largest increases were more than 160% for ζ-carotene, 31.1% for lycopene, 42.8% for β-carotene, and 28.5% for total carotenoids. [McQuinn et al., Plant Biotechnology Journal 16:482–494, published 2018; https://doi.org/10.1111/pbi.12789]. (mcquinn2018atpdsoverexpressionin pages 7-11, mcquinn2018atpdsoverexpressionin pages 26-29)

These results demonstrate practical pathway engineering but do not imply that PDS is limiting in every Arabidopsis tissue or crop. Effects were tissue dependent: ripe tomato fruit responded strongly, whereas leaves showed smaller carotenoid changes and broader transcriptional feedback. (mcquinn2018atpdsoverexpressionin pages 1-4, mcquinn2018atpdsoverexpressionin pages 14-17)

9. Evidence assessment and remaining uncertainties

The identity, plastid targeting, membrane localization, pathway position, essential genetic role, and bleaching phenotype are supported directly in Arabidopsis. The precise reaction, FAD/plastoquinone chemistry, inhibitor-binding mechanism, tetrameric assembly, substrate cavity, and channeling model are supported most deeply by biochemical and structural work on rice PDS. These properties are highly likely to apply to AtPDS because the proteins are orthologous plant-type PDS enzymes with conserved fold, catalytic chemistry, and inhibitor sensitivity, but they should not be mislabeled as direct structural measurements of Q07356. (brausemann2017structureofphytoene pages 1-3, koschmieder2017planttypephytoenedesaturase pages 1-3, ruizsola2012carotenoidbiosynthesisin pages 7-8, gemmecker2015phytoenedesaturasefrom pages 1-2)

The principal open questions are how AtPDS membrane association and oligomerization are regulated in vivo, whether its envelope-versus-thylakoid distribution changes among chloroplasts and chromoplasts, and which endogenous retinal-related metabolite mediates the newly described root–auxin effects. The 2024 work advances the signaling connection but does not yet establish a complete biosynthetic route, receptor, or direct molecular target for retinal.

Selected authoritative sources

References

  1. (ruizsola2012carotenoidbiosynthesisin pages 7-8): M. Águila Ruiz-Sola and Manuel Rodríguez-Concepción. Carotenoid biosynthesis in arabidopsis: a colorful pathway. The Arabidopsis Book, 2012:e0158, Jan 2012. URL: https://doi.org/10.1199/tab.0158, doi:10.1199/tab.0158. This article has 742 citations and is from a peer-reviewed journal.

  2. (mcquinn2018atpdsoverexpressionin pages 4-7): Ryan P. McQuinn, Breanna Wong, and James J. Giovannoni. Atpds overexpression in tomato: exposing unique patterns of carotenoid self‐regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal, 16:482-494, Sep 2018. URL: https://doi.org/10.1111/pbi.12789, doi:10.1111/pbi.12789. This article has 79 citations and is from a highest quality peer-reviewed journal.

  3. (ruizsola2012carotenoidbiosynthesisin pages 3-4): M. Águila Ruiz-Sola and Manuel Rodríguez-Concepción. Carotenoid biosynthesis in arabidopsis: a colorful pathway. The Arabidopsis Book, 2012:e0158, Jan 2012. URL: https://doi.org/10.1199/tab.0158, doi:10.1199/tab.0158. This article has 742 citations and is from a peer-reviewed journal.

  4. (koschmieder2017planttypephytoenedesaturase pages 1-3): Julian Koschmieder, Mirjam Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, and Peter Beyer. Plant-type phytoene desaturase: functional evaluation of structural implications. PLoS ONE, 12:e0187628, Nov 2017. URL: https://doi.org/10.1371/journal.pone.0187628, doi:10.1371/journal.pone.0187628. This article has 65 citations and is from a peer-reviewed journal.

  5. (koschmieder2017planttypephytoenedesaturase pages 7-8): Julian Koschmieder, Mirjam Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, and Peter Beyer. Plant-type phytoene desaturase: functional evaluation of structural implications. PLoS ONE, 12:e0187628, Nov 2017. URL: https://doi.org/10.1371/journal.pone.0187628, doi:10.1371/journal.pone.0187628. This article has 65 citations and is from a peer-reviewed journal.

