Location of B- and Z-DNA in the chromosomes of a primitive eukaryote dinoflagellate

Multifaceted Dinoflagellates and the Marine Model Prorocentrum cordatum

BACKGROUND

Dinoflagellates are a monophyletic group within the taxon Alveolata, which comprises unicellular eukaryotes. Dinoflagellates have long been studied for their organismic and morphologic diversity as well as striking cellular features. They have a main size range of 10-100 µm, a complex "cell covering", exceptionally large genomes (∼1-250 Gbp with a mean of 50,000 protein-encoding genes) spread over a variable number of highly condensed chromosomes, and perform a closed mitosis with extranuclear spindles (dinomitosis). Photosynthetic, marine, and free-living Prorocentrum cordatum is a ubiquitously occurring, bloom-forming dinoflagellate, and an emerging model system, particularly with respect to systems biology.

SUMMARY

Focused ion beam/scanning electron microscopy (FIB/SEM) analysis of P. cordatum recently revealed (i) a flattened nucleus with unusual structural features and a total of 62 tightly packed chromosomes, (ii) a single, barrel-shaped chloroplast devoid of grana and harboring multiple starch granules, (iii) a single, highly reticular mitochondrion, and (iv) multiple phosphate and lipid storage bodies. Comprehensive proteomics of subcellular fractions suggested (i) major basic nuclear proteins to participate in chromosome condensation, (ii) composition of nuclear pores to differ from standard knowledge, (iii) photosystems I and II, chloroplast complex I, and chlorophyll a-b binding light-harvesting complex to form a large megacomplex (>1.5 MDa), and (iv) an extraordinary richness in pigment-binding proteins. Systems biology-level investigation of heat stress response demonstrated a concerted down-regulation of CO2-concentrating mechanisms, CO2-fixation, central metabolism, and monomer biosynthesis, which agrees with reduced growth yields.

KEY MESSAGES

FIB/SEM analysis revealed new insights into the remarkable subcellular architecture of P. cordatum, complemented by proteogenomic unraveling of novel nuclear structures and a photosynthetic megacomplex. These recent findings are put in the wider context of current understanding of dinoflagellates.

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.

Targeted volume correlative light and electron microscopy of an environmental marine microorganism

Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.

Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions

As is true for many other aspects, genome architecture, evolution, and function in dinoflagellates are enigmatic and, in the meantime, continuous inspiration for scientific quests. Recent third-generation sequencing and Hi-C linkage analyses brought new insights into the spatial organization of symbiodiniacean genomes, revealing the topologically associated domains, discrete gene clusters and their cis and trans orientations, and relationships with transcription. Where do these new findings bring us in dinoflagellate genomics? Here, we aim to place these new results in the backdrop of the long history of research on this topic and in the context of what critical questions remain to be pursued in the future. The new data suggest, pending verification of other complete chromosome assemblies, a potential evolutionary trend in chromosome number decrease and length increase within the Symbiodiniaceae. While questions remain about the mechanics of the three-dimensional chromosome structure and cell cycle-related DNA replication, the mechanisms of gene transcription and genome size evolution, these latest findings set new starting points for further inquiries.

The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin

DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling and is considered to be transient. To determine whether the presence of Z-DNA can be detected immunochemically, the binding of monoclonal and polyclonal anti-Z-DNA antibodies to a panel of natural DNA antigens was assessed by an ELISA using brominated poly(dG-dC) as a control for Z-DNA. As these studies showed, among natural DNA tested (Micrococcus luteus, calf thymus, Escherichiacoli, salmon sperm, lambda phage), micrococcal (MC) DNA showed the highest binding with both anti-Z-DNA preparations, and E. coli DNA showed binding with the monoclonal anti-DNA preparation. The specificity for Z-DNA conformation in MC DNA was demonstrated by an inhibition binding assay. An algorithm to identify propensity to form Z-DNA indicated that DNA from Mycobacterium tuberculosis could form Z-DNA, a prediction confirmed by immunoassay. Together, these findings indicate that anti-Z-DNA antibodies can serve as probes for the presence of Z-DNA in DNA of various species origin and that the content of Z-DNA varies significantly among DNA sources.

