Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates

Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum

Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.

The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum

The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.

Glomerulosomes: morphologically distinct nuclear organelles of unknown nature

The nucleus of some representatives of the genus Pelomyxa (Amoebozoa, Archamoebae, Pelobiontida) contains specific bodies (membrane-less organelles). They may be either embedded in the nucleolar mass or detached from the nucleolus. We termed these nuclear bodies the glomerulosomes for their characteristic ultrastructural appearance. The glomerulosomes are distinct nuclear bodies, about 1 μm in diameter. The morphological and diagnostic unit of a glomerulosome is an electron-dense thread/string, about 30-40 nm in thickness. These threads are not direct continuation of the nucleolar material. The threads create the unique geometric appearance of the glomerulosome by being organized into precisely parallel rows/cords. Each cord of the threads can curve at different angles within the glomerulosome body, but the threads themselves are not coiled. Nowadays, the glomerulosomes have been discovered in P. palustris, P. stagnalis, P. paradoxa, and Pelomyxa sp. Despite the unique appearance of glomerulosomes, their existence may be a more common phenomenon in eukaryotic cells than just a specific feature of the nucleus of elected pelomyxes.

First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

Dinoflagellates are a group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in the nucleus of Gambierdiscus australes. The results showed an increased relative abundance of the different microsatellite motifs with increasing GC content. Two ND-FISH probes, (A)₂₀ and (AAT)₅ , did not yield signals whereas the remainder revealed a dispersed but nonrandom distribution of the microsatellites, mostly in clusters. The bean-shaped interphase nucleus of G. australes contained a region with a high density of trinucleotides. This nuclear compartment was located between the nucleolar organizer region (NOR), located on the concave side of the nucleus, and the convex side. Telomeric DNA was grouped in multiple foci and distributed in two polarized compartments: one associated with the NOR and the other peripherally located along the convex side of the nucleus. Changes in the position of the telomeres during cell division evidenced their dynamic distribution and thus that of the chromosomes during dinomitosis. These insights into the spatial organization of microsatellites and telomeres and thus into the nuclear architecture of G. australes will open up new lines of research into the structure and function of the nucleosome-less chromatin of dinoflagellates.

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum

Dinoflagellates are main primary producers in the oceans, the cause of algal blooms and endosymbionts of marine invertebrates. Much remains to be understood about their biology, including their peculiar crystalline chromosomes. We assembled 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum and analyzed their organization. Genes are enriched towards the ends of chromosomes and are arranged in alternating unidirectional blocks. Some chromosomes are enriched for genes involved in specific biological processes. The chromosomes fold as linear rods and each is composed of a series of structural domains separated by boundaries. Domain boundaries are positioned at sites where transcription of two gene blocks converges and disappear when cells are treated with chemicals that block transcription, indicating correlations between gene orientation, transcription and chromosome folding. The description of the genetic and spatial organization of the S. microadriaticum genome provides a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.

The 5S rRNA genes in Alexandrium: their use as a FISH chromosomal marker in studies of the diversity, cell cycle and sexuality of dinoflagellates

Chromosomal markers of the diversity and evolution of dinoflagellates are scarce because the genomes of these organisms are unique among eukaryotes in terms of their base composition and chromosomal structure. Similarly, a lack of appropriate tools has hindered studies of the chromosomal localization of 5S ribosomal DNA (rDNA) in the nucleosome-less chromosomes of dinoflagellates. In this study, we isolated and cloned 5S rDNA sequences from various toxin-producing species of the genus Alexandrium and developed a fluorescence in situ hybridization (FISH) probe that allows their chromosomal localization. Our results can be summarized as follows: 1) The 5S rDNA unit is composed of a highly conserved 122-bp coding region and an intergenic spacer (IGS), the length and sequence of which are variable even within strains. 2) Three different IGS types, one containing the U6 small nuclear RNA (snRNA) gene, were found among four of the studied species (A. minutum, A. tamarense, A. catenella and A. pacificum). 3) In all strains investigated by FISH (A. minutum, A. tamarense, A. pacificum, A. catenella, A. andersonii and A. ostenfeldii), 5S rDNA gene arrays were separate from the nucleolar organizer region, which contains the genes for the large 45S pre-ribosomal RNA. 4) One to three 5S rDNA sites per haploid genome were detected, depending on the strains/species. Intraspecific variability in the number of 5S rDNA sites was determined among strains of A. minutum and A. pacificum. 5) 5S rDNA is a useful chromosomal marker of mitosis progression and can be employed to differentiate vegetative (haploid) vs. planozygotes (diploid) cells. Thus, the FISH probe (oligo-Dino5Smix5) developed in this study facilitates analyses of the diversity, cell cycle and life stages of the genus Alexandrium.

