Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways

The potential of Pavlovophyceae species as a source of valuable carotenoids and polyunsaturated fatty acids for human consumption

Microalgae are a group of microorganisms, mostly photoautotrophs with high CO2 fixation capacity, that have gained increased attention in the last decades due to their ability to produce a wide range of valuable metabolites, such as carotenoids and polyunsaturated fatty acids, for application in food/feed, pharmaceutical, and cosmeceutical industries. Their increasing relevance has highlighted the importance of identifying and culturing new bioactive-rich microalgae species, as well as of a thorough understanding of the growth conditions to optimize the biomass production and master the biochemical composition according to the desired application. Thus, this review intends to describe the main cell processes behind the production of carotenoids and polyunsaturated fatty acids, in order to understand the possible main triggers responsible for the accumulation of those biocompounds. Their economic value and the biological relevance for human consumption are also summarized. In addition, an extensive review of the impact of culture conditions on microalgae growth performance and their biochemical composition is presented, focusing mainly on the studies involving Pavlovophyceae species. A complementary description of the biochemical composition of these microalgae is also presented, highlighting their potential applications as a promising bioresource of compounds for large-scale production and human and animal consumption.

Dual plastid targeting of protoporphyrinogen oxidase 2 in Amaranthaceae promotes herbicide tolerance

Plant tetrapyrrole biosynthesis (TPB) takes place in plastids and provides the chlorophyll and heme required for photosynthesis and many redox processes throughout plant development. TPB is strictly regulated, since accumulation of several intermediates causes photodynamic damage and cell death. Protoporphyrinogen oxidase (PPO) catalyzes the last common step before TPB diverges into chlorophyll and heme branches. Land plants possess two PPO isoforms. PPO1 is encoded as a precursor protein with a transit peptide, but in most dicotyledonous plants PPO2 does not possess a cleavable N-terminal extension. Arabidopsis (Arabidopsis thaliana) PPO1 and PPO2 localize in chloroplast thylakoids and envelope membranes, respectively. Interestingly, PPO2 proteins in Amaranthaceae contain an N-terminal extension that mediates their import into chloroplasts. Here, we present multiple lines of evidence for dual targeting of PPO2 to thylakoid and envelope membranes in this clade and demonstrate that PPO2 is not found in mitochondria. Transcript analyses revealed that dual targeting in chloroplasts involves the use of two transcription start sites and initiation of translation at different AUG codons. Among eudicots, the parallel accumulation of PPO1 and PPO2 in thylakoid membranes is specific for the Amaranthaceae and underlies PPO2-based herbicide resistance in Amaranthus species.

Multi-omics analyses reveal the importance of chromoplast plastoglobules in carotenoid accumulation in citrus fruit

Chromoplasts act as a metabolic sink for carotenoids, in which plastoglobules serve as versatile lipoprotein particles. PGs in chloroplasts have been characterized. However, the features of PGs from non-photosynthetic plastids are poorly understood. We found that the development of chromoplast plastoglobules (CPGs) in globular and crystalloid chromoplasts of citrus is associated with alterations in carotenoid storage. Using Nycodenz density gradient ultracentrifugation, an efficient protocol for isolating highly purified CPGs from sweet orange (Citrus sinensis) pulp was established. Forty-four proteins were defined as likely comprise the core proteome of CPGs using comparative proteomics analysis. Lipidome analysis of different chromoplast microcompartments revealed that the nonpolar microenvironment within CPGs was modified by 35 triacylglycerides, two sitosterol esters, and one stigmasterol ester. Manipulation of the CPG-localized gene CsELT1 (esterase/lipase/thioesterase) in citrus calli resulted in increased lipids and carotenoids, which is further evidence that the nonpolar microenvironment of CPGs contributes to carotenoid accumulation and storage in the chromoplasts. This multi-feature analysis of CPGs sheds new light on the role of chromoplasts in carotenoid metabolism, paving the way for manipulating carotenoid content in citrus fruit and other crops.

The Main Functions of Plastids

Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops

Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.

Chloroplast SRP43 and SRP54 independently promote thermostability and membrane binding of light-dependent protochlorophyllide oxidoreductases

Protochlorophyllide oxidoreductase (POR), which converts protochlorophyllide into chlorophyllide, is the only light-dependent enzyme in chlorophyll biosynthesis. While its catalytic reaction and importance for chloroplast development are well understood, little is known about the post-translational control of PORs. Here, we show that cpSRP43 and cpSRP54, two components of the chloroplast signal recognition particle pathway, play distinct roles in optimizing the function of PORB, the predominant POR isoform in Arabidopsis. The chaperone cpSRP43 stabilizes the enzyme and provides appropriate amounts of PORB during leaf greening and heat shock, whereas cpSRP54 enhances its binding to the thylakoid membrane, thereby ensuring adequate levels of metabolic flux in late chlorophyll biosynthesis. Furthermore, cpSRP43 and the DnaJ-like protein CHAPERONE-LIKE PROTEIN of POR1 concurrently act to stabilize PORB. Overall, these findings enhance our understanding of the coordinating role of cpSPR43 and cpSRP54 in the post-translational control of chlorophyll synthesis and assembly of photosynthetic chlorophyll-binding proteins.

Comparative transcriptomic and plastid development analysis sheds light on the differential carotenoid accumulation in kiwifruit flesh

Carotenoids are colorful lipophilic isoprenoids synthesized in all photosynthetic organisms which play roles in plant growth and development and provide numerous health benefits in the human diet (precursor of Vitamin A). The commercially popular kiwifruits are golden yellow-fleshed (Actinidia chinensis) and green fleshed (A. deliciosa) cultivars which have a high carotenoid concentration. Understanding the molecular mechanisms controlling the synthesis and sequestration of carotenoids in Actinidia species is key to increasing nutritional value of this crop via breeding. In this study we analyzed fruit with varying flesh color from three Actinidia species; orange-fleshed A. valvata (OF), yellow-fleshed A. polygama (YF) and green-fleshed A. arguta (GF). Microscopic analysis revealed that carotenoids accumulated in a crystalline form in YF and OF chromoplasts, with the size of crystals being bigger in OF compared to YF, which also contained globular substructures in the chromoplast. Metabolic profiles were investigated using ultra-performance liquid chromatography (UPLC), which showed that β-carotene was the predominant carotenoid in the OF and YF species, while lutein was the dominant carotenoid in the GF species. Global changes in gene expression were studied between OF and GF (both tetraploid) species using RNA-sequencing which showed higher expression levels of upstream carotenoid biosynthesis-related genes such as DXS, PSY, GGPPS, PDS, ZISO, and ZDS in OF species compared to GF. However, low expression of downstream pathway genes was observed in both species. Pathway regulatory genes (OR and OR-L), plastid morphology related genes (FIBRILLIN), chlorophyll degradation genes (SGR, SGR-L, RCCR, and NYC1) were upregulated in OF species compared to GF. This suggests chlorophyll degradation (primarily in the initial ripening stages) is accompanied by increased carotenoid production and localization in orange flesh tissue, a contrast from green flesh tissue. These results suggest a coordinated change in the carotenoid pathway, as well as changes in plastid type, are responsible for an orange phenotype in certain kiwifruit species.