Protistology and Cell Biology at the Marine Arago Laboratory of Banyuls-sur-Mer (1961-2000): Personal Recollections

The history of protistology and the introduction of modern methods of unicell observations is described in a large maritime laboratory over a period of forty years by the initiator of this new team. The development of this team and the doctoral theses developed there are described as well as the major discoveries made. The Arago Laboratory, which was then in 1960 a field laboratory mainly devoted to the collection of biological material, becomes a research laboratory specializing in the study of the major fundamental problems which govern life: the organization and expression of the genome, mitotic processes and their nuclear and cytoplasmic components, cell cycle and its regulation as well as molecular phylogeny. The biological models chosen were essentially the dinoflagellate protists in their great variety: autotrophs, heterotrophs, myxotrophs and able of proliferating at sea, thus disrupting their cell cycle. Coupled with the techniques of biochemistry and molecular biology which it was in its infancy, the most advanced observation methods used electron and confocal microscopy often after use of ultra-cold cryopreparations, necessary to preserve the antigenic sites and allow the highlighting new proteins. The dinoflagellate model was then abandoned in favor of unicellular micro-eukaryotes allowing the development of environmental genomics.

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.

Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes

Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.

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.

Effects of the bacterial algicide IRI-160AA on cellular morphology of harmful dinoflagellates

The algicide, IRI-160AA, induces mortality in dinoflagellates but not other species of algae, suggesting that a shared characteristic or feature renders this class of phytoplankton vulnerable to the algicide. In contrast to other eukaryotic species, the genome of dinoflagellates is stabilized by high concentrations of divalent cations and transition metals and contains large amounts of DNA with unusual base modifications. These distinctions set dinoflagellates apart from other phytoplankton and suggest that the nucleus may be a dinoflagellate-specific target for IRI-160AA. In this study, morphological and ultrastructural changes in three dinoflagellate species, Prorocentrum minimum, Karlodinium veneficum and Gyrodinium instriatum, were evaluated after short-term exposure to IRI-160AA using super resolution structured illumination microscopy (SR-SIM) and transmission electron microscopy (TEM). Exposure to the algicide resulted in cytoplasmic membrane blebbing, differing chloroplast morphologies, nuclear expansion, and chromosome expulsion and/or destabilization. TEM analysis showed that chromosomes of algicide-treated K. veneficum appeared electron dense with fibrous protrusions. In algicide-treated P. minimum and G. instriatum, chromosome decompaction occurred, while for P. minimum, nuclear expulsion was also observed for several cells. Results of this investigation demonstrate that exposure to the algicide destabilizes dinoflagellate chromosomes, although it was not clear if the nucleus was the primary target of the algicide or if the observed effects on chromosomal structure were due to downstream impacts. In all cases, changes in cellular morphology and ultrastructure were observed within two hours, suggesting that the algicide may be an effective and rapid approach to mitigate dinoflagellate blooms.

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.

Methods for studying the nuclei and chromosomes of dinoflagellates

Dinoflagellates are unicellular eukaryotic organisms whose nuclear structure, chromosome architecture, chromatin organization, DNA composition, and mitosis show original features. It has been necessary to adapt techniques and to create innovative methods for growing cells, isolating nuclei, and studies of their chromosomes by transmission electron microscope (TEM). Among these are innovative squash and whole-mount preparations for light and TEM observations of chromosome architecture and the spatial organization of nucleofilaments. Particular attention was given to adapt high-pressure freezing (fast-freeze fixation) techniques for the best preservation of delicate antigenic sites, and good immunodetection. The study of DNA replication with or without incorporation of bromodeoxyuridine (BrdU) was also refined to use confocal laser scanning microscopy. In this chapter, we describe methods that we have invented and/or improved from existing techniques in order to better understand this fragile chromosome architecture and the mechanisms intervening during mitosis and the cell cycle. These methods allowed us to detect specific DNA-binding proteins and the distribution of B-and Z-DNA in chromosomes during the cell cycle and mitosis, and to focus on the indissoluble link between chromosome structure and function.

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.

