Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis

Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gb of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669.0 Mb, a scaffold N50 of 288.6 kb, and predicted 18,545 genes. We also established a robust phylogenetic tree from 14 representative algae species. With additional transcriptome data, we revealed some novel potential genes that are involved in the synthesis, accumulation, and regulation of astaxanthin production. In addition, we generated an isoform-level reference transcriptome set of 18,483 transcripts with high confidence. Alternative splicing analysis demonstrated that intron retention is the most frequent mode. In summary, we report the first draft genome of H. pluvialis. These genomic resources along with transcriptomic data provide a solid foundation for the discovery of the genetic basis for theoretical and commercial astaxanthin enrichment.

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by High Light with Acetate and Fe2

Haematococcus pluvialis is a commercial microalga, that produces abundant levels of astaxanthin under stress conditions. Acetate and Fe²⁺ are reported to be important for astaxanthin accumulation in H. pluvialis. In order to study the synergistic effects of high light stress and these two factors, we obtained transcriptomes for four groups: high light irradiation (HL), addition of 25 mM acetate under high light (HA), addition of 20 μM Fe²⁺ under high light (HF) and normal green growing cells (HG). Among the total clean reads of the four groups, 156,992 unigenes were found, of which 48.88% were annotated in at least one database (Nr, Nt, Pfam, KOG/COG, SwissProt, KEGG, GO). The statistics for DEGs (differentially expressed genes) showed that there were more than 10 thousand DEGs caused by high light and 1800–1900 DEGs caused by acetate or Fe²⁺. The results of DEG analysis by GO and KEGG enrichments showed that, under the high light condition, the expression of genes related to many pathways had changed, such as the pathway for carotenoid biosynthesis, fatty acid elongation, photosynthesis-antenna proteins, carbon fixation in photosynthetic organisms and so on. Addition of acetate under high light significantly promoted the expression of key genes related to the pathways for carotenoid biosynthesis and fatty acid elongation. Furthermore, acetate could obviously inhibit the expression of genes related to the pathway for photosynthesis-antenna proteins. For addition of Fe²⁺, the genes related to photosynthesis-antenna proteins were promoted significantly and there was no obvious change in the gene expressions related to carotenoid and fatty acid synthesis.

Horizontal Transfer of a Synthetic Metabolic Pathway between Plant Species

Transgene expression from the plastid (chloroplast) genome provides unique advantages, including high levels of foreign protein accumulation, convenient transgene stacking in operons, and increased biosafety due to exclusion of plastids from pollen transmission [1, 2]. However, applications in biotechnology and synthetic biology are severely restricted by the very small number of plant species whose plastid genomes currently can be transformed [3, 4]. Here we report a simple method for the introduction of useful plastid transgenes into non-transformable species. The transgenes tested comprised a synthetic operon encoding three components of a biosynthetic pathway for producing the high-value ketocarotenoid astaxanthin in the plastids of the cigarette tobacco, Nicotiana tabacum. Transplastomic N. tabacum plants accumulated astaxanthin to up to 1% of the plants' dry weight. We then used grafting, a procedure recently shown to facilitate horizontal genome transfer between plants [5-7], to let the transgenic chloroplast genome move across the graft junction from N. tabacum plants into plants of the nicotine-free tree species Nicotiana glauca. Transplastomic N. glauca trees expressing the synthetic pathway were recovered at high frequency, thus providing a straightforward method for extension of the transplastomic technology to new species.

Engineering the lutein epoxide cycle into Arabidopsis thaliana

Although sunlight provides the energy necessary for plants to survive and grow, light can also damage reaction centers of photosystem II (PSII) and reduce photochemical efficiency. To prevent damage, plants possess photoprotective mechanisms that dissipate excess excitation. A subset of these mechanisms is collectively referred to as NPQ, or nonphotochemical quenching of chlorophyll a fluorescence. The regulation of NPQ is intrinsically linked to the cycling of xanthophylls that affects the kinetics and extent of the photoprotective response. The violaxanthin cycle (VAZ cycle) and the lutein epoxide cycle (LxL cycle) are two xanthophyll cycles found in vascular plants. The VAZ cycle has been studied extensively, owing in large part to its presence in model plant species where mutants are available to aid in its characterization. In contrast, the LxL cycle is not found in model plants, and its role in photosynthetic processes has been more difficult to define. To address this challenge, we introduced the LxL cycle into Arabidopsis thaliana and functionally isolated it from the VAZ cycle. Using these plant lines, we showed an increase in dark-acclimated PSII efficiency associated with Lx accumulation and demonstrated that violaxanthin deepoxidase is responsible for the light-driven deepoxidation of Lx. Conversion of Lx to L was reversible during periods of low light and occurred considerably faster than rates previously described in nonmodel species. Finally, we present clear evidence of the LxL cycle's role in modulating a rapid component of NPQ that is necessary to prevent photoinhibition in excess light.

Regulation of carotenogenesis in the red yeast Xanthophyllomyces dendrorhous: the role of the transcriptional co-repressor complex Cyc8-Tup1 involved in catabolic repression

BACKGROUND

The yeast Xanthophyllomyces dendrorhous produces carotenoids of commercial interest, including astaxanthin and β-carotene. Although carotenogenesis in this yeast and the expression profiles of the genes controlling this pathway are known, the mechanisms regulating this process remain poorly understood. Several studies have demonstrated that glucose represses carotenogenesis in X. dendrorhous, suggesting that this pathway could be regulated by catabolic repression. Catabolic repression is a highly conserved regulatory mechanism in eukaryotes and has been widely studied in Saccharomyces cerevisiae. Glucose-dependent repression is mainly observed at the transcriptional level and depends on the DNA-binding regulator Mig1, which recruits the co-repressor complex Cyc8-Tup1, which then represses the expression of target genes. In this work, we studied the regulation of carotenogenesis by catabolic repression in X. dendrorhous, focusing on the role of the co-repressor complex Cyc8-Tup1.

