Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms

Screening of Diatom Strains and Characterization of Cyclotella cryptica as A Potential Fucoxanthin Producer

Fucoxanthin has been receiving ever-increasing interest due to its broad health beneficial effects. Currently, seaweeds are the predominant source of natural fucoxanthin. However, the disappointingly low fucoxanthin content has impeded their use, driving the exploration of alternative fucoxanthin producers. In the present study, thirteen diatom strains were evaluated with respect to growth and fucoxanthin production potential. Cyclotella cryptica (CCMP 333), which grew well for fucoxanthin production under both photoautotrophic and heterotrophic growth conditions, was selected for further investigation. The supply of nitrate and light individually or in combination were all found to promote growth and fucoxanthin accumulation. When transferring heterotrophic cultures to light, fucoxanthin responded differentially to light intensities and was impaired by higher light intensity with a concomitant increase in diadinoxanthin and diatoxanthin, indicative of the modulation of Diadinoxanthin Cycle to cope with the light stress. Taken together, we, for the first time, performed the screening of diatom strains for fucoxanthin production potential and investigated in detail the effect of nutritional and environmental factors on C. cryptica growth and fucoxanthin accumulation. These results provide valuable implications into future engineering of C. cryptica culture parameters for improved fucoxanthin production and C. cryptica may emerge as a promising microalgal source of fucoxanthin.

The color of mass culture: spectral characteristics of a shallow water column through shade-limited algal growth dynamics(1)

It is envisioned that mass algal cultivation for commercial biofuels production will entail the use of large raceway pond systems, which typically have shade-limited photosynthetic growth within depths of 20-30 cm. The attenuation of light and spectral qualities of red, green, and blue wavelengths in a 20-cm water column as a function of Chl-a concentration during exponential and linear phases of growth dynamics for the marine diatom Thalassiosira pseudonana was examined under laboratory conditions. While photosynthetically available radiation (PAR) was in excess throughout the water column during the phase of exponential growth, PAR became rate limiting differently for red, green, and blue wavelengths during the phase of linear growth. The transition from exponential to linear growth occurred at 1-2 mg Chl-a · L-1, whereby a scalar ~5 μmol photons · m-2 · s-1 at 20-cm depth was found to occur as would be anticipated having the compensation point for where rates of photosynthesis and respiration are equal. During the phase of linear growth, red wavelengths became increasingly dominant at depth as Chl-a concentrations increased, being contrary to the optical conditions for those natural bodies of water that forced the evolution of phytoplankton photosynthesis. It is hypothesized this dramatic difference in water column optics between natural and synthetic environments could influence a variety of biological reactions, importantly non-photochemical quenching capacities, which could negatively impact crop yield.

Identification of genes coding for functional zeaxanthin epoxidases in the diatom Phaeodactylum tricornutum

Phaeodactylum tricornutum like other diatoms synthesizes fucoxanthin and diadinoxanthin as major carotenoid end products. The genes involved have recently been assigned for early pathway steps. Beyond β-carotene, only gene candidates for β-carotene hydroxylase, zeaxanthin epoxidase and zeaxanthin de-epoxidase have been proposed from the available genome sequence. The two latter enzymes may be involved in the two different xanthophyll cycles which operate in P. tricornutum. The function of three putative zeaxanthin epoxidase genes (zep) was addressed by pathway complementation in the Arabidopsis thaliana Zep mutant npq2. Genes zep2 and zep3 were able to restore zeaxanthin epoxidation and a functional xanthophyll cycle but the corresponding enzymes exhibited different catalytic activities. Zep3 functioned as a zeaxanthin epoxidase whereas Zep2 exhibited a broader substrate specificity additionally converting lutein to lutein-5,6-epoxide. Although zep1 was transcribed and the protein could be identified after import into the chloroplast in A. thaliana, Zep1 was found not to be functional in zeaxanthin epoxidation. The non-photochemical quenching kinetics of wild type A. thaliana was only restored in transformant npq2-zep3.

De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.

Carotenoids in Microalgae

Carotenoids are a class of isoprenoids synthesized by all photosynthetic organisms as well as by some non-photosynthetic bacteria and fungi with broad applications in food, feed and cosmetics, and also in the nutraceutical and pharmaceutical industries. Microalgae represent an important source of high-value products, which include carotenoids, among others. Carotenoids play key roles in light harvesting and energy transfer during photosynthesis and in the protection of the photosynthetic apparatus against photooxidative damage. Carotenoids are generally divided into carotenes and xanthophyls, but accumulation in microalgae can also be classified as primary (essential for survival) and secondary (by exposure to specific stimuli).In this chapter, we outline the high value carotenoids produced by commercially important microalgae, their production pathways, the improved production rates that can be achieved by genetic engineering as well as their biotechnological applications.

Role of MGDG and Non-bilayer Lipid Phases in the Structure and Dynamics of Chloroplast Thylakoid Membranes

In this chapter we focus our attention on the enigmatic structural and functional roles of the major, non-bilayer lipid monogalactosyl-diacylglycerol (MGDG) in the thylakoid membrane. We give an overview on the state of the art on the role of MGDG and non-bilayer lipid phases in the xanthophyll cycles in different organisms. We also discuss data on the roles of MGDG and other lipid molecules found in crystal structures of different photosynthetic protein complexes and in lipid-protein assemblies, as well as in the self-assembly of the multilamellar membrane system. Comparison and critical evaluation of different membrane models--that take into account and capitalize on the special properties of non-bilayer lipids and/or non-bilayer lipid phases, and thus to smaller or larger extents deviate from the 'standard' Singer-Nicolson model--will conclude this review. With this chapter the authors hope to further stimulate the discussion about, what we think, is perhaps the most exciting question of membrane biophysics: the why and wherefore of non-bilayer lipids and lipid phases in, or in association with, bilayer biological membranes.

