Shear Stress-Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates

Some marine plankton called dinoflagellates emit light in response to the movement of surrounding water, resulting in a phenomenon called milky seas or sea sparkle. The underlying concept, a shear-stress induced permeabilisation of biocatalytic reaction compartments, is transferred to polymer-based nanoreactors. Amphiphilic block copolymers that carry nucleobases in their hydrophobic block are self-assembled into polymersomes. The membrane of the vesicles can be transiently switched between an impermeable and a semipermeable state by shear forces occurring in flow or during turbulent mixing of polymersome dispersions. Nucleobase pairs in the hydrophobic leaflet separate when mechanical force is applied, exposing their hydrogen bonding motifs and therefore making the membrane less hydrophobic and more permeable for water soluble compounds. This polarity switch is used to release payload of the polymersomes on demand, and to activate biocatalytic reactions in the interior of the polymersomes.

Transcriptome survey and toxin measurements reveal evolutionary modification and loss of saxitoxin biosynthesis genes in the dinoflagellates Amphidinium carterae and Prorocentrum micans

In the present study, we characterized the potential toxin genes for polyketide synthase (PKS) and saxitoxin (STX) biosynthesis using the transcriptomes of two non-STX producing dinoflagellates Amphidinium carterae and Prorocentrum micans. RNA sequencing revealed 94 and 166 PKS contigs in A. carterae and P. micans, respectively. We first detected type III PKS, which was closely related to bacteria. In addition, dozens of homologs of 20 STX biosynthesis genes were identified. Interestingly, the core STX-synthesizing genes sxtA and sxtB were only found in P. micans, whereas sxtD was detected in A. carterae alone. Bioinformatic analysis showed that the first two core genes (sxtA and sxtG) had a low sequence similarity (37.0-67.6%) and different domain organization compared to those of other toxigenic dinoflagellates, such as Alexandrium pacificum. These might result in the breakdown of the initial reactions in STX production and ultimately the loss of the ability to synthesize the toxins in both dinoflagellates. Our findings suggest that toxin-related PKS and sxt genes are commonly found in non-STX producing dinoflagellates. In addition to their involvement in the synthesis of toxins, our result indicates that genes may also have other molecular metabolic functions.

Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia

Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce toxins responsible for ciguatera poisoning (CP), which causes over 50,000 cases of illness annually worldwide. The biosynthetic machinery for dinoflagellate polyketides remains poorly understood. Recent transcriptomic and genomic sequencing projects have revealed the presence of Type I modular polyketide synthases in dinoflagellates, as well as a plethora of single domain transcripts with Type I sequence homology. The current transcriptome analysis compares polyketide synthase (PKS) gene transcripts expressed in two species of Gambierdiscus from French Polynesia: a highly toxic ciguatoxin producer, G. polynesiensis, versus a non-ciguatoxic species G. pacificus, each assembled from approximately 180 million Illumina 125 nt reads using Trinity, and compares their PKS content with previously published data from other Gambierdiscus species and more distantly related dinoflagellates. Both modular and single-domain PKS transcripts were present. Single domain β-ketoacyl synthase (KS) transcripts were highly amplified in both species (98 in G. polynesiensis, 99 in G. pacificus), with smaller numbers of standalone acyl transferase (AT), ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), and thioesterase (TE) domains. G. polynesiensis expressed both a larger number of multidomain PKSs, and larger numbers of modules per transcript, than the non-ciguatoxic G. pacificus. The largest PKS transcript in G. polynesiensis encoded a 10,516 aa, 7 module protein, predicted to synthesize part of the polyether backbone. Transcripts and gene models representing portions of this PKS are present in other species, suggesting that its function may be performed in those species by multiple interacting proteins. This study contributes to the building consensus that dinoflagellates utilize a combination of Type I modular and single domain PKS proteins, in an as yet undefined manner, to synthesize polyketides.

New Perspectives Related to the Bioluminescent System in Dinoflagellates: Pyrocystis lunula, a Case Study

Pyrocystis lunula is considered a model organism due to its bioluminescence capacity linked to circadian rhythms. The mechanisms underlying the bioluminescent phenomenon have been well characterized in dinoflagellates; however, there are still some aspects that remain an enigma. Such is the case of the presence and diversity of the luciferin-binding protein (LBP), as well as the synthesis process of luciferin. Here we carry out a review of the literature in relation to the molecular players responsible for bioluminescence in dinoflagellates, with particular interest in P. lunula. We also carried out a phylogenetic analysis of the conservation of protein sequence, structure and evolutionary pattern of these key players. The basic structure of the luciferase (LCF) is quite conserved among the sequences reported to date for dinoflagellate species, but not in the case of the LBP, which has proven to be more variable in terms of sequence and structure. In the case of luciferin, its synthesis has been shown to be complex process with more than one metabolic pathway involved. The glutathione S-transferase (GST) and the P630 or blue compound, seem to be involved in this process. In the same way, various hypotheses regarding the role of bioluminescence in dinoflagellates are exposed.

Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea

Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l^-1, with more than half recording stations registering concentrations below 0.10 μmol l^-1. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l^-1. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.

Isolation and characterization of a tandem-repeated cysteine protease from the symbiotic dinoflagellate Symbiodinium sp. KB8

A cysteine protease belonging to peptidase C1A superfamily from the eukaryotic, symbiotic dinoflagellate, Symbiodinium sp. strain KB8, was characterized. The protease was purified to near homogeneity (566-fold) by (NH4)2SO4 fractionation, ultrafiltration, and column chromatography using a fluorescent peptide, butyloxycarbonyl-Val-Leu-Lys-4-methylcoumaryl-7-amide (Boc-VLK-MCA), as a substrate for assay purposes. The enzyme was termed VLKP (VLK protease), and its activity was strongly inhibited by cysteine protease inhibitors and activated by reducing agents. Based on the results for the amino acid sequence determined by liquid chromatography-coupled tandem mass spectrometry, a cDNA encoding VLKP was synthesized. VLKP was classified into the peptidase C1A superfamily of cysteine proteases (C1AP). The predicted amino acid sequence of VLKP indicated a tandem array of highly conserved precursors of C1AP with a molecular mass of approximately 71 kDa. The results of gel-filtration chromatography and SDS-PAGE suggested that VLKP exists as a monomer of 31-32 kDa, indicating that the tandem array is likely divided into two mass-equivalent halves that undergo equivalent posttranslational modifications. The VLKP precursor contains an inhibitor prodomain that might become activated after acidic autoprocessing at approximately pH 4. Both purified and recombinant VLKPs had a similar substrate specificity and kinetic parameters for common C1AP substrates. Most C1APs reside in acidic organelles such as the vacuole and lysosomes, and indeed VLKP was most active at pH 4.5. Since VLKP exhibited maximum activity during the late logarithmic growth phase, these attributes suggest that, VLKP is involved in the metabolism of proteins in acidic organelles.