The cellular landscape of mid-size noncoding RNA

Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates

Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.

Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net

Dinoflagellates are some of the most common eukaryotic cells in the ocean, but have very unusual nuclei. Many exhibit a form of closed mitosis (dinomitosis) wherein the nuclear envelope (NE) invaginates to form one or more trans-nuclear tunnels. Rather than contact spindles directly, the chromatids then bind to membrane-based kinetochores on the NE. To better understand these unique mitotic features, we reconstructed the nuclear architecture of Polykrikos kofoidii in 3D using focused ion beam scanning electron microscopy (FIB-SEM) in conjunction with high-pressure freezing, freeze-substitution, TEM, and confocal microscopy. We found that P. kofoidii possessed six nuclear tunnels, which were continuous with a reticulating network of membranes that has thus far gone unnoticed. These membranous extensions interconnect the six tunnels while ramifying throughout the nucleus to form a “nuclear net.” To our knowledge, the nuclear net is the most elaborate endomembrane structure described within a nucleus. Our findings demonstrate the utility of tomographic approaches for detecting 3D membrane networks and show that nuclear complexity has been underestimated in Polykrikos kofoidii and, potentially, in other dinoflagellates.

Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins

Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates "dinokaryon" have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented.

Impact of light quality and space weather in Alexandrium catenella (Dinophyceae) cultures

The chain-forming dinoflagellate Alexandrium catenella was grown with LED or fluorescent light. With LED light, the pool of mycosporine-like amino acids (MAAs) with strong antioxidant properties, such as mycosporine-glycine and palythene, was reduced in comparison to fluorescent light. The conjugated MAAs M-320 and M-335/360 presented similar stability to light and oxidation than their respective more sensitive moiety: mycosporine-glycine and palythene, respectively. A. catenella was exposed to extracellular hydrogen peroxide under LED or fluorescent light. It triggered an increase in chain formation at a final concentration of 98 and 196 µM, typical of an inverted U-shaped hormetic response, and reduced cell survival above 294 µM. LED light, minimizing UV-stress photoprotection, was chosen to render cells more susceptible to space weather. Cultures were exposed to 490 µM H₂O₂ multiple times between November 2017 and February 2018, close to the minimum of solar cycle 24. Cell survival was dependent on temperature, geomagnetic activity, solar X-rays and neutron flux. Geomagnetic activity originated an inverted U-shaped survival curve and X-ray flux a J-shaped survival curve, this second type of hormetic response being more rarely found. The percentage of cells in chains increased moderately with temperature, and more significantly with solar X-ray flux. Chain formation reduced along culture growth, but these observations were dependent on the occurring X-ray flux.

A novel FISH technique for labeling the chromosomes of dinoflagellates in suspension

Dinoflagellates possess some of the largest known genomes. However, the study of their chromosomes is complicated by their similar size and their inability to be distinguished by traditional banding techniques. Dinoflagellate chromosomes lack nucleosomes and are present in a liquid crystalline state. In addition, approaches such as fluorescent in situ hybridization (FISH) are problematic because chromosomes are difficult to isolate from the nuclear membrane, which in dinoflagellates remains intact, also during mitosis. Here we describe a novel, reliable and effective technique to study dinoflagellate chromosomes by physical mapping of repetitive DNA sequences in chromosomes in suspension (FISH-IS), rather than on a microscope slide. A suspension of non-fixed chromosomes was achieved by lysing the cells and destabilizing the nuclear envelope. This treatment resulted in the release of the permanently condensed chromosomes in a high-quality chromosomal suspension. Nevertheless, slide preparations of the chromosomes were not suitable for conventional FISH because the nuclear integrity and chromosomal morphology was destroyed. Our newly developed, simple and efficient FISH-IS technique employs fluorescently labeled, synthetic short sequence repeats that are hybridized with suspended, acetic-acid-pretreated chromosomes for 1 h at room temperature. The method can be successfully used to discriminate single chromosomes or specific chromosomal regions, depending on the specificity of the repeat sequences used as probes. The combination of FISH-IS and flow sorting will improve genomic studies of dinoflagellates, overcoming the difficulties posed by their huge genomes, including long stretches of non-coding sequences in multiple copies and the presence of high-copy-number tandem gene arrays.

Translation and Translational Control in Dinoflagellates

Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.

