Peter J. Rizzo

Those amazing dinoflagellate chromosomes.

ABSTRACTDinoflagellates are a very large and diverse group of eukaryotic algae that play a major role in aquatic food webs of both fresh water and marine habitats. Moreover, the toxic members of this group pose a health threat in the form of red tides. Finally, dinoflagellates are of great evolutionary importance, because of their taxonomic position, and their unusual chromosome structure and composition. While the cytoplasm of dinoflagellates is typically eukaryotic, the nucleus is unique when compared to the nucleus of other eukaryotes. More specifically, while the chromosomes of all other eukaryotes contain histones, dinoflagellate chromosomes lack histones completely. There are no known exceptions to this observation: all dinoflagellates lack histones, and all other eukaryotes contain histones. Nevertheless, dinoflagellates remain a relatively unstudied group of eukaryotes.

Comparative aspects of basic chromatin proteins in dinoflagellates

Previous work on histone-like proteins in dinoflagellates is summarized, together with some new data to give an overview of basic proteins in these algae. The first two dinoflagellates studied were both found to contain one major acid-soluble protein that migrated to the same position in acidic-urea gels. When several other genera were studied however, it became apparent that the histone-like proteins from different dinoflagellates were similar but not identical. In view of the great diversity of living dinoflagellates it is speculated that further differences in dinoflagellate basic chromatin proteins will be revealed. Electrophoretic data from the eukaryotic (endosymbiont) nucleus of Peridinium balticum showed the presence of five major components. It is speculated that two of these proteins represent an H1-like doublet and two others correspond to the highly conserved histones H3 and H4. The fifth component is a new histone that may substitute for H2A and H2B in the nucleosome. Because histones and nucleosomes are present in all higher organisms but completely lacking in procaryotes, studies on basic proteins in dinoflagellates will provides insights into the evolution of histones and eucaryotic chromatin organization.

Kryptoperidinium foliaceum blooms in South Carolina: a multi–analytical approach to identification

Abstract Observations following the discovery of Kryptoperidinium foliaceum blooms in South Carolina (SC), USA, suggest that a multi-analytical approach, using a standard, minimal set of criteria, should be adopted for determining dinoflagellate species identity and taxonomic placement. A combination of morphological, molecular, and biochemical analyses were used to determine the identity of this “red tide” dinoflagellate, first documented in SC waters in the spring of 1998. Results from thecal plate tabulations (based on scanning electron and epifluorescence microscopy), gene sequence data, species-specific PCR probe assays, and microalgal pigment profiles were analyzed and compared to reference cultures of K. foliaceum . Comparative data showed marked inconsistencies among the K. foliaceum reference culture isolates. In addition, the SC bloom isolate was shown to be mononucleate, contrary to previous reports for K. foliaceum , suggesting a more transient endosymbiotic association than previously considered.

Histone-like protein and chromatin structure in the wall-less dinoflagellate Gymnodinium nelsoni

Basic nuclear proteins from the wall-less dinoflagellate Gymnodinium nelsoni were analyzed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS). One major histone-like protein with a molecular weight of about 10 000 was present in acid extracts of whole nuclei and chromatin isolated from growing cultures. In addition, two minor components of 17 000 and 13 000 daltons were also noted. Chromatin fibers spread by the microcentrifugation technique showed no indication of a subunit structure, but instead appeared as smooth threads with diameter of about 6.5 nm.

CLONING, EXPRESSION, AND CHARACTERIZATION OF A HISTONE‐LIKE PROTEIN FROM THE MARINE DINOFLAGELLATE LINGULODINIUM POLYEDRUM (DINOPHYCEAE)1

Although nucleosomes and histones are lacking in dinoflagellate nuclei, small basic histone‐like proteins have been reported, but their function(s) is unknown. In this study we cloned and sequenced a gene for a histone‐like protein from the dinoflagellate Lingulodinium polyedrum (Stein) Dodge (HLp) (formerly Gonyaulax polyedra Stein) and investigated its post‐translational modification and DNA‐binding activities. HLp appears to be acetylated in L. polyedrum, and we identified several L. polyedrum proteins that possess histone acetyltransferase activity and may be responsible for this modification. HLp binds weakly to L. polyedrum DNA but to certain specific sequences with higher affinity, consistent with its having a regulatory function.

Histones in protistan evolution

The potential of comparative studies on histones for use in protistan evolution is discussed, using algal histones as specific examples. A basic premise for the importance of histones in protistan evolution is the observation that these proteins are completely absent in prokaryotes (and cytoplasmic organelles), but with few exceptions, the same five major histone types are found in all higher plants and animals. Since the histone content of the algae and other protists is not constant, some of these organisms may represent transition forms between the prokaryotic and eukaryotic modes of packaging the genetic material. Comparative studies of protistan histones may thus be of help in determining evolutionary relationships. However, several problems are encounter with protistan histones, including difficulties in isolating nuclei, proteolytic degradation, anomalous gel migration of histones, and difficulties in histone identification. Because of the above problems, and the observed variability in protistan histones, it is suggested that several criteria be employed for histone identification in protists.

