Nuclease Digestion of Chromatin from the Eukaryotic Algae Olisthodiscus luteus,Peridinium balticum,and Crypthecodinium cohnii 1, 2

Chromatin from a uninucleate dinoflagellate, Crypthecodinium cohnii, a binucleate dinoflagellate, Peridinium balticum, and a chromophyte, Olisthodiscus luteus, was examined by nuclease digestion and the results were compared to those from vertebrates. Gel analysis of the products of staphylococcal (micrococcal) nuclease digestion revealed a DNA repeat unit of 220(±5) base pairs for O. luteus and 215(±5) for P. balticum. Limit digestion gave a core particle of 140 base pairs, revealing that these longer repeat sizes are due to longer linker regions. No repeating subunit structure was found upon electrophoresis of digests of C. cohnii nuclei. Examination of the DNA fragments produced by DNAse I digestion of nuclei isolated from P. balticum and O. luteus showed the same ladder of ten base multiples as seen in chromatin from other eukaryotes. Examination of the kinetics of digestion by DNAse II of Peridinium chromatin revealed less susceptibility when compared to DNAse I digestions while 70% of Olisthodiscus chromatin and 35% of C. cohnii chromatin was sensitive to DNAse II. These data, taken together with previous results from Euglena, indicate that while algal chromatin is similar to that of higher eukaryotes in regard to DNAse I and II action, it differs in that the linker DNA is longer. In addition, the Hl-like histone from O. luteus and P. balticum is located in the linker DNA as in higher eukaryotes.     

Subunit organization of Euglena chromatin

Digestion of $\text{Euglena}$ nuclei or extracted chromatin with micrococcal nuclease results in the identification of a repeating structure. The DNA repeat size, analyzed on agarose and polyacrylamide gels, is found to be 225±13 base pairs. DNase I digestion produces a serie of fragments multiples of roughly 10 bases. Eventhough pressure shearing is necessary to disrupt the though pellicule of the phytoflagellate, we confirm that, in $\text{Euglena}$, chromatin organization is similar to that of other eukaryotes.     

Cytochromec oxidase ofEuglena gracilis: Purification,characterization, and identification of mitochondrially synthesized subunits

Cytochromec oxidase was purified from mitochondria ofEuglena gracilis and separated into 15 different polypeptide subunits by polyacrylamide gel electrophoresis. All 15 subunits copurify through various purification procedures, and the subunit composition of the isolated enzyme is identical to that of the immunoprecipitated one. Therefore, the 15 protein subunits represent integral components of theEuglena oxidase. In anin vitro protein-synthesizing system using isolated mitochondria, polypeptides 1–3 were radioactive labeled in the presence of [³⁵S]methionine. This further identifies these polypeptides with the three largest subunits of cytochromec oxidse encoded by mitochondrial DNA in other eukaryotic organisms. By subtraction, the other 12 subunits can be assigned to nuclear genes. The isolatedEuglena oxidase was highly active withEuglena cytochromec ₅₅₈ and has monophasic kinetics. Using horse cytochromec ₅₅₀ as a substrate, activity of the isolated oxidase was rather low. These findings correlate with the oxidase activity of mitochondrial membranes. Again, reactivity was low with cytochromec ₅₅₀ and 35-fold higher with theEuglena cytochromec ₅₅₈. The data show that the cytochromec oxidase of the protistEuglena is different from other eukaryotic cytochromec oxidases in number and size of subunits, and also with regard to kinetic properties and substrate specificity.Abbreviations kDa kilodalton - PAGE polyacrylamide gel electrophoresis - SDS sodium dodecyl sulfate - TN turnover number     

Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba balamuthi, and from the chloroplast and cytosol of Euglena gracilis: pieces in the evolutionary puzzle of the eukaryotic glycolytic pathway