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

Dinoflagellates are fascinating protists that have attracted researchers from different fields. The free-living species are major primary producers and the cause of harmful algal blooms sometimes associated with red tides. Dinoflagellates lack histones and nucleosomes and present a unique genome and chromosome organization, being considered the only living knockouts of histones. Their plastids contain genes organized in unigenic minicircles. Basic cell structure, biochemistry and molecular phylogeny place the dinoflagellates firmly among the eukaryotes. They have G1-S-G2-M cell cycles, repetitive sequences, ribosomal genes in tandem, nuclear matrix, snRNAs, and eukaryotic cytoplasm, whereas their nuclear DNA is different, from base composition to chromosome organization. They have a high G + C content, highly methylated and rare bases such as 5-hydroxymethyluracil (HOMeU), no TATA boxes, and form distinct interphasic dinochromosomes with a liquid crystalline organization of DNA, stabilized by metal cations and structural RNA. Without histones and with a protein:DNA mass ratio (1:10) lower than prokaryotes, they need a different way of packing their huge amounts of DNA into a functional chromatin. In spite of the high interest in the dinoflagellate system in genetics, molecular and cellular biology, their analysis until now has been very restricted. We review here the main achievements in the characterization of the genome, nucleus and chromosomes in this diversified phylum. The recent discovery of a eukaryotic structural and functional differentiation in the dinochromosomes and of the organization of gene expression in them, demonstrate that in spite of the secondary loss of histones, that produce a lack of nucleosomal and supranucleosomal chromatin organization, they keep a functional nuclear organization closer to eukaryotes than to prokaryotes.

Insights into a dinoflagellate genome through expressed sequence tag analysis

Background

Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

Results

Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion

This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

Architecture and evolution of dinoflagellate chromosomes: an enigmatic origin

Dinoflagellates are a highly diversified group of unicellular protists that present fascinating nuclear features which have intrigued researchers for many years. As examples, a dense nuclear matrix accommodates permanently condensed chromosomes that are composed of fibers organized without histones and nucleosomes in stacked rows of parallel nested arches. The macromolecular chromosome structure corresponds to cholesteric liquid crystals with a constant left-handed twist. RNA acts to maintain the chromosome structure. Whole mounted chromosomes have a left-handed screw-like configuration with coils which progressively increase their pitch. This helical arrangement seems to be the result of a couple of narrow strands coiling together. Chromosomes do not show Q, G and C banding patterns. However, a roughly spherical differentiated upper end (primitive kinetochore?) and two differentiated coiling regions, the upper one composed of two to three coils where a couple of sister strands run together and parallel to each other, and the lower one where sister strands run out of phase by 180 degrees angular difference along the immediate next turns, can be distinguished. The chromosome segregation into two daughter chromatids begins at the telomere that attaches to the nuclear envelope, follows along the chromosome axis constituting first a Y-shaped and afterwards a V-shaped chromosome, which packs the newly synthesized DNA inside the "old" chromosome. Dividing chromosomes remain highly condensed, and the diameters of the new chromatids and the undivided chromosome are similar, but the number of arches is twice as large in G1 as in G2. The nuclear envelope remains through the cell cycle and shows spindle fibers, which penetrate intranuclear cytoplasmic channels during mitosis constituting an extra nuclear spindle. These and other cytogenetic features suggest that dinoflagellates are a group of enigmatic protists, unique and different from the usual eukaryotes. In contrast, DNA sequence studies propose that dinoflagellates are true eukaryotes, closely related to Apicomplexa, and ciliates (Alveolata), suggesting that the unusual features of chromosome and nuclear organization are not primitive but derived characters. Nevertheless, dinoflagellates have reached enigmatic specific nuclear and chromosome solutions, extremely far from those of other living beings.

Proliferation of dinoflagellates: blooming or bleaching

The dinoflagellates, a diverse sister group of the malaria parasites, are the major agents causing harmful algal blooms and are also the symbiotic algae of corals. Dinoflagellate nuclei differ significantly from other eukaryotic nuclei by having extranuclear spindles, no nucleosomes and enormous genomes in liquid crystal states. These cytological characteristics were related to the acquisition of prokaryotic genes during evolution (hence Mesokaryotes), which may also account for the biochemical diversity and the relatively slow growth rates of dinoflagellates. The fact that the proliferation of many dinoflagellates is sensitive to turbulence may be due to the physiological requirements of the genome's liquid crystal states. Mechanical stress and anti-microtubule drugs induce cell cycle arrest mainly in G1, implicating a role for the permanent cortical microtubular cytoskeleton in mechanotransduction. The cell cycles of photosynthetic dinoflagellates are also gated by the circadian rhythm, with cell division occurring mainly at the end of the dark phase. Cell growth and the biosynthesis of many toxins occur during the light phase, corresponding to G1 in the cell cycle. The dinoflagellates also embody several options for coupling cell cycle progression to cell growth, enabling them to make the best use of available resources and possibly preparing them for a symbiotic existence.