  6. (gupta2022thegeneticcomponents pages 4-5): Prateek Gupta and Joseph Hirschberg. The genetic components of a natural color palette: a comprehensive list of carotenoid pathway mutations in plants. Frontiers in Plant Science, Jan 2022. URL: https://doi.org/10.3389/fpls.2021.806184, doi:10.3389/fpls.2021.806184. This article has 25 citations.

  7. (chen2010isolationandcharacterization pages 1-2): Yu Chen, Faqiang Li, and Eleanore T. Wurtzel. Isolation and characterization of the z-iso gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiology, 153:66-79, Mar 2010. URL: https://doi.org/10.1104/pp.110.153916, doi:10.1104/pp.110.153916. This article has 301 citations and is from a highest quality peer-reviewed journal.

  8. (koschmieder2017planttypephytoenedesaturase pages 20-22): Julian Koschmieder, Mirjam Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, and Peter Beyer. Plant-type phytoene desaturase: functional evaluation of structural implications. PLoS ONE, 12:e0187628, Nov 2017. URL: https://doi.org/10.1371/journal.pone.0187628, doi:10.1371/journal.pone.0187628. This article has 65 citations and is from a peer-reviewed journal.

  9. (gemmecker2015phytoenedesaturasefrom pages 17-18): Sandra Gemmecker, Patrick Schaub, Julian Koschmieder, Anton Brausemann, Friedel Drepper, Marta Rodriguez-Franco, Sandro Ghisla, Bettina Warscheid, Oliver Einsle, and Peter Beyer. Phytoene desaturase from oryza sativa: oligomeric assembly, membrane association and preliminary 3d-analysis. PLoS ONE, 10:e0131717, Jul 2015. URL: https://doi.org/10.1371/journal.pone.0131717, doi:10.1371/journal.pone.0131717. This article has 40 citations and is from a peer-reviewed journal.

  10. (gemmecker2015phytoenedesaturasefrom pages 1-2): Sandra Gemmecker, Patrick Schaub, Julian Koschmieder, Anton Brausemann, Friedel Drepper, Marta Rodriguez-Franco, Sandro Ghisla, Bettina Warscheid, Oliver Einsle, and Peter Beyer. Phytoene desaturase from oryza sativa: oligomeric assembly, membrane association and preliminary 3d-analysis. PLoS ONE, 10:e0131717, Jul 2015. URL: https://doi.org/10.1371/journal.pone.0131717, doi:10.1371/journal.pone.0131717. This article has 40 citations and is from a peer-reviewed journal.

  11. (koschmieder2017planttypephytoenedesaturase pages 24-25): Julian Koschmieder, Mirjam Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, and Peter Beyer. Plant-type phytoene desaturase: functional evaluation of structural implications. PLoS ONE, 12:e0187628, Nov 2017. URL: https://doi.org/10.1371/journal.pone.0187628, doi:10.1371/journal.pone.0187628. This article has 65 citations and is from a peer-reviewed journal.

  12. (ruizsola2012carotenoidbiosynthesisin pages 5-7): M. Águila Ruiz-Sola and Manuel Rodríguez-Concepción. Carotenoid biosynthesis in arabidopsis: a colorful pathway. The Arabidopsis Book, 2012:e0158, Jan 2012. URL: https://doi.org/10.1199/tab.0158, doi:10.1199/tab.0158. This article has 742 citations and is from a peer-reviewed journal.

  13. (brausemann2017structureofphytoene pages 1-3): Anton Brausemann, Sandra Gemmecker, Julian Koschmieder, Sandro Ghisla, Peter Beyer, and Oliver Einsle. Structure of phytoene desaturase provides insights into herbicide binding and reaction mechanisms involved in carotene desaturation. Structure, 25 8:1222-1232.e3, Aug 2017. URL: https://doi.org/10.1016/j.str.2017.06.002, doi:10.1016/j.str.2017.06.002. This article has 89 citations and is from a domain leading peer-reviewed journal.