Genomic or cDNA clones for the glycolytic enzyme enolase wereisolated from the amitochondriate pelobiont Mastigamoeba balamuthi,from the kinetoplastid Trypanosoma brucei, and from the euglenidEuglena gracilis. Clones for the cytosolic enzyme were foundin all three organisms, whereas Euglena was found to also expressmRNA for a second isoenzyme that possesses a putative N-terminalplastid-targeting peptide and is probably targeted to the chloroplast.Database searching revealed that Arabidopsis also possessesa second enolase gene that encodes an N-terminal extension andis likely targeted to the chloroplast. A phylogeny of enolaseamino acid sequences from 6 archaebacteria, 24 eubacteria, and32 eukaryotes showed that the Mastigamoeba enolase tended tobranch with its homologs from Trypanosoma and from the amitochondriateprotist Entamoeba histolytica. The compartment-specific isoenzymesin Euglena arose through a gene duplication independent of thatwhich gave rise to the compartment-specific isoenzymes in Arabidopsis,as evidenced by the finding that the Euglena enolases are moresimilar to the homolog from the eubacterium Treponema pallidumthan they are to homologs from any other organism sampled. Inmarked contrast to all other glycolytic enzymes studied to date,enolases from all eukaryotes surveyed here (except Euglena)are not markedly more similar to eubacterial than to archaebacterialhomologs. An intriguing indel shared by enolase from eukaryotes,from the archaebacterium Methanococcus jannaschii, and fromthe eubacterium Campylobacter jejuni maps to the surface ofthe three-dimensional structure of the enzyme and appears tohave occurred at the same position in parallel in independentlineages.     

The Ribonucleic Acids of Crithidia fasciculata*

SYNOPSIS. Crithidia fasciculata ribosomes were found to be 80S and to dissociate into 58 and 41S subunits; on 5 to 50% sucrose gradients, rRNA was separated into 25, 18, and 5S components. The molecular sizes of the heavier rRNA species, estimated by polyacrylamide gel electrophoresis were 1.24 and 0.84 M (×10⁶ daltons). The 25S RNA has a tendency to interact with the 18S RNA to give a complex that is difficult to separate by sucrose gradient centrifugation. The 25S RNA is also unstable and dissociates into 0.73 and 0.57 M components. The 18S RNA has molecular size (0.84 M) higher than the 0.7 M reported for most eukaryotes, but similar to that of Euglena and Amoeba. Ribosomal RNA hybridized 0.29% of the nuclear DNA. Mitochondrial RNA, extracted by a rapid procedure was resolved into 16 and 5S components in sucrose gradients.     

Presence of an unusually high concentration of an ubiquitinated histone-like protein in Trypanosoma cruzi

The conjugation of ubiquitin to histones H2A and H2B has been established in higher eukaryotes and has been related to changes in chromatin organization. In Trypanosoma cruzi, no condensation of chromatin occurs during mitosis. In order to determine the presence of histone ubiquitination in T. cruzi epimastigotes, histones were extracted from chromatin and analyzed by three electrophoretic systems: acid-urea, triton-acid-urea and sodium-dodecyl-sulphate polyacrylamide gel. The immunochemical detection of ubiquitin-histone conjugates by Western blotting showed a strong reaction with a slow migrating band of M_r 19 kDa. The high percentage of ubiquitin-histone conjugates present in T. cruzi chromatin may be related to the inability of this parasite to condense chromatin into a 30 nm fiber. J. Cell. Biochem. 66:433–440, 1997. © 1997 Wiley-Liss, Inc.     

The structure of Sipunculus nudus erythrocyte chromatin

The structure of the Sipunculus erythrocyte chromatin has been characterized by electron microscopy and nuclease digestion (staphylococcal nuclease and pancreatic nuclease). Contrary to previous results [1], we were able to isolate and characterize a histone H_2B in sipunculid nuclei. Though the histones H_2A and H_2B were markedly different from their vertebrate homologues, the subunit structure of the chromatin is the same. But the length of the repeat unit of DNA in the chromatin, is 177 ± 5 bp for the sipunculid erythrocyte nuclei, close to that reported for the chromatin of some lower eukaryotes.     

Growth of Euglena gracilis on whey

Summary To extend the use of industrial wastes, we have studied the growth of Euglena cells on demineralized whey powder, an industrial dairy waste from cheese making. The demineralized whey powder was solubilized (15 g/l) in 0.04 N HCl and autoclaved for two hours at 120°C. The solution was then brought to pH 3.5 with NH₄OH and tested for its ability to support Euglena growth. In the dark, cell densities of 4.5 to 5.5×10⁶ cells/ml were obtained when vitamin B₁₂, thiamine and minerals were added to the hydrolyzed whey solution. Although growth of Euglena is possible on whey, the industrial application may be limited due to the need to hydrolyze the whey and to the low utilization of carbon (20%) as the glucose, but not the galactose, released during hydrolysis is used.     