Dinoflagellates: a remarkable evolutionary experiment

In this paper, we focus on dinoflagellate ecology, toxin production, fossil record, and a molecular phylogenetic analysis of hosts and plastids. Of ecological interest are the swimming and feeding behavior, bioluminescence, and symbioses of dinoflagellates with corals. The many varieties of dinoflagellate toxins, their biological effects, and current knowledge of their origin are discussed. Knowledge of dinoflagellate evolution is aided by a rich fossil record that can be used to document their emergence and diversification. However, recent biogeochemical studies indicate that dinoflagellates may be much older than previously believed. A remarkable feature of dinoflagellates is their unique genome structure and gene regulation. The nuclear genomes of these algae are of enormous size, lack nucleosomes, and have permanently condensed chromosomes. This chapter reviews the current knowledge of gene regulation and transcription in dinoflagellates with regard to the unique aspects of the nuclear genome. Previous work shows the plastid genome of typical dinoflagellates to have been reduced to single-gene minicircles that encode only a small number of proteins. Recent studies have demonstrated that the majority of the plastid genome has been transferred to the nucleus, which makes the dinoflagellates the only eukaryotes to encode the majority of typical plastid genes in the nucleus. The evolution of the dinoflagellate plastid and the implications of these results for understanding organellar genome evolution are discussed.

First evidence to show the topological change of DNA from B-dNA to Z-DNA conformation in the hippocampus of Alzheimer's brain

Alzheimer's disease (AD) is a complex neurodegenerative disorder. Our studies for the first time showed evidence for altered DNA conformation in the hippocampus of Alzheimer's disease affected brain. The Circular dichroism spectra of severely affected AD DNA showed a typical left-handed Z-DNA conformation, whereas normal, young, and aged brain DNA have the usual B-DNA conformation. Moderately affected AD DNA has modified B-DNA conformation (probable B-Z intermediate form). The ELISA, ethidium bromide binding pattern to DNA and melting temperature (Tm) profiles also revealed the conformational transition from B to Z DNA in AD brain DNA. The altered conformation of DNA will have tremendous implications in gene expressions.

Morphology and behaviour of dinoflagellate chromosomes during the cell cycle and mitosis

The morphology and behaviour of the chromosomes of dinoflagellates during the cell cycle appear to be unique among eukaryotes. We used synchronized and aphidicolin-blocked cultures of the dinoflagellate Crypthecodinium cohnii to describe the successive morphological changes that chromosomes undergo during the cell cycle. The chromosomes in early G(1) phase appeared to be loosely condensed with numerous structures protruding toward the nucleoplasm. They condensed in late G(1), before unwinding in S phase. The chromosomes in cells in G(2) phase were tightly condensed and had a double number of arches, as visualised by electron microscopy. During prophase, chromosomes elongated and split longitudinally, into characteristic V or Y shapes. We also used confocal microscopy to show a metaphase-like alignment of the chromosomes, which has never been described in dinoflagellates. The metaphase-like nucleus appeared flattened and enlarged, and continued to do so into anaphase. Chromosome segregation occurred via binding to the nuclear envelope surrounding the cytoplasmic channels and microtubule bundles. Our findings are summarized in a model of chromosome behaviour during the cell cycle.

Ultrastructural methods for nucleic acid detection by immunocytology

In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.

Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks

CD spectroscopy was used to analyze conformational properties of a self-complementary 54-mer DNA composed of alternating (CG)3 and (TA)3 hexamers. NaCl induced the Z-form in poly(GC), but the 54-mer remained the B-form under the same conditions. The B-Z transition was induced only after the addition of NiCl2. However, the Z-form was adopted by the whole molecule, not by the (CG)3 blocks alone. Two orders of magnitude higher concentrations of NiCl2 were required to induce the Z-form in poly(AT). The Z-form was also induced in poly(GC) by CsF that switched poly(AT) into the X-form, which seems to be a solution counterpart of D-DNA. Under these conditions the CD spectrum of the 54-mer was consistent with the (TA)3 blocks being in the X-form and the (CG)3 blocks in the B-form. At high concentrations of ethanol or trifluoroethanol, poly(AT) was an A-form, while poly(GC) adopted either Z-form, A-form or Z'-form. At the high trifluoroethanol concentrations the 54-mer cooperatively switched into a conformation whose CD spectrum was most consistent with the A-form in the (TA)3 blocks and the Z'-form in the (CG)3 blocks. This suggests that the base pairs are tilted in the Z'-form as in the A-form. The present article illustrates that CD spectroscopy can provide interesting pieces of information about conformational isomerizations and coexistence of multiple conformations in DNA molecules containing blocks of different simple sequence repeats.