RESULTS

The X. dendrorhous CYC8 and TUP1 genes were identified, and their functions were demonstrated by heterologous complementation in S. cerevisiae. In addition, cyc8 - and tup1 - mutant strains of X. dendrorhous were obtained, and both mutations were shown to prevent the glucose-dependent repression of carotenogenesis in X. dendrorhous, increasing the carotenoid production in both mutant strains. Furthermore, the effects of glucose on the transcript levels of genes involved in carotenogenesis differed between the mutant strains and wild-type X. dendrorhous, particularly for genes involved in the synthesis of carotenoid precursors, such as HMGR, idi and FPS. Additionally, transcriptomic analyses showed that cyc8 - and tup1 - mutations affected the expression of over 250 genes in X. dendrorhous.

CONCLUSIONS

The CYC8 and TUP1 genes are functional in X. dendrorhous, and their gene products are involved in catabolic repression and carotenogenesis regulation. This study presents the first report involving the participation of Cyc8 and Tup1 in carotenogenesis regulation in yeast.

ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed

Elucidation of the carotenoid biosynthetic pathway has enabled altering the composition and content of carotenoids in various plants, but to achieve desired nutritional impacts, the genetic components regulating carotenoid homeostasis in seed, the plant organ consumed in greatest abundance, must be elucidated. We used a combination of linkage mapping, genome-wide association studies (GWAS), and pathway-level analysis to identify nine loci that impact the natural variation of seed carotenoids in Arabidopsis (Arabidopsis thaliana). ZEAXANTHIN EPOXIDASE (ZEP) was the major contributor to carotenoid composition, with mutants lacking ZEP activity showing a remarkable 6-fold increase in total seed carotenoids relative to the wild type. Natural variation in ZEP gene expression during seed development was identified as the underlying mechanism for fine-tuning carotenoid composition, stability, and ultimately content in Arabidopsis seed. We previously showed that two CAROTENOID CLEAVAGE DIOXYGENASE enzymes, CCD1 and CCD4, are the primary mediators of seed carotenoid degradation, and here we demonstrate that ZEP acts as an upstream control point of carotenoid homeostasis, with ZEP-mediated epoxidation targeting carotenoids for degradation by CCD enzymes. Finally, four of the nine loci/enzymatic activities identified as underlying natural variation in Arabidopsis seed carotenoids also were identified in a recent GWAS of maize (Zea mays) kernel carotenoid variation. This first comparison of the natural variation in seed carotenoids in monocots and dicots suggests a surprising overlap in the genetic architecture of these traits between the two lineages and provides a list of likely candidates to target for selecting seed carotenoid variation in other species.

Evolutionary aspects of plant photoreceptors

Plant photoreceptors link environmental light cues with physiological responses, determining how individual plants complete their life cycles. Structural and functional evolution of photoreceptors has co-occurred as plants diversified and faced the challenge of new light environments, during the transition of plants to land and as substantial plant canopies evolved. Large-scale comparative sequencing projects allow us for the first time to document photoreceptor evolution in understudied clades, revealing some surprises. Here we review recent progress in evolutionary studies of three photoreceptor families: phytochromes, phototropins and neochromes.

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA)

Haematococcus pluvialis is an astaxanthin-rich microalga that can increase its astaxanthin production by salicylic acid (SA) or jasmonic acid (JA) induction. The genetic transcriptome details of astaxanthin biosynthesis were analyzed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress). Based on the RNA-seq analysis, 56,077 unigenes (51.7%) were identified with functions in response to the hormone stress. The top five identified subcategories were cell, cellular process, intracellular, catalytic activity and cytoplasm, which possessed 5600 (~9.99%), 5302 (~9.45%), 5242 (~9.35%), 4407 (~7.86%) and 4195 (~7.48%) unigenes, respectively. Furthermore, 59 unigenes were identified and assigned to 26 putative transcription factors (TFs), including 12 plant-specific TFs. They were likely associated with astaxanthin biosynthesis in Haematococcus upon SA and JA stress. In comparison, the up-regulation of differential expressed genes occurred much earlier, with higher transcript levels in the JA treatment (about 6 h later) than in the SA treatment (beyond 24 h). These results provide valuable information for directing metabolic engineering efforts to improve astaxanthin biosynthesis in H. pluvialis.

Effect of an Introduced Phytoene Synthase Gene Expression on Carotenoid Biosynthesis in the Marine Diatom Phaeodactylum tricornutum

Carotenoids exert beneficial effects on human health through their excellent antioxidant activity. To increase carotenoid productivity in the marine Pennales Phaeodactylum tricornutum, we genetically engineered the phytoene synthase gene (psy) to improve expression because RNA-sequencing analysis has suggested that the expression level of psy is lower than other enzyme-encoding genes that are involved in the carotenoid biosynthetic pathway. We isolated psy from P. tricornutum, and this gene was fused with the enhanced green fluorescent protein gene to detect psy expression. After transformation using the microparticle bombardment technique, we obtained several P. tricornutum transformants and confirmed psy expression in their plastids. We investigated the amounts of PSY mRNA and carotenoids, such as fucoxanthin and β-carotene, at different growth phases. The introduction of psy increased the fucoxanthin content of a transformants by approximately 1.45-fold relative to the levels in the wild-type diatom. However, some transformants failed to show a significant increase in the carotenoid content relative to that of the wild-type diatom. We also found that the amount of PSY mRNA at log phase might contribute to the increase in carotenoids in the transformants at stationary phase.