A Novel Cyclophilin B Gene in the Red Tide Dinoflagellate Cochlodinium polykrikoides: Molecular Characterizations and Transcriptional Responses to Environmental Stresses

The marine dinoflagellate Cochlodinium polykrikoides is one of the most common ichthyotoxic species that causes harmful algal blooms (HABs), which leads to ecological damage and huge economic loss in aquaculture industries. Cyclophilins (CYPs) belong to the immunophilin superfamily, and they may play a role in the survival mechanisms of the dinoflagellate in stress environments. In the present study, we identified a novel cyclophilin gene from C. polykrikoides and examined physiological and gene transcriptional responses to biocides copper sulphate (CuSO₄) and sodium hypochlorite (NaOCl). The full length of CpCYP was 903 bp, ranging from the dinoflagellate splice leader (DinoSL) sequence to the polyA tail, comprising a 639 bp ORF, a 117 bp 5′-UTR, and a 147 bp 3′-UTR. Motif and phylogenetic comparisons showed that CpCYP was affiliated to group B of CYP. In biocide stressors, cell counts, chlorophyll a, and photosynthetic efficiency (Fv/Fm) of C. polykrikoides were considerably decreased in both exposure time- and dose-dependent manners. In addition, CpCYP gene expression was significantly induced after 24 h exposure to the biocide-treated stress conditions. These results indicate an effect of the biocides on the cell physiology and expression profile of CpCYP, suggesting that the gene may play a role in environmental stress responses.

Whole Transcriptomic Analysis Provides Insights into Molecular Mechanisms for Toxin Biosynthesis in a Toxic Dinoflagellate Alexandrium catenella (ACHK-T)

Paralytic shellfish toxins (PSTs), a group of neurotoxic alkaloids, are the most potent biotoxins for aquatic ecosystems and human health. Marine dinoflagellates and freshwater cyanobacteria are two producers of PSTs. The biosynthesis mechanism of PSTs has been well elucidated in cyanobacteria; however, it remains ambiguous in dinoflagellates. Here, we compared the transcriptome profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) at different toxin biosynthesis stages within the cell cycle using RNA-seq. The intracellular toxin content increased gradually in the middle G1 phase and rapidly in the late G1 phase, and then remained relatively stable in other phases. Samples from four toxin biosynthesis stages were selected for sequencing, and finally yielded 110,370 unigenes, of which 66,141 were successfully annotated in the known databases. An analysis of differentially expressed genes revealed that 2866 genes altered significantly and 297 were co-expressed throughout the four stages. These genes participated mainly in protein metabolism, carbohydrate metabolism, and the oxidation-reduction process. A total of 138 homologues of toxin genes were identified, but they altered insignificantly among different stages, indicating that toxin biosynthesis might be regulated translationally or post-translationally. Our results will serve as an important transcriptomic resource to characterize key molecular processes underlying dinoflagellate toxin biosynthesis.

Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata

The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features.

Dynamics of histone H2A, H4 and HS1ph during spermatogenesis with a focus on chromatin condensation and maturity of spermatozoa

Histones and histone phosphorylation play vital roles during animal spermatogenesis and spermatozoa maturation. The dynamic distribution of histones H2A and H4 and phosphorylated H2A and H4 at serine 1 (HS1ph) was explored in mammalian and Decapoda germ cells, with a special focus on the distribution of H2A, H4 and HS1ph between mouse condensed spermatozoa chromatin and crab non-condensed spermatozoa chromatin. The distribution of histone marks was also analysed in mature spermatozoa with different chromatin structures. Histone H2A and H4 marks were closely associated with the relatively loose chromatin structure in crab spermatozoa. The significant decrease in the HS1ph signal during spermatogenesis suggests that eliminating most of these epigenetic marks in the nucleusis closely associated with spermatozoa maturity.

Uniquely designed nuclear structures of lower eukaryotes

The nuclear structures of lower eukaryotes, specifically protists, often vary from those of yeasts and metazoans. Several studies have demonstrated the unique and fascinating features of these nuclear structures, such as a histone-independent condensed chromatin in dinoflagellates and two structurally distinct nuclear pore complexes in ciliates. Despite their unique molecular/structural features, functions required for formation of their cognate molecules/structures are highly conserved. This provides important information about the structure-function relationship of the nuclear structures. In this review, we highlight characteristic nuclear structures found in lower eukaryotes, and discuss their attractiveness as potential biological systems for studying nuclear structures.

Chromatin Dynamics in Vivo: A Game of Musical Chairs

Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.

Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes

The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

BACKGROUND

Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution.

RESULTS

We identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis. We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum, whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution.