Identification and phylogeny of putative PEPC genes in three toxin-producing Karenia (Dinophyta) species

Dense blooms of toxin-producing Karenia brevis increase local surface ocean pH through CO2 uptake. To identify genes that may contribute to bloom-related environmental pH and pCO2 changes, transcriptomes with RNA from K. brevis Wilson cultures that had been acclimated to low CO2 (250 ppm) or recent CO2 (350 ppm) pCO2 levels were assembled. Among the annotated transcripts were PEPC, PPDK, and PEPCK enzymes found in the model C4 carbon fixation pathway. Previous studies have demonstrated that the enzymatic activity of PEPC, PPDK, and/or PEPCK in some algae species, including marine diatoms, is influenced by variations in dissolved inorganic carbon. We found significantly similar PEPC, PPDK, and PEPCK enzymes in the transcriptomes of K. brevis and two sister species Karenia papilionacea, and Karenia mikimotoi. One or more isoforms of PEPC were also identified in the transcriptomes of thirty additional photosynthetic phytoplankton species from nine phyla. Phylogenetic trees were constructed with neighbor joining and maximum likelihood techniques to characterize the evolutionary relationship among phytoplankton, terrestrial plant C4, and terrestrial plant C3 PEPC sequences. Based on the nucleotide trees constructed during this study, the Karenia PEPC transcripts were more closely related to the terrestrial C4 genes than the terrestrial C3 genes. Furthermore, PEPC phylogeny among phytoplankton closely resembles phylogenetic trees constructed with ribosomal RNA. This study confirmed that the toxin-producing dinoflagellates K. brevis, K. mikimotoi, and K. papilionacea express putative PEPC, PEPCK, and PPDK transcripts.

A Type-1 Phosphoprotein Phosphatase from a Dinoflagellate as a Possible Component of the Circadian Mechanism

Indicative of the importance of protein phosphorylation in the core circadian clock mechanism, chronically applied inhibitors of both protein kinases and phosphoprotein phosphatases have significant effects on the period, phase, and light-dependent regulation of circadian rhythms in the dinoflagellate Lingulodinium polyedrum. This study was aimed at identifying the presence of the affected phosphatase(s). Dephosphorylation of a PP1/PP2A-specific substrate by L. polyedrum extracts was inhibited by okadaic acid only at concentrations greater than 100 nM, as in vivo, by mammalian inhibitor-2 (I-2), and by an endogenous inhibitor with properties similar to I-2, indicating that a type-1 protein phosphatase (PP1) was predominant. A cDNA encoding a highly conserved PP1 was isolated, the 1st such signaling molecule identified in dinoflagellates. Anti-sera specific for this type of phosphatase recognized a 34 kDa protein in L. polyedrum extract, this being the same size as the PP1 encoded by the isolated cDNA. These findings are consistent with the suggestion that the L. polyedrum PP1 may be a part of the clock mechanism in this species.

Characterization of an epoxide hydrolase from the Florida red tide dinoflagellate, Karenia brevis

Epoxide hydrolases (EH, EC 3.3.2.3) have been proposed to be key enzymes in the biosynthesis of polyether (PE) ladder compounds such as the brevetoxins which are produced by the dinoflagellate Karenia brevis. These enzymes have the potential to catalyze kinetically disfavored endo-tet cyclization reactions. Data mining of K. brevis transcriptome libraries revealed two classes of epoxide hydrolases: microsomal and leukotriene A4 (LTA4) hydrolases. A microsomal EH was cloned and expressed for characterization. The enzyme is a monomeric protein with molecular weight 44kDa. Kinetic parameters were evaluated using a variety of epoxide substrates to assess substrate selectivity and enantioselectivity, as well as its potential to catalyze the critical endo-tet cyclization of epoxy alcohols. Monitoring of EH activity in high and low toxin producing cultures of K. brevis over a three week period showed consistently higher activity in the high toxin producing culture implicating the involvement of one or more EH in brevetoxin biosynthesis.

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi

The dinoflagellate Karenia mikimotoi forms blooms in the coastal waters of temperate regions and occasionally causes massive fish and invertebrate mortality. This study aimed to elucidate the toxic effect of K. mikimotoi on marine organisms by using the genomics approach; RNA-sequence libraries were constructed, and data were analyzed to identify toxin-related genes. Next-generation sequencing produced 153,406 transcript contigs from the axenic culture of K. mikimotoi. BLASTX analysis against all assembled contigs revealed that 208 contigs were polyketide synthase (PKS) sequences. Thus, K. mikimotoi was thought to have several genes encoding PKS metabolites and to likely produce toxin-like polyketide molecules. Of all the sequences, approximately 30 encoded eight PKS genes, which were remarkably similar to those of Karenia brevis. Our phylogenetic analyses showed that these genes belonged to a new group of PKS type-I genes. Phylogenetic and active domain analyses showed that the amino acid sequence of four among eight Karenia PKS genes was not similar to any of the reported PKS genes. These PKS genes might possibly be associated with the synthesis of polyketide toxins produced by Karenia species. Further, a homology search revealed 10 contigs that were similar to a toxin gene responsible for the synthesis of saxitoxin (sxtA) in the toxic dinoflagellate Alexandrium fundyense. These contigs encoded A1-A3 domains of sxtA genes. Thus, this study identified some transcripts in K. mikimotoi that might be associated with several putative toxin-related genes. The findings of this study might help understand the mechanism of toxicity of K. mikimotoi and other dinoflagellates.

Effects of Biocide Chlorine on Biochemical Responses of the Dinoflagellate Prorocentrum minimum

Effects of the biocide sodium hypochlorite (NaOCl) on the dinoflagellate Prorocentrum minimum were assessed. Growth rate, pigment concentrations, and chlorophyll autofluorescence were monitored up to 72 hours after NaOCl exposure, and these parameters showed dose- and time-dependent decrease. The 72-hour EC₅₀ was 0.983 mg/L. Additionally, enzymatic activities of lipid peroxidation and reduced glutathione were significantly altered with increasing NaOCl and exposure time. Thus, NaOCl at doses of 0.5 mg/L induces physiological and biochemical changes in P. minimum, suggesting that chlorine concentrations observed in power plant discharges and in drinking water systems are potentially detrimental to microalgae.

[Algicidal effect of (2-isobutoxyphenyl) amine on Alexandrium tamarense]

OBJECTIVE

A strain named BS01 showed strong algicidal activity to Alexandrium tamarense and we got algicidal compound (2-isobutoxyphenyl) amine from BS01 to study its algicidal effect on A. tamarense.

METHODS

We studied the algicidal mechanism of (2-isobutoxyphenyl) amine on photosynthetic process, antioxidant enzyme activities and morphological change of A. tamarense.

RESULTS

After 24 hours treatment with (2-isobutoxyphenyl) amine, algicidal activity was 84. 1% with the concentration of 20 µg/mL. The compound could induce a reactive oxygen species burst in P. globosa in 0. 5 hours which could cause serious oxidative damage to algal cells. The Fv/Fm value which could reflect photosystem II (PS II) electron flow status also decreased. To eliminate the excess ROS, the activities of the antioxidant systems (including superoxide dismutase and catalase) increased significantly during exposure. Transmission electron microscope analysis showed obvious morphological modifications of chloroplast dismantling as a part of the algicidal process.

