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Information on EC 1.3.5.5 - 15-cis-phytoene desaturase
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1.3.5.5 15-cis-phytoene desaturaseIUBMB Comments
This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria. The enzyme from Synechococcus can also use NAD+ and NADP+ as electron acceptor under anaerobic conditions. The enzyme from Gentiana lutea shows no activity with NAD+ or NADP+ .
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Word Map
- 1.3.5.5
-
carotenoid
-
herbicide
- zeta-carotene
- agriculture
-
bleaching
- norflurazon
- synthesis
-
phytofluene
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
ospds, bopds, citpds1, plant-type phytoene desaturase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PDS
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
15,9'-dicis-phytofluene + plastoquinone = 9,15,9'-tricis-zeta-carotene + plastoquinol
(1b)
-
15,9'-dicis-phytofluene + plastoquinone = 9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
-
15-cis-phytoene + 2 plastoquinone = 9,15,9'-tricis-zeta-carotene + 2 plastoquinol
overall reaction
-
15-cis-phytoene + 2 plastoquinone = 9,15,9'-tricis-zeta-carotene + 2 plastoquinol
overall reaction, ordered ping-pong bi-bi mechanism, both lipophilic substrates are bound inside the same substrate cavity that cannot be occupied by both simultaneously. The central 15-cis configuration of phytoene mediates the regiospecificity in catalysis
15-cis-phytoene + 2 plastoquinone = 9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
15-cis-phytoene + plastoquinone = 15,9'-dicis-phytofluene + plastoquinol
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
15-cis-phytoene:plastoquinone oxidoreductase
This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria. The enzyme from Synechococcus can also use NAD+ and NADP+ as electron acceptor under anaerobic conditions. The enzyme from Gentiana lutea shows no activity with NAD+ or NADP+ [1].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
15-cis-phytoene + 2 decyl-plastoquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
15-cis-phytoene + 2 decyl-ubiquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
-
this quinone derivative is used in the study because the natural C45-ubiquinone is not available commercially
-
-
?
15-cis-phytoene + 2 decylubiquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
-
this quinone derivative is used in the study because the natural C45-ubiquinone is not available commercially
-
-
?
15-cis-phytoene + 2,5-dibromo-3-methyl-6-isopropyl-1,4-benzoquinone
9,15,9'-tricis-zeta-carotene + 2,5-dibromo-3-methyl-6-isopropyl-1,4-benzoquinol
-
-
-
-
?
15-cis-phytoene + 5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole + H2O
9,15,9'-tricis-zeta-carotene + 5-n-undecyl-4,6,7-trihydroxybenzothiazole
-
-
-
-
?
15-cis-phytoene + duroquinone
9,15,9'-tricis-zeta-carotene + duroquinol
-
-
-
-
?
15-cis-phytoene + plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
the biosynthetic pathway of carotenoid synthesis involves several steps of desaturation requiring free energy, for instance the transition from phytoene to phytofluene achieved by phytoene desaturase. This reaction is associated with a reduction of plastoquinone. The oxidation of the plastoquinol is then achieved by a plastoquinol:oxygen oxidoreductase. Might additionally mediate the reduction of plastoquinone by internal reductants
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
Dunaliella salina CCAP 19/41 (PLY DF15)
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
?
15-cis-phytoene + 2 decyl-plastoquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
-
this quinone derivative is used in the study because the natural C45-plastoquinone is not available commercially. Decyl-plastoquinone is very effective as a cofactor of desaturation. The simultanous presence of NADP+ has no influence on the activity
-
-
?
15-cis-phytoene + 2 decyl-plastoquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
-
-
-
?
15-cis-phytoene + 2 decyl-plastoquinone
9,15,9'-tricis-zeta-carotene + 2 decyl-plastoquinol
-
this quinone derivative is used in the study because the natural C45-plastoquinone is not available commercially
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
overall reaction
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
overall reaction. The conversion rate with all-trans-phytoene is 10% of the value with the 15-cis isomer
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
the biosynthetic pathway of carotenoid synthesis involves several steps of desaturation requiring free energy, for instance the transition from phytoene to phytofluene achieved by phytoene desaturase. This reaction is associated with a reduction of plastoquinone. The oxidation of the plastoquinol is then achieved by a plastoquinol:oxygen oxidoreductase. Might additionally mediate the reduction of plastoquinone by internal reductants
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
phytoene desaturase is an enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
phytoene desaturase is an enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
Dunaliella salina CCAP 19/41 (PLY DF15)
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
decyl-plastoquinone is used for enzyme assays
-
-
?
additional information
?