The diadinoxanthin diatoxanthin cycle induces structural rearrangements of the isolated FCP antenna complexes of the pennate diatom Phaeodactylum tricornutum

The study investigated the influence of the xanthophyll cycle pigments diadinoxanthin (DD) and diatoxanthin (Dt) on the spectroscopic characteristics, structure and protein composition of isolated fucoxanthin chlorophyll protein (FCP) complexes of the pennate diatom Phaeodactylum tricornutum. 77 K fluorescence emission spectra revealed that Dt-containing FCP complexes showed a characteristic long wavelength fluorescence emission at 700 nm at a pH-value of 5 whereas DD-enriched FCPs retained the typical 680 nm fluorescence emission maximum of isolated FCPs. The 700 nm emission in Dt-containing FCPs indicates an aggregation of antenna complexes and is a typical feature of the quenching site Q1 in recent models for non-photochemical fluorescence quenching (NPQ). A comparable long-wavelength fluorescence emission was found in FCP complexes prepared with either triton X-100 or n-dodecyl β-D-maltoside as detergent. A treatment of the FCP complexes at low pH-values in the presence of a high concentration of Mg(2+) ions showed that the extent of FCP aggregation which leads to the 700 nm fluorescence emission is different from the macro-aggregation of antenna complexes in higher plants. Protein analyses by mass spectrometry showed that the protein composition of the DD- and Dt-enriched FCP complexes was comparable. However, the Lhcf6 and Lhcr1 polypeptides were only found in Dt-enriched FCPs isolated with dodecyl maltoside whereas the Lhcf17 protein was only detected in DD-enriched FCPs prepared with triton. With respect to low pH-induced antenna aggregation it is important that the Lhcx1 protein was found in both DD- and Dt-enriched FCPs, albeit with only two peptides with confident scores.

Photosynthetic Pigments in Diatoms

Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

Production of carotenoids by microalgae: achievements and challenges

Carotenoids are a wide group of lipophylic isoprenoids synthesized by all photosynthetic organisms and also by some non-photosynthetic bacteria and fungi. Animals, which cannot synthesize carotenoids de novo, must include them in their diet to fulfil essential provitamin, antioxidant, or colouring requirements. Carotenoids are indispensable in light harvesting and energy transfer during photosynthesis and in the protection of the photosynthetic apparatus against photooxidative damage. In this review, we outline the factors inducing carotenoid accumulation in microalgae, the knowledge acquired on the metabolic pathways responsible for their biosynthesis, and the recent achievements in the genetic engineering of this pathway. Despite the considerable progress achieved in understanding and engineering algal carotenogenesis, many aspects remain to be elucidated. The increasing number of sequenced microalgal genomes and the data generated by high-throughput technologies will enable a better understanding of carotenoid biosynthesis in microalgae. Moreover, the growing number of industrial microalgal species genetically modified will allow the production of novel strains with enhanced carotenoid contents.

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.

Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis

Diatoms are abundant and important biological components of the marine environment that biosynthesize diverse natural products. These microalgae are rich in various lipids, carotenoids, sterols and isoprenoids, some of them containing toxins and other metabolites. Several groups of diatom natural products have attracted great interest due to their potential practical application as energy sources (biofuel), valuable food constituents, and prospective materials for nanotechnology. In addition, hydrocarbons, which are used in climate reconstruction, polyamines which participate in biomineralization, new apoptotic agents against tumor cells, attractants and deterrents that regulate the biochemical communications between marine species in seawaters have also been isolated from diatoms. However, chemical studies on these microalgae are complicated by difficulties, connected with obtaining their biomass, and the influence of nutrients and contaminators in their environment as well as by seasonal and climatic factors on the biosynthesis of the corresponding natural products. Overall, the number of chemically studied diatoms is lower than that of other algae, but further studies, particularly those connected with improvements in the isolation and structure elucidation technique as well as the genomics of diatoms, promise both to increase the number of studied species with isolated biologically active natural products and to provide a clearer perception of their biosynthesis.

Protein redox regulation in the thylakoid lumen: the importance of disulfide bonds for violaxanthin de-epoxidase

When exposed to saturating light conditions photosynthetic eukaryotes activate the xanthophyll cycle where the carotenoid violaxanthin is converted into zeaxanthin by the enzyme violaxanthin de-epoxidase (VDE). VDE protein sequence includes 13 cysteine residues, 12 of which are strongly conserved in both land plants and algae. Site directed mutagenesis of Arabidopsis thaliana VDE showed that all these 12 conserved cysteines have a major role in protein function and their mutation leads to a strong reduction of activity. VDE is also shown to be active in its completely oxidized form presenting six disulfide bonds. Redox titration showed that VDE activity is sensitive to variation in redox potential, suggesting the possibility that dithiol/disulfide exchange reactions may represent a mechanism for VDE regulation.