CONCLUSIONS

Overall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates.

The precarious prokaryotic chromosome

Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other "precarious" features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.

Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution

BACKGROUND

The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates. Collectively alveolates are present in virtually every environment and include a vast diversity of cell shapes, molecular and cellular features and feeding modes including lifestyles such as phototrophy, phagotrophy/predation and intracellular parasitism, in addition to a variety of symbiotic associations. Oxyrrhis marina is a well-known model for heterotrophic protist biology, and is now emerging as a useful organism to explore the many changes that occurred during the origin and diversification of dinoflagellates by virtue of its phylogenetic position at the base of the dinoflagellate tree.

RESULTS

We have generated and analysed expressed sequence tag (EST) sequences from the alveolate Oxyrrhis marina in order to shed light on the evolution of a number of dinoflagellate characteristics, especially regarding the emergence of highly unusual genomic features. We found that O. marina harbours extensive gene redundancy, indicating high rates of gene duplication and transcription from multiple genomic loci. In addition, we observed a correlation between expression level and copy number in several genes, suggesting that copy number may contribute to determining transcript levels for some genes. Finally, we analyze the genes and predicted products of the recently discovered Dinoflagellate Viral Nuclear Protein, and several cases of horizontally acquired genes.

CONCLUSION

The dataset presented here has proven very valuable for studying this important group of protists. Our analysis indicates that gene redundancy is a pervasive feature of dinoflagellate genomes, thus the mechanisms involved in its generation must have arisen early in the evolution of the group.

The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome

Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.

Chromatin: packaging without nucleosomes

Dinoflagellates are unique among eukaryotes in their unusual 'dinokaryons' - nuclei that lack bulk histones. A new study finds that acquisition of a novel dinoflagellate chromatin protein was an early step in the transition to a nucleus lacking detectable nucleosomes.

Transcriptional responses of heat shock protein 70 (Hsp70) to thermal, bisphenol A, and copper stresses in the dinoflagellate Prorocentrum minimum

The heat shock protein 70 (Hsp70) family is an important part of the cell's machinery for protein folding, and helps to protect cells from environmental stress. Although Hsp70 functions have been discovered in various organisms, studies on dinoflagellate Hsps are limited, except for a few phylogenetic attempts. In this study, we sequenced the complete open reading frame of the dinoflagellate Prorocentrum minimum Hsp70 (PmHsp70), and characterized its molecular functions. The putative PmHsp70 protein contained 3 signature patterns of the Hsp70 family. Phylogenetic analysis revealed that PmHsp70 belonged to the dinoflagellate clade. Real-time (RT)-PCR analyses revealed that PmHsp70 was upregulated by thermal stress. Further, we examined the transcriptional response of PmHsp70 to copper (Cu) and bisphenol A (BPA) exposures. In toxicity assays, Cu and BPA exhibited EC(50)-72 h values of 1.07 ± 0.138 mg L(-1) and 1.51 ± 0.110 mg L(-1), respectively, in P. minimum. Expression of PmHsp70 was significantly upregulated in response to Cu and BPA exposures (one-way ANOVA, P<0.05). PmHsp70 displayed different expression patterns in response to different concentrations of Cu and BPA. This study evaluated typical characteristics and, for the first time, toxicant-related functions of PmHsp70. The results suggest that Hsp70 genes may play a vital role in the environmental stress responses of dinoflagellates.

Bioactives from microalgal dinoflagellates

Dinoflagellate microalgae are an important source of marine biotoxins. Bioactives from dinoflagellates are attracting increasing attention because of their impact on the safety of seafood and potential uses in biomedical, toxicological and pharmacological research. Here we review the potential applications of dinoflagellate toxins and the methods for producing them. Only sparing quantities of dinoflagellate toxins are generally available and this hinders bioactivity characterization and evaluation in possible applications. Approaches to production of increased quantities of dinoflagellate bioactives are discussed. Although many dinoflagellates are fragile and grow slowly, controlled culture in bioreactors appears to be generally suitable for producing many of the metabolites of interest.

Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

A full suite of histone and histone modifying genes are transcribed in the dinoflagellate Lingulodinium

BACKGROUND

Dinoflagellates typically lack histones and nucleosomes are not observed in DNA spreads. However, recent studies have shown the presence of core histone mRNA sequences scattered among different dinoflagellate species. To date, the presence of all components required for manufacturing and modifying nucleosomes in a single dinoflagellate species has not been confirmed.