-
geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene
-
-
-
additional information
?
-
Dunaliella salina CCAP 19/41 (PLY DF15)
geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene
-
-
-
additional information
?
-
benzoquinone cosubstrates are strongly preferred over naphthoquinones
-
-
?
additional information
?
-
PDS requires plastoquinone as a directly interacting co-substrate to reoxidize the enzyme-bound FADred formed upon desaturation. The enzyme structure has led to the conclusion that both lipophilic substrates are bound inside the same substrate cavity that cannot be occupied by both simultaneously. The central 15-cis configuration of phytoene mediates the regiospecificity in catalysis, overview. LC-MS analysis of PDS desaturation products produced from asymmetric (C35) 15-cis-norphytoene
-
-
-
additional information
?
-
-
the enzyme also shows activity with NADP+ as cosubstrate, the affinity for NADP+ is lower than for decylplastoquinone or decylubioquinone
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
15-cis-phytoene + plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
the biosynthetic pathway of carotenoid synthesis involves several steps of desaturation requiring free energy, for instance the transition from phytoene to phytofluene achieved by phytoene desaturase. This reaction is associated with a reduction of plastoquinone. The oxidation of the plastoquinol is then achieved by a plastoquinol:oxygen oxidoreductase. Might additionally mediate the reduction of plastoquinone by internal reductants
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
Dunaliella salina CCAP 19/41 (PLY DF15)
-
-
-
?
15,9'-dicis-phytofluene + plastoquinone
9,15,9'-tricis-zeta-carotene + plastoquinol
-
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
overall reaction
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
the biosynthetic pathway of carotenoid synthesis involves several steps of desaturation requiring free energy, for instance the transition from phytoene to phytofluene achieved by phytoene desaturase. This reaction is associated with a reduction of plastoquinone. The oxidation of the plastoquinol is then achieved by a plastoquinol:oxygen oxidoreductase. Might additionally mediate the reduction of plastoquinone by internal reductants
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + 2 plastoquinone
9,15,9'-tricis-zeta-carotene + 2 plastoquinol
-
-
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + acceptor
9,15,9'-tricis-zeta-carotene + reduced acceptor
phytoene desaturase is an enzyme of the carotenoid biosynthetic pathway
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
Dunaliella salina CCAP 19/41 (PLY DF15)
-
-
-
?
15-cis-phytoene + plastoquinone
15,9'-dicis-phytofluene + plastoquinol
-
-
-
?
additional information
?
-
geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene
-
-
-
additional information
?