Effects of silencing key genes in the capsanthin biosynthetic pathway on fruit color of detached pepper fruits

BACKGROUND

There are many varieties of carotenoids in pepper fruits. Capsanthin is a red carotenoid that gives mature pepper fruits their red color. The red color in pepper fruits is regulated mainly by the genes capsanthin/capsorubin synthase(Ccs), phytoene synthase(Psy), lycopene-β-cyclase(Lcyb) and β-carotene hydroxylase(Crtz). There has been very limited research work related to the development and change in the red color during fruit formation and when a certain gene or several genes are deleted. In this paper, we constructed viral vectors, using the tobacco rattle virus (TRV), to carry the target gene to infect detached pepper fruits, and observed the fruits' color change. We used real-time quantitative PCR to analyze the gene silencing efficiency. At the same time, HPLC was used to determine the content of capsanthin and carotenoids that are associated with capsanthin synthesis when key genes in the pepper fruits were silenced.

RESULTS

These genes (Ccs, Psy, Lcyb and Crtz) were individually silenced through virus induced gene silencing (VIGS) technology, and pepper fruits from red fruit cultivars showed an orange or yellow color. When several genes were silenced simultaneously, the fruit also did not show the normal red color. Gene expression analysis by real-time quantitative PCR showed 70-80% efficiency of target gene silencing when using the VIGS method. HPLC analysis showed that the contents of carotenoids associated with capsanthin synthesis (e.g. β-carotene, β-cryptoxanthin or zeaxanthin) were decreased in varying degrees when silencing a gene or several genes together, however, the content of capsanthin reduced significantly. The synthesis of capsanthin was influenced either directly or indirectly when any key gene was silenced. The influence of the target genes on color changes in pepper fruits was confirmed via the targeted silencing of them.

CONCLUSIONS

VIGS was a good method to study the molecular mechanism of pepper fruit color formation. By using virus induced gene silencing technology, capsanthin synthesis genes in pepper fruits were silenced individually or simultaneously, and pepper fruit color changes were observed. This provides a platform to further explore the molecular mechanism of pepper fruit color formation.

Quantitative proteomic analysis of thylakoid from two microalgae (Haematococcus pluvialis and Dunaliella salina) reveals two different high light-responsive strategies

Under high light (HL) stress, astaxanthin-accumulating Haematococcus pluvialis and β-carotene-accumulating Dunaliella salina showed different responsive patterns. To elucidate cellular-regulating strategies photosynthetically and metabolically, thylakoid membrane proteins in H. pluvialis and D. salina were extracted and relatively quantified after 0 h, 24 h and 48 h of HL stress. Proteomic analysis showed that three subunits of the cytochrome b6/f complex were greatly reduced under HL stress in H. pluvialis, while they were increased in D. salina. Additionally, the major subunits of both photosystem (PS) II and PSI reaction center proteins were first reduced and subsequently recovered in H. pluvialis, while they were gradually reduced in D. salina. D. salina also showed a greater ability to function using the xanthophyll-cycle and the cyclic photosynthetic electron transfer pathway compared to H. pluvialis. We propose a reoriented and effective HL-responsive strategy in H. pluvialis, enabling it to acclimate under HL. The promising metabolic pathway described here contains a reorganized pentose phosphate pathway, Calvin cycle and glycolysis pathway participating in carbon sink formation under HL in H. pluvialis. Additionally, the efficient carbon reorientation strategy in H. pluvialis was verified by elevated extracellular carbon assimilation and rapid conversion into astaxanthin.

Metabolomic and network analysis of astaxanthin-producing Haematococcus pluvialis under various stress conditions

Various combinations of acetate (Ac), Fe(2+) and high light (HL) stress conditions were evaluated to maximize astaxanthin accumulation and biomass production in Haematococcus pluvialis, and then GC-MS and LC-MS based metabolomics were applied to determine molecular mechanisms responsible for enhancing astaxanthin accumulation under the stress conditions. With the optimized analytical protocols, the GC-MS and LC-MS analyses allowed identification of 93 stable and 24 unstable intracellular metabolites from H. pluvialis, respectively. In addition, a metabolic network was constructed based on GC-MS metabolomic datasets using a weighted correlation network analysis (WGCNA) approach. The network analysis uncovered 2, 1 and 1 distinguished metabolic modules highly associated with HL, Fe(2+) & HL, and Ac & Fe(2+) & HL conditions, respectively. Finally, LC-MS analysis found that AKG, Glu and R5P may be metabolites associated with the Fe(2+) & HL condition. The study provided the first metabolomic view of cell growth and astaxanthin accumulation in H. pluvialis.

Comparison of carotenoid accumulation and biosynthetic gene expression between Valencia and Rohde Red Valencia sweet oranges

Carotenoid accumulation and biosynthetic gene expression levels during fruit maturation were compared between ordinary Valencia (VAL) and its more deeply colored mutant Rohde Red Valencia orange (RRV). The two cultivars exhibited different carotenoid profiles and regulatory mechanisms in flavedo and juice sacs, respectively. In flavedo, there was uncoordinated carotenoid accumulation and gene expression in RRV during green stages, which might be related to the expression of certain gene(s) in the MEP (methylerythritol phosphate) pathway. The carotenoid biosynthesis pathway shifting from α,β-xanthophylls to β,β-xanthophylls synthesis occurred in RRV earlier than VAL during orange stages. In juice sacs, the low carotenoid content in both cultivars coincided with low expression of LCYE-Contig03 and LCYE-Contig24 during green stages, suggesting LCYE might be a limiting step for carotenoid accumulation. VAL mainly accumulated violaxanthin, but RRV accumulated β-cryptoxanthin and violaxanthin during orange stages, which corresponded to differences in juice color. Several upstream genes (PDS-Contig17, LCYB-Contig19, and ZDS members) and a downstream gene (ZEP) were expressed at higher levels in RRV than VAL, which might be responsible for greater accumulation of β-cryptoxanthin and violaxanthin in RRV, respectively.

Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum)

Xanthophylls, the pigments responsible for yellow to red coloration, are naturally occurring carotenoid compounds in many colored tissues of plants. These pigments are esterified within the chromoplast; however, little is known about the mechanisms underlying their accumulation in flower organs. In this study, we characterized two allelic tomato (Solanum lycopersicum L.) mutants, pale yellow petal (pyp) 1-1 and pyp1-2, that have reduced yellow color intensity in the petals and anthers due to loss-of-function mutations. Carotenoid analyses showed that the yellow flower organs of wild-type tomato contained high levels of xanthophylls that largely consisted of neoxanthin and violaxanthin esterified with myristic and/or palmitic acids. Functional disruption of PYP1 resulted in loss of xanthophyll esters, which was associated with a reduction in the total carotenoid content and disruption of normal chromoplast development. These findings suggest that xanthophyll esterification promotes the sequestration of carotenoids in the chromoplast and that accumulation of these esters is important for normal chromoplast development. Next-generation sequencing coupled with map-based positional cloning identified the mutant alleles responsible for the pyp1 phenotype. PYP1 most likely encodes a carotenoid modifying protein that plays a vital role in the production of xanthophyll esters in tomato anthers and petals. Our results provide insight into the molecular mechanism underlying the production of xanthophyll esters in higher plants, thereby shedding light on a longstanding mystery.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.

Biosynthetic pathway and health benefits of fucoxanthin, an algae-specific xanthophyll in brown seaweeds

Fucoxanthin is the main carotenoid produced in brown algae as a component of the light-harvesting complex for photosynthesis and photoprotection. In contrast to the complete elucidation of the carotenoid biosynthetic pathways in red and green algae, the biosynthetic pathway of fucoxanthin in brown algae is not fully understood. Recently, two models for the fucoxanthin biosynthetic pathway have been proposed in unicellular diatoms; however, there is no such information for the pathway in brown seaweeds to date. Here, we propose a biosynthetic pathway for fucoxanthin in the brown seaweed, Ectocarpus siliculosus, derived from comparison of carotenogenic genes in its sequenced genome with those in the genomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum. Currently, fucoxanthin is receiving attention, due to its potential benefits for human health. Therefore, new knowledge regarding the medical and nutraceutical properties of fucoxanthin from brown seaweeds is also summarized here.

Effect of environmental stress factors on ecophysiological traits and susceptibility to pathogens of five Populus clones throughout the growing season

The variability of ecophysiological traits associated with productivity (e.g., water relations, leaf structure, photosynthesis and nitrogen (N) content) and susceptibility to fungal and insect infection were investigated in five poplar clones (Populus deltoides Batr.-Lux clone; Populus nigra L.-58-861 clone and Populus × canadensis Mönch.-Luisa Avanzo, I-214 and Adige clones) during their growing season. The objective of the study was to determine their physiological responses under summer constraints (characteristic of the Mediterranean climate) and to propose clone candidates for environmental restoration activities such as phytoremediation. Relative water content, the radiometric water index and (13)C isotope discrimination (Δ(13)C) results reflected improved water relations in Adige and Lux during summer drought. Leaf structural parameters such as leaf area, leaf mass per area, density (D) and thickness (T) indicated poorer structural adaptations to summer drought in clone 58-861. Nitrogen content and Δ(13)C results pointed to a stomatal component as the main limitant of photosynthesis in all clones. Adige and Lux showed enhanced photoprotection as indicated by the size and the de-epoxidation index of the xanthophyll-cycle pool, and also improved antioxidant defence displayed by higher ascorbate, reduced glutathione, total phenolics and α-tocopherol levels. Photoprotective and antioxidative responses allowed all clones to maintain a high maximum quantum yield of PSII (Fv/Fm) with the exception of Luisa Avanzo and 58-861 which experienced slight photoinhibition in late spring. The study of susceptibility to rust (Melampsora sp.) and lace bug (Monosteira unicostata Muls. and Rey) infections showed Adige and Lux to be the most tolerant. Overall, these two clones presented high adaptability to summer conditions and improved resistance to abiotic and biotic stress, thereby making them highly commendable clones for use in environmental remediation programmes.

Molecular characterisation of colour formation in the prawn Fenneropenaeus merguiensis

Introduction

Body colouration in animals can have a range of functions, with predator protection an important aspect of colour in crustaceans. Colour determination is associated with the carotenoid astaxanthin, which is taken up through the diet and stabilised in the tissues by the protein crustacyanin. As a variety of genes are found to play a role in colour formation in other systems, a holistic approach was employed in this study to determine the factors involved in Fenneropenaeus merguiensis colouration.

Results

Full length F. merguiensis crustacyanin subunit A and C sequences were isolated. Crustacyanin subunit A and C were found in the F. merguiensis transcriptomes of the muscle/cuticle tissue, hepatopancreas, eye stalk and nervous system, using 454 next generation sequencing technology. Custom microarray analysis of albino, light and dark F. merguiensis cuticle tissue showed genes encoding actin, sarcoplasmic calcium-binding protein and arginine kinase to be 4-fold or greater differentially expressed (p<0.05) and down-regulated in albinos when compared to light and dark samples. QPCR expression analysis of crustacyanin and total astaxanthin pigment extraction revealed significantly (p<0.05) lower crustacyanin subunit A and C gene transcript copy numbers and total astaxanthin levels in albinos than in the light and dark samples. Additionally, crustacyanin subunit A and C expression levels correlated positively with each other.

Conclusions

This study identified gene products putatively involved in crustacean colouration, such as crustacyanin, sarcoplasmic calcium-binding protein and forms of actin, and investigated differences in gene expression and astaxanthin levels between albino, light and dark coloured prawns. These genes open a path to enhance our understanding of the biology and regulation of colour formation.