Histones from Saccharomyces cerevisiae

Total histones and histone fractions isolated from Saccharomyces cerevisiae chromatin were analysed by polyacrylamide gel electrophoresis. The presence of the four histone fractions H2a, H2b, H3 and H4 was demonstrated. In addition, yeast chromatin contained a protein similar to histone H1 from mammals in molecular weight, charge and association properties with Triton X-100. However, it had a much lower lysine to arginine ratio, equal to about 3, as compared with H1 histones from higher eukaryotes. The order of electrophoretic mobilities of yeast histone fractions in acidic urea-polyacrylamide gels was similar to that observed for histones from plant sources, i.e. H4>H3>H2a>H2b>H1. Previously undetected protein (protein X) was extracted from yeast chromatin with 5 % HClO₄. The properties of this protein are under investigation.     

Formation of Chromoneme-like Fibrils Induced in Infusorian Somatic Nuclei by Magnesium Ions

A study was made of the effect of Mg²⁺ on higher-order chromatin structure in macronuclei (Ma) of infusoria Paramecium aurelia and Bursaria truncatella. In infusorian Ma, inactive chromatin is commonly packed in chromatin bodies sized 60–200 nm. When isolated chromatin or Ma were treated with Mg²⁺ (about 3 mM), chromatin bodies arranged into fibrils 100–300 nm in diameter, which resembled higher eukaryotic chromonemes. The dynamics of chromoneme-like fibril formation was described. The results testified to the similarity of chromatin bodies to chromomeres of higher eukaryotes. Structurally intact central chromomere cores proved to be essential for the formation of chromoneme-like fibrils. Chromatin organization in infusoria was shown to follow the discrete-level model (nucleosomes–nucleomeres–chromomeres–chromonemes) assumed for higher eukaryotes.     

Effects of Photosynthetic Intermediates on the Activation State of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Euglena gracilis Z

The half-saturating concentration of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from Euglena gracilis Z for CO₂ in its activation by CO₂ in the presence of a saturating concentration of MgCl₂ (KJ was measured by analyzing the partial reversible inactivation of the fully activated enzyme in the medium with dilute CO₂. The K_d of the Euglena enzyme was 12.5 μm. The K,_d values were 6.3/im for the enzyme from soybean, 10.8 fiM from maize, 23.3 jiM from Scenedesmus obliquus, and 20.8 μm from Anabaena 7120. The activated state of Euglena RuBisCO was stabilized by 6-phosphogluconate, fructose 1,6-bisphosphate, and 3-phosphoglycerate in the medium containing low concentrations of CO₂. Both fructose 6-phosphate and ATP stimulated inactivation in the medium. NADPH not only stabilized the activated state of the enzyme, but also enhanced the enzyme activity over the full activity measured in the absence of NADPH. NADP⁺ did not nullify the effects of NADPH on the activation at all. The physiological significance of the effects of these photosynthetic metabolites on the activated state of Euglena RuBisCO is discussed.     

Purification of Euglena EF-1L: A cytoplasmic factor that also functions on procaryotic and organellar ribosomes

The low-molecular-weight form of the cytoplasmic protein synthesis elongation factor-1 (EF-1_L) from Euglena gracilis has been purified extensively from whole-cell extracts. A four-step purification procedure has been developed which results in a 45-fold enrichment in EF-1_L with 10% recovery of the total EF-1 activity present in the post-ribosomal supernatant. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicates that the EF-1_L is greater than 90% pure. The purified factor is composed of a single subunit of molecular weight 56,000 as determined by gel filtration and polyacrylamide gel electrophoresis under denaturing conditions. Unlike EF-1s purified to date from other organisms, Euglena EF-1_L catalyzes polymerization on Escherichia coli and Euglena chloroplast ribosomes, as well as on wheat germ ribosomes. The activity of this factor on 70 S ribosomes is about 5% that observed on eucaryotic 80 S ribosomes. This level of catalytic activity is sufficient to obscure the activity of chloroplast EF-Tu and mitochondrial EF-Tu in whole-cell extracts of Euglena. The activity of EF-1_L as measured on either wheat germ or E. coli ribosomes is unstable in the absence of glycerol, is inhibited only slightly by 20 mm, N-ethylmaleimide, is not stimulated by E. coli EF-Ts, and is not inhibited by the antibiotic kirromycin. The relative affinity of EF-1_L for guanine nucleotides was also measured and it was observed that its affinity for GTP is approximately six- to eightfold greater than that for GDP.     