-
Dunaliella salina CCAP 19/41 (PLY DF15)
geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
decyl-plastoquinone
-
this quinone derivative is used in the study because the natural C45-plastoquinone is not available commercially
quinone
-
since phytoene desaturation responds to the redox state of quinones, which is adjusted by the respiratory redox pathway, the two reactions must be regarded as being mechanistically linked. Using redox titrations, it is shown that the optimal activity lies in the range of the midpoint potential of the plastoquinone/plastohydroquinone redox couple
Ubiquinone-10
-
this quinone derivative is used in the study because the natural C45-plastoquinone is not available commercially
FAD
the deduced amino acid sequence of wheat phytoene desaturase reveals a typical pyridine dinucleotide binding motif generally associated with the binding of FAD
FAD
PDS requires plastoquinone as a directly interacting co-substrate to reoxidize the enzyme-bound FADred formed upon desaturation
plastoquinone
-
decyl-plastoquinone or decyl-ubiquinone is used in the study because the natural C45-plastoquinone is not available commercially. The affinity of the enzyme for plastoquinone is higher than for NADP+
plastoquinone
-
plastoquinone is an essential component of phytoene desaturation
additional information
-
5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole, 2,5-dibromo-3-methyl-6-isopropyl-l,4-benzoquinone, duroquinon are used as artificial electron acceptor
-
additional information
-
the enzyme also shows activity with NADP+ as cosubstrate, the affinity for NADP+ is lower than for decylplastoquinone or decylubioquinone
-
additional information
-
the soluble form of the enzyme is able to associate on to/into protein-free liposomal membranes made from chromoplast lipids, thereby gaining activity by binding added FAD. Once bound to membranes, activated phytoene desaturase works independently of any added FAD, employing membrane-bound electron acceptors. FAD exerts no positive effect on the membrane-association process, its role is confined to enzymatic activation
-
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2R,5S)-5-methyl-2-(3-trifluoromethylbenzyl)-3-oxomorpholine
-
less active inhibitor compared to (2R,5S)-5-methyl-2-(3-trifluoromethylbenzyl)-3-ketomorpholine; very low inhibition
O-[1-ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-(2-chlorobenzyl)carbamate
-
-
O-[1-ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-(2-phenylethyl)carbamate
-
-
O-[1-methyl-2-(3-trifluoromethylphenoxy)]ethyl-N-benzylcarbamate
-
-
additional information
-
with respect to a structure-activity relationship the oxygen atom of the phenoxy group and a carbamate structure in O-(1-ethyl-2-phenoxy)ethyl-N-aralkylcarbamates studied are found to be essential for strong PDS inhibitors. phytoene desaturase inhibitor
-
fluridone
-
arginine304 present in the wild-type Hydrilla verticillata phytoene desaturase is substituted with all 19 other natural amino acids. In vitro the threonine (Thr), cysteine (Cys), alanine (Ala) and glutamine (Gln) mutations impart the highest resistance to fluridone. The three natural mutations [Cys, serine (Ser), histidine (His)] and the wild-type phytoene desaturase protein are tested in vitro against seven inhibitors of phytoene desaturase representing several classes of herbicides. These mutations confer cross-resistance to norflurazon and overall negative cross-resistance to beflubutamid, picolinafen and diflufenican. The Thr304 Hydrilla pds mutant is an excellent marker for the selection of transgenic plants. Seedlings harbouring Thr304 pds have a maximum resistance to sensitivity (R/S) ratio of 57 and 14 times higher than that of the wild-type for treatments with norflurazon and fluridone, respectively. These plants exhibit normal growth and development, even after long-term exposure to herbicide. As Thr304 pds is of plant origin, it could become more acceptable than other selectable markers for use in genetically modified food
norflurazon
-
arginine304 present in the wild-type Hydrilla verticillata phytoene desaturase is substituted with all 19 other natural amino acids. In vitro the threonine (Thr), cysteine (Cys), alanine (Ala) and glutamine (Gln) mutations impart the highest resistance to fluridone. The three natural mutations [Cys, serine (Ser), histidine (His)] and the wild-type phytoene desaturase protein are tested in vitro against seven inhibitors of phytoene desaturase representing several classes of herbicides. These mutations confer cross-resistance to norflurazon and overall negative cross-resistance to beflubutamid, picolinafen and diflufenican. The Thr304 Hydrilla pds mutant is an excellent marker for the selection of transgenic plants. Seedlings harbouring Thr304 pds have a maximum resistance to sensitivity (R/S) ratio of 57 and 14 times higher than that of the wild-type for treatments with norflurazon and fluridone, respectively. These plants exhibit normal growth and development, even after long-term exposure to herbicide. As Thr304 pds is of plant origin, it could become more acceptable than other selectable markers for use in genetically modified food