METHODOLOGY AND RESULTS

Analysis of a Lingulodinium transcriptome obtained by Illumina sequencing of mRNA shows several different copies of each of the four core histones as well as a suite of histone modifying enzymes and histone chaperone proteins. Phylogenetic analysis shows one of each Lingulodinium histone copies belongs to the dinoflagellate clade while the second is more divergent and does not share a common ancestor. All histone mRNAs are in low abundance (roughly 25 times lower than higher plants) and transcript levels do not vary over the cell cycle. We also tested Lingulodinium extracts for histone proteins using immunoblotting and LC-MS/MS, but were unable to confirm histone expression at the protein level.

CONCLUSION

We show that all core histone sequences are present in the Lingulodinium transcriptome. The conservation of these sequences, even though histone protein accumulation remains below currently detectable levels, strongly suggests dinoflagellates possess histones.

Evaluation and validation of internal control genes for studying gene expression in the dinoflagellate Prorocentrum minimum using real-time PCR

Housekeeping genes (HKGs) are required for the normalization of expression levels in real-time PCR, and their selection is critical for gene expression studies. However, stable expressions of candidate HKGs vary among organisms and tissues and even according to environmental conditions. Here, we evaluated the gene expressions of 10 frequently used HKGs, including 18S rRNA, P2, ACT, TUA, TUB, CYC, eIF4E, MDH, UBQ, and GAPDH, with a total of 17 RNA samples extracted from the dinoflagellate Prorocentrum minimum. All the RNAs were prepared from various cells cultured under different conditions, including thermal shocks, toxic chemical exposures, and different life stages. Via C(T) analyses of the 10 HKGs using the geNorm software, TUA was selected as the most stable HKG for gene expression studies of the dinoflagellate, followed by MDH. Pair-wise variation (V) analysis showed that at least 2 genes were required for accurate normalization of gene expression studies depending on the experimental conditions. These HKGs are useful internal controls for the normalization of gene expression in P. minimum.

Comparative genomic and transcriptomic characterization of the toxigenic marine dinoflagellate Alexandrium ostenfeldii

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins.

Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data

The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Pentapharsodinium and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.

Evolution of light-harvesting complex proteins from Chl c-containing algae

Background

Light harvesting complex (LHC) proteins function in photosynthesis by binding chlorophyll (Chl) and carotenoid molecules that absorb light and transfer the energy to the reaction center Chl of the photosystem. Most research has focused on LHCs of plants and chlorophytes that bind Chl a and b and extensive work on these proteins has uncovered a diversity of biochemical functions, expression patterns and amino acid sequences. We focus here on a less-studied family of LHCs that typically bind Chl a and c, and that are widely distributed in Chl c-containing and other algae. Previous phylogenetic analyses of these proteins suggested that individual algal lineages possess proteins from one or two subfamilies, and that most subfamilies are characteristic of a particular algal lineage, but genome-scale datasets had revealed that some species have multiple different forms of the gene. Such observations also suggested that there might have been an important influence of endosymbiosis in the evolution of LHCs.

Results

We reconstruct a phylogeny of LHCs from Chl c-containing algae and related lineages using data from recent sequencing projects to give ~10-fold larger taxon sampling than previous studies. The phylogeny indicates that individual taxa possess proteins from multiple LHC subfamilies and that several LHC subfamilies are found in distantly related algal lineages. This phylogenetic pattern implies functional differentiation of the gene families, a hypothesis that is consistent with data on gene expression, carotenoid binding and physical associations with other LHCs. In all probability LHCs have undergone a complex history of evolution of function, gene transfer, and lineage-specific diversification.

Conclusion

The analysis provides a strikingly different picture of LHC diversity than previous analyses of LHC evolution. Individual algal lineages possess proteins from multiple LHC subfamilies. Evolutionary relationships showed support for the hypothesized origin of Chl c plastids. This work also allows recent experimental findings about molecular function to be understood in a broader phylogenetic context.

Trans-splicing

Trans-splicing is the joining together of portions of two separate pre-mRNA molecules. The two distinct categories of spliceosomal trans-splicing are genic trans-splicing, which joins exons of different pre-mRNA transcripts, and spliced leader (SL) trans-splicing, which involves an exon donated from a specialized SL RNA. Both depend primarily on the same signals and components as cis-splicing. Genic trans-splicing events producing protein-coding mRNAs have been described in a variety of organisms, including Caenorhabditis elegans and Drosophila. In mammalian cells, genic trans-splicing can be associated with cancers and translocations. SL trans-splicing has mainly been studied in nematodes and trypanosomes, but there are now numerous and diverse phyla (including primitive chordates) where this type of trans-splicing has been detected. Such diversity raises questions as to the evolutionary origin of the process. Another intriguing question concerns the function of trans-splicing, as operon resolution can only account for a small proportion of the total amount of SL trans-splicing.