Stepwise protein targeting into plastoglobules are facilitated by three hydrophobic regions of rice phytoene synthase 2

Plastoglobules (PGs) are plastidial lipid droplets enclosed by a polar monolayer born from the thylakoid membrane when plants require active lipid metabolism, including carotenogenesis, under the environmental stress and during plastid transition. Despite the fact that many proteins are reported to target PGs, their translocation mechanism has remained largely unexplored. To elucidate this process, we studied the influence of three hydrophobic regions (HR)-HR1 (1-45^th aa), HR2 (46-80^th aa), and HR3 (229-247^th aa)-of rice phytoene synthase 2 (OsPSY2, 398 aa), which has previously shown to target PGs. As results, HR1 includes the crucial sequence (31-45^th aa) for chloroplast import and the stromal cleavage occurs at a specific alanine site (64^th aa) within HR2, verifying that a N-terminal 64-aa-region works as the transit peptide (Tp). HR2 has a weak PG-targeting signal by showing synchronous and asynchronous localization patterns in both PGs and stroma of chloroplasts. HR3 exhibited a strong PG-targeting role with the required positional specificity to prevent potential issues such as non-accumulation, aggregation, and folding errors in proteins. Herein, we characterized a Tp and two transmembrane domains in three HRs of OsPSY2 and propose a spontaneous pathway for its PG-translocation with a shape embedded in the PG-monolayer. Given this subplastidial localization, we suggest six sophisticated tactics for plant biotechnology applications, including metabolic engineering and molecular farming.

Two isoforms of Arabidopsis protoporphyrinogen oxidase localize in different plastidal membranes

All land plants encode 2 isoforms of protoporphyrinogen oxidase (PPO). While PPO1 is predominantly expressed in green tissues and its loss is seedling-lethal in Arabidopsis (Arabidopsis thaliana), the effects of PPO2 deficiency have not been investigated in detail. We identified 2 ppo2 T-DNA insertion mutants from publicly available collections, one of which (ppo2-2) is a knock-out mutant. While the loss of PPO2 did not result in any obvious phenotype, substantial changes in PPO activity were measured in etiolated and root tissues. However, ppo1 ppo2 double mutants were embryo-lethal. To shed light on possible functional differences between the 2 isoforms, PPO2 was overexpressed in the ppo1 background. Although the ppo1 phenotype was partially complemented, even strong overexpression of PPO2 was unable to fully compensate for the loss of PPO1. Analysis of subcellular localization revealed that PPO2 is found exclusively in chloroplast envelopes, while PPO1 accumulates in thylakoid membranes. Mitochondrial localization of PPO2 in Arabidopsis was ruled out. Since Arabidopsis PPO2 does not encode a cleavable transit peptide, integration of the protein into the chloroplast envelope must make use of a noncanonical import route. However, when a chloroplast transit peptide was fused to the N-terminus of PPO2, the enzyme was detected predominantly in thylakoid membranes and was able to fully complement ppo1. Thus, the 2 PPO isoforms in Arabidopsis are functionally equivalent but spatially separated. Their distinctive localizations within plastids thus enable the synthesis of discrete subpools of the PPO product protoporphyrin IX, which may serve different cellular needs.

"Omics" insights into plastid behavior toward improved carotenoid accumulation

Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.

Dissecting the Chloroplast Proteome of the Potato (Solanum Tuberosum L.) and Its Comparison with the Tuber Amyloplast Proteome

The chloroplast, the energy organelle unique to plants and green algae, performs many functions, including photosynthesis and biosynthesis of metabolites. However, as the most critical tuber crop worldwide, the chloroplast proteome of potato (Solanum tuberosum) has not been explored. Here, we use Percoll density gradient centrifugation to isolate intact chloroplasts from leaves of potato cultivar E3 and establish a reference proteome map of potato chloroplast by bottom-up proteomics. A total of 1834 non-redundant proteins were identified in the chloroplast proteome, including 51 proteins encoded by the chloroplast genome. Extensive sequence-based localization prediction revealed over 62% of proteins to be chloroplast resident by at least one algorithm. Sixteen proteins were selected to evaluate the prediction result by transient fluorescence assay, which confirmed that 14 were distributed in distinct internal compartments of the chloroplast. In addition, we identified 136 phosphorylation sites in 61 proteins encoded by chloroplast proteome. Furthermore, we reconstruct the snapshots along starch metabolic pathways in the two different types of plastids by a comparative analysis between chloroplast and previously reported amyloplast proteomes. Altogether, our results establish a comprehensive proteome map with post-translationally modified sites of potato chloroplast, which would provide the theoretical principle for the research of the photosynthesis pathway and starch metabolism.

Chloroplast-localized PITP7 is essential for plant growth and photosynthetic function in Arabidopsis

Recent studies of chloroplast-localized Sec14-like protein (CPSFL1, also known as phosphatidylinositol transfer protein 7, PITP7) showed that CPSFL1 is necessary for photoautotropic growth and chloroplast vesicle formation in Arabidopsis (Arabidopsis thaliana). Here, we investigated the functional roles of CPSFL1/PITP7 using two A. thaliana mutants carrying a putative null allele (pitp7-1) and a weak allele (pitp7-2), respectively. PITP7 transcripts were undetectable in pitp7-1 and less abundant in pitp7-2 than in the wild-type (WT). The severity of mutant phenotypes, such as plant developmental abnormalities, levels of plastoquinone-9 (PQ-9) and chlorophylls, photosynthetic protein complexes, and photosynthetic performance, were well related to PITP7 transcript levels. The pitp7-1 mutation was seedling lethal and was associated with significantly lower levels of PQ-9 and major photosynthetic proteins. pitp7-2 plants showed greater susceptibility to high-intensity light stress than the WT, attributable to defects in nonphotochemical quenching and photosynthetic electron transport. PITP7 is specifically bound to phosphatidylinositol phosphates (PIPs) in lipid-binding assays in vitro, and the point mutations R82, H125, E162, or K233 reduced the binding affinity of PITP7 to PIPs. Further, constitutive expression of PITP7^H125Q or PITP7^E162K in pitp7-1 homozygous plants restored autotrophic growth in soil but without fully complementing the mutant phenotypes. Consistent with a previous study, our results demonstrate that PITP7 is essential for plant development, particularly the accumulation of PQ-9 and photosynthetic complexes. We propose a possible role for PITP7 in membrane trafficking of hydrophobic ligands such as PQ-9 and carotenoids through chloroplast vesicle formation or direct binding involving PIPs.