norflurazon
arrests the reaction by stabilizing the intermediary FADred. An excess of the quinone acceptor relieves this blockage
norflurazon
NFZ, competitive inhibition, inhibition kinetics with enzyme mutant R300S
norflurazon
-
0.0001 mM, Vmax values are very little influenced by norflurazon, which reveals a competition between NADP+ or plastoquinone and norflurazon for the cofactor binding site of phytoene desaturase
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
light wavelengths affect the synthesis of carotenoids in Dunaliella salina. The red light increases the cellular content of all major carotenoids and total carotenoids. Concentrations of 15-cis-phytoene in cultures increase with light intensity under both red and blue light, being generally higher under red than blue light (more than double)
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.039
5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole
-
pH 7.8, 27°C, chromoplast homogenate
additional information
additional information
Michaelis-Menten kinetics
-
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.2
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
obtained from Escherichia coli transformant
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
siliques and roots show the lowest levels of expression
brenda
additional information
PDS transcripts are nearly absent in the roots and seeds
brenda
BoPDS has the highest level of expression in flowers with an approximate 4.5fold increase of BoPDS transcript level compared with leaf tissue
brenda
BoPDS has the highest level of expression in flowers with an approximate 4.5fold increase of BoPDS transcript level compared with leaf tissue
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
BoPDS is present at similar levels in chromoplasts and leucoplasts
brenda
the plastid membrane enzyme form is present in a large protein complex of approximately 350000 Da, the enzyme from stroma is in an approximately 660000 Da complex
brenda
-
phytoene desaturase is restricted to the chloroplast
brenda
BoPDS is present at similar levels in chromoplasts and leucoplasts
brenda
-
the soluble form is enzymatically inactive and a constituent of a larger Hsp 70-containing protein complex in the stroma, whereas the membrane-bound form is functional
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
additional information
using the crystal structure of Oryza sativa PDS in complex with norflurazon, the relevance of homotetrameric assembly of the enzyme observed in crystallo is determined by dynamic mathematical modeling of reaction time courses, substrate channeling occurs of the intermediate phytofluene between individual subunits at membrane surfaces
malfunction
both the albino and dwarf phenotypes of the pds3 mutant result from functional disruption of the PDS3 gene. Chloroplast development is arrested at the proplastid stage in the pds3 mutant. Further analysis shows that a high level of phytoene is accumulated in the pds3 mutant. Disrupting PDS3 gene results in gene expression changes involved in at least 20 metabolic pathways, including the inhibition of many genes in carotenoid, chlorophyll, and GA biosynthesis pathways. The accumulated phytoene in the pds3 mutant might play an important role in certain negative feedbacks to affect gene expression of diverse cellular pathways
malfunction
high light stress, red light stress, or use of a phytoene desaturase inhibitor or a mitotic disrupter herbicide lead to the accumulation of 15-cis phytoene but not all-trans phytoene. Bleaching herbicides such as norflurazon are known to boost phytoene accumulation in the cells of Dunaliella salina and other higher plants, by inhibiting PDS, which prevents the conversion of phytoene to phytofluene
malfunction
Dunaliella salina CCAP 19/41 (PLY DF15)
-
high light stress, red light stress, or use of a phytoene desaturase inhibitor or a mitotic disrupter herbicide lead to the accumulation of 15-cis phytoene but not all-trans phytoene. Bleaching herbicides such as norflurazon are known to boost phytoene accumulation in the cells of Dunaliella salina and other higher plants, by inhibiting PDS, which prevents the conversion of phytoene to phytofluene
-
metabolism