Characterization and heterologous expression of a new matrix attachment region binding protein from the unicellular green alga Dunaliella salina

Although interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) are implicated in various nuclear functions, the understanding of the regulatory mechanism of MARs is still poor. A few MAR-binding proteins (MARBP) have been isolated from some plants and animals, but not from the unicellular algae. Here, we identify a novel MAR-binding protein, namely DMBP-1, from the halotolerant alga Dunaliella salina. The cDNA of DMBP-1 is 2322-bp long and contains a 1626 bp of an open reading frame encoding a polypeptide of 542 amino acids (59 kDa). The DMBP-1 expressed in Escherichia coli specifically binds A/T-rich MAR DNA. The DMBP-1 fused to green fluorescent protein appears only inside the nuclei of Chinese hamster ovarian cells transfected with the pEGFP-MBP, indicating that the protein is located in the nuclei. The findings mentioned above may contribute to better understanding of the nuclear matrix-MAR interactions.

The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms

BACKGROUND

The phenotype of an organism is an outcome of both its genotype, encoding the primary sequence of proteins, and the developmental orchestration of gene expression. The substrate of gene expression in eukaryotes is the chromatin, whose fundamental units are nucleosomes composed of DNA wrapped around each two of the core histone types H2A, H2B, H3 and H4. Key regulatory steps involved in the determination of chromatin conformations are posttranslational modifications (PTM) at histone tails as well as the assembly of histone variants into nucleosomal arrays. Although the mechanistic background is fragmentary understood, it appears that the chromatin signature of metazoan cell types is inheritable over generations. Even less understood is the conservation of epigenetic mechanisms among eukaryotes and their origins.

RESULTS

In the light of recent progress in understanding the tree of eukaryotic life we discovered the origin of histone H3 by phylogenetic analyses of variants from all supergroups, which allowed the reconstruction of ancestral states. We found that H3 variants evolved frequently but independently within related species of almost all eukaryotic supergroups. Interestingly, we found all core histone types encoded in the genome of a basal dinoflagellate and H3 variants in two other species, although is was reported that dinoflagellate chromatin is not organized into nucleosomes.Most probably one or more animal/nuclearid H3.3-like variants gave rise to H3 variants of all opisthokonts (animals, choanozoa, fungi, nuclearids, Amoebozoa). H3.2 and H3.1 as well as H3.1t are derivatives of H3.3, whereas H3.2 evolved already in early branching animals, such as Trichoplax. H3.1 and H3.1t are probably restricted to mammals.We deduced a model for protoH3 of the last eukaryotic common ancestor (LECA) confirming a remarkable degree of sequence conservation in comparison to canonical human H3.1. We found evidence that multiple PTMs are conserved even in putatively early branching eukaryotic taxa (Euglenozoa/Excavata).

CONCLUSIONS

At least a basal repertoire of chromatin modifying mechanisms appears to share old common ancestry and may thus be inherent to all eukaryotes. We speculate that epigenetic principles responsive to environmental triggers may have had influenced phenotypic variation and concomitantly may potentially have had impact on eukaryotic diversification.

Functional nuclear architecture studied by microscopy: present and future

In this review we describe major contributions of light and electron microscopic approaches to the present understanding of functional nuclear architecture. The large gap of knowledge, which must still be bridged from the molecular level to the level of higher order structure, is emphasized by differences of currently discussed models of nuclear architecture. Molecular biological tools represent new means for the multicolor visualization of various nuclear components in living cells. New achievements offer the possibility to surpass the resolution limit of conventional light microscopy down to the nanometer scale and require improved bioinformatics tools able to handle the analysis of large amounts of data. In combination with the much higher resolution of electron microscopic methods, including ultrastructural cytochemistry, correlative microscopy of the same cells in their living and fixed state is the approach of choice to combine the advantages of different techniques. This will make possible future analyses of cell type- and species-specific differences of nuclear architecture in more detail and to put different models to critical tests.

Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum

Background

The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin gene cluster has recently been characterized in cyanobacteria, the genetic background of PSP toxin production in dinoflagellates remains elusive.

Results

We constructed and analysed an expressed sequence tag (EST) library of A. minutum, which contained 15,703 read sequences yielding a total of 4,320 unique expressed clusters. Of these clusters, 72% combined the forward-and reverse reads of at least one bacterial clone. This sequence resource was then used to construct an oligonucleotide microarray. We analysed the expression of all clusters in three different strains. While the cyanobacterial PSP toxin genes were not found among the A. minutum sequences, 192 genes were differentially expressed between toxic and non-toxic strains.