Identification, In Silico Characterization, and Differential Expression Profiles of Carotenoid, Xanthophyll, Apocarotenoid Biosynthetic Pathways Genes, and Analysis of Carotenoid and Xanthophyll Accumulation in Heracleum moellendorffii Hance

Heracleum moellendorffii Hance is a non-woody forest plant widely used in China, Korea, and Japan because of its various therapeutic properties. However, the genetic details of the carotenoid pathway (CP), xanthophyll pathway (XP), and apocarotenoid pathway (AP) genes have not been studied. Thus, the CP, XP, and AP genes of H. moellendorffii were detected and analyzed. A total of fifteen genes were identified, of which eight, four, and three belonged to CP, XP, and AP, respectively. All identified genes possessed full open reading frames. Phylogenetic characterization of the identified gene sequences showed the highest similarity with other higher plants. Multiple alignments and 3D dimensional structures showed several diverse conserved motifs, such as the carotene-binding motif, dinucleotide-binding motif, and aspartate or glutamate residues. The results of real-time PCR showed that the CP, XP, and AP genes were highly expressed in leaves, followed by the stems and roots. In total, eight different individual carotenoids were identified using HPLC analysis. The highest individual and total carotenoid content were achieved in the leaves, followed by the stems and roots. This study will provide more information on the gene structure of the CP, XP, and AP genes, which may help to increase the accumulation of carotenoids in H. moellendorffii through genetic engineering. These results could be helpful for further molecular and functional studies of CP, XP, and AP genes.

Critical role for isoprenoids in apicoplast biogenesis by malaria parasites

Isopentenyl pyrophosphate (IPP) is an essential metabolic output of the apicoplast organelle in Plasmodium falciparum malaria parasites and is required for prenylation-dependent vesicular trafficking and other cellular processes. We have elucidated a critical and previously uncharacterized role for IPP in apicoplast biogenesis. Inhibiting IPP synthesis blocks apicoplast elongation and inheritance by daughter merozoites, and apicoplast biogenesis is rescued by exogenous IPP and polyprenols. Knockout of the only known isoprenoid-dependent apicoplast pathway, tRNA prenylation by MiaA, has no effect on blood-stage parasites and thus cannot explain apicoplast reliance on IPP. However, we have localized an annotated polyprenyl synthase (PPS) to the apicoplast. PPS knockdown is lethal to parasites, rescued by IPP and long- (C₅₀) but not short-chain (≤C₂₀) prenyl alcohols, and blocks apicoplast biogenesis, thus explaining apicoplast dependence on isoprenoid synthesis. We hypothesize that PPS synthesizes long-chain polyprenols critical for apicoplast membrane fluidity and biogenesis. This work critically expands the paradigm for isoprenoid utilization in malaria parasites and identifies a novel essential branch of apicoplast metabolism suitable for therapeutic targeting.

Exogenous gibberellin induced regreening through the regulation of chlorophyll and carotenoid metabolism in Valencia oranges

In the present study, we studied the effects of gibberellic acid (GA) on chlorophyll and carotenoid metabolites and related gene expression during the regreening process in Valencia orange fruits (Citrus sinensis Osbeck). During the regreening, fruits treated with GA turned green much faster than those of the control. Compared with untreated fruits, chlorophyll accumulation was induced and the content of carotenoids (β-cryptoxanthin, all-trans-violaxanthin, and 9-cis-violaxanthin) was decreased by the GA treatment. Chlorophyll and carotenoid contents following GA treatment appeared to be highly regulated at the gene transcription level. Correspondingly, the up-regulation of chlorophyll biosynthesis genes (CitGGDR, CitCHL27, CitPORA, and CitCAO) and down-regulation of degradation genes (CitCLH1, CitSGR, CitPPH, CitPAO, and CitRCCR) led to the increase of chlorophyll contents, and the down-regulation of carotenoid biosynthesis genes (CitPSY, CitPDS, CitZDS, CitLCYb2, and CitHYb) led to the decrease of carotenoid contents. These observations indicated that GA acted as a crucial regulator in the regreening process of citrus fruits.

Fruit ripening: dynamics and integrated analysis of carotenoids and anthocyanins

BACKGROUND

Fruits are vital food resources as they are loaded with bioactive compounds varying with different stages of ripening. As the fruit ripens, a dynamic color change is observed from green to yellow to red due to the biosynthesis of pigments like chlorophyll, carotenoids, and anthocyanins. Apart from making the fruit attractive and being a visual indicator of the ripening status, pigments add value to a ripened fruit by making them a source of nutraceuticals and industrial products. As the fruit matures, it undergoes biochemical changes which alter the pigment composition of fruits.

RESULTS

The synthesis, degradation and retention pathways of fruit pigments are mediated by hormonal, genetic, and environmental factors. Manipulation of the underlying regulatory mechanisms during fruit ripening suggests ways to enhance the desired pigments in fruits by biotechnological interventions. Here we report, in-depth insight into the dynamics of a pigment change in ripening and the regulatory mechanisms in action.

CONCLUSIONS

This review emphasizes the role of pigments as an asset to a ripened fruit as they augment the nutritive value, antioxidant levels and the net carbon gain of fruits; pigments are a source for fruit biofortification have tremendous industrial value along with being a tool to predict the harvest. This report will be of great utility to the harvesters, traders, consumers, and natural product divisions to extract the leading nutraceutical and industrial potential of preferred pigments biosynthesized at different fruit ripening stages.

Transcriptomic analyses reveal variegation-induced metabolic changes leading to high L-theanine levels in albino sectors of variegated tea (Camellia sinensis)

Camellia sinensis cv. 'Yanling Huayecha' (YHC) is an albino-green chimaeric tea mutant with stable genetic traits. Here, we analysed the cell ultrastructure, photosynthetic pigments, amino acids, and transcriptomes of the albino, mosaic, and green zones of YHC. Well-organized thylakoids were found in chloroplasts in mesophyll cells of the green zone but not the albino zone. The albino zone of the leaves contained almost no photosynthetic pigment. However, the levels of total amino acids and theanine were higher in the albino zone than in the mosaic and green zones. A transcriptomic analysis showed that carbon metabolism, nitrogen metabolism and amino acid biosynthesis showed differences among the different zones. Metabolite and transcriptomic analyses revealed that (1) downregulation of CsPPOX1 and damage to thylakoids in the albino zone may block chlorophyll synthesis; (2) downregulation of CsLHCB6, CsFdC2 and CsSCY1 influences chloroplast biogenesis and thylakoid membrane formation, which may contribute to the appearance of variegated tea leaves; and (3) tea plant variegation disrupts the balance between carbon and nitrogen metabolism and promotes the accumulation of amino acids, and upregulation of CsTSⅠ and CsAlaDC may enhance L-theanine synthesis. In summary, our study provides a theoretical basis and valuable insights for elucidating the molecular mechanisms and promoting the economic utilization of variegation in tea.