maize phytoene desaturase and zeta-carotene desaturase catalyse a poly-Z desaturation pathway to the predominate geometric isomer 7,9,7',9'-tetra-Z-lycopene (poly-Z-lycopene or prolycopene), and not the all-trans substrate required by the downstream lycopene cyclase enzymes
metabolism
determination of the phytoene isomers in Dunaliella salina by NMR spectrocopy and analysis of the carotenoid synthesis pathway of Dunaliella salina, overview
metabolism
Dunaliella salina CCAP 19/41 (PLY DF15)
-
determination of the phytoene isomers in Dunaliella salina by NMR spectrocopy and analysis of the carotenoid synthesis pathway of Dunaliella salina, overview
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physiological function
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
physiological function
-
phytoene desaturase is an early enzyme of the carotenoid biosynthetic pathway
physiological function
phytoene desaturase is an enzyme of the carotenoid biosynthetic pathway
physiological function
three functional units, comprising genes PSY1, PDS/ZISO, and ZDS/CrtISO, are responsible for the synthesis of 15-cis-phytoene, 9,9'-di-cis-zeta-carotene, and all-trans-lycopene, respectively. Silencing of desaturase PDS results in the induction of the isomerase in the same functional unit, ZISO. PDS-silenced fruits show a 55% reduction of total carotenoids, with phytoene and phytofluene being the most abundant compounds. All-trans-zeat-carotene is detectable in nonsilenced fruits
physiological function
upon transfer to high light, the transcript levels of all investigated carotenogenic genes including those coding for phytoene synthase, phytoene desaturase and both ketolases are increased
physiological function
carotenoids comprise a diverse range of naturally occurring stereoisomers, which differ in their physico-chemical properties. Their biosynthesis begins with phytoene, which is a rarity among carotenoids because it is colourless. Geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene. The marine microalga Dunaliella salina is the richest source of beta-carotene, but it can accumulate phytoene and phytofluene as well. Dunaliella salina, similar to tomato, produces predominantly 15-cis phytoene isomer (over 98%) and a trace amount of all-trans phytoene (below 2%). 9-cis phytoene is not detected in any of the extracts of Dunaliella salina biomass. 15-cis phytoene is the most abundant isomer in Dunaliella salina and that it is subject to a series of isomerisation and desaturation reactions to form all-trans and 9-cis beta-carotene
physiological function
phytoene desaturase (PDS) is an essential plant carotenoid biosynthetic enzyme. PDS catalyzes the introduction of two double bonds into 15-cis-phytoene, yielding 9,15,9'-tri-cis-zeta-carotene via the intermediate 9,15-di-cis-phytofluene
physiological function
Dunaliella salina CCAP 19/41 (PLY DF15)
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carotenoids comprise a diverse range of naturally occurring stereoisomers, which differ in their physico-chemical properties. Their biosynthesis begins with phytoene, which is a rarity among carotenoids because it is colourless. Geranylgeranyl diphosphate is catalysed by phytoene synthase and phytoene desaturase to phytoene and phytofluene, respectively. The subsequent steps involve desaturation, isomerisation and cyclisation reactions to form alpha- and beta-carotene stereoisomers, via all-trans lycopene. The marine microalga Dunaliella salina is the richest source of beta-carotene, but it can accumulate phytoene and phytofluene as well. Dunaliella salina, similar to tomato, produces predominantly 15-cis phytoene isomer (over 98%) and a trace amount of all-trans phytoene (below 2%). 9-cis phytoene is not detected in any of the extracts of Dunaliella salina biomass. 15-cis phytoene is the most abundant isomer in Dunaliella salina and that it is subject to a series of isomerisation and desaturation reactions to form all-trans and 9-cis beta-carotene
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Show AA Sequence and Transmembrane Helices (1470 entries)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
350000
the plastid membrane enzyme form is present in a large protein complex of approximately 350000 Da, the stroma version is in an approximately 660000 Da complex
55000
x * 55000, SDS-PAGE, the plastid membrane enzyme form is present in a large protein complex of approximately 350000 Da, the stroma version is in an approximately 660000 Da complex
660000
the plastid membrane enzyme form is present in a large protein complex of approximately 350000 Da, the stroma version is in an approximately 660000 Da complex
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
octamer
8 * 56200, calculated, 8 * 56000, SDS-PAGE, recombinant protein with His-tag
?