Biodiversity of NPQ

In their natural environment plants and algae are exposed to rapidly changing light conditions and light intensities. Illumination with high light intensities has the potential to overexcite the photosynthetic pigments and the electron transport chain and thus induce the production of toxic reactive oxygen species (ROS). To prevent damage by the action of ROS, plants and algae have developed a multitude of photoprotection mechanisms. One of the most important protection mechanisms is the dissipation of excessive excitation energy as heat in the light-harvesting complexes of the photosystems. This process requires a structural change of the photosynthetic antenna complexes that are normally optimized with regard to efficient light-harvesting. Enhanced heat dissipation in the antenna systems is accompanied by a strong quenching of the chlorophyll a fluorescence and has thus been termed non-photochemical quenching of chlorophyll a fluorescence, NPQ. The general importance of NPQ for the photoprotection of plants and algae is documented by its wide distribution in the plant kingdom. In the present review we will summarize the present day knowledge about NPQ in higher plants and different algal groups with a special focus on the molecular mechanisms that lead to the structural rearrangements of the antenna complexes and enhanced heat dissipation. We will present the newest models for NPQ in higher plants and diatoms and will compare the features of NPQ in different algae with those of NPQ in higher plants. In addition, we will briefly address evolutionary aspects of NPQ, i.e. how the requirements of NPQ have changed during the transition of plants from the aquatic habitat to the land environment. We will conclude with a presentation of open questions regarding the mechanistic basis of NPQ and suggestions for future experiments that may serve to obtain this missing information.

Synthetic biology and metabolic engineering for marine carotenoids: new opportunities and future prospects

Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

Spectral radiation dependent photoprotective mechanism in the diatom Pseudo-nitzschia multistriata

Phytoplankton, such as diatoms, experience great variations of photon flux density (PFD) and light spectrum along the marine water column. Diatoms have developed some rapidly-regulated photoprotective mechanisms, such as the xanthophyll cycle activation (XC) and the non-photochemical chlorophyll fluorescence quenching (NPQ), to protect themselves from photooxidative damages caused by excess PFD. In this study, we investigate the role of blue fluence rate in combination with red radiation in shaping photoacclimative and protective responses in the coastal diatom Pseudo-nitzschia multistriata. This diatom was acclimated to four spectral light conditions (blue, red, blue-red, blue-red-green), each of them provided with low and high PFD. Our results reveal that the increase in the XC pool size and the amplitude of NPQ is determined by the blue fluence rate experienced by cells, while cells require sensing red radiation to allow the development of these processes. Variations in the light spectrum and in the blue versus red radiation modulate either the photoprotective capacity, such as the activation of the diadinoxanthin-diatoxanthin xanthophyll cycle, the diadinoxanthin de-epoxidation rate and the capacity of non-photochemical quenching, or the pigment composition of this diatom. We propose that spectral composition of light has a key role on the ability of diatoms to finely balance light harvesting and photoprotective capacity.

Plastids of marine phytoplankton produce bioactive pigments and lipids

Phytoplankton is acknowledged to be a very diverse source of bioactive molecules. These compounds play physiological roles that allow cells to deal with changes of the environmental constrains. For example, the diversity of light harvesting pigments allows efficient photosynthesis at different depths in the seawater column. Identically, lipid composition of cell membranes can vary according to environmental factors. This, together with the heterogenous evolutionary origin of taxa, makes the chemical diversity of phytoplankton compounds much larger than in terrestrial plants. This contribution is dedicated to pigments and lipids synthesized within or from plastids/photosynthetic membranes. It starts with a short review of cyanobacteria and microalgae phylogeny. Then the bioactivity of pigments and lipids (anti-oxidant, anti-inflammatory, anti-mutagenic, anti-cancer, anti-obesity, anti-allergic activities, and cardio- neuro-, hepato- and photoprotective effects), alone or in combination, is detailed. To increase the cellular production of bioactive compounds, specific culture conditions may be applied (e.g., high light intensity, nitrogen starvation). Regardless of the progress made in blue biotechnologies, the production of bioactive compounds is still limited. However, some examples of large scale production are given, and perspectives are suggested in the final section.

Molecular characterization and primary functional analysis of PeVDE, a violaxanthin de-epoxidase gene from bamboo (Phyllostachys edulis)

PeVDE was expressed primarily in bamboo leaves, which was up-regulated under high light. The protein encoded by PeVDE had enzyme activity of catalyzing violaxanthin (V) to zeaxanthin (Z) through antheraxanthin (A) as assay shown in vitro. Violaxanthin de-epoxidase (VDE), a key enzyme of xanthophyll cycle, catalyzes conversion from violaxanthin (V) to zeaxanthin (Z) through antheraxanthin (A) to protect photosynthesis apparatus. A cDNA, PeVDE, encoding a VDE was isolated from bamboo (Phyllostachys edulis) by RT-PCR and RACE methods. PeVDE is 1,723 bp and contains an ORF encoding 451 amino acids, with a transit peptide of 103 amino acids. The mature protein is deduced to have 348 amino acids with a calculated molecular weight of 39.6 kDa and a theoretic isoelectric point of 4.5. Semi-quantitative RT-PCR assay indicated that the highest expression level of PeVDE was in leaf, which agreed with the accumulation pattern of PeVDE protein. Real time PCR results showed that PeVDE was up-regulated and reached the highest level after the treatment (1,200 μmo1 m(-2) s(-1)) for 2 h, then decreased and kept at the level similar to that of 0.5 h after treatment for 8 h. To investigate the function of PeVDE, mature protein was heterologously expressed in Escherichia coli and the enzymatic activity assay was carried out using V as substrate. The pigments that formed in the reaction mixture were extracted and analyzed by HPLC method. Besides V, A and Z were detected in the reaction mixture, which indicated that the recombinant protein exhibited enzymatic activity of catalyzing V into Z through A. This study indicates that PeVDE functions through regulating the components of xanthophyll cycle, which might be one of the critical factors that contribute to the growth of bamboo under naturally varying light conditions.