Divalent cation distribution in dinoflagellate chromosomes imaged by high-resolution ion probe mass spectrometry

From a variety of analytical electron microscopy experiments, the chromosomes of dinoflagellates are known to contain sizeable amounts of cations, the latter thought to contribute to the neutralization of the negative charge carried by the phosphate groups in the DNA backbone. From previous Ca and Mg chelation experiments, it is also known that these cations are necessary for the compaction and preservation of the chromosome architecture. Similar conclusions have been recently presented by our group concerning mammalian mitotic chromosomes, in studies based on secondary ion mass spectrometry (SIMS) carried out with the University of Chicago high-resolution scanning ion microprobe (UC-SIM). We have now applied this instrument to image the distribution of DNA-bound Ca(2+) and Mg(2+) in dinoflagellate chromosomes, a goal that could not be attained earlier by analytical electron microscopy. Analyzed quantitatively and imaged here by SIMS for the first time, through their cation content, are the chromosomes of the dinoflagellates Prorocentrum micans, Gymnodinium mikimotoi and Gymnodinium dorsum. The cell nuclei were isolated and prepared for SIMS analysis with a minimal protocol (mechanical fractionation in culture medium followed by ethanol drying), which did not expose the samples to artifact-creating, alien chemical agents. By this approach, we have confirmed the earlier findings by several authors, and contributed new structural information provided by our ion probe capability to erode the sample surface layer by layer (SIMS tomography). Dinoflagellates, due to the absence of histones, represent an ideal model system where cations may bind directly with DNA, allowing comparisons to be made with recently reported X-ray crystallography results at atomic resolution. Such comparisons yielded quantitative confirmation that the Ca(2+)+Mg(2+) concentrations found for e.g. P. micans are consistent with those anticipated to provide complete charge neutralization of naked DNA by cations, also resulting in maximal DNA compaction.

Evidence For the Presence of A Cdc2‐Like Protein Kinase In the Dinoflagellate Crypthecodinium Cohnii

ABSTRACT. The unusual nature of mitosis and ancestral organization of the dinoflagellate nucleus prompted the question of whether the cdc2‐like histone H1 kinase, a presumed ubiquitous cell cycle regulator in eukaryotes, is present in these primitive organisms. Western blotting of Crypthecodinium cohnii protein extracts using antibody against the Pro‐Ser‐Thr‐Ala‐Ile‐Arg‐Glu (=PSTAIRE) amino acid sequence motif, conserved in all cdc2 homologues known, revealed one prominent band corresponding to a protein with an apparent relative molecular weight ≈ 34,000, identical in mobility to that from HeLa cells and Physarum polycephalum, higher and lower eukaryotic controls, respectively. Incubation of C. cohnii cell lysates with p13suc1‐sepharose beads, which preferentially, though not exclusively, bind p34cdc2, resulted in precipitation of a 34‐kDa protein which was reactive with anti‐PSTAIRE antibody, selectively competed for by the PSTAIRE peptide and able to phosphorylate histone H1 in vitro. We conclude that the dinoflagellate C. cohnii contains a protein very similar to the cdc2 gene product from fission yeast and its homologues in all eukaryotes studied thus far.

Some properties of the histone-like protein from crypthecodinium cohnii (HCc)

The histone-like protein from Crypthecodinium cohnii (HCc) was examined in regard to its amino acid composition and the peptide pattern resulting from protease digestion. A revised amino acid composition indicated a higher lysine and arginine content and a lower glycine content than that determined previously. Comparative peptide mapping of HCc with HTa, a histone-like protein from Thermoplasma acidophilum, and with a histone-like protein from the dinoflagellate Gyrodinium dorsum showed significant differences in the peptide patterns produced.

THE MAJOR HISTONE-LIKE PROTEIN FROM THE NONPHOTOSYNTHETIC DINOFLAGELLATE CRYPTHECODINIUM COHNII (PYRROPHYTA) IS PRESENT IN STATIONARY PHASE CULTURES1

An improved method is described for the isolation of nuclei from the nonphotosynthetic dinoflagellate Crypthecodinium cohnii (Seligo) Chatton in Grassé. The new method results in an increase in yield from about 13% to 45% or higher, with no loss in purity or activity of endogenous RNA polymerase. Most of this increase in yield is from the ability of 25% Ficoll to cause many cells to shed their walls, and from the stabilizing effect of hexylene glycol during cell disruption. The histone‐like protein, previously undetectable in chromatin from stationary phase cells, can now be demonstrated in chromatin from stationary as well as log phase cells. Preliminary experiments indicate that this protein inhibits transcription.