Carotenoid Biosynthesis in Arabidopsis: A Colorful Pathway

Ruiz-Sola, M. Águila; Rodríguez‐Concepción, Manuel

doi:10.1199/tab.0158

Cited by 475 publications

(390 citation statements)

References 281 publications

(476 reference statements)

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“…Of the 155 carotenoid metabolism genes, 13% can be described as oscillating, a similar proportion as found in the whole genome (17%), with similar proportions oscillating in either phase or antiphase with pDR5 expression. Of the 16 genes encoding core carotenoid biosynthesis enzymes (35), three are present among the oscillating genes (12); however, they are not confined to a specific branch or part of the biosynthesis pathway (Table S2), and each shows a low mean expression value (<1 in all but two of 39 samples for one of the three genes). These results indicate that, overall, carotenoid metabolism or biosynthesis genes are not part of the oscillatory transcriptional output of the LR clock.…”

Section: Resultsmentioning

confidence: 99%

“…The carotenoid metabolism gene list was generated by compiling the genes associated with GO categories describing carotenoid and apocarotenoid processes (www.arabidopsis.org) and from recent publications (Table S2). This list and the 16 core carotenoid biosynthesis genes (35) were examined in the OZ dataset (12). Hierarchical clustering was conducted using the Multiple Experiment Viewer (version 4.8) program (81).…”

Section: Methodsmentioning

confidence: 99%

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Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Norman

Zhang

Cazzonelli

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

122

120

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In plants, continuous formation of lateral roots (LRs) facilitates efficient exploration of the soil environment. Roots can maximize developmental capacity in variable environmental conditions through establishment of sites competent to form LRs. This LR prepattern is established by a periodic oscillation in gene expression near the root tip. The spatial distribution of competent (prebranch) sites results from the interplay between this periodic process and primary root growth; yet, much about this oscillatory process and the formation of prebranch sites remains unknown. We find that disruption of carotenoid biosynthesis results in seedlings with very few LRs. Carotenoids are further required for the output of the LR clock because inhibition of carotenoid synthesis also results in fewer sites competent to form LRs. Genetic analyses and a carotenoid cleavage inhibitor indicate that an apocarotenoid, distinct from abscisic acid or strigolactone, is specifically required for LR formation. Expression of a key carotenoid biosynthesis gene occurs in a spatially specific pattern along the root's axis, suggesting spatial regulation of carotenoid synthesis. These results indicate that developmental prepatterning of LRs requires an uncharacterized carotenoid-derived molecule. We propose that this molecule functions non-cell-autonomously in establishment of the LR prepattern.root development | patterning | secondary metabolite synthesis A nchorage and uptake of water and soluble nutrients are essential functions of plant root systems and key to plant productivity and survival. The capacity of a root system to carry out these functions can be maximized by iterative root branching. Root branches are formed de novo during primary root growth, which allows for the elaboration of a complex root system that effectively enables the plant to navigate and exploit the resources of diverse, locally variable subterranean environments. Understanding the developmental mechanisms underlying the pattern of root branches has broad significance in both basic and applied research.As with other dicotyledonous plants, formation of a complex root system in the model plant Arabidopsis thaliana (Arabidopsis) occurs through iterative production of branches, or lateral roots (LRs), from the primary root. The simplified root system of Arabidopsis has yielded considerable insight into the cellular events and molecular regulators required for LR formation (recently reviewed in refs.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Norman

Zhang

Cazzonelli

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

122

120

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“…Although LCYE has not been reported to be a carotenoid regulatory gene target, its elevated expression may account for the relative abundance of lutein in yellow carrots and alpha-carotene in orange carrots. DXS1 is a limiting factor in upregulation of the carotenoid pathway in A. thaliana 49 . DXS1 expression is induced by light 50,51 , and it is the main DXS isoform catalyzing the biosynthesis of isoprenoid and carotenoid precursors in photosynthetic metabolism 52,53 .…”

Section: A Model For Carotenoid Accumulation In Carrot Rootsmentioning

confidence: 99%

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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“…1), which produces isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the common precursors of monoterpenes (Croteau, 1987), diterpenes, carotenoids (Ruiz-Sola and Rodríguez-Concepción, 2012), the prenyl chains of chlorophyll and plastoquinones, and some sesquiterpenes (Dudareva et al, 2005). Many volatile compounds that play roles in plant defense are also made from precursors supplied by the MEP pathway (Gershenzon and Dudareva, 2007).…”

mentioning

confidence: 99%

Deoxyxylulose 5-Phosphate Synthase Controls Flux through the Methylerythritol 4-Phosphate Pathway in Arabidopsis

Rohwer²,

et al. 2014

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The 2-C-methylerythritol 4-phosphate (MEP) pathway supplies precursors for plastidial isoprenoid biosynthesis including carotenoids, redox cofactor side chains, and biogenic volatile organic compounds. We examined the first enzyme of this pathway, 1-deoxyxylulose 5-phosphate synthase (DXS), using metabolic control analysis. Multiple Arabidopsis (Arabidopsis thaliana) lines presenting a range of DXS activities were dynamically labeled with 13 CO 2 in an illuminated, climate-controlled, gas exchange cuvette. Carbon was rapidly assimilated into MEP pathway intermediates, but not into the mevalonate pathway. A flux control coefficient of 0.82 was calculated for DXS by correlating absolute flux to enzyme activity under photosynthetic steady-state conditions, indicating that DXS is the major controlling enzyme of the MEP pathway. DXS manipulation also revealed a second pool of a downstream metabolite, 2-Cmethylerythritol-2,4-cyclodiphosphate (MEcDP), metabolically isolated from the MEP pathway. DXS overexpression led to a 3-to 4-fold increase in MEcDP pool size but to a 2-fold drop in maximal labeling. The existence of this pool was supported by residual MEcDP levels detected in dark-adapted transgenic plants. Both pools of MEcDP are closely modulated by DXS activity, as shown by the fact that the concentration control coefficient of DXS was twice as high for MEcDP (0.74) as for 1-deoxyxylulose 5-phosphate (0.35) or dimethylallyl diphosphate (0.34). Despite the high flux control coefficient for DXS, its overexpression led to only modest increases in isoprenoid end products and in the photosynthetic rate. Diversion of flux via MEcDP may partly explain these findings and suggests new opportunities to engineer the MEP pathway.

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Carotenoid Biosynthesis in Arabidopsis: A Colorful Pathway

Cited by 475 publications

References 281 publications

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Deoxyxylulose 5-Phosphate Synthase Controls Flux through the Methylerythritol 4-Phosphate Pathway in Arabidopsis

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