Zeaxanthin binds to light-harvesting complex stress-related protein to enhance nonphotochemical quenching in Physcomitrella patens

Nonphotochemical quenching (NPQ) dissipates excess energy to protect the photosynthetic apparatus from excess light. The moss Physcomitrella patens exhibits strong NPQ by both algal-type light-harvesting complex stress-related (LHCSR)-dependent and plant-type S subunit of Photosystem II (PSBS)-dependent mechanisms. In this work, we studied the dependence of NPQ reactions on zeaxanthin, which is synthesized under light stress by violaxanthin deepoxidase (VDE) from preexisting violaxanthin. We produced vde knockout (KO) plants and showed they underwent a dramatic reduction in thermal dissipation ability and enhanced photoinhibition in excess light conditions. Multiple mutants (vde lhcsr KO and vde psbs KO) showed that zeaxanthin had a major influence on LHCSR-dependent NPQ, in contrast with previous reports in Chlamydomonas reinhardtii. The PSBS-dependent component of quenching was less dependent on zeaxanthin, despite the near-complete violaxanthin to zeaxanthin exchange in LHC proteins. Consistent with this, we provide biochemical evidence that native LHCSR protein binds zeaxanthin upon excess light stress. These findings suggest that zeaxanthin played an important role in the adaptation of modern plants to the enhanced levels of oxygen and excess light intensity of land environments.

Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae

BACKGROUND

Xanthophylls, oxygenated derivatives of carotenes, play critical roles in photosynthetic apparatus of cyanobacteria, algae, and higher plants. Although the xanthophylls biosynthetic pathway of algae is largely unknown, it is of particular interest because they have a very complicated evolutionary history. Carotenoid hydroxylase (CHY) is an important protein that plays essential roles in xanthophylls biosynthesis. With the availability of 18 sequenced algal genomes, we performed a comprehensive comparative analysis of chy genes and explored their distribution, structure, evolution, origins, and expression.

RESULTS

Overall 60 putative chy genes were identified and classified into two major subfamilies (bch and cyp97) according to their domain structures. Genes in the bch subfamily were found in 10 green algae and 1 red alga, but absent in other algae. In the phylogenetic tree, bch genes of green algae and higher plants share a common ancestor and are of non-cyanobacterial origin, whereas that of red algae is of cyanobacteria. The homologs of cyp97a/c genes were widespread only in green algae, while cyp97b paralogs were seen in most of algae. Phylogenetic analysis on cyp97 genes supported the hypothesis that cyp97b is an ancient gene originated before the formation of extant algal groups. The cyp97a gene is more closely related to cyp97c in evolution than to cyp97b. The two cyp97 genes were isolated from the green alga Haematococcus pluvialis, and transcriptional expression profiles of chy genes were observed under high light stress of different wavelength.

CONCLUSIONS

Green algae received a β-xanthophylls biosynthetic pathway from host organisms. Although red algae inherited the pathway from cyanobacteria during primary endosymbiosis, it remains unclear in Chromalveolates. The α-xanthophylls biosynthetic pathway is a common feature in green algae and higher plants. The origination of cyp97a/c is most likely due to gene duplication before divergence of green algae and higher plants. Protein domain structures and expression analyses in green alga H. pluvialis indicate that various chy genes are in different manners response to light. The knowledge of evolution of chy genes in photosynthetic eukaryotes provided information of gene cloning and functional investigation of chy genes in algae in the future.

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.

Molecular cloning and characterization of violaxanthin de-epoxidase (CsVDE) in cucumber

Violaxanthin de-epoxidase (VDE) plays an important role in protecting the photosynthetic apparatus from photo-damage by dissipating excessively absorbed light energy as heat, via the conversion of violaxanthin (V) to intermediate product antheraxanthin (A) and final product zeaxanthin (Z) under high light stress. We have cloned a violaxanthin de-epoxidase gene (CsVDE) from cucumber. The amino acid sequence of CsVDE has high homology with VDEs in other plants. RT-PCR analysis and histochemical staining show that CsVDE is expressed in all green tissues in cucumber and Arabidopsis. Using GFP fusion protein and immunogold labeling methods, we show that CsVDE is mainly localized in chloroplasts in cucumber. Under high light stress, relative expression of CsVDE and the de-epoxidation ratio (A+Z)/(V+A+Z) is increased rapidly, and abundance of the gold particles was also increased. Furthermore, CsVDE is quickly induced by cold and drought stress, reaching maximum levels at the 2(nd) hour and the 9(th) day, respectively. The ratio of (A+Z)/(V+A+Z) and non-photochemical quenching (NPQ) is reduced in transgenic Arabidopsis down-regulated by the antisense fragment of CsVDE, compared to wild type (WT) Arabidopsis under high light stress. This indicates decreased functionality of the xanthophyll cycle and increased sensitivity to photoinhibition of photosystem II (PSII) in transgenic Arabidopsis under high light stress.