Emerging trade-offs - impact of photoprotectants (PsbS, xanthophylls, and vitamin E) on oxylipins as regulators of development and defense

This review summarizes evidence for a mechanistic link between plant photoprotection and the synthesis of oxylipin hormones as regulators of development and defense. Knockout mutants of Arabidopsis, deficient in various key components of the chloroplast photoprotection system, consistently produced greater concentrations of the hormone jasmonic acid or its precursor 12- oxo-phytodienoic acid (OPDA), both members of the oxylipin messenger family. Characterized plants include several mutants deficient in PsbS (an intrinsic chlorophyll-binding protein of photosystem II) or pigments (zeaxanthin and/or lutein) required for photoprotective thermal dissipation of excess excitation energy in the chloroplast and a mutant deficient in reactive oxygen detoxification via the antioxidant vitamin E (tocopherol). Evidence is also presented that certain plant defenses against herbivores or pathogens are elevated for these mutants. This evidence furthermore indicates that wild-type Arabidopsis plants possess less than maximal defenses against herbivores or pathogens, and suggest that plant lines with superior defenses against abiotic stress may have lower biotic defenses. The implications of this apparent trade-off between abiotic and biotic plant defenses for plant ecology as well as for plant breeding/engineering are explored, and the need for research further addressing this important issue is highlighted.

The Arabidopsis nox mutant lacking carotene hydroxylase activity reveals a critical role for xanthophylls in photosystem I biogenesis

Carotenes, and their oxygenated derivatives xanthophylls, are essential components of the photosynthetic apparatus. They contribute to the assembly of photosynthetic complexes and participate in light absorption and chloroplast photoprotection. Here, we studied the role of xanthophylls, as distinct from that of carotenes, by characterizing a no xanthophylls (nox) mutant of Arabidopsis thaliana, which was obtained by combining mutations targeting the four carotenoid hydroxylase genes. nox plants retained α- and β-carotenes but were devoid in xanthophylls. The phenotype included depletion of light-harvesting complex (LHC) subunits and impairment of nonphotochemical quenching, two effects consistent with the location of xanthophylls in photosystem II antenna, but also a decreased efficiency of photosynthetic electron transfer, photosensitivity, and lethality in soil. Biochemical analysis revealed that the nox mutant was specifically depleted in photosystem I function due to a severe deficiency in PsaA/B subunits. While the stationary level of psaA/B transcripts showed no major differences between genotypes, the stability of newly synthesized PsaA/B proteins was decreased and translation of psaA/B mRNA was impaired in nox with respect to wild-type plants. We conclude that xanthophylls, besides their role in photoprotection and LHC assembly, are also needed for photosystem I core translation and stability, thus making these compounds indispensable for autotrophic growth.

Coexistence of plant and algal energy dissipation mechanisms in the moss Physcomitrella patens

Although light is the source of energy for photosynthetic organisms, it causes oxidative stress when in excess. Plants and algae prevent reactive oxygen species (ROS) formation by activation of nonphotochemical quenching (NPQ), which dissipates excess excitation energy as heat. Although NPQ is found in both algae and plants, these organisms rely on two different proteins for its activation, Light harvesting complex stress-related (LHCSR) and Photosystem II subunit S (PSBS). In the moss Physcomitrella patens, both proteins are present and active. Several P. patens lines depleted in or over-expressing PSBS and/or LHCSR at various levels were generated by exploiting the ability of Physcomitrella to undergo homologous recombination. The analysis of the transgenic lines showed that either protein is sufficient, alone, for NPQ activation independently of the other, supporting the idea that they rely on different activation mechanisms. Modulation of PSBS and/or LHCSR contents was found to be correlated with NPQ amplitude, indicating that plants and algae can directly modulate their ability to dissipate energy simply by altering the accumulation level of one or both of these proteins. The availability of a large range of P. patens genotypes differing in PSBS and LHCSR content allowed comparison of their activation mechanisms and discussion of implications for the evolution of photoprotection during land colonization.

Comparative analysis of β-carotene hydroxylase genes for astaxanthin biosynthesis

Astaxanthin (3,3'-dihydroxy-4,4'-diketo-β-carotene) (1) is a carotenoid of significant commercial value due to its superior antioxidant potential, application as a component of animal feeds, and ongoing research that links its application to the treatment and prevention of human pathologies. The high commercial cost of 1 is also based upon its complex synthesis. Chemical synthesis has been demonstrated, but produces a mixture of stereoisomers with limited applications. Production from biological sources is limited to natural producers with complex culture requirements. The biosynthetic pathway for 1 is well studied; however, questions remain that prevent optimized production in heterologous systems. Presented is a direct comparison of 12 β-carotene (2) hydroxylases derived from archaea, bacteria, cyanobacteria, and plants. Expression in Escherichia coli enables a comparison of catalytic activity with respect to zeaxanthin (3) and 1 biosynthesis. The most suitable β-carotene hydroxylases were subsequently expressed from an efficient dual expression vector, enabling 1 biosynthesis at levels up to 84% of total carotenoids. This supports efficient 1 biosynthesis by balanced expression of β-carotene ketolase and β-carotene hydroxylase genes. Moreover, our work suggests that the most efficient route for astaxanthin biosynthesis proceeds by hydroxylation of β-carotene to zeaxanthin, followed by ketolation.

Depletion of leaf-type ferredoxin-NADP(+) oxidoreductase results in the permanent induction of photoprotective mechanisms in Arabidopsis chloroplasts

Arabidopsis thaliana contains two photosynthetically competent chloroplast-targeted ferredoxin-NADP(+) oxidoreductase (FNR) isoforms that are largely redundant in their function. Nevertheless, the FNR isoforms also display distinct molecular phenotypes, as only the FNR1 is able to directly bind to the thylakoid membrane. We report the consequences of depletion of FNR in the F(1) (fnr1 × fnr2) and F(2) (fnr1 fnr2) generation plants of the fnr1 and fnr2 single mutant crossings. The fnr1 × fnr2 plants, with a decreased total content of FNR, showed a small and pale green phenotype, accompanied with a marked downregulation of photosynthetic pigment-protein complexes. Specifically, when compared with the wild type (WT), the quantum yield of photosystem II (PSII) electron transport was lower, non-photochemical quenching (NPQ) was higher and the rate of P700(+) re-reduction was faster in the mutant plants. The slight over-reduction of the plastoquinone pool detected in the mutants resulted in the adjustment of the reactive oxygen species (ROS) scavenging systems, as both the content and de-epoxidation state of xanthophylls, as well as the content of α-tocopherol, were higher in the leaves of the mutant plants when compared with the WT. The fnr1 fnr2 double mutant plants, which had no detectable FNR and possessed an extremely downregulated photosynthetic machinery, survived only when grown heterotrophically in the presence of sucrose. Intriguingly, the fnr1 fnr2 plants were still capable of sustaining the biogenesis of a few malformed chloroplasts.