  14. (xu2024exogenousapplicationof pages 2-4): Kang Xu, Haoran Zeng, Feiyang Lin, Emi Yumoto, Masashi Asahina, Ken-ichiro Hayashi, Hidehiro Fukaki, Hisashi Ito, and Masaaki K Watahiki. Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth. Plant Physiology, 196:1659-1673, Aug 2024. URL: https://doi.org/10.1093/plphys/kiae405, doi:10.1093/plphys/kiae405. This article has 6 citations and is from a highest quality peer-reviewed journal.

  15. (xu2024exogenousapplicationof pages 8-9): Kang Xu, Haoran Zeng, Feiyang Lin, Emi Yumoto, Masashi Asahina, Ken-ichiro Hayashi, Hidehiro Fukaki, Hisashi Ito, and Masaaki K Watahiki. Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth. Plant Physiology, 196:1659-1673, Aug 2024. URL: https://doi.org/10.1093/plphys/kiae405, doi:10.1093/plphys/kiae405. This article has 6 citations and is from a highest quality peer-reviewed journal.

  16. (xu2024exogenousapplicationof pages 1-2): Kang Xu, Haoran Zeng, Feiyang Lin, Emi Yumoto, Masashi Asahina, Ken-ichiro Hayashi, Hidehiro Fukaki, Hisashi Ito, and Masaaki K Watahiki. Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth. Plant Physiology, 196:1659-1673, Aug 2024. URL: https://doi.org/10.1093/plphys/kiae405, doi:10.1093/plphys/kiae405. This article has 6 citations and is from a highest quality peer-reviewed journal.

  17. (xu2024exogenousapplicationof pages 9-10): Kang Xu, Haoran Zeng, Feiyang Lin, Emi Yumoto, Masashi Asahina, Ken-ichiro Hayashi, Hidehiro Fukaki, Hisashi Ito, and Masaaki K Watahiki. Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth. Plant Physiology, 196:1659-1673, Aug 2024. URL: https://doi.org/10.1093/plphys/kiae405, doi:10.1093/plphys/kiae405. This article has 6 citations and is from a highest quality peer-reviewed journal.

  18. (mcquinn2018atpdsoverexpressionin pages 7-11): Ryan P. McQuinn, Breanna Wong, and James J. Giovannoni. Atpds overexpression in tomato: exposing unique patterns of carotenoid self‐regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal, 16:482-494, Sep 2018. URL: https://doi.org/10.1111/pbi.12789, doi:10.1111/pbi.12789. This article has 79 citations and is from a highest quality peer-reviewed journal.

  19. (mcquinn2018atpdsoverexpressionin pages 26-29): Ryan P. McQuinn, Breanna Wong, and James J. Giovannoni. Atpds overexpression in tomato: exposing unique patterns of carotenoid self‐regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal, 16:482-494, Sep 2018. URL: https://doi.org/10.1111/pbi.12789, doi:10.1111/pbi.12789. This article has 79 citations and is from a highest quality peer-reviewed journal.

  20. (xu2024exogenousapplicationof pages 11-12): Kang Xu, Haoran Zeng, Feiyang Lin, Emi Yumoto, Masashi Asahina, Ken-ichiro Hayashi, Hidehiro Fukaki, Hisashi Ito, and Masaaki K Watahiki. Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth. Plant Physiology, 196:1659-1673, Aug 2024. URL: https://doi.org/10.1093/plphys/kiae405, doi:10.1093/plphys/kiae405. This article has 6 citations and is from a highest quality peer-reviewed journal.

  21. (mcquinn2018atpdsoverexpressionin pages 1-4): Ryan P. McQuinn, Breanna Wong, and James J. Giovannoni. Atpds overexpression in tomato: exposing unique patterns of carotenoid self‐regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal, 16:482-494, Sep 2018. URL: https://doi.org/10.1111/pbi.12789, doi:10.1111/pbi.12789. This article has 79 citations and is from a highest quality peer-reviewed journal.