Making extra room for carotenoids in plant cells: New opportunities for biofortification

Plant carotenoids are essential for photosynthesis and photoprotection and provide colors in the yellow to red range to non-photosynthetic organs such as petals and ripe fruits. They are also the precursors of biologically active molecules not only in plants (including hormones and retrograde signals) but also in animals (including retinoids such as vitamin A). A carotenoid-rich diet has been associated with improved health and cognitive capacity in humans, whereas the use of carotenoids as natural pigments is widespread in the agrofood and cosmetic industries. The nutritional and economic relevance of carotenoids has spurred a large number of biotechnological strategies to enrich plant tissues with carotenoids. Most of such approaches to alter carotenoid contents in plants have been focused on manipulating their biosynthesis or degradation, whereas improving carotenoid sink capacity in plant tissues has received much less attention. Our knowledge on the molecular mechanisms influencing carotenoid storage in plants has substantially grown in the last years, opening new opportunities for carotenoid biofortification. Here we will review these advances with a particular focus on those creating extra room for carotenoids in plant cells either by promoting the differentiation of carotenoid-sequestering structures within plastids or by transferring carotenoid production to the cytosol.

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L

Chelidonium majus L. is a perennial herbaceous plant that has various medicinal properties. However, the genomic information about its carotenoid biosynthesis pathway (CBP), xanthophyll biosynthesis pathway (XBP), and apocarotenoid biosynthesis pathway (ABP) genes were limited. Thus, the CBP, XBP, and ABP genes of C. majus were identified and analyzed. Among the 15 carotenoid pathway genes identified, 11 full and 4 partial open reading frames were determined. Phylogenetic analysis of these gene sequences showed higher similarity with higher plants. Through 3D structural analysis and multiple alignments, several distinct conserved motifs were identified, including dinucleotide binding motif, carotene binding motif, and aspartate or glutamate residues. Quantitative RT-PCR showed that CBP, XBP, and ABP genes were expressed in a tissue-specific manner; the highest expression levels were achieved in flowers, followed by those in leaves, roots, and stems. The HPLC analysis of the different organs showed the presence of eight different carotenoids. The highest total carotenoid content was found in leaves, followed by that in flowers, stems, and roots. This study provides information on the molecular mechanisms involved in CBP, XBP, and ABP genes, which might help optimize the carotenoid production in C. majus. The results could also be a basis of further studies on the molecular genetics and functional analysis of CBP, XBP, and ABP genes.

ChloroKB, a cell metabolism reconstruction of the model plant Arabidopsis thaliana

Can we understand how plant cell metabolism really works? An integrated large-scale modelling of plant metabolism predictive model would make possible to analyse the impact of disturbances in environmental conditions on cellular functioning and diversity of plant-made molecules of interest. ChloroKB, a Web application initially developed for exploration of Arabidopsis chloroplast metabolic network now covers Arabidopsis mesophyll cell metabolism. Interconnected metabolic maps show subcellular compartments, metabolites, proteins, complexes, reactions, and transport. Data in ChloroKB have been structured to allow for mathematical modelling and will be used as a reference for modelling work dedicated to a particular issue.

Challenges and Potential in Increasing Lutein Content in Microalgae

Research on enhancing lutein content in microalgae has made significant progress in recent years. However, strategies are needed to address the possible limitations of microalgae as practical lutein producers. The capacity of lutein sequestration may determine the upper limit of cellular lutein content. The preliminary estimation presented in this work suggests that the lutein sequestration capacity of the light-harvesting complex (LHC) of microalgae is most likely below 2% on the basis of dry cell weight (DCW). Due to its nature as a structural pigment, higher lutein content might interfere with the LHC in fulfilling photosynthetic functions. Storing lutein in a lipophilic environment is a mechanism for achieving high lutein content but several critical barriers must be overcome such as lutein degradation and access to lipid droplet to be stored through esterification. Understanding the mechanisms underlying lipid droplet biogenesis in chloroplasts, as well as carotenoid trafficking through chloroplast membranes and carotenoid esterification, may provide insight for new approaches to achieve high lutein contents in algae. In the meantime, building the machinery for esterification and sequestration of lutein and other hydroxyl-carotenoids in model microorganisms, such as yeast, with synthetic biology technology provides a promising option.

The Role of Membranes and Lipid-Protein Interactions in the Mg-Branch of Tetrapyrrole Biosynthesis

Chlorophyll (Chl) is essential for photosynthesis and needs to be produced throughout the whole plant life, especially under changing light intensity and stress conditions which may result in the destruction and elimination of these pigments. All steps of the Mg-branch of tetrapyrrole biosynthesis leading to Chl formation are carried out by enzymes associated with plastid membranes. Still the significance of these protein-membrane and protein-lipid interactions in Chl synthesis and chloroplast differentiation are not very well-understood. In this review, we provide an overview on Chl biosynthesis in angiosperms with emphasis on its association with membranes and lipids. Moreover, the last steps of the pathway including the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the biosynthesis of the isoprenoid phytyl moiety and the esterification of Chlide are also summarized. The unique biochemical and photophysical properties of the light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR) enzyme catalyzing Pchlide photoreduction and located to peculiar tubuloreticular prolamellar body (PLB) membranes of light-deprived tissues of angiosperms and to envelope membranes, as well as to thylakoids (especially grana margins) are also reviewed. Data about the factors influencing tubuloreticular membrane formation within cells, the spectroscopic properties and the in vitro reconstitution of the native LPOR enzyme complexes are also critically discussed.

Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria

β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.

Plastoquinone In and Beyond Photosynthesis

Plastoquinone-9 (PQ-9) is an essential component of photosynthesis that carries electrons in the linear and alternative electron transport chains, and is also a redox sensor that regulates state transitions and gene expression. However, a large fraction of the PQ pool is located outside the thylakoid membranes, in the plastoglobules and the chloroplast envelopes, reflecting a wider range of functions beyond electron transport. This review describes new functions of PQ in photoprotection, as a potent antioxidant, and in chloroplast metabolism as a cofactor in the biosynthesis of chloroplast metabolites. It also focuses on the essential need for tight environmental control of PQ biosynthesis and for active exchange of this compound between the thylakoid membranes and the plastoglobules. Through its multiple functions, PQ connects photosynthesis with metabolism, light acclimation, and stress tolerance.

Carotenoid accumulation in the eyespot apparatus required for phototaxis is independent of chloroplast development in Euglena gracilis

Euglena gracilis exhibits photomovements in response to various light stimuli, such as phototactic and photophobic responses. Our recent study revealed that carotenoids in the eyespot apparatus are required for triggering phototaxis in this alga. However, the role of chloroplasts in eyespot formation is not understood. Here, we isolated carotenoid-less (cl) strains of E. gracilis from cells silenced gene expression of phytoene synthase (EgcrtB). Unlike WT, the culture colors of cl1, cl3, and the non-photosynthetic mutant SM-ZK were orange, while that of cl4 was white. Electron microscope observations showed that SM-ZK, cl1, and cl3 had no developed chloroplast and formed a normal eyespot apparatus, similar to that of WT, but this was not the case for cl4. Carotenoids detected in WT were diadinoxanthin, neoxanthin, and β-carotene. However, the most abundant species of SM-ZK, cl1, and cl3 was zeaxanthin, and there was no diadinoxanthin or neoxanthin. Photomovement analysis showed that SM-ZK, cl1, and cl3 exhibited negative phototactic and photophobic responses, similar to those of WT, whereas cl4 lacked negative phototaxis. Taken together, the formation of the eyespot apparatus required for phototaxis is independent of chloroplast development in E. gracilis, suggesting that this property is different from other photosynthetic flagellates.