Molecular and photosynthetic responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum

Photosynthetic diatoms that live suspended throughout the water column will constantly be swept up and down by vertical mixing. When returned to the photic zone after experiencing longer periods in darkness, mechanisms exist that enable the diatoms both to survive sudden light exposure and immediately utilize the available energy in photosynthesis and growth. We have investigated both the response to prolonged darkness and the re-acclimation to moderate intensity white irradiance (E = 100 µmol m⁻² s⁻¹) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance. The analyses resulted in several intriguing findings. Dark treatment of the cells led to 1) significantly decreased nuclear transcriptional activity, 2) distinct intracellular changes, 3) fixed ratios of the light-harvesting pigments despite a decrease in the total cell pigment pool, and 4) only a minor drop in photosynthetic efficiency (Φ_{PSII_max}). Re-introduction of the cells to the initial light conditions revealed 5) distinct expression profiles for nuclear genes involved in photosynthesis and those involved in photoprotection, 6) rapid rise in photosynthetic parameters (α and rETR_max) within 0.5 h of re-exposure to light despite a very modest de novo synthesis of photosynthetic compounds, and 7) increasingly efficient resonance energy transfer from fucoxanthin chlorophyll a/c-binding protein complexes to photosystem II reaction centers during the first 0.5 h, supporting the observations stated in 6). In summary, the results show that despite extensive transcriptional, metabolic and intracellular changes, the ability of cells to perform photosynthesis was kept intact during the length of the experiment. We conclude that P. tricornutum maintains a functional photosynthetic apparatus during dark periods that enables prompt recovery upon re-illumination.

High light acclimation in the secondary plastids containing diatom Phaeodactylum tricornutum is triggered by the redox state of the plastoquinone pool

In diatoms, the process of energy-dependent chlorophyll fluorescence quenching (qE) has an important role in photoprotection. Three components are essential for qE: (1) the light-dependent generation of a transthylakoidal proton gradient; (2) the deepoxidation of the xanthophyll diadinoxanthin (Dd) into diatoxanthin (Dt); and (3) specific nucleus-encoded antenna proteins, called Light Harvesting Complex Protein X (LHCX). We used the model diatom Phaeodactylum tricornutum to investigate the concerted light acclimation response of the qE key components LHCX, proton gradient, and xanthophyll cycle pigments (Dd+Dt) and to identify the intracellular light-responsive trigger. At high-light exposure, the up-regulation of three of the LHCX genes and the de novo synthesis of Dd+Dt led to a pronounced rise of qE. By inhibiting either the conversion of Dd to Dt or the translation of LHCX genes, qE amplification was abolished and the diatom cells suffered from stronger photoinhibition. Artificial modification of the redox state of the plastoquinone (PQ) pool via 3-(3,4-dichlorophenyl)-1,1-dimethylurea and 5-dibromo-6-isopropyl-3-methyl-1,4-benzoquinone resulted in a disturbance of Dd+Dt synthesis in an opposite way. Moreover, we could increase the transcription of two of the four LHCX genes under low-light conditions by reducing the PQ pool using 5-dibromo-6-isopropyl-3-methyl-1,4-benzoquinone. Altogether, our results underline the central role of the redox state of the PQ pool in the light acclimation of diatoms. Additionally, they emphasize strong evidence for the existence of a plastid-to-nucleus retrograde signaling mechanism in an organism with plastids that derived from secondary endosymbiosis.

Blue light is essential for high light acclimation and photoprotection in the diatom Phaeodactylum tricornutum

The objective of the present study was to test the hypothesis that the acclimation to different light intensities in the diatom Phaeodactylum tricornutum is controlled by light quality perception mechanisms. Therefore, semi-continuous cultures of P. tricornutum were illuminated with equal amounts of photosynthetically absorbed radiation of blue (BL), white (WL), and red light (RL) and in combination of two intensities of irradiance, low (LL) and medium light (ML). Under LL conditions, growth rates and photosynthesis rates were similar for all cultures. However, BL cultures were found to be in an acclimation state with an increased photoprotective potential. This was deduced from an increased capacity of non-photochemical quenching, a larger pool of xanthophyll cycle pigments, and a higher de-epoxidation state of xanthophyll cycle pigments compared to WL and RL cultures. Furthermore, in the chloroplast membrane proteome of BL cells, an upregulation of proteins involved in photoprotection, e.g. the Lhcx1 protein and zeaxanthin epoxidase, was evident. ML conditions induced increased photosynthesis rates and a further enhanced photoprotective potential for algae grown under BL and WL. In contrast, RL cultures exhibited no signs of acclimation towards increased irradiance. The data implicate that in diatoms the photoacclimation to high light intensities requires the perception of blue light.

Cell biology of chromerids: autotrophic relatives to apicomplexan parasites

Chromerida are algae possessing a complex plastid surrounded by four membranes. Although isolated originally from stony corals in Australia, they seem to be globally distributed. According to their molecular phylogeny, morphology, ultrastructure, structure of organellar genomes, and noncanonical pathway for tetrapyrrole synthesis, these algae are thought to be the closest known phototrophic relatives to apicomplexan parasites. Here, we summarize the current knowledge of cell biology and evolution of this novel group of algae, which contains only two formally described species, but is apparently highly diverse and virtually ubiquitous in marine environments.

Efficient heterologous transformation of Chlamydomonas reinhardtii npq2 mutant with the zeaxanthin epoxidase gene isolated and characterized from Chlorella zofingiensis

In the violaxanthin cycle, the violaxanthin de-epoxidase and zeaxanthin epoxidase catalyze the inter-conversion between violaxanthin and zeaxanthin in both plants and green algae. The zeaxanthin epoxidase gene from the green microalga Chlorella zofingiensis (Czzep) has been isolated. This gene encodes a polypeptide of 596 amino acids. A single copy of Czzep has been found in the C. zofingiensis genome by Southern blot analysis. qPCR analysis has shown that transcript levels of Czzep were increased after zeaxanthin formation under high light conditions. The functionality of Czzep gene by heterologous genetic complementation in the Chlamydomonas mutant npq2, which lacks zeaxanthin epoxidase (ZEP) activity and accumulates zeaxanthin in all conditions, was analyzed. The Czzep gene was adequately inserted in the pSI105 vector and expressed in npq2. The positive transformants were able to efficiently convert zeaxanthin into violaxanthin, as well as to restore their maximum quantum efficiency of the PSII (Fv/Fm). These results show that Chlamydomonas can be an efficient tool for heterologous expression and metabolic engineering for biotechnological applications.