  22. (mcquinn2018atpdsoverexpressionin pages 14-17): Ryan P. McQuinn, Breanna Wong, and James J. Giovannoni. Atpds overexpression in tomato: exposing unique patterns of carotenoid self‐regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal, 16:482-494, Sep 2018. URL: https://doi.org/10.1111/pbi.12789, doi:10.1111/pbi.12789. This article has 79 citations and is from a highest quality peer-reviewed journal.

Artifacts

Citations

  1. mcquinn2018atpdsoverexpressionin pages 4-7
  2. gupta2022thegeneticcomponents pages 4-5
  3. chen2010isolationandcharacterization pages 1-2
  4. brausemann2017structureofphytoene pages 1-3
  5. ruizsola2012carotenoidbiosynthesisin pages 7-8
  6. ruizsola2012carotenoidbiosynthesisin pages 3-4
  7. koschmieder2017planttypephytoenedesaturase pages 1-3
  8. koschmieder2017planttypephytoenedesaturase pages 7-8
  9. koschmieder2017planttypephytoenedesaturase pages 20-22
  10. gemmecker2015phytoenedesaturasefrom pages 17-18
  11. gemmecker2015phytoenedesaturasefrom pages 1-2
  12. koschmieder2017planttypephytoenedesaturase pages 24-25
  13. ruizsola2012carotenoidbiosynthesisin pages 5-7
  14. xu2024exogenousapplicationof pages 2-4
  15. xu2024exogenousapplicationof pages 8-9
  16. xu2024exogenousapplicationof pages 1-2
  17. xu2024exogenousapplicationof pages 9-10
  18. mcquinn2018atpdsoverexpressionin pages 7-11
  19. mcquinn2018atpdsoverexpressionin pages 26-29
  20. xu2024exogenousapplicationof pages 11-12
  21. mcquinn2018atpdsoverexpressionin pages 1-4
  22. mcquinn2018atpdsoverexpressionin pages 14-17
  23. DOI
  24. Xu et al., Plant Physiology 196:1659–1673, published August 2024; https://doi.org/10.1093/plphys/kiae405
  25. McQuinn et al., Plant Biotechnology Journal 16:482–494, published 2018; https://doi.org/10.1111/pbi.12789
  26. https://doi.org/10.1199/tab.0158
  27. https://doi.org/10.1111/pbi.12789
  28. https://doi.org/10.1104/pp.110.153916
  29. https://doi.org/10.1371/journal.pone.0187628
  30. https://doi.org/10.1105/tpc.7.12.2139
  31. https://doi.org/10.1371/journal.pone.0131717
  32. https://doi.org/10.1016/j.str.2017.06.002
  33. https://doi.org/10.3389/fpls.2021.806184
  34. https://doi.org/10.1093/plphys/kiae405
  35. https://doi.org/10.1093/plphys/kiae405].
  36. https://doi.org/10.1111/pbi.12789].
  37. https://doi.org/10.1199/tab.0158.
  38. https://doi.org/10.1104/pp.110.153916.
  39. https://doi.org/10.1371/journal.pone.0131717.
  40. https://doi.org/10.1016/j.str.2017.06.002.
  41. https://doi.org/10.1371/journal.pone.0187628.
  42. https://doi.org/10.3389/fpls.2021.806184.
  43. https://doi.org/10.1093/plphys/kiae405.
  44. https://doi.org/10.1111/pbi.12789.
  45. https://doi.org/10.1199/tab.0158,
  46. https://doi.org/10.1111/pbi.12789,
  47. https://doi.org/10.1371/journal.pone.0187628,
  48. https://doi.org/10.3389/fpls.2021.806184,
  49. https://doi.org/10.1104/pp.110.153916,
  50. https://doi.org/10.1371/journal.pone.0131717,
  51. https://doi.org/10.1016/j.str.2017.06.002,
  52. https://doi.org/10.1093/plphys/kiae405,