Cyclic expression of a nuclear protein in a dinoflagellate

Nuclei of the dinoflagellate Crypthecodinium cohnii strain Whd were isolated and nuclear proteins were extracted in three fractions, corresponding to the increasing affinity of these proteins to genomic DNA. One fraction contained two major bands (48- and 46-kDa) and antibodies specific to this fraction revealed two major bands by Western blot on nuclear extracts, corresponding to the 46- and 48-kDa bands. The 48-kDa protein was detected in G1 phase but not in M phase cells. An expression cDNA library of C. cohnii was screened with these antibodies, and two different open reading frames were isolated. Dinoflagellate nuclear associated protein (Dinap1), one of these coding sequences, was produced in E. coli and appeared to correspond to the 48-kDa nuclear protein. No homologue of this sequence was found in the data bases, but two regions were identified, one including two putative zinc finger repeats, and one coding for two potential W/W domains. The second coding sequence showed a low similarity to non-specific sterol carrier proteins. Immunocytolocalization with specific polyclonal antibodies to recombinant Dinap1 showed that the nucleus was immunoreactive only during the G1 phase: the nucleoplasm was immunostained, while chromosome cores and nuclear envelopes were negative.

Localization of B-DNA and Z-DNA in terminally differentiating fiber cells in the adult lens

We examined histochemically and immunohistochemically the distribution of B- and Z-DNA in the epithelium and terminally differentiating dog lens fiber cells. On the basis of anti-DNA antibody reactivity, qualitative and quantitative data on B- and Z-DNA in cells were determined. Anti-B-DNA immunoreactivity gradually declined throughout nucleated fibers, with a precipitous decrease at approximately 90 microns. Anti-Z-DNA antibody binding decreased with a sudden loss of immunoreactivity at approximately 90 microns. The pattern of anti-B- and Z-DNA staining correlates with the loss of alpha-crystallin immunoreactivity, the major lens crystallin, and decreased eosin staining of proteins. Germinative zone cell nuclei showed the highest DNA probe binding values, followed by the superficial fibers, central zone, middle fibers, and deep fibers. The presence of single-stranded (ss)DNA in deeper fibers was detected by anti-ss-DNA antibodies. This is indicative of DNA degradation. These observations suggest that a dramatic reorganization of lens fiber cells' supramolecular order occurs at approximately 90 microns, the phase transition zone.

Dinoflagellates have a eukaryotic nuclear matrix with lamin-like proteins and topoisomerase II

Unicellular Dinoflagellates represent the only eukaryotic Phylum lacking histones and nucleosomes. To investigate whether Dinoflagellates do have a nuclear matrix that would modulate the supramolecular organization of their non-nucleosomal DNA and chromosomes, cells of the free-living unarmored Dinoflagellate Amphidinium carterae were encapsulated in agarose microbeads and submitted to sequential extraction with non-ionic detergents, nucleases and 2 M NaCl. Our results demonstrate that this species has a residual nuclear matrix similar to that of vertebrates and higher plants. The cytoskeleton-nuclear matrix complex of A. carterae shows a relatively intricate polypeptide pattern. Immunoblots with different antibodies reveal several intermediate filament types of proteins, one of which is immunologically related to vertebrate lamins, confirming that these proteins are ancestral members of the IF family, which is highly conserved in eukaryotes. A topoisomerase II homologue has also been identified in the nuclear matrix, suggesting that these structures could play a role in organizing the Dinoflagellate DNA in loop domains. Taken together our results demonstrate that the nuclear matrix is an early acquisition of the eukaryotic nucleus, independent of histones and nucleosomes in such a way that the mechanisms controlling the two levels of organization in eukaryotic chromatin would be molecularly and evolutionarily independent.