Biosynthesis of fucoxanthin and diadinoxanthin and function of initial pathway genes in Phaeodactylum tricornutum

The biosynthesis pathway to diadinoxanthin and fucoxanthin was elucidated in Phaeodactylum tricornutum by a combined approach involving metabolite analysis identification of gene function. For the initial steps leading to β-carotene, putative genes were selected from the genomic database and the function of several of them identified by genetic pathway complementation in Escherichia coli. They included genes encoding a phytoene synthase, a phytoene desaturase, a ζ-carotene desaturase, and a lycopene β-cyclase. Intermediates of the pathway beyond β-carotene, present in trace amounts, were separated by TLC and identified as violaxanthin and neoxanthin in the enriched fraction. Neoxanthin is a branching point for the synthesis of both diadinoxanthin and fucoxanthin and the mechanisms for their formation were proposed. A single isomerization of one of the allenic double bounds in neoxanthin yields diadinoxanhin. Two reactions, hydroxylation at C8 in combination with a keto-enol tautomerization and acetylation of the 3'-HO group results in the formation of fucoxanthin.

Silencing of the violaxanthin de-epoxidase gene in the diatom Phaeodactylum tricornutum reduces diatoxanthin synthesis and non-photochemical quenching

Diatoms are a major group of primary producers ubiquitous in all aquatic ecosystems. To protect themselves from photooxidative damage in a fluctuating light climate potentially punctuated with regular excess light exposures, diatoms have developed several photoprotective mechanisms. The xanthophyll cycle (XC) dependent non-photochemical chlorophyll fluorescence quenching (NPQ) is one of the most important photoprotective processes that rapidly regulate photosynthesis in diatoms. NPQ depends on the conversion of diadinoxanthin (DD) into diatoxanthin (DT) by the violaxanthin de-epoxidase (VDE), also called DD de-epoxidase (DDE). To study the role of DDE in controlling NPQ, we generated transformants of P. tricornutum in which the gene (Vde/Dde) encoding for DDE was silenced. RNA interference was induced by genetic transformation of the cells with plasmids containing either short (198 bp) or long (523 bp) antisense (AS) fragments or, alternatively, with a plasmid mediating the expression of a self-complementary hairpin-like construct (inverted repeat, IR). The silencing approaches generated diatom transformants with a phenotype clearly distinguishable from wildtype (WT) cells, i.e. a lower degree as well as slower kinetics of both DD de-epoxidation and NPQ induction. Real-time PCR based quantification of Dde transcripts revealed differences in transcript levels between AS transformants and WT cells but also between AS and IR transformants, suggesting the possible presence of two different gene silencing mediating mechanisms. This was confirmed by the differential effect of the light intensity on the respective silencing efficiency of both types of transformants. The characterization of the transformants strengthened some of the specific features of the XC and NPQ and confirmed the most recent mechanistic model of the DT/NPQ relationship in diatoms.

Identification of key residues for pH dependent activation of violaxanthin de-epoxidase from Arabidopsis thaliana

Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pK(a) values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121-Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role.

De novo transcriptomic analysis of an oleaginous microalga: pathway description and gene discovery for production of next-generation biofuels

Background

Eustigmatos cf. polyphem is a yellow-green unicellular soil microalga belonging to the eustimatophyte with high biomass and considerable production of triacylglycerols (TAGs) for biofuels, which is thus referred to as an oleaginous microalga. The paucity of microalgae genome sequences, however, limits development of gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for a non-model microalgae species, E. cf. polyphem, and identify pathways and genes of importance related to biofuel production.

Results

We performed the de novo assembly of E. cf. polyphem transcriptome using Illumina paired-end sequencing technology. In a single run, we produced 29,199,432 sequencing reads corresponding to 2.33 Gb total nucleotides. These reads were assembled into 75,632 unigenes with a mean size of 503 bp and an N50 of 663 bp, ranging from 100 bp to >3,000 bp. Assembled unigenes were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. These analyses identified the majority of carbohydrate, fatty acids, TAG and carotenoids biosynthesis and catabolism pathways in E. cf. polyphem.

Conclusions

Our data provides the construction of metabolic pathways involved in the biosynthesis and catabolism of carbohydrate, fatty acids, TAG and carotenoids in E. cf. polyphem and provides a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.

Exploring the molecular basis of responses to light in marine diatoms

Light is an essential source of energy for life on Earth and is one of the most important signals that organisms use to obtain information from the surrounding environment, on land and in the oceans. Prominent marine microalgae, such as diatoms, display a suite of sophisticated responses (physiological, biochemical, and behavioural) to optimize their photosynthesis and growth under changing light conditions. However, the molecular mechanisms controlling diatom responses to light are still largely unknown. Recent progress in marine diatom genomics and genetics, combined with well-established (eco) physiological and biophysical approaches, now offers novel opportunities to address these issues. This review provides a description of the molecular components identified in diatom genomes that are involved in light perception and acclimation mechanisms. How the initial functional characterizations of specific light regulators provide the basis to investigate the conservation or diversification of light-mediated processes in diatoms is also discussed. Hypotheses on the role of the identified factors in determining the growth, distribution, and adaptation of diatoms in different marine environments are reported.