CONCLUSION

These results indicated that the lysis mechanism of algicidal compound on algae may primarily be the increasing level of ROS in the algal cells.

The dinoflagellate Lingulodinium has predicted casein kinase 2 sites in many RNA binding proteins

Many cellular processes in the dinoflagellate Lingulodinium polyedrum are controlled by a circadian (daily) clock. Since the activity of proteins involved in various metabolic pathways or in regulating gene expression can be affected by phosphorylation, we established a generalized phosphoproteome catalog using LC-MS/MS to analyze a phosphoprotein-enriched fraction. Over 11,000 peptides were identified by comparison to a Lingulodinium transcriptome, and 527 of these had at least one identified phosphosite. Gene ontology analysis revealed that RNA binding and translation were one of the major categories among these proteins identified by these peptides. Since casein kinase 2 (CK2) is known to be important in eukaryotic circadian biology substrates, we next tried to identify specific substrates for this kinase. To achieve this we first classified and catalogued the kinases in the Lingulodinium transcriptome then assigned the different phosphosites to the different kinase classes. Interestingly, potential CK2 targets include a substantial proportion of RNA binding proteins. Phosphosite identification thus provides a promising new approach to investigate the Lingulodinium circadian system.

Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms

A tertiary endosymbiosis between a dinoflagellate host and diatom endosymbiont gave rise to "dinotoms," cells with a unique nuclear and mitochondrial redundancy derived from two evolutionarily distinct eukaryotic lineages. To examine how this unique redundancy might have affected the evolution of metabolic systems, we investigated the transcription of genes involved in biosynthesis of the amino acid tryptophan in three species, Durinskia baltica, Kryptoperidinium foliaceum, and Glenodinium foliaceum. From transcriptome sequence data, we recovered two distinct sets of protein-coding transcripts covering the entire tryptophan biosynthetic pathway. Phylogenetic analyses suggest a diatom origin for one set of the proteins, which we infer to be expressed in the endosymbiont, and that the other arose from multiple horizontal gene transfer events to the dinoflagellate ancestor of the host lineage. This is the first indication that these cells retain redundant sets of transcripts and likely metabolic pathways for the biosynthesis of small molecules and extend their redundancy to their two distinct nuclear genomes.

Molybdate:sulfate ratio affects redox metabolism and viability of the dinoflagellate Lingulodinium polyedrum

Molybdenum is a transition metal used primarily (90% or more) as an additive to steel and corrosion-resistant alloys in metallurgical industries and its release into the environment is a growing problem. As a catalytic center of some redox enzymes, molybdenum is an essential element for inorganic nitrogen assimilation/fixation, phytohormone synthesis, and free radical metabolism in photosynthesizing species. In oceanic and estuarine waters, microalgae absorb molybdenum as the water-soluble molybdate anion (MoO4(2-)), although MoO4(2-) uptake is thought to compete with uptake of the much more abundant sulfate anion (SO4(2-), approximately 25 mM in seawater). Thus, those aspects of microalgal biology impacted by molybdenum would be better explained by considering both MoO4(2-) and SO4(2-) concentrations in the aquatic milieu. This work examines toxicological, physiological and redox imbalances in the dinoflagellate Lingulodinium polyedrum that have been induced by changes in the molybdate:sulfate ratios. We prepared cultures of Lingulodinium polyedrum grown in artificial seawater containing eight different MoO4(2-) concentrations (from 0 to 200 μM) and three different SO4(2-) concentrations (3.5 mM, 9.6 mM and 25 mM). We measured sulfur content in cells, the activities of the three major antioxidant enzymes (superoxide dismutase, catalase, and ascorbate peroxidase), indexes of oxidative modifications in proteins (carbonyl content) and lipids (thiobarbituric acid-reactive substances, TBARS), the activities of the molybdenum-dependent enzymes xanthine oxidase and nitrate reductase, expression of key protein components of dinoflagellate photosynthesis (peridinin-chlorophyll a protein and ribulose-1,5-biphosphate carboxylase/oxidase) and growth curves. We find evidence for Mo toxicity at relatively high [MoO4(2-)]:[SO4(2-)] ratios. We also find evidence for extensive redox adaptations at Mo levels well below lethal levels.

[Illumination's effect on the growth and nitrate reductase activity of typical red-tide algae in the East China Sea]

Two typical red-tide algae, Skeletonema costatum and Prorocentrum donghaiense were selected as studied objects. The nitrate reductase activity (NRA) and the growth of the two algae under different illuminations through incubation experiment were studied. The illumination condition was consistent with in situ. Results showed that P. donghaiense and S. costatum could grow normally in the solar radiation ranged from 30-60 W x m(-2), and the growth curve was "S" type. However, when solar radiation was below 9 W x m(-2), the two alga could hardly grow. In the range of 0-60 W x m(-2), three parameters (NRAmax, micro(max), Bf) increased with the increasing of light intensity, indicating that the light intensity can influence the grow of alga indirectly through influencing the nitrate reductase activity. The micro(max) and NRAmax in unite volume of Skeletonema costatum were higher than those of Prorocentrum donghaiense, indicating that Skeletonema costatum can better utilize the nitrate than Prorocentrum donghaiense.

A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria

Cytochrome oxidase subunit 3 (Cox3) is a mitochondrion-encoded core membrane protein of complex IV of the mitochondrial respiratory chain, and consists of seven trans-membrane helices. Here we show that in diverse later-branching dinoflagellates, cox3 is consistently split into two exons in the mitochondrial genome between helices six and seven. Gene exons are transcribed as two discrete oligoadenylated precursor RNAs, and these are subsequently trans-spliced to form a complete coding mRNA. This trans-splicing is highly unusual in that some of the oligoadenylated tail is incorporated at the splice site, such that a short string of adenosines links the two coding exons. This feature is consistently represented in diverse dinoflagellates, however the number of adenosines added varies according to the size of the coding gap between the two exons. Thus we observed between zero (Amphidinium carterae) and 10 (Symbiodinium sp.) adenosines added in different taxa, but the final coding sequence length is identical with the reading frame maintained. Northern analyses show that precursor cox3 transcripts are approximately equally abundant as mature cox3 mRNAs, suggesting a slow or regulated maturation process. These data indicate that the splicing mechanism in dinoflagellate mitochondria is tolerant of variations in the length of the precursor coding sequence, and implicates the use of a splicing template, or guide molecule, during splicing that controls mature mRNA length.

Putative monofunctional type I polyketide synthase units: a dinoflagellate-specific feature?