Efficient photosynthesis in dynamic light environments: a chloroplast's perspective

In nature, light availability for photosynthesis can undergo massive changes on a very short timescale. Photosynthesis in such dynamic light environments requires that plants can respond swiftly. Expanding our knowledge of the rapid responses that underlie dynamic photosynthesis is an important endeavor: it provides insights into nature's design of a highly dynamic energy conversion system and hereby can open up new strategies for improving photosynthesis in the field. The present review focuses on three processes that have previously been identified as promising engineering targets for enhancing crop yield by accelerating dynamic photosynthesis, all three of them involving or being linked to processes in the chloroplast, i.e. relaxation of non-photochemical quenching, Calvin–Benson–Bassham cycle enzyme activation/deactivation and dynamics of stomatal conductance. We dissect these three processes on the functional and molecular level to reveal gaps in our understanding and critically discuss current strategies to improve photosynthesis in the field.

Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas

Carotenoids are essential molecules in oxygenic photoautotrophs, and they fulfill essential requirements for human and animal nutrition. How carotenoid accumulation is regulated in the chloroplast, a cyanobacterium-derived organelle, remains poorly understood, despite significant advancements in identifying enzymes of the carotenoid biosynthetic pathway. This study identifies a role of chloroplast Sec14-like 1 (CPSFL1), a CRAL-TRIO protein of eukaryotic origin, in modulation of carotenoid biosynthesis and accumulation in the chloroplast. The CPSFL1 protein represents an isoprenoid- and carotenoid-binding protein that associates with membranes through interactions with the phospholipid phosphatidic acid. These findings have implications for understanding carotenoid biosynthesis and optimizing algal carotenoid nutritional quality.

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of Chlamydomonas reinhardtii and isolated cpsfl1. The cpsfl1 mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The CPSFL1 gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The cpsfl1 mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and β-carotene when expressed in Escherichia coli and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.

Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids

Plant specialized terpenoids are natural products that have no obvious role in growth and development, but play many important functional roles to improve the plant's overall fitness. Besides, plant specialized terpenoids have immense value to humans due to their applications in fragrance, flavor, cosmetic, and biofuel industries. Understanding the fundamental aspects involved in the biosynthesis and regulation of these high-value molecules in plants not only paves the path to enhance plant traits, but also facilitates homologous or heterologous engineering for overproduction of target molecules of importance. Recent developments in functional genomics and high-throughput analytical techniques have led to unraveling of several novel aspects involved in the biosynthesis and regulation of plant specialized terpenoids. The knowledge thus derived has been successfully utilized to produce target specialized terpenoids of plant origin in homologous or heterologous host systems by metabolic engineering and synthetic biology approaches. Here, we provide an overview and highlights on advances related to the biosynthetic steps, regulation, and metabolic engineering of plant specialized terpenoids.

A Sec14 domain protein is required for photoautotrophic growth and chloroplast vesicle formation in Arabidopsis thaliana

In eukaryotic photosynthetic organisms, the conversion of solar into chemical energy occurs in thylakoid membranes in the chloroplast. How thylakoid membranes are formed and maintained is poorly understood. However, previous observations of vesicles adjacent to the stromal side of the inner envelope membrane of the chloroplast suggest a possible role of membrane transport via vesicle trafficking from the inner envelope to the thylakoids. Here we show that the model plant Arabidopsis thaliana has a chloroplast-localized Sec14-like protein (CPSFL1) that is necessary for photoautotrophic growth and vesicle formation at the inner envelope membrane of the chloroplast. The cpsfl1 mutants are seedling lethal, show a defect in thylakoid structure, and lack chloroplast vesicles. Sec14 domain proteins are found only in eukaryotes and have been well characterized in yeast, where they regulate vesicle budding at the trans-Golgi network. Like the yeast Sec14p, CPSFL1 binds phosphatidylinositol phosphates (PIPs) and phosphatidic acid (PA) and acts as a phosphatidylinositol transfer protein in vitro, and expression of Arabidopsis CPSFL1 can complement the yeast sec14 mutation. CPSFL1 can transfer PIP into PA-rich membrane bilayers in vitro, suggesting that CPSFL1 potentially facilitates vesicle formation by trafficking PA and/or PIP, known regulators of membrane trafficking between organellar subcompartments. These results underscore the role of vesicles in thylakoid biogenesis and/or maintenance. CPSFL1 appears to be an example of a eukaryotic cytosolic protein that has been coopted for a function in the chloroplast, an organelle derived from endosymbiosis of a cyanobacterium.

Post-translational coordination of chlorophyll biosynthesis and breakdown by BCMs maintains chlorophyll homeostasis during leaf development

Chlorophyll is indispensable for life on Earth. Dynamic control of chlorophyll level, determined by the relative rates of chlorophyll anabolism and catabolism, ensures optimal photosynthesis and plant fitness. How plants post-translationally coordinate these two antagonistic pathways during their lifespan remains enigmatic. Here, we show that two Arabidopsis paralogs of BALANCE of CHLOROPHYLL METABOLISM (BCM) act as functionally conserved scaffold proteins to regulate the trade-off between chlorophyll synthesis and breakdown. During early leaf development, BCM1 interacts with GENOMES UNCOUPLED 4 to stimulate Mg-chelatase activity, thus optimizing chlorophyll synthesis. Meanwhile, BCM1’s interaction with Mg-dechelatase promotes degradation of the latter, thereby preventing chlorophyll degradation. At the onset of leaf senescence, BCM2 is up-regulated relative to BCM1, and plays a conserved role in attenuating chlorophyll degradation. These results support a model in which post-translational regulators promote chlorophyll homeostasis by adjusting the balance between chlorophyll biosynthesis and breakdown during leaf development.

Plants regulate chlorophyll levels to optimise photosynthesis. Here Wang et al. describe two paralogous thylakoid proteins, BCM1 and BCM2, which stimulate chlorophyll biosynthesis and attenuate chlorophyll degradation respectively through interaction with the Mg-chelatase-stimulating factor GUN4 and Mg-dechelatase isoform SGR1.

Differential role of the two ζ-carotene desaturase paralogs in carrot (Daucus carota): ZDS1 is a functional gene essential for plant development and carotenoid synthesis

Daucus carota is a biennale crop that develops an edible storage root. Orange carrots, the most consumed cultivar worldwide, accumulate high levels of β-carotene and α-carotene in the storage root during secondary growth. Genes involved in β-carotene synthesis have been identified in carrots and unlike most species, D. carota has two ζ-carotene desaturase genes, named ZDS1 and ZDS2, that share 91.3 % identity in their coding regions. ZDS1 expression falls during leaf, but not root development, while ZDS2 is induced in leaves and storage roots of a mature plant. In this work, by means of post-transcriptional gene silencing, we determined that ZDS1 is essential for initial carrot development. The suppression of the expression of this gene by RNAi triggered a reduction in the transcript levels of ZDS2 and PSY2 genes, with a concomitant decrease in the carotenoid content in both, leaves and storage roots. On the contrary, transgenic lines with reduced ZDS2 transcript abundance maintain the same levels of expression of endogenous ZDS1 and PSY2 and carotenoid profile as wild-type plants. The simultaneous silencing of ZDS1 and ZDS2 resulted in lines with a negligible leaf and root development, as well as significantly lower endogenous PSY2 expression. Further functional analyses, such as a plastidial subcellular localization of ZDS1:GFP and the increment in carotenoid content in transgenic tobacco plants overexpressing the carrot ZDS1, confirmed that ZDS1 codifies for a functional enzyme. Overall, these results lead us to propose that the main ζ-carotene desaturase activity in carrot is encoded by the ZDS1 gene and ZDS2 gene has a complementary and non essential role.