Pathways of carotenoid biosynthesis in bacteria and microalgae

The carotenoids, a subfamily of the isoprenoids, are among the most widespread, ancient, diverse, and rich class of all natural products and biomolecules. Microorganisms, as well as microalgae and bacteria synthesize isoprenoids from isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). For long time, mevalonic acid was assumed to be the only natural precursor for IPP and DMAPP in the cytosolic acetate/mevalonate pathway for the biosynthesis of sterols, sesquiterpenes, triterpenoids, and carotenoids. At present, it is accepted that the relatively new route, the methylerythritol 4-phosphate (MEP), or 1-deoxy-D: -xylulose-5-phosphate (DOXP) is the main pathway for the biosynthesis of plastidic isoprenoids, such as carotenoids, phytol (a side chain of chlorophylls), plastoquinone-9, isoprene, mono-, and diterpenes. Cytosolic isoprenoids (sterols) biosynthesized by MEP have been reported in eubacteria and algae (Chlorella, Chlamydomonas, Scenedesmus, and Dunaliella). This review summarizes current knowledge of the biosynthetic pathways leading to the formation of different isoprenoids and carotenoids in bacteria and microalgae. Particular attention was given to the last early steps of the biosynthesis of the key C(5)-precursor and the final steps of the biosynthesis of carotenoids including selected examples in microalgae and bacteria as well as the recent advances in genomics and metabolic engineering.

Whole genome studies of Tetrahymena

Within the past decade, genomic studies have emerged as essential and highly productive tools to explore the biology of Tetrahymena thermophila. The current major resources, which have been extensively mined by the research community, are the annotated macronuclear genome assembly, transcriptomic data and the databases that house this information. Efforts in progress will soon improve these data sources and expand their scope, including providing annotated micronuclear and comparative genomic sequences. Future studies of Tetrahymena cell and molecular biology, development, physiology, evolution and ecology will benefit greatly from these resources and the advanced genomic technologies they enable.

Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates

The chromalveolate "supergroup" is of key interest in contemporary phycology, as it contains the overwhelming majority of extant algal species, including several phyla of key importance to oceanic net primary productivity such as diatoms, kelps, and dinoflagellates. There is also intense current interest in the exploitation of these algae for industrial purposes, such as biodiesel production. However, the evolution of the constituent species, and in particular the origin and radiation of the chloroplast genomes, remains poorly understood. In this review, we discuss current theories of the origins of the extant red alga-derived chloroplast lineages in the chromalveolates and the potential ramifications of the recent discovery of large numbers of green algal genes in chromalveolate genomes. We consider that the best explanation for this is that chromalveolates historically possessed a cryptic green algal endosymbiont that was subsequently replaced by a red algal chloroplast. We consider how changing selective pressures acting on ancient chromalveolate lineages may have selectively favored the serial endosymbioses of green and red algae and whether a complex endosymbiotic history facilitated the rise of chromalveolates to their current position of ecological prominence.

Evolution and functional properties of photosystem II light harvesting complexes in eukaryotes

Photoautotrophic organisms, the major agent of inorganic carbon fixation into biomass, convert light energy into chemical energy. The first step of photosynthesis consists of the absorption of solar energy by pigments binding protein complexes named photosystems. Within photosystems, a family of proteins called Light Harvesting Complexes (LHC), responsible for light harvesting and energy transfer to reaction centers, has evolved along with eukaryotic organisms. Besides light absorption, these proteins catalyze photoprotective reactions which allowed functioning of oxygenic photosynthetic machinery in the increasingly oxidant environment. In this work we review current knowledge of LHC proteins serving Photosystem II. Balance between light harvesting and photoprotection is critical in Photosystem II, due to the lower quantum efficiency as compared to Photosystem I. In particular, we focus on the role of each antenna complex in light harvesting, energy transfer, scavenging of reactive oxygen species, chlorophyll triplet quenching and thermal dissipation of excess energy. This article is part of a Special Issue entitled: Photosystem II.

Carotenoid biosynthesis in diatoms

Diatoms are ubiquitous and constitute an important group of the phytoplankton community having a major contribution to the total marine primary production. These microalgae exhibit a characteristic golden-brown colour due to a high amount of the xanthophyll fucoxanthin that plays a major role in the light-harvesting complex of photosystems. In the water column, diatoms are exposed to light intensities that vary quickly from lower to higher values. Xanthophyll cycles prevent photodestruction of the cells in excessive light intensities. In diatoms, the diadinoxanthin-diatoxanthin cycle is the most important short-term photoprotective mechanism. If the biosynthetic pathways of chloroplast pigments have been extensively studied in higher plants and green algae, the research on carotenoid biosynthesis in diatoms is still in its infancy. In this study, the data on the biosynthetic pathway of diatom carotenoids are reviewed. The early steps occur through the 2-C-methyl-D: -erythritol 4-phosphate (MEP) pathway. Then a hypothetical pathway is suggested from dimethylallyl diphosphate (DMAPP) and isopentenyl pyrophosphate (IPP). Most of the enzymes of the pathway have not been so far isolated from diatoms, but candidate genes for each of them were identified using protein similarity searches of genomic data.