Properties of soluble chromatins isolated from apical and axial parts of cauliflower inflorescence

Soluble chromatins were isolated from apical and axial parts of the cauliflower inflorescence. The template activities of the two chromatins were found to differ significantly, when using RNA polymerase of Escherichia coli. The derivative thermal melting profiles showed at least three melting peaks for each chromatin, indicating that higher T_m values could be distinguished in the apical chromatin in each peak. Histones extracted from both chromatins were analysed by acrylamide disc-electrophoresis. A much smaller amount of presumed F1 fraction was observed in the sample from axial chromatin.     

Hetero- and euchromatin of synchronous Euglena cells : I. Physical fractionation of nuclei into differentially condensed chromatin

Several attempts were made to isolate intact nuclei and fractionate condensed and extended chromatin from synchronized cells of Euglena gracilis Z. Different factors affecting the recovery and the intactness of nuclei have been tested: detergent concentration, incubation time and addition of Mn²⁺ (0.13 mM) and/or spermidine (0.14 mM) as protective agents. Interphase and mitotic nuclei show preserved chromatin when Mn²⁺ is included, while the combination of Mn²⁺ and spermidine—and, to a lesser extent, spermidine alone—leads to mitotic nuclei with enhanced clumped chromatin. The common procedure to fractionate Euglena chromatin involves swelling of nuclei before disruption. We proved that this step induces artefactual decondensation of packed heterochromatin. Two alternative methods are compared with separate condensed and dispersed chromatin: (1) breakage of swollen nuclei and subsequent addition of divalent cations and/or spermidine with mild pressure shearing forces; (2) disruption of nuclei in a medium containing Mn²⁺ as a protective agent, without swelling. Electron microscopy study indicates that the normal packed appearance of condensed chromatin is preserved, according to the second procedure, while extensive shearing is necessary. Template capacity of the extended chromatin is significantly higher in both methods. Relative amounts of condensed and dispersed chromatin during interphase and mitosis are discussed.     

Distinct chromatin organization in the germ line founder cell of the Caenorhabditis elegans embryo

Cells belonging to the germ lineage segregate physically and molecularly from their somatic neighbors during embryogenesis. While germ line‐specific chromatin modifications have been identified at later stages in the Caenorhabditis elegans nematode, none have been found in the single P₄ germ line founder cell that arises at the beginning of gastrulation. Using light and electron microscopy, we now report that the chromatin organization in the germ line founder cell of the early C. elegans embryo is distinct from that in the neighboring somatic cells. This unique organization is characterized by a greater chromatin compaction and an expansion of the interchromatin compartment. The ultrastructure of individual chromatin domains does not differ between germ line and somatic cells, pointing to a specific organization mainly at the level of the whole nucleus. We show that this higher order reorganization of chromatin is not a consequence of the P₄ nucleus being smaller than somatic nuclei or having initiated mitosis. Imaging of living embryos expressing fluorescent markers for both chromatin and P granules revealed that the appearance of a distinct chromatin organization in the P₄ cell occurs approximately 10 min after its birth and coincides with the aggregation of P granules around the nucleus, suggesting a possible link between these two events. The higher order reorganization of chromatin that is reported here occurs during the establishment of definitive germ cell identity. The changes we have observed could therefore be a prerequisite for the programming of chromatin totipotency.     