Effects of nanoTiO2 on tomato plants under different irradiances

In this study, we investigated the physiological and photochemical influences of nanoTiO₂ exposure on tomato plants (Lycopersicum esculentum Mill.). Tomato plants were exposed to 100 mg L^-1 of nanoTiO₂ for 90 days in a hydroponic system. Light irradiances of 135 and 550 μmol_photon m^-2 s^-1 were applied as environmental stressors that could affect uptake of nanoTiO₂. To quantify nanoTiO₂ accumulation in plant bodies and roots, we used transmission electron microscopy, energy-dispersive X-ray spectroscopy, inductively coupled plasma mass spectrometry, and X-ray powder diffraction. Phenotypic and physiological influences such as color change, growth rate, fruit productivity, pigment concentration, and enzyme activity (SOD, CAT, APX) were monitored. We observed numerous effects caused by high irradiance and nanoTiO₂ exposure, such as rapid chlorophyll decrease, increased anthocyanin and carotenoid concentrations, high enzymatic activity, and an approximately eight-fold increase in fruit production. Moreover, light absorption in the nanoTiO₂-treated tomato plants, as measured by a ultraviolet-visible light spectrometer, increased by a factor of approximately 19, likely due to natural pigments that worked as sensitizers, and this resulted in an ∼120% increase in photochemical activities on A, ФPSII, ФCO₂, g_sw, and E.

Contrasting patterns of hormonal and photoprotective isoprenoids in response to stress in Cistus albidus during a Mediterranean winter

Seasonal accumulation of hormonal and photoprotective isoprenoids, particularly α-tocopherol, carotenoids and abscisic acid, indicate their important role in protecting Cistus albidus plants from environmental stress during a Mediterranean winter. The high diurnal amounts of α-tocopherol and xanthophylls 3 h before maximum light intensity suggest a photoprotective response against the prevailing diurnal changes. The timing to modulate acclimatory/defense responses under changing environmental conditions is one of the most critical points for plant fitness and stress tolerance. Here, we report seasonal and diurnal changes in the contents of isoprenoids originated from the methylerythritol phosphate pathway, including chlorophylls, carotenoids, tocochromanols, and phytohormones (abscisic acid, cytokinins, and gibberellins) in C. albidus during a Mediterranean winter. Plants were subjected not only to typically low winter temperatures but also to drought, as shown by a mean plant water status of 54% during the experimental period. The maximum PSII efficiency, however, remained consistently high (F_v/F_m > 0.8), proving that C. albidus had efficient mechanisms to tolerate combined stress conditions during winter. While seasonal α-tocopherol contents remained high (200-300 µg/g DW) during the experimental period, carotenoid contents increased during winter attaining maximum levels in February (minimum air temperature ≤ 5 °C for 13 days). Following the initial transient increases of bioactive trans-zeatin (about fivefold) during winter, the increased abscisic acid contents proved its important role during abiotic stress tolerance. Diurnal amounts of α-tocopherol and xanthophylls, particularly lutein, zeaxanthin and neoxanthin including the de-epoxidation state, reached maximum levels as early as 2 h after dawn, when solar intensity was 68% lower than the maximum solar radiation at noon. It is concluded that (1) given their proven antioxidant properties, both α-tocopherol and carotenoids seem to play a crucial role protecting the photosynthetic apparatus under severe stress conditions; (2) high seasonal amounts of abscisic acid indicate its important role in abiotic stress tolerance within plant hormones, although under specific environmental conditions, accumulation of bioactive cytokinins appears to be involved to enhance stress tolerance; (3) the concerted diurnal adjustment of α-tocopherol and xanthophylls as early as 3 h before maximum light intensity suggests that plants anticipated the predictable diurnal changes in the environment to protect the photosynthetic apparatus.

Measurement of the redox state of the plastoquinone pool in cyanobacteria

Here, we developed a method for measuring the in vivo redox state of the plastoquinone (PQ) pool in the cyanobacteria Synechocystis sp. PCC 6803. Cells were illuminated on a glass fiber filter, PQ was extracted with ethyl acetate and determined with HPLC. Control samples with fully oxidized and reduced photoactive PQ pool were prepared by far-red and high light treatments, respectively, or by blocking the photosynthetic electron transfer chemically before or after PQ in moderate light. The photoactive pool comprised 50% of total PQ. We find that the PQ pool of cyanobacteria behaves under light treatments qualitatively similarly as in plant chloroplasts, is less reduced during growth under high than under ambient CO₂ and remains partly reduced in darkness.

Dynamic metabolic solutions to the sessile life style of plants

Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand dynamic biosynthesis and storage of a plethora of phytochemicals.

Covering: up to 2018

Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand synthesis of a plethora of phytochemicals to specifically respond to the challenges arising during plant ontogeny. Key steps in the biosynthesis of phytochemicals are catalyzed by membrane-bound cytochrome P450 enzymes which in plants constitute a superfamily. In planta, the P450s may be organized in dynamic enzyme clusters (metabolons) and the genes encoding the P450s and other enzymes in a specific pathway may be clustered. Metabolon formation facilitates transfer of substrates between sequential enzymes and therefore enables the plant to channel the flux of general metabolites towards biosynthesis of specific phytochemicals. In the plant cell, compartmentalization of the operation of specific biosynthetic pathways in specialized plastids serves to avoid undesired metabolic cross-talk and offers distinct storage sites for molar concentrations of specific phytochemicals. Liquid–liquid phase separation may lead to formation of dense biomolecular condensates within the cytoplasm or vacuole allowing swift activation of the stored phytochemicals as required upon pest or herbivore attack. The molecular grid behind plant plasticity offers an endless reservoir of functional modules, which may be utilized as a synthetic biology tool-box for engineering of novel biological systems based on rational design principles. In this review, we highlight some of the concepts used by plants to coordinate biosynthesis and storage of phytochemicals.

Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

Background

Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible.

Results

The comparative analysis of the constitutive transcriptomic profiles suggests the existence of passive defense strategies against the insect and/or the phytoplasma in the scarcely-susceptible cultivar. Moreover, the attack by the infective vector on the scarcely-susceptible variety prompted immediate and substantial transcriptomic changes that led to the rapid erection of further active defenses. On the other hand, in the most susceptible variety the response was delayed and mainly consisted of the induction of phytoalexin synthesis. Surprisingly, the jasmonic acid- and ethylene-mediated defense reactions, activated by the susceptible cultivar following FD-free insect feeding, were not detected in the presence of the phytoplasma-infected vector.