Marine dinoflagellates (alveolata) are microalgae of which some cause harmful algal blooms and produce a broad variety of most likely polyketide synthesis derived phycotoxins. Recently, novel polyketide synthesase (PKS) transcripts have been described from the Florida red tide dinoflagellate Karenia brevis (gymnodiniales) which are evolutionarily related to Type I PKS but were apparently expressed as monofunctional proteins, a feature typical of Type II PKS. Here, we investigated expression units of PKS I-like sequences in Alexandrium ostenfeldii (gonyaulacales) and Heterocapsa triquetra (peridiniales) at the transcript and protein level. The five full length transcripts we obtained were all characterized by polyadenylation, a 3′ UTR and the dinoflagellate specific spliced leader sequence at the 5′end. Each of the five transcripts encoded a single ketoacylsynthase (KS) domain showing high similarity to K. brevis KS sequences. The monofunctional structure was also confirmed using dinoflagellate specific KS antibodies in Western Blots. In a maximum likelihood phylogenetic analysis of KS domains from diverse PKSs, dinoflagellate KSs formed a clade placed well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes. These findings indicate that the atypical PKS I structure, i.e., expression as putative monofunctional units, might be a dinoflagellate specific feature. In addition, the sequenced transcripts harbored a previously unknown, apparently dinoflagellate specific conserved N-terminal domain. We discuss the implications of this novel region with regard to the putative monofunctional organization of Type I PKS in dinoflagellates.

Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker

Background

DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.

Methodology/Principal Findings

The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.

Conclusions/Significance

The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.

Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (Amphidinium, Dinoflagellata)

Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

Dozens of toxin-related genes are expressed in a nontoxic strain of the dinoflagellate Heterocapsa circularisquama

The dinoflagellate Heterocapsa circularisquama is lethal to a variety of marine organisms, in particular, commercially important farmed bivalves. Unlike most dinoflagellate toxins, which are polyketides, the only described toxin from H. circularisquama (H2-a) is a porphyrin derivative that functions in light. It is unknown whether H2-a is produced specifically for its lytic properties. We searched for toxin-related genes in the transcriptome of a nontoxic strain of H. circularisquama, and surprisingly found the richest set of toxin-related genes yet described in dinoflagellates. There are 87 distinct expressed sequence tag contigs that encode polyketide synthases and nonribosomal peptide synthases, as well as 8 contigs that are involved in porphyrin biosynthesis. Phylogenomic analysis shows that many toxin-related genes are widely distributed among dinoflagellates. Our data likely indicate a variety of unknown metabolic functions for the toxin-related genes in H. circularisquama because they were identified in a nontoxic strain raised in unialgal culture.

[Toxic effects of nano-TiO2 on Gymnodinium breve]

In order to reveal the toxicity and mechanism of nano-TiO2 on algae, the inhibition effect, enzyme activity, oxygen free radicals of nano-TiO2 on the growth of G. breve were investigated. The results showed that G. breve was inhibited by nano-TiO2, and the 72 h-EC50 was 9.7 mg x L(-1). With the increasing concentration of nano-titanium dioxide, the activities of SOD decrease significantly (P < 0.05). The content of hydrogen peroxide radicals and the activities of CAT increase significantly (P < 0.05), and the content of superoxide anion shows the increasing trend. The content of hydrogen peroxide radicals was 0.083 U x mL(-1) in 0 mg x L(-1) nano-TiO2 suspension while that was 1.1 U x mL(-1) in control after 48 h. Through the study of 20 mg x L(-1) nano-titanium dioxide on G. breve at different times, the activities of SOD and CAT, the content of MDA are consistent, which the highest values is achieved at the exposure time of 12 hours and the lowest value is found at the exposure time of 48 hours. The content of hydroxyl radical increased significantly at the exposure time of 48 hours. The activity of SOD was 0.14 U x (10(7) cell x min)(-1) in G. breve at 12 h which was ten times higher than that at 48 h.

Chemical chaperone therapy: luciferase assay for screening of β-galactosidase mutations

β-Galactosidosis is a group of disorder based on heterogeneous mutations of GLB1 gene coding for the lysosomal acid β-galactosidase (β-gal). A decrease of the β-gal enzyme activity results in progressive accumulation of substrates in somatic cells, particularly in neurons, leading to severe neuronal dysfunction. We have previously reported that N-octyl-4-epi-β-valienamine (NOEV), a chemical chaperone compound, stabilized various mutant human β-gal proteins and increased residual enzyme activities in cultured fibroblasts from human patients. These data proved a potential therapeutic benefit of chemical chaperone therapy for patients with missense β-gal. This effect is mutation specific. In this study, we have established a sensitive luciferase-based assay for measuring chaperone effect on mutant human β-gal. A dinoflagellate luciferase (Dluc) cDNA was introduced to the C-terminus of human β-gal. When COS7 cells expressing the Dluc-tagged human R201C β-gal was treated with NOEV, there happened a remarkable increase of the mutant β-gal activity. In the presence of NH(4)Cl, luciferase level in the medium increased in parallel with the enzyme activity in cell lysates. We also found that proteasome inhibitors enhance chaperone effect of NOEV. These results demonstrate that the luciferase-based assay is a reliable and convenient method for screening and evaluation of chaperone effects on human β-gal mutants, and that it will be a useful tool for finding novel chaperone compounds in the future study.

The determination of activity of the enzyme Rubisco in cell extracts of the dinoflagellate alga Symbiodinium sp. by manganese chemiluminescence and its response to short-term thermal stress of the alga

The dinoflagellate alga Symbiodinium sp., living in symbiosis with corals, clams and other invertebrates, is a primary producer in coral reefs and other marine ecosystems. The function of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in dinoflagellates is difficult to study because its activity is rapidly lost after extraction from the cell. We report procedures for the extraction of Rubisco from Symbiodinium cells and for stable storage. We describe a continuous assay for Rubisco activity in these crude cell extracts using the Mn(2+) chemiluminescence of Rubisco oxygenase. Chemiluminescence time courses exhibited initial transients resembling bacterial Form II Rubisco, followed by several minutes of linearly decreasing activity. The initial activity was determined from extrapolation of this linear section of the time course. The activity of fast-frozen cell extracts was stable at -80 degrees C and, after thawing and storage on ice, remained stable for up to 1 h before declining non-linearly. Crude cell extracts bound [(14)C] 2-carboxy-D-arabitinol 1,5-bisphosphate to a high molecular mass fraction separable by gel filtration chromatography. After pre-treatment of Symbiodinium cell cultures in darkness at temperatures above 30 degrees C, the extracted Rubisco activities decreased, with almost complete loss of activity above 36 degrees C. The implications for the sensitivity to elevated temperature of Symbiodinium photosynthesis are assessed.

Characterisation of nitric oxide synthase in three cnidarian-dinoflagellate symbioses

Background

Nitric oxide synthase (NOS) is an enzyme catalysing the conversion of L-arginine to L-citrulline and nitric oxide (NO), the latter being an essential messenger molecule for a range of biological processes. Whilst its role in higher vertebrates is well understood little is known about the role of this enzyme in early metazoan groups. For instance, NOS-mediated signalling has been associated with Cnidaria-algal symbioses, however controversy remains about the contribution of enzyme activities by the individual partners of these mutualistic relationships.