Z-DNA binding and inhibition by GTP of Drosophila topoisomerase II

A Z-DNA binding protein has been isolated and characterized by biochemical means from Drosophila melanogaster tissue culture cells and embryos. This protein shares the following properties with the known, cloned Drosophila topoisomerase II: (1) expression of an ATP-dependent relaxation activity on supercoiled DNA; (2) a monomer mass of 165 kDa in SDS denaturing gels; (3) a sedimentation coefficient, S20,w, of approximately 10 S for the active enzyme; (4) cross-reactivity for the respective monoclonal and polyclonal antibodies; (5) generation of covalent enzyme-DNA intermediates at preferred cutting sites in the Drosophila HSP70 intergenic spacer region; (6) inhibition of DNA relaxation activity by antitumor drugs, e.g., the etoposide VM26, and by monospecific antibodies raised against the protein; and (7) in vitro phosphorylation by a casein kinase activity. However, we have identified new properties for our topoisomerase II preparation not previously reported for the conventionally isolated enzyme: (1) The enzyme binds to Z-DNA with an affinity 2 orders of magnitude greater than that for B-DNA. (2) The binding to Z-DNA is increased 5-10-fold by GTP or GTP-gamma-S. (3) GTP and GTP-gamma-S inhibit the catalytic activity of topoisomerase II through a proposed allosteric mechanism. (4) Z-DNA inhibits the relaxation of closed circular supercoiled DNA. (5) The preparation consists of a single polypeptide chain of 165 kDa on denaturing SDS gels with no evidence of proteolytic degradation. We postulate that the Z-DNA binding activity of undegraded topoisomerase II may be important in targeting the enzyme both to structural motifs required for chromatin organization and to sites of local supercoiling. Some of these features arise during processes such as replication and gene expression and may be more frequent during embryogenesis and early development.

Molecular cloning and immunolocalization of two variants of the major basic nuclear protein (HCc) from the histone-less eukaryote Crypthecodinium cohnii (Pyrrhophyta)

Two clones that encode variants (HCc1 and HCc2) of the major basic nuclear protein of the dinoflagellate Crypthecodinium cohnii, were identified by immunoscreening of a cDNA expression library. The first clone carries a full-length cDNA with an open reading frame (HCc1) encoding 113 amino acids. The cDNA from the second clone lacks some of the 5' end, and the coding sequence is only 102 residues. The two proteins display 77% sequence similarity and their NH2-ends are homologous to the NH2-peptide of the HCc protein determined by P. Rizzo. The amino acid composition, which confirms the basic nature of lysine-rich HCc proteins, differs markedly from other known DNA-binding proteins such as histones, HMGs or prokaryotic histone-like proteins. No convincing homology was found with other proteins. HCc antigens were localized on C. cohnii by immunofluorescence, and by electron microscopy (EM) with immunogold labelling. HCc proteins are mainly detected at the periphery of the permanently condensed chromosomes, where active chromatin is located, as well as in the nucleolar organizing region (NOR). This suggests that these basic, non-histone proteins, with a moderate affinity for DNA, are involved at some level in the regulation of gene expression.

Nucleolar localization of rRNA coding sequences in Prorocentrum micans Ehr. (dinomastigote, kingdom Protoctist) by in situ hybridization

To define the molecular mechanisms of ribosome biogenesis and to find out in which nucleolar compartment transcription of rDNA occurs, we have performed in situ hybridization (ISH) of RNase-treated cryosections using biotinylated rRNA coding sequences as a probe and the eukaryotic dinoflagellate nucleolar system as a model. Recent data from ISH of eukaryotic ribosomal genes by electron microscopy (EM) has so far failed to establish a consensus which clearly defines the function of the three compartments of the nucleolus. Dinomastigote protoctists are the only known eukaryotes whose chromatin is totally devoid of nucleosomes. Their chromosomes remain permanently condensed during the entire cell cycle and active nucleoli arise from an unwound part of some of the otherwise compact chromosomes. In this work, DNA-DNA hybrids were detected either by fluorescent avidin or by indirect immunogold staining procedures in EM; this is the first use of cryosections to detect hybrids in EM not only in the nucleolus sensu lato but also in a dinomastigote cell. Coding sequences of ribosomal genes were detected both in the periphery of the nucleolar organizer region (NOR), which corresponds to the unwound part of the nucleolar chromosome, and in the proximal part of the fibrillo-granular (FG) region. These results suggest that the rRNA gene transcription predominantly occurs at the periphery of the NOR where the coding sequences are located. A predictive model summarizes and allows discussions and comparisons with other eukaryotes in which nucleolar mechanisms were previously studied. This leads to the conclusion that dinoflagellate cells constitute an excellent model for the study of the functional structure of the eukaryotic nucleolus.(ABSTRACT TRUNCATED AT 250 WORDS)

Local supercoil-stabilized DNA structures

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.