Conclusions

Based on this study and on the lack of identified PSP synthesis genes in the two existent Alexandrium tamarense EST libraries, we propose that the PSP toxin genes in dinoflagellates might be more different from their cyanobacterial counterparts than would be expected in the case of a recent gene transfer. As a starting point to identify possible PSP toxin-associated genes in dinoflagellates without relying on a priori sequence information, the sequences only present in mRNA pools of the toxic strain can be seen as putative candidates involved in toxin synthesis and regulation, or acclimation to intracellular PSP toxins.

Paternal DNA packaging in spermatozoa: more than the sum of its parts? DNA, histones, protamines and epigenetics

Haploid male germ cells package their DNA into a volume that is typically 10% or less that of a somatic cell nucleus. To achieve this remarkable level of compaction, spermatozoa replace most of their histones with smaller, highly basic arginine and (in eutherians) cysteine rich protamines. One reason for such a high level of compaction is that it may help optimise nuclear shape and hence support the gametes' swimming ability for the long journey across the female reproductive tract to the oocyte. Super-compaction of the genome may confer additional protection from the effects of genotoxic factors. However, many species including the human retain a fraction of their chromatin in the more relaxed nucleosomal configuration that appears to run counter to the ergonomic, toroidal and repackaging of sperm DNA. Recent research suggests that the composition of this 'residual' nucleosomal compartment, a generally overlooked feature of the male gamete, is far more significant and important than previously thought. In this respect, the transport and incorporation of modified paternal histones by the spermatozoon to the zygote has been demonstrated and indicates another potential paternal effect in the epigenetic reprogramming of the zygote following fertilisation that is independent of imprinting status. In this review, the most recent research into mammalian spermatozoal chromatin composition is discussed alongside evidence for conserved, non-randomly located nucleosomal domains in spermatozoal nuclei, all supporting the hypothesis that the spermatozoon delivers a novel epigenetic signature to the egg that may be crucial for normal development. We also provide some thoughts on why this signature may be required in early embryogenesis.

The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes

The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.

Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin

Non-coding RNAs (ncRNAs) play an important role in a variety of nuclear processes, including genetic imprinting, RNA interference-mediated transcriptional repression, and dosage compensation. These transcripts are thought to influence chromosome organization and, in some cases, gene expression by directing the assembly of specific chromatin modifications to targeted regions of the genome. In the malaria parasite Plasmodium falciparum, little is known about the regulation of nuclear organization or gene expression, although a notable scarcity of identifiable transcription factors encoded in its genome has led to speculation that this organism may be unusually reliant on chromatin modifications as a mechanism for regulating gene expression. To study the mechanisms that regulate chromatin structure in malaria parasites, we examined the role of ncRNAs in the assembly of chromatin at the centromeres of P. falciparum. We show that centromeric regions within the Plasmodium genome contain bidirectional promoter activity driving the expression of short ncRNAs that are localized within the nucleus and appear to associate with the centromeres themselves, strongly suggesting that they are central characters in the maintenance and function of centromeric chromatin. These observations support the hypothesis that ncRNAs play an important role in the proper organizational assembly of chromatin in P. falciparum, perhaps compensating for a lack of both regulatory transcription factors and RNA interference machinery.

Spliced Leader RNA-Mediated trans-Splicing in a Dinoflagellate, Karenia brevis

Spliced leader (SL) trans-splicing is a form of mRNA processing originally described in parasitic kinetoplastids. During this reaction, a short RNA sequence is transferred from the 5'-end of an SL transcript to a splice acceptor site on pre-mRNA molecules. Here we report numerous mRNAs from a dinoflagellate, Karenia brevis, which contain an identical leader sequence at their 5'-terminal end. Furthermore, we have isolated a gene from K. brevis encoding a putative SL RNA containing the conserved splice donor site immediately following the leader sequence. A 1,742-bp DNA fragment encoding a K. brevis 5S gene repeat was found to encode the SL RNA gene, as well as a U6 small nuclear RNA (snRNA) gene, and binding sites for the core components of the splicesome (Sm proteins) involved in RNA splicing. Therefore the K. brevis SL RNA appears to be in a genomic arrangement typical of SL genes in a number of species known to mature their mRNAs by trans-splicing. Additionally, we show that the SL gene exists as a stable snRNA and has a predicted secondary structure typical of SL RNAs. The data presented here support the hypothesis that an SL RNA is present in K. brevis and that maturation of a percentage of mRNAs in K. brevis occurs via a trans-splicing process in which a common SL sequence is added to the 5'-end of mature mRNAs. The occurrence of SL trans-splicing in a dinoflagellate extends the known phylogenetic range of this process.