x * 55000, SDS-PAGE, the plastid membrane enzyme form is present in a large protein complex of approximately 350000 Da, the stroma version is in an approximately 660000 Da complex
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
the enzyme form from stroma appears to be slightly larger in size than the membrane version, which may be because of different posttranslational modifications of BoPDS in these two locations
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
low-resolution model, homotetrameric arrangement of the protein
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
L504R
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the modified phytoene desaturase is still active in conversion of phytoene to zeta-carotene and exhibits 43fold-higher resistance to the bleaching herbicide norflurazon. The norflurazon-resistant phytoene desaturase gene is used for successful nuclear transformation and genetic engineering of the carotenoid biosynthesis pathway for accelerated astaxanthin biosynthesis
R304X
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substitution of arginine304 present in the wild-type Hydrilla verticillata phytoene desaturase with all 19 other natural amino acids. In vitro the threonine (Thr), cysteine (Cys), alanine (Ala) and glutamine (Gln) mutations impart the highest resistance to fluridone. The three natural mutations [Cys, serine (Ser), histidine (His)] and the wild-type phytoene desaturase protein are tested in vitro against seven inhibitors of phytoene desaturase representing several classes of herbicides. These mutations confer cross-resistance to norflurazon and overall negative cross-resistance to beflubutamid, picolinafen and diflufenican. The Thr304 Hydrilla pds mutant is an excellent marker for the selection of transgenic plants. Seedlings harbouring Thr304 pds have a maximum resistance to sensitivity (R/S) ratio of 57 and 14 times higher than that of the wild-type for treatments with norflurazon and fluridone, respectively. These plants exhibit normal growth and development, even after long-term exposure to herbicide. As Thr304 pds is of plant origin, it could become more acceptable than other selectable markers for use in genetically modified food
F162V
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
L538F
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
L538R
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
R300S
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
R300T
site-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
T508V
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
Y506F
-directed mutagenesis, the mutant shows below 5% activity compared to wild-type enzyme
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
reduced form of protein is stable for over 2 h in ambient oxygen atmosphere, rapid reoxidation can be achieved with excess decyl-plastoquinone
743580
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant protein. High-order oligomers formed in solution are the basis for an active preparation
recombinant wild-type and mutant His6-tagged enzymes OsPDS from Escherichia coli by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene OsI_010044 or PDS1, recombinant expression of wild-type and mutant His6-tagged enzymes OsPDS in Escherichia coli
heterologous expression in a strain of Escherichia coli containing a carotenoid-producing plasmid
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
although carotenoid accumulation is strongly induced during flower development, only very low concentrations of phytoene desaturase transcripts are detectable, while the corresponding protein accumulates in low, but measurable amounts, appearing in soluble and membrane-bound states
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Pds is constitutively expressed. Endosperm carotenogenesis is not regulated by increasing the level of phytoene desaturase transcripts
presence of 5-chloro-3-methyl-4-nitro-1H-pyrazole activates phytoene desaturase (Pds) and zeta-carotene desaturase Zds gene expression from early to midmaturation stages of fruit
regulation of phytoene desaturase occurs primarily at the mRNA level, most likely by transcriptional control. The enzyme is induced in response to stress conditions leading to biosynthesis of secondary carotenoids
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the CitPDS1 transcript in the juice sacs/segment epidermis (edible part) is at a low level in the young fruit, and it increases toward maturation. In the peel the level of the CitPDS1 transcript remains constant after an increase in July
there is no significant induction of phytoene desaturase gene expression specific to white tissue, indicating that phytoene desaturase expression is independent of the pigment status of the cells
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upon transfer to high light, the transcript levels of all investigated carotenogenic genes including those coding for phytoene synthase, phytoene desaturase and both ketolases are increased. Transcription changes proceed via binding of the transcription factor NtcA to the promoter regions of the carotenogenic genes. The binding is absolutely dependent on the presence of reductants and oxo-glutarate and inhibited by 3-(3, 4-dichlorophenyl)-1,1-dimethyl urea
presence of 5-chloro-3-methyl-4-nitro-1H-pyrazole activates phytoene desaturase (Pds) and zeta-carotene desaturase Zds gene expression from early to midmaturation stages of fruit
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presence of 5-chloro-3-methyl-4-nitro-1H-pyrazole activates phytoene desaturase (Pds) and zeta-carotene desaturase Zds gene expression from early to midmaturation stages of fruit
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
agriculture
synthesis
agriculture
-
the Thr304 Hydrilla pds mutant is an excellent marker for the selection of transgenic plants. Seedlings harbouring Thr304 pds have a maximum resistance to sensitivity (R/S) ratio of 57 and 14 times higher than that of the wild-type for treatments with norflurazon and fluridone, respectively. These plants exhibit normal growth and development, even after long-term exposure to herbicide. As Thr304 pds is of plant origin, it could become more acceptable than other selectable markers for use in genetically modified food
agriculture
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fruit treated with 5-chloro-3-methyl-4-nitro-1H-pyrazole appear more yellow and/or orange than ethephon or control fruit at any harvest date
agriculture
phytoene desaturase is a prominent target of certain inhibitors, such as norflurazon, acting as bleaching herbicides
agriculture
-
fruit treated with 5-chloro-3-methyl-4-nitro-1H-pyrazole appear more yellow and/or orange than ethephon or control fruit at any harvest date
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synthesis
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the norflurazon-resistant phytoene desaturase gene is used for successful nuclear transformation and genetic engineering of the carotenoid biosynthesis pathway for accelerated astaxanthin biosynthesis (astaxanthin as a food supplement for humans)
synthesis
Dunalielle salina can be used as a cell factory for phytoene production
synthesis
Dunaliella salina CCAP 19/41 (PLY DF15)
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Dunalielle salina can be used as a cell factory for phytoene production
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Mayer, M.P.; Beyer, P.; Kleinig, H.