Overlapping photoprotective function of vitamin E and carotenoids in Chlamydomonas

Tocopherols (vitamin E) and carotenoids are the two most abundant groups of lipid-soluble antioxidants in the chloroplast. Carotenoids are well known for their roles in protecting against photooxidative stress, whereas the photoprotective functions of tocopherols have only recently been examined experimentally. In addition, little is known about the functional overlap of carotenoids and tocopherols in vivo. To investigate this possible overlap, Chlamydomonas reinhardtii strains were engineered to overproduce tocopherols by chloroplast transformation with non-codon-optimized and codon-optimized versions of the homogentisate phytyltransferase vitamin E2 (VTE2) from Synechocystis and by nuclear transformation with VTE2 from C. reinhardtii, which resulted in 1.6-fold, 5-fold to 10-fold, and more than 10-fold increases in total tocopherol content, respectively. To test if tocopherol overproduction can compensate for carotenoid deficiency in terms of antioxidant function, the nuclear VTE2 gene from C. reinhardtii was overexpressed in the npq1 lor1 double mutant, which lacks zeaxanthin and lutein. Following transfer to high light, the npq1 lor1 strains that overaccumulated tocopherols showed increased resistance for up to 2 d and higher efficiency of photosystem II, and they were also much more resistant to other oxidative stresses. These results suggest an overlapping functions of tocopherols and carotenoids in protection against photooxidative stress.

Restoration of rapidly reversible photoprotective energy dissipation in the absence of PsbS protein by enhanced DeltapH

Variations in the light environment require higher plants to regulate the light harvesting process. Under high light a mechanism known as non-photochemical quenching (NPQ) is triggered to dissipate excess absorbed light energy within the photosystem II (PSII) antenna as heat, preventing photodamage to the reaction center. The major component of NPQ, known as qE, is rapidly reversible in the dark and dependent upon the transmembrane proton gradient (ΔpH), formed as a result of photosynthetic electron transport. Using diaminodurene and phenazine metasulfate, mediators of cyclic electron flow around photosystem I, to enhance ΔpH, it is demonstrated that rapidly reversible qE-type quenching can be observed in intact chloroplasts from Arabidopsis plants lacking the PsbS protein, previously believed to be indispensible for the process. The qE in chloroplasts lacking PsbS significantly quenched the level of fluorescence when all PSII reaction centers were in the open state (F(o) state), protected PSII reaction centers from photoinhibition, was modulated by zeaxanthin and was accompanied by the qE-typical absorption spectral changes, known as ΔA(535). Titrations of the ΔpH dependence of qE in the absence of PsbS reveal that this protein affects the cooperativity and sensitivity of the photoprotective process to protons. The roles of PsbS and zeaxanthin are discussed in light of their involvement in the control of the proton-antenna association constant, pK, via regulation of the interconnected phenomena of PSII antenna reorganization/aggregation and hydrophobicity.

Photometrical analysis with photosensory domains of photoreceptors in green algae

Chloroplast photoorientation in the green alga Mougeotia scalaris is controlled by blue and red light. The properties of the LOV domains of phototropin A and B were consistent with previous data of action spectra and photoreceptor lifetime for blue light-mediated photoorientation. The LOV domains of the neochromes did not bind flavin, while the domains of neochrome 2 contributed to multimer formation. The absorption spectra of the neochrome phytochrome photosensory domain with phytochromobilin were very similar to the action spectra for red light-induced photoorientation. These results indicate that phototropin and neochrome work as the blue and red photoreceptors involved in photoorientation.

Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis

We attempted to optimize the production of zeaxanthin in Escherichia coli by reordering five biosynthetic genes in the natural carotenoid cluster of Pantoea ananatis. Newly designed operons for zeaxanthin production were constructed by the ordered gene assembly in Bacillus subtilis (OGAB) method, which can assemble multiple genes in one step using an intrinsic B. subtilis plasmid transformation system. The highest level of production of zeaxanthin in E. coli (820 microg/g [dry weight]) was observed in the transformant with a plasmid in which the gene order corresponds to the order of the zeaxanthin metabolic pathway (crtE-crtB-crtI-crtY-crtZ), among a series of plasmids with circularly permuted gene orders. Although two of five operons using intrinsic zeaxanthin promoters failed to assemble in B. subtilis, the full set of operons was obtained by repressing operon expression during OGAB assembly with a p(R) promoter-cI repressor system. This result suggests that repressing the expression of foreign genes in B. subtilis is important for their assembly by the OGAB method. For all tested operons, the abundance of mRNA decreased monotonically with the increasing distance of the gene from the promoter in E. coli, and this may influence the yield of zeaxanthin. Our results suggest that rearrangement of biosynthetic genes in the order of the metabolic pathway by the OGAB method could be a useful approach for metabolic engineering.

Staphyloxanthin plays a role in the fitness of Staphylococcus aureus and its ability to cope with oxidative stress

Staphyloxanthin is a membrane-bound carotenoid of Staphylococcus aureus. Here we studied the interaction of staphyloxanthin with reactive oxygen substances (ROS) and showed by comparative analysis of the wild type (WT) and an isogenic crtM mutant that the WT is more resistant to hydrogen peroxide, superoxide radical, hydroxyl radical, hypochloride, and neutrophil killing.