Conclusions

The comparison of the transcriptomic response in two grapevine varieties with different levels of susceptibility to Flavescence dorèe highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5908-6) contains supplementary material, which is available to authorized users.

Isolation and functional characterization of two dioxygenases putatively involved in bixin biosynthesis in annatto (Bixa orellana L.)

Carotenoid cleavage dioxygenases (CCDs) are enzymes that have been implicated in the biosynthesis of a wide diversity of secondary metabolites with important economic value, including bixin. Bixin is the second most used pigment in the world's food industry worldwide, and its main source is the aril of achiote (Bixa orellana L.) seeds. A recent transcriptome analysis of B. orellana identified a new set of eight CCD members (BoCCD4s and BoCCD1s) potentially involved in bixin synthesis. We used several approaches in order to discriminate the best candidates with CCDs genes. A reverse transcription-PCR (RT-qPCR) expression analysis was carried out in five developmental stages of two accessions of B. orellana seeds with different bixin contents: (P13W, low bixin producer and N4P, high bixin producer). The results showed that three BoCCDs (BoCCD4-1, BoCCD4-3, and BoCCD1-1) had an expression pattern consistent with bixin accumulation during seed development. Additionally, an alignment of the CCD enzyme family and homology models of proteins were generated to verify whether the newly proposed CCD enzymes were bona fide CCDs. The study confirmed that these three enzymes were well-preserved and belonged to the CCD family. In a second selection round, the three CCD genes were analyzed by in situ RT-qPCR in seed tissue. Results indicated that BoCCD4-3 and BoCCD1-1 exhibited tissue-specific expressions in the seed aril. To test whether the two selected CCDs had enzymatic activity, they were expressed in Escherichia coli; activity was determined by identifying their products in the crude extract using UHPLC-ESI-QTOF-MS/MS. The cleavage product (bixin aldehyde) was also analyzed by Fourier transform infrared. The results indicated that both BoCCD4-3 and BoCCD1-1 cleave lycopene in vitro at 5,6-5',6'.

Inside and Beyond Color: Comparative Overview of Functional Quality of Tomato and Watermelon Fruits

The quali-quantitative evaluation and the improvement of the levels of plant bioactive secondary metabolites are increasingly gaining consideration by growers, breeders and processors, particularly in those fruits and vegetables that, due to their supposed health promoting properties, are considered "functional." Worldwide, tomato and watermelon are among the main grown and consumed crops and represent important sources not only of dietary lycopene but also of other health beneficial bioactives. Tomato and watermelon synthesize and store lycopene as their major ripe fruit carotenoid responsible of their typical red color at full maturity. It is also the precursor of some characteristic aroma volatiles in both fruits playing, thus, an important visual and olfactory impact in consumer choice. While sharing the same main pigment, tomato and watermelon fruits show substantial biochemical and physiological differences during ripening. Tomato is climacteric while watermelon is non-climacteric; unripe tomato fruit is green, mainly contributed by chlorophylls and xanthophylls, while young watermelon fruit mesocarp is white and contains only traces of carotenoids. Various studies comparatively evaluated in vivo pigment development in ripening tomato and watermelon fruits. However, in most cases, other classes of compounds have not been considered. We believe this knowledge is fundamental for targeted breeding aimed at improving the functional quality of elite cultivars. Hence, in this paper, we critically review the recent understanding underlying the biosynthesis, accumulation and regulation of different bioactive compounds (carotenoids, phenolics, aroma volatiles, and vitamin C) during tomato and watermelon fruit ripening. We also highlight some concerns about possible harmful effects of excessive uptake of bioactive compound on human health. We found that a complex interweaving of anabolic, catabolic and recycling reactions, finely regulated at multiple levels and with temporal and spatial precision, ensures a certain homeostasis in the concentrations of carotenoids, phenolics, aroma volatiles and Vitamin C within the fruit tissues. Nevertheless, several exogenous factors including light and temperature conditions, pathogen attack, as well as pre- and post-harvest manipulations can drive their amounts far away from homeostasis. These adaptive responses allow crops to better cope with abiotic and biotic stresses but may severely affect the supposed functional quality of fruits.

AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins

Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( http://at-chloro.prabi.fr/at_chloro/ ) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.

Phytol metabolism in plants

Phytol, the prenyl side chain of chlorophyll, is derived from geranylgeraniol by reduction of three double bonds. Recent results demonstrated that the conversion of geranylgeraniol to phytol is linked to chlorophyll synthesis, which is catalyzed by protein complexes associated with the thylakoid membranes. One of these complexes contains light harvesting chlorophyll binding like proteins (LIL3), enzymes of chlorophyll synthesis (protoporphyrinogen oxidoreductase, POR; chlorophyll synthase, CHLG) and geranylgeranyl reductase (GGR). Phytol is not only employed for the synthesis of chlorophyll, but also for tocopherol (vitamin E), phylloquinol (vitamin K) and fatty acid phytyl ester production. Previously, it was believed that phytol is derived from reduction of geranylgeranyl-diphosphate originating from the 4-methylerythritol-5-phosphate (MEP) pathway. The identification and characterization of two kinases, VTE5 and VTE6, involved in phytol and phytyl-phosphate phosphorylation, respectively, indicated that most phytol employed for tocopherol synthesis is derived from reduction of geranylgeranylated chlorophyll to (phytol-) chlorophyll. After hydrolysis from chlorophyll, free phytol is phosphorylated by the two kinases, and phytyl-diphosphate employed for the synthesis of tocopherol and phylloquinol. The reason why some chloroplast lipids, i.e. chlorophyll, tocopherol and phylloquinol, are derived from phytol, while others, i.e. carotenoids and tocotrienols (in some plant species) are synthesized from geranylgeraniol, remains unclear.

Effect of diflufenican on total carotenoid and phytoene production in carrot suspension-cultured cells

Diflufenican increased 493-fold the level of phytoene. Diflufenican-induced inhibition of phytoene desaturase gene expression in carrot cells resulted in an increased production of phytoene. This work analyzes the effect of diflufenican, an inhibitor of phytoene desaturase, on the gene expression profiles of the biosynthetic pathway of carotenoids related with the production of these compounds in carrot cell cultures. The results showed that the presence of 10 µM diflufenican in the culture medium increased phytoene levels, which was 493-fold higher than in control cells after 7 days of treatment but did not alter cell growth in carrot cell cultures. The maximal production of phytoene was reached with 10 µM diflufenican after 7 days of incubation in the presence of light and with 30 g/L sucrose in the culture medium. Moreover, diflufenican decreased the expression of phytoene synthase and phytoene desaturase genes at all the times studied. This diflufenican-induced inhibition of phytoene desaturase gene expression in carrot cell cultures resulted in an increased production of phytoene. Our results provide new insights into the action of diflufenican in carrot cell cultures, which could represent an alternative more sustainable and environmentally friendly system to produce phytoene than those currently used.