Lateral Transfer and Recompartmentalization of Calvin Cycle Enzymes of Plants and Algae

Certain Calvin cycle enzymes also function in glycolysis or gluconeogenisis, thus photosynthetic eukaryotes would be predicted to have ancestrally possessed cytosolic homologues of these enzymes derived from the eukaryotic host and plastid homologues from the cyanobacterial endosymbiont. In practice, the evolutionary histories of these enzymes are often more complex. Focusing on eukaryotes with secondary plastids, we have examined the evolution of four such genes: class I and II fructose bisphosphate aldolase (FBA), sedoheptulose bisphosphatase (SBPase), and fructose bisphosphatase (FBPase). We show that previously observed distributions of plastid and cytosolic homologues are not always found in algae with secondary plastids: there is evidence for multiple events of both lateral gene transfer and retargeting to a new cellular compartment for both cytosolic and plastid enzymes of plants and algae. In particular, we show that a clade of class II FBAs spans a greater diversity of eukaryotes that previously recognized and contains both plastid-targeted (Phaeodactylum, Odontella) and cytosolic (ascomycetes, oomycetes, Euglena, and Bigelowiella) forms. Lateral transfer events also gave rise to a subset of plant cytosolic FBA, as well as cytosolic FBPase in Toxoplasma and other coccidian apicomplexa. In contrast, it has recently been suggested that the Trypanosoma FBA and SBPase are derived from a plastid, however, greater taxonomic sampling shows that these enzymes provide no evidence for a plastid-containing ancestor of Trypanosoma. Altogether, the evolutionary histories of the FBA and SBPase/FBPase gene families are complex, including extensive paralogy, lateral transfer, and retargeting between cellular compartments.     

Tubulin Genes in the Algal Protist Euglena gracilis

ABSTRACT Alpha- and beta-tubulin cDNA were selected from a Euglenaλgt11 expression library, recloned and either sequenced (α-tubulin cDNA) or hybridized to Euglena RNA and DNA (α- and β-tubulin cDNA). RNA for hybridization was extracted at 30 minute intervals after flagellar amputation and quantitated for cDNA binding. Unlike previous reports on most other flagellates, no net increase in either α- or β-tubulin RNA could be detected during regeneration—suggesting steady state or constitutive tubulin RNA synthesis. Incubation of the cDNA with genomic DNA after restriction digestion produced patterns of hybridization consistent with the presence of one to two kinds each of the α- and β-tubulin genes. The deduced amino acid sequence of the α-tubulin cDNA was more than 90% identical to the α-tubulins of Trypanosoma, Chlamydomonas, Naegleria, Tetrahymena and higher plants. The carboxy terminus of the α-tubulin cDNA and the previously sequenced β-tubulin of Euglena showed greatest identity to the carboxy terminus of the tubulins from Trypanosoma brucei. The sequence data for α and β-tubulins of Euglena provides direct evidence for the similarity of two gene products from euglenas and trypanosomes and adds support to earlier suggestions that these organisms are phylogenetically related.     

Variation of DNA Levels in Euglena Related to pH of Culture Medium1

Variations in DNA levels for log-phase Euglena have been shown to be directly related to the pH of the culture medium. Data are presented here for cultures grown in Cramer and Myer's medium at pH 3.0 and 6.8. DNA levels are ～50% greater for Euglena at the higher pH value, confirming earlier reports.     

Genome balance in six successive generations of the allotetraploid Festuca pratensis × Lolium perenne

In the allotetraploid, Festuca pratensis Huds. (2n = 4x = 28) × Lolium perenne L. (2n = 4x = 28) the balance of chromatin, as determined by GISH, changes over successive generations of open pollination in favour of L. perenne. There is extensive recombination between chromosomes of the two parental genomes, as well as substitution of whole Festuca chromosomes by whole Lolium chromosomes. The total number of Lolium chromosomes increased from a mean 14.36 in the F₂ to 16.26 in the F₆, and the total number of Festuca chromosomes decreased correspondingly from a mean of 13.57 to a value of 11.56. The number of recombinant chromosomes and recombination breakpoints per genotype also increased from generation to generation, although the respective values of both characters were higher for Festuca (0.86–8.41 and 1.14–15.22) than for Lolium (0.68–4.59 and 0.68–6.0). The proportion of total genome length contributed by the L. perenne chromatin increased from about 50% in F₂ to 59.5% in F₆. The results are based on the sample of 134 plants studied (26–28 plants per generation), and are discussed in terms of the dominance of Lolium chromosomes over those of Festuca, and possible mechanisms underlying this phenomenon of chromatin substitution.