Functional expression of the astaxanthin biosynthesis genes from a marine bacterium, Paracoccus haeundaensis

The astaxanthin biosynthesis gene cluster in Paracoccus haeundaensis consists of six genes: crtW, crtZ, crtY, crtI, crtB, and crtE contain 726, 486, 1158, 1503, 912, and 879 base pairs, respectively. Individual carotenoid biosynthesis genes of P. haeundaensis have now been expressed in E. coli and each gene product has been purified to homogeneity. Their molecular characteristics, including enzymatic activities, are reported here.

Cloning and characterization of the astaxanthin biosynthesis gene cluster from the marine bacterium Paracoccus haeundaensis

Carotenoids are important natural pigments produced by many microorganisms and plants. In a previous study, we isolated and characterized a marine bacterium, Paracoccus haeundaensis, which produces carotenoids, mainly astaxanthin. In the present study, a carotenoid biosynthesis gene cluster involved in the production of astaxanthin was isolated and characterized from this marine bacterium. The cluster contained six carotenogenic genes, five of which, with the same orientation, were designated crtW, crtZ, crtY, crtI, and crtB, and one of which, with the opposite orientation, was designated crtE. The crtW, crtZ, crtY, crtI, crtB, and crtE genes contained 726, 486, 1158, 1503, 912, and 879 base pairs, respectively, and encoded polypeptides of 242, 162, 386, 501, 304, and 293 amino acid residues, respectively. The stop codon of each crt gene, except crtE, overlapped the start codon of the following crt gene. Comparisons of the structures and nucleotide sequences of the crt genes showed that the signature domains of the carotenoid biosynthesis genes are highly conserved. The molecular phylogenetic tree analysis showed the evolutionary relationships among the carotenoid biosynthesis genes of various organisms. An expression vector (pCR-XR-TOPO-Crt-full vector) containing the astaxanthin biosynthesis genes was constructed and transformed into Escherichia coli BL21(DE3) Codon Plus cells. The E. coli transformants produced 400 microg astaxanthin per gram of dry cell weight.

Ketocarotenoid formation in transgenic potato

Potato has been genetically engineered for the production of commercially important ketocarotenoids including astaxanthin (3,3'-dihydroxy 4,4'-diketo-beta-carotene). To support the formation of 3-hydroxylated and 4-ketolated beta-carotene, a transgenic potato line accumulating zeaxanthin due to inactivated zeaxanthin epoxidase was co-transformed with the crtO beta-carotene ketolase gene from the cyanobacterium Synechocystis under a constitutive promoter. Plants were generated which exhibited expression of this gene, resulting in an accumulation of echinenone, 3'-hydroxyechinenone, and 4-ketozeaxanthin in leaves, as well as 3'-hydroxyechinenone, 4-ketozeaxanthin together with astaxanthin in the tuber. The amount of ketocarotenoids formed represent approximately 10-12% of total carotenoids in leaves and tubers. Negative effects on photosynthesis due to the presence of the ketocarotenoids in leaves could be excluded by the determination of variable fluorescence.

Light-Modulated Exposure of the Light-Harvesting Complex II (LHCII) to Protein Kinase(s) and State Transition in Chlamydomonas reinhardtii Xanthophyll Mutants

Reversible phosphorylation of chl a/b protein complex II (LHCII), the mobile light-harvesting antenna, regulates its association and energy transfer/dissipation to photosystem (PS) II or I (state transition). Excitation of LHCII induces conformational changes affecting the exposure of the phosphorylation site at the N-terminal domain to protein kinase(s) [Zer, H., et al. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 8277-8282; Zer, H., et al. (2003) Biochemistry 42, 728-738]. Thus, it was of interest to examine whether the pigment composition of LHCII affects the light-induced modulation of LHCII phosphorylation and state transition. To this end, we have used thylakoids of wild-type Chlamydomonas reinhardtii and xanthophyll deficient mutants npq1, lor1, npq2, npq1 lor1, and npq2 lor1. Phosphorylated protein bands P11, P13, and P17 are considered components of the mobile C. reinhardtii LHCII complex. The protein composition of these bands has been analyzed by mass spectrometry using Qtof-2 with a nanospray attachment. P11 and P13 contain C. reinhardtii light-harvesting chlorophyll a/b binding protein LhcII type I. P17 contains C. reinhardtii LhcII types III and IV. Illumination of isolated thylakoids inhibits the redox-controlled phosphorylation of polypeptide bands P13 and P17 and to a lower extent that of P11. The light-induced inhibition of LHCII phosphorylation and the state transition process are not influenced by extensive differences in the xanthophyll composition of the mutants. Thus, LHCII can be visualized as possessing two functionally distinct, independent domains: (i) the pigment binding transmembrane domain regulating the extent of energy transfer/dissipation and (ii) the surface-exposed phosphorylation site regulating the association of LHCII with PSII or PSI.

Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat

EST and genomic DNA sequencing efforts for rice and wheat have provided the basis for interpreting genome organization and evolution. In this study we have used EST and genomic sequencing information and a bioinformatic approach in a two-step strategy to align portions of the wheat and rice genomes. In the first step, wheat ESTs were used to identify rice orthologs and it was shown that wheat 3S and rice 1 contain syntenic units with intrachromosomal rearrangements. Further analysis using anchored rice contiguous sequences and TBLASTX alignments in a second alignment step showed interruptions by orthologous genes that map elsewhere in the wheat genome. This indicates that gene content and order is not as conserved as large chromosomal blocks as previously predicted. Similarly, chromosome 7L contains syntenic units with rice 6 and 8 but is interrupted by combinations of intrachromosomal and interchromosomal rearrangements involving syntenic units and single gene orthologs from other rice chromosome groups. We have used the rice sequence annotations to identify genes that can be used to develop markers linked to biosynthetic pathways on 3BS controlling xanthophyll production in wheat and thus involved in determining flour colour.

