Purification and the histones of Dictyostelium discoideum chromatin

Toxic effects of mercury on the cell nucleus of Dictyostelium discoideum

Governmental agencies (www.epa.gov/mercury) and the scientific community have reported on the high toxicity due to mercury. Indeed, exposure to mercury can cause severe injury to the central nervous system and kidney in humans. Beyond its recognized toxicity, little is known regarding the molecular mechanisms involved in the actions of this heavy metal. Mercury has been also observed to form insoluble fibrous protein aggregates in the cell nucleus. We used D. discoideum to evaluate micronuclei formation and, since mercury is able to induce oxidative stress that could bring to protein aggregation, we assessed nuclear protein carbonylation by Western Blot. We observed a significant increase in micronuclei formation and 14 carbonylated proteins were identified. Moreover, we used isotope-coded protein label (ICPL) and mass spectrometry analysis of proteins obtained by lysis of purified nuclei, before of tryptic digestion to quantify nuclear proteins affected by mercury. In particular, we examined the effects of mercury that associate a classical genotoxic assay to proteomic effects into the nucleus. The data present direct evidences for mercury genotoxicity, nuclear protein carbonylation, quantitative change in core histones, and the involvement of pseudouridine synthase in mercury toxicity. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 417-425, 2017.

Copine A is required for cytokinesis, contractile vacuole function, and development in Dictyostelium

Copines make up a family of soluble, calcium-dependent, membrane binding proteins found in a variety of eukaryotic organisms. In an earlier study, we identified six copine genes in the Dictyostelium discoideum genome and focused our studies on cpnA. Our previous localization studies of green fluorescent protein-tagged CpnA in Dictyostelium suggested that CpnA may have roles in contractile vacuole function, endolysosomal trafficking, and development. To test these hypotheses, we created a cpnA- knockout strain, and here we report the initial characterization of the mutant phenotype. The cpnA- cells exhibited normal growth rates and a slight cytokinesis defect. When placed in starvation conditions, cpnA- cells appeared to aggregate into mounds and form fingers with normal timing; however, they were delayed or arrested in the finger stage. When placed in water, cpnA- cells formed unusually large contractile vacuoles, indicating a defect in contractile vacuole function, while endocytosis and phagocytosis rates for the cpnA- cells were similar to those seen for wild-type cells. These studies indicate that CpnA plays a role in cytokinesis and contractile vacuole function and is required for normal development, specifically in the later stages prior to culmination. We also used real-time reverse transcription-PCR to determine the expression patterns of all six copine genes during development. The six copine genes were expressed in vegetative cells, with each gene exhibiting a distinct pattern of expression throughout development. All of the copine genes except cpnF showed an upregulation of mRNA expression at one or two developmental transitions, suggesting that copines may be important regulators of Dictyostelium development.

ATP-independent DNA renaturation catalyzed by a protein from Ustilago maydis

A protein that catalyzes the renaturation of complementary strands of DNA has been purified from mitotic cells of the lower eukaryote Ustilago maydis. The most highly purified fraction contains a polypeptide with a molecular mass of 20 kDa as determined by SDS/PAGE and glycerol gradient sedimentation. DNA reannealing is enhanced by the presence of a divalent cation but does not require ATP nor any other nucleotide triphosphate. Reassociation proceeds with fast kinetics as more than 60% of the DNA is reannealed within 4 min at a 30:1 nucleotide/protein monomer ratio, results which suggest that the protein acts in a stoichiometric fashion. Amino acid analysis revealed that the protein contained an elevated level of basic residues and low levels of tryptophan and tyrosine. The protein binds to an oligonucleotide of ten residues but not to one having only five. As judged by agarose gel assays, the protein does not catalyze strand-transfer reactions but does promote the annealing of a 58-residue polynucleotide onto single-stranded circles and gapped linear duplexes. These latter reactions are dependent on the presence of DNA sequence similarity between the pairing partners.

Gene expression and chromatin structure in the cellular slime mold, Dictyostelium discoideum

Micrococcal nuclease digestion of chromatin from growing cells reveals a structural organization which differs for genes transcribed at diverse rates. The late cAMP dependent prespore genes which are not transcribed in growing cells are found in growing cells in a regular nucleosomal repeat with an average spacing of 168 nucleotides. By contrast genes expressed at a low level in growing cells show an irregular pattern of bands with an average distance between bands of 80 nucleotides. The sizes of the bands generated from the transcribed genes are consistent with the concept that transcription results in the loss of the linker region histone H1 with concomitant sliding of nucleosomes to generate close packed ("slipped") di, tri, and tetra nucleosomes lacking the linker region. Further analysis of dinucleosomes released by micrococcal nuclease digestion reveals that transcriptionally active genes are found associated with dinucleosomes species which may be lacking histone H1. The length of DNA protected by these dinucleosomes is heterogeneous, ranging from 250 to 300 nucleotides. Methodology is described which has been adapted to allow two dimensional hybridization mapping of nucleoprotein complexes on single copy Dictyostelium genes.

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.

Electrophoretic study of histones in the unicellular alga Olisthodiscus luteus

Basic proteins were prepared from isolated nuclei of the unicellular alga Olisthodiscus luteus. The ratio of DNA/RNA/basic protein for these nuclei was 1:0.17:1.1, respectively, and the amino acid composition of the basic protein was very similar to that of Euglena and calf histones. The Olisthodiscus basic proteins were separated into four major components by polyacrylamide gel electrophoresis in four gel systems: (1) low pH disc gels containing 2.5 M urea; (2) two-dimensional low pH-urea gels in which the second dimension contained 1% Triton X-100; (3) slab gels containing 0.1% sodium dodecyl sulfate (SDS); (4) two-dimensional gels combining systems (1) and (3). The presence of four rather than five major histone fractions was shown to be not merely the result of proteolytic degradation. Results from the urea-containing gels suggest that an H1-like histone is missing, while electrophoresis in the SDS-containing gels shows the presence of a component resembling H1. In view of recent reports documenting the presence of five major histones in lower eukaryotes as well as in higher organisms, the presence of only four histones in Olisthodiscus suggests that this primitive eukaryote is unusual in its histone complement.