Thylakoid proteome modulation in pea plants grown at different irradiances: quantitative proteomic profiling in a non-model organism aided by transcriptomic data integration

Plant thylakoid membranes contain hundreds of proteins that closely interact to cope with ever-changing environmental conditions. We investigated how Pisum sativum L. (pea) grown at different irradiances optimizes light-use efficiency through the differential accumulation of thylakoid proteins. Thylakoid membranes from plants grown under low (LL), moderate (ML) and high (HL) light intensity were characterized by combining chlorophyll fluorescence measurements with quantitative label-free proteomic analysis. Protein sequences retrieved from available transcriptomic data considerably improved thylakoid proteome profiling, increasing the quantifiable proteins from 63 to 194. The experimental approach used also demonstrates that this integrative omics strategy is powerful for unravelling protein isoforms and functions that are still unknown in non-model organisms. We found that the different growth irradiances affect the electron transport kinetics but not the relative abundance of photosystems (PS) I and II. Two acclimation strategies were evident. The behaviour of plants acclimated to LL was compared at higher irradiances: (i) in ML, plants turn on photoprotective responses mostly modulating the PSII light-harvesting capacity, either accumulating Lhcb4.3 or favouring the xanthophyll cycle; (ii) in HL, plants reduce the pool of light-harvesting complex II and enhance the PSII repair cycle. When growing at ML and HL, plants accumulate ATP synthase, boosting both cyclic and linear electron transport by finely tuning the ΔpH across the membrane and optimizing protein trafficking by adjusting the thylakoid architecture. Our results provide a quantitative snapshot of how plants coordinate light harvesting, electron transport and protein synthesis by adjusting the thylakoid membrane proteome in a light-dependent manner.

Characterization of Ferredoxin-Dependent Biliverdin Reductase PCYA1 Reveals the Dual Function in Retrograde Bilin Biosynthesis and Interaction With Light-Dependent Protochlorophyllide Oxidoreductase LPOR in Chlamydomonas reinhardtii

Bilins are linear tetrapyrroles commonly used as chromophores of phycobiliproteins and phytochromes for light-harvesting or light-sensing in photosynthetic organisms. Many eukaryotic algae lack both phycobiliproteins and phytochromes, but retain the bilin biosynthetic enzymes including heme oxygenase (HO/HMOX) and ferredoxin-dependent biliverdin reductase (FDBR). Previous studies on Chlamydomonas reinhardtii heme oxygenase mutant (hmox1) have shown that bilins are not only essential retrograde signals to mitigate oxidative stress during diurnal dark-to-light transitions, they are also required for chlorophyll accumulation and maintenance of a functional photosynthetic apparatus in the light. However, the underlying mechanism of bilin-mediated regulation of chlorophyll biosynthesis is unclear. In this study, Chlamydomonas phycocyanobilin:ferredoxin oxidoreductase PCYA1 FDBR domain was found to specifically interact with the rate-limiting chlorophyll biosynthetic enzyme LPOR (light-dependent protochlorophyllide oxidoreductase). PCYA1 is partially associated with chloroplast envelope membrane, consistent with the observed export of bilin from chloroplast to cytosol by cytosolic expression of a bilin-binding reporter protein in Chlamydomonas. Both the pcya1-1 mutant with the carboxyl-terminal extension of PCYA1 eliminated and efficient knockdown of PCYA1 expression by artificial microRNA exhibited no significant impact on algal phototrophic growth and photosynthetic proteins accumulation, indicating that the conserved FDBR domain is sufficient and minimally required for bilin biosynthesis and functioning. Taken together, these studies provide novel insights into the regulatory role of PCYA1 in chlorophyll biosynthesis via interaction with key Chl biosynthetic enzyme.

A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health

Carotenoids are lipophilic isoprenoid compounds synthesized by all photosynthetic organisms and some non-photosynthetic prokaryotes and fungi. With some notable exceptions, animals (including humans) do not produce carotenoids de novo but take them in their diets. In photosynthetic systems carotenoids are essential for photoprotection against excess light and contribute to light harvesting, but perhaps they are best known for their properties as natural pigments in the yellow to red range. Carotenoids can be associated to fatty acids, sugars, proteins, or other compounds that can change their physical and chemical properties and influence their biological roles. Furthermore, oxidative cleavage of carotenoids produces smaller molecules such as apocarotenoids, some of which are important pigments and volatile (aroma) compounds. Enzymatic breakage of carotenoids can also produce biologically active molecules in both plants (hormones, retrograde signals) and animals (retinoids). Both carotenoids and their enzymatic cleavage products are associated with other processes positively impacting human health. Carotenoids are widely used in the industry as food ingredients, feed additives, and supplements. This review, contributed by scientists of complementary disciplines related to carotenoid research, covers recent advances and provides a perspective on future directions on the subjects of carotenoid metabolism, biotechnology, and nutritional and health benefits.

The Intracellular Localization of the Vanillin Biosynthetic Machinery in Pods of Vanilla planifolia

Vanillin is the most important flavor compound in the vanilla pod. Vanilla planifolia vanillin synthase (VpVAN) catalyzes the conversion of ferulic acid and ferulic acid glucoside into vanillin and vanillin glucoside, respectively. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) of vanilla pod sections demonstrates that vanillin glucoside is preferentially localized within the mesocarp and placental laminae whereas vanillin is preferentially localized within the mesocarp. VpVAN is present as the mature form (25 kDa) but, depending on the tissue and isolation procedure, small amounts of the immature unprocessed form (40 kDa) and putative oligomers (50, 75 and 100 kDa) may be observed by immunoblotting using an antibody specific to the C-terminal sequence of VpVAN. The VpVAN protein is localized within chloroplasts and re-differentiated chloroplasts termed phenyloplasts, as monitored during the process of pod development. Isolated chloroplasts were shown to convert [14C]phenylalanine and [14C]cinnamic acid into [14C]vanillin glucoside, indicating that the entire vanillin de novo biosynthetic machinery converting phenylalanine to vanillin glucoside is present in the chloroplast.

Carotenoid Metabolism in Plants: The Role of Plastids

Carotenoids are indispensable to plants and critical in human diets. Plastids are the organelles for carotenoid biosynthesis and storage in plant cells. They exist in various types, which include proplastids, etioplasts, chloroplasts, amyloplasts, and chromoplasts. These plastids have dramatic differences in their capacity to synthesize and sequester carotenoids. Clearly, plastids play a central role in governing carotenogenic activity, carotenoid stability, and pigment diversity. Understanding of carotenoid metabolism and accumulation in various plastids expands our view on the multifaceted regulation of carotenogenesis and facilitates our efforts toward developing nutrient-enriched food crops. In this review, we provide a comprehensive overview of the impact of various types of plastids on carotenoid biosynthesis and accumulation, and discuss recent advances in our understanding of the regulatory control of carotenogenesis and metabolic engineering of carotenoids in light of plastid types in plants.