Methodology/Principal Findings

Using a modified citrulline assay we successfully measured NOS activity in three cnidarian-algal symbioses: the sea anemone Aiptasia pallida, the hard coral Acropora millepora, and the soft coral Lobophytum pauciflorum, so demonstrating a wide distribution of this enzyme in the phylum Cnidaria. Further biochemical (citrulline assay) and histochemical (NADPH-diaphorase) investigations of NOS in the host tissue of L. pauciflorum revealed the cytosolic and calcium dependent nature of this enzyme and its in situ localisation within the coral's gastrodermal tissue, the innermost layer of the body wall bearing the symbiotic algae. Interestingly, enzyme activity could not be detected in symbionts freshly isolated from the cnidarians, or in cultured algal symbionts.

Conclusions/Significance

These results suggest that NOS-mediated NO release may be host-derived, a finding that has the potential to further refine our understanding of signalling events in cnidarian-algal symbioses.

The activity of a wall-bound cellulase is required for and is coupled to cell cycle progression in the dinoflagellate Crypthecodinium cohnii

Cellulose synthesis, but not its degradation, is generally thought to be required for plant cell growth. In this work, we cloned a dinoflagellate cellulase gene, dCel1, whose activities increased significantly in G(2)/M phase, in agreement with the significant drop of cellulose content reported previously. Cellulase inhibitors not only caused a delay in cell cycle progression at both the G(1) and G(2)/M phases in the dinoflagellate Crypthecodinium cohnii, but also induced a higher level of dCel1p expression. Immunostaining results revealed that dCel1p was mainly localized at the cell wall. Accordingly, the possible role of cellulase activity in cell cycle progression was tested by treating synchronized cells with exogenous dCelp and purified antibody, in experiments analogous to overexpression and knockdown analyses, respectively. Cell cycle advancement was observed in cells treated with exogenous dCel1p, whereas the addition of purified antibody resulted in a cell cycle delay. Furthermore, delaying the G(2)/M phase independently with antimicrotubule inhibitors caused an abrupt and reversible drop in cellulase protein level. Our results provide a conceptual framework for the coordination of cell wall degradation and reconstruction with cell cycle progression in organisms with cell walls. Since cellulase activity has a direct bearing on the cell size, the coupling between cellulase expression and cell cycle progression can also be considered as a feedback mechanism that regulates cell size.

Characterization and localization of a hybrid non-ribosomal peptide synthetase and polyketide synthase gene from the toxic dinoflagellate Karenia brevis

The toxic dinoflagellate Karenia brevis, a causative agent of the red tides in Florida, produces a series of toxic compounds known as brevetoxins and their derivatives. Recently, several putative genes encoding polyketide synthase (PKS) were identified from K. brevis in an effort to elucidate the genetic systems involved in brevetoxin production. In this study, novel PKS sequences were isolated from three clones of K. brevis. Eighteen unique sequences were obtained for the PKS ketosynthase (KS) domain of K. brevis. Phylogenetic comparison with closely related PKS genes revealed that 16 grouped with cyanobacteria sequences, while the remaining two grouped with Apicomplexa and previously reported sequences for K. brevis. A fosmid library was also constructed to further characterize PKS genes detected in K. brevis Wilson clone. Several fosmid clones were positive for the presence of PKS genes, and one was fully sequenced to determine the full structure of the PKS cluster. A hybrid non ribosomal peptide synthetase and PKS (NRPS-PKS) gene cluster of 16,061 bp was isolated. In addition, we assessed whether the isolated gene was being actively expressed using reverse transcription polymerase chain reaction (RT-PCR) and determined its localization at the cellular level by chloroplast isolation. RT-PCR analyses revealed that this gene was actively expressed in K. brevis cultures. The hybrid NRPS-PKS gene cluster was located in the chloroplast, suggesting that K. brevis acquired the ability to produce some of its secondary metabolites through endosymbiosis with ancestral cyanobacteria. Further work is needed to determine the compound produced by the NRPS-PKS hybrid, to find other PKS gene sequences, and to assess their role in K. brevis toxin biosynthetic pathway.

An external delta-carbonic anhydrase in a free-living marine dinoflagellate may circumvent diffusion-limited carbon acquisition

The oceans globally constitute an important sink for carbon dioxide (CO(2)) due to phytoplankton photosynthesis. However, the marine environment imposes serious restraints to carbon fixation. First, the equilibrium between CO(2) and bicarbonate (HCO(3)(-)) is pH dependent, and, in normal, slightly alkaline seawater, [CO(2)] is typically low (approximately 10 mum). Second, the rate of CO(2) diffusion in seawater is slow, so, for any cells unable to take up bicarbonate efficiently, photosynthesis could become carbon limited due to depletion of CO(2) from their immediate vicinity. This may be especially problematic for those dinoflagellates using a form II Rubisco because this form is less oxygen tolerant than the usually found form I enzyme. We have identified a carbonic anhydrase (CA) from the free-living marine dinoflagellate Lingulodinium polyedrum that appears to play a role in carbon acquisition. This CA shares 60% sequence identity with delta-class CAs, isoforms so far found only in marine algae. Immunoelectron microscopy indicates that this enzyme is associated exclusively with the plasma membrane. Furthermore, this enzyme appears to be exposed to the external medium as determined by whole-cell CA assays and vectorial labeling of cell surface proteins with (125)I. The fixation of (14)CO(2) is strongly pH dependent, suggesting preferential uptake of CO(2) rather than HCO(3)(-), and photosynthetic rates decrease in the presence of 1 mm acetazolamide, a non-membrane-permeable CA inhibitor. This constitutes the first CA identified in the dinoflagellates, and, taken together, our results suggest that this enzyme may help to increase CO(2) availability at the cell surface.

Diverse bacterial PKS sequences derived from okadaic acid-producing dinoflagellates

Okadaic acid (OA) and the related dinophysistoxins are isolated from dinoflagellates of the genus Prorocentrum and Dinophysis. Bacteria of the Roseobacter group have been associated with okadaic acid producing dinoflagellates and have been previously implicated in OA production. Analysis of 16S rRNA libraries reveals that Roseobacter are the most abundant bacteria associated with OA producing dinoflagellates of the genus Prorocentrum and are not found in association with non-toxic dinoflagellates. While some polyketide synthase (PKS) genes form a highly supported Prorocentrum clade, most appear to be bacterial, but unrelated to Roseobacter or Alpha-Proteobacterial PKSs or those derived from other Alveolates Karenia brevis or Crytosporidium parvum.

An unusual S-adenosylmethionine synthetase gene from dinoflagellate is methylated

Background

S-Adenosylmethionine synthetase (AdoMetS) catalyzes the formation of S-Adenosylmethionine (AdoMet), the major methyl group donor in cells. AdoMet-mediated methylation of DNA is known to have regulatory effects on DNA transcription and chromosome structure. Transcription of environmental-responsive genes was demonstrated to be mediated via DNA methylation in dinoflagellates.