A dinoflagellate AAA family member rescues a conditional yeast G1/S phase cyclin mutant through increased CLB5 accumulation

An AAA protein from the dinoflagellate Gonyaulax polyedra (GpAAA) with the unusual ability to rescue the phenotype of a yeast mutant lacking G1/S phase cyclins (cln1cln2cln3) has been isolated and the mechanism of rescue was characterized. We find that GpAAA is not a cyclin and has no similarity to any known cell cycle regulators. Instead, GpAAA forms a novel and strongly supported clade with bacterial spoIIIAA proteins and an Arabidopsis gene of unknown function. Since dinoflagellates cannot be transformed, we took advantage of the powerful genetic tools available for yeast. We find that rescue of the cln1cln2cln3 phenotype does not involve an effect on the CDK-inhibitor (CKI) Sic1p, as GpAAA does not alter the sensitivity to an inducible SIC1. Instead, Northern blot analyses show that GpAAA expression increases levels of CLB5, in agreement with the observation that GpAAA is unable to rescue the quadruple mutant cln1cln2cln3clb5. We propose that the increased transcription of CLB5 may be due to a protein remodeling function of GpAAA alleviating inhibition of the transcription factor SBF. Thus, although no known equivalents to the yeast SBF have been documented in dinoflagellates, we conclude that dinoflagellates could indeed utilize GpAAA as a cell cycle regulator.

Telomeric DNA localization on dinoflagellate chromosomes: structural and evolutionary implications

Dinoflagellates are eukaryotic microalgae with distinct chromosomes throughout the cell cycle which lack histones and nucleosomes. The molecular organization of these chromosomes is still poorly understood. We have analysed the presence of telomeres in two evolutionarily distant and heterogeneous dinoflagellate species (Prorocentrum micans and Amphidinium carterae) by FISH with a probe containing the Arabidopsis consensus telomeric sequence. Telomere structures were identified at the chromosome ends of both species during interphase and mitosis and were frequently associated with the nuclear envelope. These results identify for the first time telomere structures in dinoflagellate chromosomes, which are formed in the absence of histones. The presence of telomeres supports the linear nature of dinoflagellate chromosomes.

Topology of splicing and snRNP biogenesis in dinoflagellate nuclei

BACKGROUND INFORMATION

Dinoflagellates are protists that are hypothesized to have experienced a secondary loss of histones. Amongst eukaryotes, they are unique in lacking these proteins. To date, information on the mechanisms involving remodelling, transcription and splicing of their chromatin is limited. Dinoflagellate genes lack TATA boxes and downstream polyadenylation sites and particular linear arrangements. They have an alpha-amanitin-sensitive RNA polymerase, specific transcription factors and regulators, and both transcriptional and post-transcriptional regulation of gene expression. Dinoflagellates produce either polycistronic or discrete mRNAs, and have conserved snRNAs (small nuclear RNAs), indicating that their genes are spliced.

RESULTS

Five representative dinoflagellate species (Amphidinium carterae, Akashiwo sanguinea, Alexandrium lusitanicum, Alexandrium fundyense and Prorocentrum micans), which show diversity in their DNA content, nuclear organization and taxonomic position, were investigated. The nuclear distribution and ultrastructural organization of splicing and snRNP (small nuclear ribonucleoprotein) biogenesis were determined by fluorescent and electron microscopy immunolabelling with Y12 sera [recognizing the sDMA (symmetrical dimethylarginine) domain of Sm and other nuclear proteins], anti-p105-PANA [proliferation-associated nuclear antigen; a marker of IGs (interchromatin granules)] and anti-DNA antibodies. In parallel, ultrastructural analysis, including cytochemical staining for RNA, phosphorylated proteins and DNA, was carried out. Splicing factors were distributed in a diffuse perichromosomal layer containing perichromatin granules and fibrils that co-localized with the decondensed peripheral DNA loops, but not with the main chromosome body. Interchromosomal domains with IGs and Cajal-like bodies were also detected.

CONCLUSIONS

Dinoflagellates are rather dissimilar to other eukaryotes in their genomes, their mechanisms of gene expression and their chromosome ultrastructure. However, they share common splicing nuclear domains and snRNP biogenesis with that of other eukaryotes.