Quinone compounds are able to replace molecular oxygen as terminal electron acceptor in phytoene desaturation in chromoplasts of Narcissus pseudonarcissus L.
Eur. J. Biochem.
191
359-363
1990
Narcissus pseudonarcissus
brenda
Matthews, P.D.; Luo, R.; Wurtzel, E.T.
Maize phytoene desaturase and zeta-carotene desaturase catalyse a poly-Z desaturation pathway: implications for genetic engineering of carotenoid content among cereal crops
J. Exp. Bot.
54
2215-2230
2003
Zea mays (P49086)
brenda
Breitenbach, J.; Sandmann, G.
zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene
Planta
220
785-793
2005
Capsicum annuum
brenda
Steinbrenner, J.; Sandmann, G.
Transformation of the green alga Haematococcus pluvialis with a phytoene desaturase for accelerated astaxanthin biosynthesis
Appl. Environ. Microbiol.
72
7477-7484
2006
Haematococcus lacustris
brenda
Kita, M.; Komatsu, A.; Omura, M.; Yano, M.; Ikoma, Y.; Moriguchi, T.
Cloning and expression of CitPDS1, a gene encoding phytoene desaturase in citrus
Biosci. Biotechnol. Biochem.
65
1424-1428
2001
Citrus unshiu (Q7GCA8)
brenda
Qin, G.; Gu, H.; Ma, L.; Peng, Y.; Deng, X.W.; Chen, Z.; Qu, L.J.
Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis
Cell Res.
17
471-482
2007
Arabidopsis thaliana (Q07356)
brenda
Nievelstein, V.; Vandekerchove, J.; Tadros, M.H.; Lintig, J.V.; Nitschke, W.; Beyer, P.
Carotene desaturation is linked to a respiratory redox pathway in Narcissus pseudonarcissus chromoplast membranes. Involvement of a 23-kDa oxygen-evolving-complex-like protein
Eur. J. Biochem.
233
864-872
1995
Narcissus pseudonarcissus
brenda
Sandmann, G.; Mitchell, G.
In vitro inhibition studies of phytoene desaturase by bleaching ketomorpholine derivatives
J. Agric. Food Chem.
49
138-141
2001
Synechococcus sp.
brenda
Breitenbach, J.; Zhu, C.; Sandmann, G.
Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors
J. Agric. Food Chem.
49
5270-5272
2001
Synechococcus sp., Gentiana lutea
brenda
Ohki, S.; Miller-Sulger, R.; Wakabayashi, K.; Pfleiderer, W.; Bger, P.
Phytoene desaturase inhibition by O-(2-phenoxy)ethyl-N-aralkylcarbamates
J. Agric. Food Chem.
51
3049-3055
2003
Synechococcus elongatus PCC 7942 = FACHB-805
brenda
Zhu, Y.H.; Jiang, J.G.; Yan, Y.; Chen, X.W.
Isolation and characterization of phytoene desaturase cDNA involved in the beta-carotene biosynthetic pathway in Dunaliella salina
J. Agric. Food Chem.
53
5593-5597
2005
Dunaliella salina (Q3ZDQ0)
brenda
Cong, L.; Wang, C.; Li, Z.; Chen, L.; Yang, G.; Wang, Y.; He, G.
cDNA cloning and expression analysis of wheat (Triticum aestivum L.) phytoene and zeta-carotene desaturase genes
Mol. Biol. Rep.
37
3351-3361
2010
Triticum aestivum (B8YDB8)
brenda
Bennoun, P.
The present model for chlororespiration
Photosynth. Res.