Results

A full-length cDNA encoding AdoMetS was cloned from the dinoflagellate Crypthecodinium cohnii. Phylogenetic analysis suggests that the CcAdoMetS gene, is associated with the clade of higher plant orthrologues, and not to the clade of the animal orthrologues. Surprisingly, three extra stretches of residues (8 to 19 amino acids) were found on CcAdoMetS, when compared to other members of this usually conserved protein family. Modeled on the bacterial AdeMetS, two of the extra loops are located close to the methionine binding site. Despite this, the CcAdoMetS was able to rescue the corresponding mutant of budding yeast. Southern analysis, coupled with methylation-sensitive and insensitive enzyme digestion of C. cohnii genomic DNA, demonstrated that the AdoMetS gene is itself methylated. The increase in digestibility of methylation-sensitive enzymes on AdoMet synthetase gene observed following the addition of DNA methylation inhibitors L-ethionine and 5-azacytidine suggests the presence of cytosine methylation sites within CcAdoMetS gene. During the cell cycle, both the transcript and protein levels of CcAdoMetS peaked at the G1 phase. L-ethionine was able to delay the cell cycle at the entry of S phase. A cell cycle delay at the exit of G2/M phase was induced by 5-azacytidine.

Conclusion

The present study demonstrates a major role of AdoMet-mediated DNA methylation in the regulation of cell proliferation and that the CcAdoMetS gene is itself methylated.

Horizontal gene transfer in chromalveolates

BACKGROUND

Horizontal gene transfer (HGT), the non-genealogical transfer of genetic material between different organisms, is considered a potentially important mechanism of genome evolution in eukaryotes. Using phylogenomic analyses of expressed sequence tag (EST) data generated from a clonal cell line of a free living dinoflagellate alga Karenia brevis, we investigated the impact of HGT on genome evolution in unicellular chromalveolate protists.

RESULTS

We identified 16 proteins that have originated in chromalveolates through ancient HGTs before the divergence of the genera Karenia and Karlodinium and one protein that was derived through a more recent HGT. Detailed analysis of the phylogeny and distribution of identified proteins demonstrates that eight have resulted from independent HGTs in several eukaryotic lineages.

CONCLUSION

Recurring intra- and interdomain gene exchange provides an important source of genetic novelty not only in parasitic taxa as previously demonstrated but as we show here, also in free-living protists. Investigating the tempo and mode of evolution of horizontally transferred genes in protists will therefore advance our understanding of mechanisms of adaptation in eukaryotes.

The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages

Background

The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them.

Results

We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate.

Conclusion

Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport.

The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes

The mitochondrial genome and the expression of the genes within it have evolved to be highly unusual in several lineages. Within alveolates, apicomplexans and dinoflagellates share the most reduced mitochondrial gene content on record, but differ from one another in organisation and function. To clarify how these characteristics originated, we examined mitochondrial genome form and expression in a key lineage that arose close to the divergence of apicomplexans and dinoflagellates, Oxyrrhis marina. We show that Oxyrrhis is a basal member of the dinoflagellate lineage whose mitochondrial genome has some unique characteristics while sharing others with apicomplexans or dinoflagellates. Specifically, Oxyrrhis has the smallest gene complement known, with several rRNA fragments and only two protein coding genes, cox1 and a cob-cox3 fusion. The genome appears to be highly fragmented, like that of dinoflagellates, but genes are frequently arranged as tandem copies, reminiscent of the repeating nature of the Plasmodium genome. In dinoflagellates and Oxyrrhis, genes are found in many arrangements, but the Oxyrrhis genome appears to be more structured, since neighbouring genes or gene fragments are invariably the same: cox1 and the cob-cox3 fusion were never found on the same genomic fragment. Analysing hundreds of cDNAs for both genes and circularized mRNAs from cob-cox3 showed that neither uses canonical start or stop codons, although a UAA terminator is created in the cob-cox3 fusion mRNA by post-transcriptional oligoadenylation. mRNAs from both genes also use a novel 5' oligo(U) cap. Extensive RNA editing is characteristic of dinoflagellates, but we find no editing in Oxyrrhis. Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes.

Synchronization of cell death in a dinoflagellate population is mediated by an excreted thiol protease

Regulated programmed cell death (PCD) processes have been documented in several phytoplankton species and are hypothesized to play a role in population dynamics. However, the mechanisms leading to the coordinated collapse of phytoplankton blooms are poorly understood. We showed that the collapse of the annual bloom of Peridinium gatunense, an abundant dinoflagellate in Lake Kinneret, Israel, is initiated by CO2 limitation followed by oxidative stress that triggers a PCD-like cascade. We provide evidences that a protease excreted by senescing P. gatunense cells sensitizes younger cells to oxidative stress and may consequently trigger synchronized cell death of the population. Ageing of the P. gatunense cultures was characterized by a remarkable rise in DNA fragmentation and enhanced sensitivity to H2O2. Exposure of logarithmic phase (young) cultures to conditioning media from stationary phase (old) cells sensitized them to H2O2 and led to premature massive cell death. We detected the induction of specific extracellular protease activity, leupeptin-sensitive, in ageing cultures and in lake waters during the succession of the P. gatunense bloom. Partial purification of the conditioned media revealed that this protease activity is responsible for the higher susceptibility of young cells to oxidative stress. Inhibition of the protease activity lowered the sensitivity to oxidative stress, whereas application of papain to logarithmic phase P. gatunense cultures mimicked the effect of the spent media and enhanced cell death. We propose a novel mechanistic framework by which a population of unicellular phytoplankton orchestrates a coordinated response to stress, thereby determine the fate of its individuals.

Differences in enzyme activities between two species of Hematodinium, parasitic dinoflagellates of crustaceans

Parasitic dinoflagellates of the genus Hematodinium infect several commercially important decapod crustaceans. Different species of Hematodinium have different levels of virulence in their respective hosts. Enzyme activities were studied from two species of Hematodinium, one isolated from the Norway lobster (Nephrops norvegicus) and the other from the American blue crab (Callinectes sapidus). We report the identification of differences in secretion of acid phosphatase (AP) and leucine arylamidase from two parasite species. Leucine arylamidase was only contained and secreted by the species infecting the blue crab. Both parasite species contained AP, but only the species infecting the Norway lobster secreted this enzyme. In this species, AP activity was predominantly in the soluble fraction (69.5%). AP activity was localized to cytoplasmic granules and on the membranes surrounding the cell nucleus. In addition to providing information on the cellular metabolism of the parasite, the pattern of activities of these enzymes may also be useful in distinguishing among different species of Hematodinium.

The Expression of a Plant-type Ferredoxin Redox System provides Molecular Evidence for a Plastid in the Early Dinoflagellate Perkinsus marinus

Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).