Genomic insights into photosynthesis in eukaryotic phytoplankton

The evolution of photosynthesis completely altered the biogeochemistry of our planet and permitted the evolution of more complex multicellular organisms. Curiously, terrestrial photosynthesis is carried out largely by green algae and their descendents the higher plants, whereas in the ocean the most abundant photosynthetic eukaryotes are microscopic and have red algal affiliations. Although primary productivity is approximately equal between the land and the ocean, the marine microbes represent less than 1% of the photosynthetic biomass found on land. This review focuses on this highly successful and diverse group of organisms collectively known as phytoplankton and reviews how insights from whole genome analyses have improved our understanding of the novel innovations employed by them to maximize photosynthetic efficiency in variable light environments.

Mutation analysis of violaxanthin de-epoxidase identifies substrate-binding sites and residues involved in catalysis

Plants are able to deal with variable environmental conditions; when exposed to strong illumination, they safely dissipate excess energy as heat and increase their capacity for scavenging reacting oxygen species. Both these protection mechanisms involve activation of the xanthophyll cycle, in which the carotenoid violaxanthin is converted to zeaxanthin by violaxanthin de-epoxidase, using ascorbate as the source of reducing power. In this work, following determination of the three-dimensional structure of the violaxanthin de-epoxidase catalytic domain, we identified the putative binding sites for violaxanthin and ascorbate by in silico docking. Amino acid residues lying in close contact with the two substrates were analyzed for their involvement in the catalytic mechanism. Experimental results supported the proposed substrate-binding sites and point to two residues, Asp-177 and Tyr-198, which are suggested to participate in the catalytic mechanism, based on complete loss of activity in mutant proteins. The role of other residues and the mechanistic similarity to aspartic proteases and epoxide hydrolases are discussed.

Photoprotective compounds from marine organisms

The substantial loss in the stratospheric ozone layer and consequent increase in solar ultraviolet radiation on the earth's surface have augmented the interest in searching for natural photoprotective compounds in organisms of marine as well as freshwater ecosystems. A number of photoprotective compounds such as mycosporine-like amino acids (MAAs), scytonemin, carotenoids and several other UV-absorbing substances of unknown chemical structure have been identified from different organisms. MAAs form the most common class of UV-absorbing compounds known to occur widely in various marine organisms; however, several compounds having UV-screening properties still need to be identified. The synthesis of scytonemin, a predominant UV-A-photoprotective pigment, is exclusively reported in cyanobacteria. Carotenoids are important components of the photosynthetic apparatus that serve both light-harvesting and photoprotective functions, either by direct quenching of the singlet oxygen or other toxic reactive oxygen species or by dissipating the excess energy in the photosynthetic apparatus. The production of photoprotective compounds is affected by several environmental factors such as different wavelengths of UVR, desiccation, nutrients, salt concentration, light as well as dark period, and still there is controversy about the biosynthesis of various photoprotective compounds. Recent studies have focused on marine organisms as a source of natural bioactive molecules having a photoprotective role, their biosynthesis and commercial application. However, there is a need for extensive work to explore the photoprotective role of various UV-absorbing compounds from marine habitats so that a range of biotechnological and pharmaceutical applications can be found.

An integrated analysis of molecular acclimation to high light in the marine diatom Phaeodactylum tricornutum

Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to acclimate their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0–0.5 h), an intermediate acclimation phase (3–12 h) and a late acclimation phase (12–48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiance have been identified.

Carotenoids found in Bacillus

AIMS

To identify the diversity of pigmented aerobic spore formers found in the environment and to characterize the chemical nature of this pigmentation.

MATERIALS AND RESULTS

Sampling of heat-resistant bacterial counts from soil, sea water and the human gastrointestinal tract. Phylogenetic profiling using analysis of 16S rRNA sequences to define species. Pigment profiling using high-performance liquid chromatography-photo diode array analysis.

CONCLUSIONS

The most commonly found pigments were yellow, orange and pink. Isolates were nearly always members of the Bacillus genus and in most cases were related with known species such as Bacillus marisflavi, Bacillus indicus, Bacillus firmus, Bacillus altitudinis and Bacillus safensis. Three types of carotenoids were found with absorption maxima at 455, 467 and 492 nm, corresponding to the visible colours yellow, orange and pink, respectively. Although the presence of other carotenoids cannot be ruled out, these three predominant carotenoids appear to account for the pigments obtained in most pigmented bacilli, and our analysis reveals the existence of a C30 biosynthetic pathway. Interestingly, we report the presence of a water-soluble pigment that may also be a carotenoid. The function of carotenoids is photoprotection, and carotenoid-containing spores exhibited significantly higher levels of resistance to UV radiation than non-carotenoid-containing Bacillus species.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that pigmented bacilli are ubiquitous and contain new carotenoid biosynthetic pathways that may have industrial importance.

Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity

Members of the cryptochrome/photolyase family (CPF) are widely distributed throughout all kingdoms, and encode photosensitive proteins that typically show either photoreceptor or DNA repair activity. Animal and plant cryptochromes have lost DNA repair activity and now perform specialized photoperceptory functions, for example, plant cryptochromes regulate growth and circadian rhythms, whereas mammalian and insect cryptochromes act as transcriptional repressors that control the circadian clock. However, the functional differentiation between photolyases and cryptochromes is now being questioned. Here, we show that the PtCPF1 protein from the marine diatom Phaeodactylum tricornutum shows 6-4 photoproduct repair activity and can act as a transcriptional repressor of the circadian clock in a heterologous mammalian cell system. Conversely, it seems to have a wide role in blue-light-regulated gene expression in diatoms. The protein might therefore represent a missing link in the evolution of CPFs, and act as a novel ultraviolet/blue light sensor in marine environments.