73
273-277
2002
Embryophyta, Rhodophyta
brenda
Lopez, A.B.; Yang, Y.; Thannhauser, T.W.; Li, L.
Phytoene desaturase is present in a large protein complex in the plastid membrane
Physiol. Plant.
133
190-198
2008
Brassica oleracea (B2X8P6)
brenda
Arias, R.S.; Dayan, F.E., Michel, A.; Howell, J.; Scheffler, B.E.
Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker
Plant Biotechnol. J.
4
263-273
2006
Hydrilla verticillata
brenda
Norris, S.R.; Barrette, T.R.; DellaPenna, D.
Genetic dissection of carotenoid synthesis in arabidopsis defines plastoquinone as an essential component of phytoene desaturation
Plant Cell
7
2139-2149
1995
Arabidopsis thaliana
brenda
Al-Babili, S.; von Lintig, J.; Haubruck, H.; Beyer, P.
A novel, soluble form of phytoene desaturase from Narcissus pseudonarcissus chromoplasts is Hsp70-complexed and competent for flavinylation, membrane association and enzymatic activation
Plant J.
9
601-612
1996
Narcissus pseudonarcissus
brenda
Li, Z.H.; Matthews, P.D.; Burr, B.; Wurtzel, E.T.
Cloning and characterization of a maize cDNA encoding phytoene desaturase, an enzyme of the carotenoid biosynthetic pathway
Plant Mol. Biol.
30
269-279
1996
Zea mays (P49086)
brenda
Wetzel, C.M.; Rodermel, S.R.
Regulation of phytoene desaturase expression is independent of leaf pigment content in Arabidopsis thaliana
Plant Mol. Biol.
37
1045-1053
1998
Arabidopsis thaliana
brenda
Grnewald, K.; Eckert, M.; Hirschberg, J.; Hagen, C.
Phytoene desaturase is localized exclusively in the chloroplast and up-regulated at the mRNA level during accumulation of secondary carotenoids in Haematococcus pluvialis (Volvocales, chlorophyceae)
Plant Physiol.
122
1261-1268
2000
Haematococcus lacustris
brenda
Alferez, F.; Pozo, L.; Rouseff, R.; Burns, J.
Modification of carotenoid levels by abscission agents and expression of carotenoid biosynthetic genes in Valencia sweet orange
J. Agric. Food Chem.
61
3082-3089
2013
Citrus sinensis, Citrus sinensis L. Osbeck
brenda
Fantini, E.; Falcone, G.; Frusciante, S.; Giliberto, L.; Giuliano, G.
Dissection of tomato lycopene biosynthesis through virus-induced gene silencing
Plant Physiol.
163
986-998
2013
Solanum lycopersicum (P28554)
brenda
Gemmecker, S.; Schaub, P.; Koschmieder, J.; Brausemann, A.; Drepper, F.; Rodriguez-Franco, M.; Ghisla, S.; Warscheid, B.; Einsle, O.; Beyer, P.
Phytoene desaturase from Oryza sativa oligomeric assembly, membrane association and preliminary 3D-analysis
PLoS ONE
10
e0131717
2015
Oryza sativa Indica Group (A2XDA1)
brenda
Sandmann, G.; Mautz, J.; Breitenbach, J.
Control of light-dependent keto carotenoid biosynthesis in Nostoc 7120 by the transcription factor NtcA
Z. Naturforsch. C
71
303-311
2016
Nostoc sp. PCC 7120 = FACHB-418 (Q9R6X5)
brenda
Mazzucchi, L.; Xu, Y.; Harvey, P.
Stereoisomers of colourless carotenoids from the marine microalga Dunaliella salina
Molecules
25
1880
2020
Dunaliella salina (Q3ZDQ0), Dunaliella salina CCAP 19/41 (PLY DF15) (Q3ZDQ0)
brenda
Koschmieder, J.; Fehling-Kaschek, M.; Schaub, P.; Ghisla, S.; Brausemann, A.; Timmer, J.; Beyer, P.
Plant-type phytoene desaturase functional evaluation of structural implications
PLoS ONE
12
e0187628
2017
Oryza sativa Indica Group (A2XDA1)
brenda
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