Analysis of the targeting sequences of an iron-containing superoxide dismutase (SOD) of the dinoflagellate Lingulodinium polyedrum suggests function in multiple cellular compartments

One of the proteins targeted to the peridinin plastid of the dinoflagellate Lingulodinium polyedrum is the iron-containing superoxide dismutase (LpSOD). Like dinoflagellate plastid proteins of class II, LpSOD carries a bipartite presequence comprising a signal peptide followed by a transit peptide. Our bioinformatic studies suggest that its signal peptide is atypical, however, and that the entire presequence may function as a mitochondrial targeting signal. It is possible that LpSOD represents a new class of proteins in algae with complex plastids, which are co-targeted to the plastid and mitochondrion. In addition to the ambiguous N-terminal targeting signal, LpSOD contains a potential type-1 peroxisome-targeting signal (PTS1) located at its C-terminus. In accordance with a peroxisome localization of this dismutase, its mRNA has two in-frame AUG codons. Our bioinformatic analyses indicate that the first start codon resides in a much weaker oligonucleotide context than the second one. This suggests that synthesis of the plastid/mitochondrion-targeted and peroxisome-targeted isoforms could proceed through so-called leaky scanning. Moreover, our results show that expression of the two isoforms could be regulated by a 'hairpin' structure located between the first and second start codons.

Alveolate and chlorophycean mitochondrial cox2 genes split twice independently

The mitochondrial gene for COXII is typically encoded in the organelle genome, however in some members of two unrelated groups, Apicomplexa and Chlorophyceae, cox2 is split into two genes, and both are encoded in the nucleus. Rare genomic changes (RGCs) have acquired popularity as phylogenetic markers, and accordingly this rearrangement of cox2 has been used to infer a possible source of the apicomplexan plastid, the apicoplast, a topic that continues to attract much debate. Accurate interpretation of RGCs, however, is critically dependent on appropriate sampling of the character state of interest amongst relevant taxa. Dinoflagellates form the sister taxon to Apicomplexa, and therefore the state of their cox2 is essential to the interpretation of this apparent RGC. Here we present the first complete cox2 data from dinoflagellates, that suggests despite the remarkable similarity of cox2 seen in Alveolates and Chlorophyceae, this gene reorganization arose independently in these two groups, not through lateral transfer as previously suggested.

Cloning of polyketide synthase genes from amphidinolide-producing dinoflagellate Amphidinium sp

Cloning of polyketide synthase (PKS) gene for amphidinolide biosynthesis was attempted from a dinoflagellate Amphidinium sp. (strain Y-42). Fourteen beta-ketoacyl synthase gene fragments were obtained by Polymerase Chain Reaction (PCR) amplification from degenerated primer sets designed on the basis of the conserved amino acid sequences of beta-ketoacyl synthase domains in known type I PKSs. The PCR analysis using primer sets designed from these fourteen beta-ketoacyl synthase gene fragments revealed that these DNA sequences exist only in the dinoflagellates producing amphidinolides. The DNA sequence of the positive clone, which was isolated from genomic DNA library of Amphidinium sp. (strain Y-42) by PCR detection using the specific primer set, was analyzed by shotgun sequencing. The deduced gene products in the positive clone showed similarity with beta-ketoacyl synthase (KS), acyl transferase (AT), dehydratase (DH), ketoreductase (KR), and acyl carrier protein (ACP) in known type I PKSs and thioesterase (TE).

Circadian rhythm of a TCA cycle enzyme is apparently regulated at the translational level in the dinoflagellate Lingulodinium polyedrum

Previously, the authors have reported that intracellular amounts of several metabolic-related enzymes from the photosynthetic dinoflagellate Lingulodinium polyedrum(formerly Gonyaulax polyedra) showed a daily rhythm under a 12:12 h LD cycle. This led the authors to hypothesize that a circadian clock controls metabolism, including the tricarboxylic acid (TCA) cycle. In this study, the authors investigated daily changes in the levels of mRNA, protein, and enzyme activity of several metabolic enzymes during 12:12 h LD, 8:16 h LD, and constant light conditions. The NADP-dependent isocitrate dehydrogenase (NADPICDH) in the TCA cycle exhibited circadian changes of protein abundance and enzyme activity under all conditions, whereas its mRNA level remained constant throughout the cycle. These results indicate that the rhythm of NADPICDH is regulated by a circadian control of protein synthesis or modification rather than by message levels and suggest that the TCA cycle may be controlled by the circadian clock system.

Mitochondrial cytochrome b mRNA editing in dinoflagellates: possible ecological and evolutionary associations?

To verify the hypothesis that mt mRNA editing is widespread in dinoflagellates, we analyzed cytochrome b (cob) mRNA editing for six species representing distinct ecotypes and taxonomic classes of Dinophyceae. Editing is detected in all, which is similar to the three other species studied previously in that edited sites appear to aggregate in four clusters and occur predominantly at first and second positions of codons (93%), overwhelmingly involving A --> G, U --> C, or C --> U substitutions with a smaller number of G --> C, G --> A changes. Comparative analyses on editing characteristics reveal interesting trends related to phylogenetic relatedness and ecological features. Editing density (percentage of nucleotide that is affected by editing) increases from early to derived lineages. Higher editing densities also map to red tide-forming lineages. Furthermore, similarity of location of edited codons (LOE) and the type of nucleotide changes (TOE) in different lineages mirror the taxonomic affinity of the lineages. Phylogenetic trees constructed from LOE and TOE resemble those inferred from cob sequences. The results bolster our earlier hypothesis that cob editing is widespread in dinoflagellates and suggest that density, location, and type of editing may bear yet-to-be-defined evolutionary and ecological significance.

Type II topoisomerase activities in both the G1 and G2/M phases of the dinoflagellate cell cycle

Dinoflagellate genomes are large (up to 200 pg) and are encoded in histoneless chromosomes that are quasi-permanently condensed. This unique combination of chromosomal characteristics presents additional topological and cell cycle control problems for a eukaryotic cell, potentially exhibiting novel regulatory requirements of topoisomerase II. The heterotrophic dinoflagellate Crypthecodinium cohnii was used in this study. The topoisomerase II activities throughout its cell cycle were investigated by DNA flow cytometry following enzyme deactivation. Fluorescence microscopy was also used for studying the chromosome morphology of the treated cells. Two classes of topoisomerase II inhibitors were applied in our study, both of which caused G1 delay as well as G2/M arrest in the C. cohnii cell cycle. At high doses, the topoisomerase poisons amsacrine and ellipticine induced DNA fragmentation in C. cohnii cells. Topoisomerase II activities, as measured by the ability to decatenate kinetoplastid DNA (kDNA), are normally detected throughout the cell cycle in C. cohnii. Our results suggest that the requirement of type II topoisomerase activities during the G1 phase of the cell cycle may relate to the unwinding of quasi-permanently condensed chromosomes for the purpose of transcription. This was also the first time that topoisomerase II activity in dinoflagellate cells was detected.