The function of chloroplastic NAD(P)H dehydrogenase in tobacco during chilling stress under low irradiance

The function of chloroplastic NAD(P)H dehydrogenase (NDH) was examined by comparing a tobacco transformant (DeltandhB) in which the ndhB gene had been disrupted with its wild type, upon exposure to chilling temperature (4 degrees C) under low irradiance (100 micro mol m(-2) s(-1) PFD). During the chilling stress, the maximum photochemical efficiency of PSII (F(v)/F(m)) decreased markedly in both the wild type and DeltandhB. However, both F(v)/F(m) and P700(+), as well as the PSII-driven electron transport rate (ETR), in DeltandhB were lower than that in the wild type, implying that NDH-dependent cyclic electron flow around PSI functioned to protect the photosynthetic apparatus from chilling stress under low irradiance. Under the stress, non-photochemical quenching (NPQ), particularly the fast relaxing NPQ component (qf) and the de-epoxidized ratio of the xanthophyll cycle pigments, (A+Z)/(V+A+Z), were distinguishable in DeltandhB from those in the wild type. The lower NPQ in DeltandhB might be related to an inefficient proton gradient across thylakoid membranes (DeltapH) because of lacking an NDH-dependent cyclic electron flow around PSI at chilling temperature under low irradiance.

Photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas

When there is an imbalance between the light energy absorbed by a photosynthetic organism and that which can be utilized in photosynthesis, photo-oxidative stress can damage pigments, proteins, lipids, and nucleic acids. In this work we compared the wild type and a xanthophyll-deficient mutant of Chlamydomonas reinhardtii in their response to high amounts of light. Wild-type Chlamydomonas cells were able to acclimate to high amounts of light following transfer from low light conditions. In contrast, the npq1 lor1 double mutant, which lacks protective xanthophylls (zeaxanthin and lutein) in the chloroplast, progressively lost viability and photosynthetic capacity along with destruction of thylakoid membrane protein-pigment complexes and accumulation of reactive oxygen species and membrane lipid peroxides. Loss of viability was partially rescued by lowered oxygen tension, suggesting that the high sensitivity of the mutant to light stress is caused by the production of reactive oxygen species in the chloroplast. Cell death was not prevented by the addition of an organic carbon source to the growth medium, demonstrating that the photo-oxidative damage can target other essential chloroplast processes besides photosynthesis. From the differential sensitivity of the mutant to exogenously added pro-oxidants, we infer that the reactive oxygen species produced during light stress in npq1 lor1 may be singlet oxygen and/or superoxide but not hydrogen peroxide. The bleaching phenotype of npq1 lor1 was not due to enhanced photodamage to photosystem II but rather to a less localized phenomenon of accumulation of photo-oxidation products in chloroplast membranes.

Genetic basis of microbial carotenogenesis

The synthesis of carotenoids begins with the formation of a phytoene from geranylgeranyl pyrophosphate, a well conserved step in all carotenogenic organisms and catalyzed by a phytoene synthase, an enzyme encoded by the crtB ( spy) genes. The next step is the dehydrogenation of the phytoene, which is carried out by phytoene dehydrogenase. In organisms with oxygenic photosynthesis, this enzyme, which accomplishes two dehydrogenations, is encoded by the crtP genes. In organisms that lack oxygenic photosynthesis, dehydrogenation is carried out by an enzyme completely unrelated to the former one, which carries out four dehydrogenations and is encoded by the crtI genes. In organisms with oxygenic photosynthesis, dehydrogenation of the phytoene is accomplished by a zeta-carotene dehydrogenase encoded by the crtQ ( zds) genes. In many carotenogenic organisms, the process is completed with the cyclization of lycopene. In organisms exhibiting oxygenic photosynthesis, this step is performed by a lycopene cyclase encoded by the crtL genes. In contrast, anoxygenic photosynthetic and non-photosynthetic organisms use a different lycopene cyclase, encoded by the crtY ( lyc) genes. A third and unrelated type of lycopene beta-cyclase has been described in certain bacteria and archaea. Fungi differ from the rest of non-photosynthetic organisms in that they have a bifunctional enzyme that displays both phytoene synthase and lycopene cyclase activity. Carotenoids can be modified by oxygen-containing functional groups, thus originating xanthophylls. Only two enzymes are necessary for the conversion of beta-carotene into astaxanthin, using several ketocarotenoids as intermediates, in both prokaryotes and eukaryotes. These enzymes are a beta-carotene hydroxylase ( crtZ genes) and a beta-carotene ketolase, encoded by the crtW (bacteria) or bkt (algae) genes.

Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants

Carotenoid biosynthesis in plants has been described at the molecular level for most of the biochemical steps in the pathway. However, the cis-trans isomerization of carotenoids, which is known to occur in vivo, has remained a mystery since its discovery five decades ago. To elucidate the molecular mechanism of carotenoid isomerization, we have taken a genetic map-based approach to clone the tangerine locus from tomato. Fruit of tangerine are orange and accumulate prolycopene (7Z,9Z,7'Z,9'Z-tetra-cis-lycopene) instead of the all-trans-lycopene, which normally is synthesized in the wild type. Our data indicate that the tangerine gene, designated CRTISO, encodes an authentic carotenoid isomerase that is required during carotenoid desaturation. CRTISO is a redox-type enzyme structurally related to the bacterial-type phytoene desaturase CRTI. Two alleles of tangerine have been investigated. In tangerine(mic), loss of function is attributable to a deletion mutation in CRTISO, and in tangerine(3183), expression of this gene is impaired. CRTISO from tomato is expressed in all green tissues but is upregulated during fruit ripening and in flowers. The function of carotene isomerase in plants presumably is to enable carotenoid biosynthesis to occur in the dark and in nonphotosynthetic tissues.