Localization of polyketide synthase encoding genes to the toxic dinoflagellate Karenia brevis

Karenia brevis is a toxic marine dinoflagellate endemic to the Gulf of Mexico. Blooms of this harmful alga cause fish kills, marine mammal mortalities and neurotoxic shellfish poisonings. These harmful effects are attributed to a suite of polyketide secondary metabolites known as the brevetoxins. The carbon framework of all polyketides is assembled by a polyketide synthase (PKS). Previously, PKS encoding genes were amplified from K. brevis culture and their similarity to a PKS gene from the closely related protist, Cryptosporidium parvum, suggested that these genes originate from the dinoflagellate. However, K. brevis has not been grown axenically. The associated bacteria might be the source of the toxins or the PKS genes. Herein we report the localization of PKS encoding genes by a combination of flow cytometry/PCR and fluorescence in situ hybridization (FISH). Two genes localized exclusively to K. brevis cells while a third localized to both K. brevis and associated bacteria. While these genes have not yet been linked to toxin production, the work describes the first definitive evidence of resident PKS genes in any dinoflagellate.

A Transcriptional Fusion of Genes Encoding Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and Enolase in Dinoflagellates

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and enolase are enzymes essential for glycolysis and gluconeogenesis. Dinoflagellates possess several types of both GAPDH and enolase genes. Here, we identify a novel cytosolic GAPDH-enolase fusion protein in several dinoflagellate species. Phylogenetic analyses revealed that the GAPDH moiety of this fusion is weakly related to a cytosolic GAPDH previously reported in dinoflagellates, ciliates, and an apicomplexan. The enolase moiety has phylogenetic affinity with sequences from ciliates and apicomplexans, as expected for dinoflagellate genes. Furthermore, the enolase moiety has two insertions in a highly conserved region of the gene that are shared with ciliate and apicomplexan homologues, as well as with land plants, stramenopiles, haptophytes, and a chlorarachniophyte. Another glycolytic gene fusion in eukaryotes is the mitochondrion-targeted triose-phosphate isomerase (TPI) and GAPDH fusion in stramenopiles (i.e. diatoms and oomycetes). However, unlike the mitochondrial TPI-GAPDH fusion, the GAPDH-enolase fusion protein appears to exist in the same compartment as stand-alone homologues of each protein, and the metabolic reactions they catalyze in glycolysis and gluconeogenesis are not directly sequential. It is possible that the fusion is post-translationally processed to give separate GAPDH and enolase products, or that the fusion protein may function as a single bifunctional polypeptide in glycolysis, gluconeogenesis, or perhaps more likely in some previously unrecognized metabolic capacity.

Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole

The luciferase of Lingulodinium polyedrum, a marine bioluminescent dinoflagellate, consists of three similar but not identical domains in a single polypeptide. Each encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light. These domains share no sequence similarity with any other in the GenBank database and no structural or motif similarity with any other luciferase. We report here the 1.8-A crystal structure of the third domain, D3, at pH 8, and a mechanism for its activity regulation by pH. D3 consists of two major structural elements: a beta-barrel pocket putatively for substrate binding and catalysis and a regulatory three-helix bundle. N-terminal histidine residues previously shown to regulate activity by pH are at the interface of the helices in the bundle. Molecular dynamics calculations indicate that, in response to changes in pH, these histidines could trigger a large molecular motion of the bundle, thereby exposing the active site to the substrate.

Biological activity of a red-tide alga--A. tamarense under co-cultured condition with bacteria

The relationship between Alexandrium tamarense (Lebour) Balech, one of red-tide alga, and two strains of marine bacteria, Bacillius megaterium (S7) and B. halmapulus (S10) isolated from Xiamen Western Sea, was investigated by evaluating the growth state of A. tamarense and the variation of beta-glucosidase activity in co-culture system. The results showed the growth and multiplication of the alga were related with the concentration, genus speciality of the bacteria, and growth stage of the alga itself. The growth of A. tamarense was obviously inhibited by S7 and S10 at high concentration. Either inhibition or promotion contributed much more clearly in earlier than in later stage of the growth of the alga. Furthermore, there was a roughly similar variation trend of the activity of extra-cellular enzyme, beta-glucosidase, in the water of the separately co-cultured bacteria S7 and S10 with the alga. The beta-glucosidase activity (beta-GlcA) rapidly increased during the later algal growth accompanying the increase of the lysis of the alga cells. The obvious inhibition of A. tamarense by marine bacteria at high concentration and evident increase of beta-GlcA in co-colture system would help us in better understanding the relationship between red-tide alga and bacteria, and also enlightenedus the possible use of bacteria in the bio-control of red-tide.

A new additional reporter enzyme, dinoflagellate luciferase, for monitoring of gene expression in mammalian cells

Dinoflagellate luciferase (DL) catalyses the oxidation of dinoflagellate luciferin by molecular oxygen, resulting in an electronically excited species that emits blue light (lambda(max)=474 nm). Luciferase has three catalytic domains in its single polypeptide chain (M(r)=ca. 140 kDa), and each domain (about 40 kDa) is enzymatically active when expressed individually in recombinant fusion proteins in E. coli. Thus, DL should be useful as a reporter enzyme in studies of gene expression in mammalian cells. Expression plasmids consisting of one domain of luciferase (dDL) cDNA linked to different several promoters were introduced into a series of mammalian cell lines. Following transfection, dDL activities in cell extracts were determined by a rapid light emission assay of luciferase activity. For dual and multiple reporter assays, it is possible to exchange dDL for the firefly or renilla luciferases, and use the new luciferase for control or target reporter genes. Thus, the triple-reporter assay can identify three transcriptional activities of different genes at the same time. This work establishes the DL gene as a new efficient marker of gene expression in mammalian cells.

Molecular evolution of dinoflagellate luciferases, enzymes with three catalytic domains in a single polypeptide

Enzymes with multiple catalytic sites are rare, and their evolutionary significance remains to be established. This study of luciferases from seven dinoflagellate species examines the previously undescribed evolution of such proteins. All these enzymes have the same unique structure: three homologous domains, each with catalytic activity, preceded by an N-terminal region of unknown function. Both pairwise comparison and phylogenetic inference indicate that the similarity of the corresponding individual domains between species is greater than that between the three different domains of each polypeptide. Trees constructed from each of the three individual domains are congruent with the tree of the full-length coding sequence. Luciferase and ribosomal DNA trees both indicate that the Lingulodinium polyedrum luciferase diverged early from the other six. In all species, the amino acid sequence in the central regions of the three domains is strongly conserved, suggesting it as the catalytic site. Synonymous substitution rates also are greatly reduced in the central regions of two species but not in the other five. This lineage-specific difference in synonymous substitution rates in the central region of the domains correlates inversely with the content of GC3, which can be accounted for by the biased usage toward C-ending codons at the degenerate sites. RNA modeling of the central region of the L. polyedrum luciferase domain suggests a function of the constrained synonymous substitutions in the circadian-controlled protein synthesis.