Circular mitochondrial DNA from Acanthamoeba castellanii (Neff-strain)

The mitochondrial genomes of Ustilago cynodontis and Acanthamoeba castellanii

Mitochondrial DNA from Ustilago cynodontis has been investigated in several of its properties. Its dG + dC content is equal to 33.5%; its buoyant density (1.698 g/cm3) is higher, by 5 mg/cm3, and its melting temperature (82.5 degrees C) is lower than expected for a bacterial DNA having the same base composition; the first derivative of its melting curve indicates a large compositional heterogeneity, its molarity of elution from hydroxyapatite is high, 0.28 M phosphate, and allows its partial separation from nuclear DNA. Degradation by micrococcal nuclease indicates that about 25% of the DNA is formed by stretches having no more than 15% dG + dC. Finally, the unit size of mitochondrial genome is about 50 X 10(6). In most of its properties, the mitochondrial genome of U. cynodontis presents strong analogies with that of Saccharomyces cerevisiae. A parallel investigation on mitochondrial DNA from Acanthamoeba castellanii which has as genome unit size of only 27 X 10(6), has shown that this shares with the former the dG + dC content (32.9%), the melting temperature (82.5 degrees C), a large compositional heterogeneity and a very similar pattern of micrococcal nuclease degradation; its buoyant density (1.692 g/cm3) and its molarity of elution from hydroxyapatite (0.25 M phosphate) are, however, normal, probably because of a different short-sequence pattern and the fact that its dA + dT-rich stretches are shorter, on the average.

Evolutionary divergence of mitochondrial DNA from Paramecium aurelia

Mitochondrial (mt) DNA from four sibling species within the Paramecium aurelia complex, including stocks of different geographic origin and mutants, were analyzed using four 6-bp recognition site and one 4-bp recognition site endonucleases and the sequence divergence was estimated using Upholt's (1977) statistical procedure. All four species were readily distinguishable regardless of the restriction endonuclease employed. With intraspecies comparisons, no differences were observed which could be accounted for on the basis of geographic origin. Except for species 4, each stock (and mutant) gave a species-specific fragment pattern. For species 4, while the patterns were distinct from the other species, two species-specific type of patterns were found, designated A and B. The sequence divergence between these was estimated to be between 1 and 2 percent. With interspecies comparisons, the sequence divergence ranged from 3.9 to 10.3% with the greatest divergence being between species 1 and 4, and the least between species 1 and 5. The similarity between species 1 and 5 is in accord with other criteria for interspecies comparisons. The degree of sequence divergence measured here in Paramecium mt DNA is well within the range reported for rodents and primates. All four species mt DNA were cleaved to many DNA fragments by DPN II, an enzyme which recognizes non-methylated sites, and not by DPNI, the methyl-site specific counterpart of DPN II, suggesting that mt DNA from Paramecium aurelia is not appreciably methylated, if at all.

Chloroplast DNA from three archegoniates

1. DNA from female and male Sphaerocarpos donnellii (liverwort) plants exhibits at least two species with buoyant densities of 1.703 (main band) and 1.691 (satellite) g cm(-3) in CsCl equilibrium gradients. At least part, if not all, of the satellite DNA is localized in plastids. It consists of up to 90% of uniformly sized circular molecules of an average circumference of 38.5 μm. Compared to other Chlorophyta, the liverwort's cpDNA is unusually low both in diensity and contour length. - 2. On the hand, cpDNA from the ferns Asplenium nidus and Pteris vittata resembles those of higher plants in buoyant density (1.697 g cm(-3)) and circumference (about 44.8 μm). - 3. Analysis of DNA from the archegoniate chloroplasts with restriction endonucleases indicates chat the cyclic molecules are monomers. - 4. The results show that the circular molecules found in cpDNA of higher plants do not represent the functionally required minimum size of DNA in plastids.

Mitochondrial DNA from Podospora anserina. I. Isolation and characterization

Mitochondrial (Mt) DNA from Podospora anserina was isolated and characterized with respect to density in CsCl, contour length and endonuclease restriction enzymes. The density of Mt DNA for four races examined was 1.694 g/cm3, compared with 1.712 g/cm3 for nuclear DNA. Extraction in the presence of a nuclease inhibitor, aurintricarboxylic acid and isolation in DAPI CsCl gradients allowed us to isolate high molecular weight DNA. Mt DNA isolated by total DNA extraction contained ca. 1% of circular molecules, 31 micron in contour length; Mt DNA isolated from purified mitochondria contained 2--4% of these 31 micron circles. Analysis with Eco RI restriction endonuclease revealed that each of the four races examined, s, A, T and E had a characteristic fragment pattern. Races s and A Mt DNA differed by only one fragment after Eco RI enzymatic digestion; similarly, these two DNA differed by only one or two fragments after Hae III digestion.

Circular DNA and rolling circles in nucleolar rDNA from mitotic nuclei of Physarum polycephalum

1. About 15% of nucleolar DNA (1.712 g/cm3) from Physarum polycephalum displaying maximum hybridization to ribosomal RNA, is composed of circular DNA of 3.9 +/- 0.2 mum contour length or multiples thereof. 2. A portion of these circular molecules (25%) contained linear DNA pieces longer than circumference length. In a small fraction of circular DNA linear pieces, shorter than the unit length, were observed. 3. Most nucleolar DNA, [3H]thymidine-labeled or hybridizable to ribosomal RNA was separable from chromosomal DNA during G2 phase, mitosis and S phase of the cell cycle. 4. Ribosomal DNA content was not amplified during the cell cycle, was unchanged during exponential or stationary growth phase and amounted to about 0.11 -- 0.21% of nuclear DNA in diploid and hexaploid strains of Physarum or 100--200 ribosomal genes per diploid genome.

Characterization of the genome of the small free-living amoeba Acanthamoeba castellanii

The cellular DNAs of Acanthamoeba castellanii have been characterized by their behaviour in CsC1 density gradients, by their thermal denaturation and by their renaturation kinetics. Whole-cell DNA exhibits, on CsC1 density gradients, a major peak with a density of 1.717 g/cm3 (major component) and a minor peak with a density of 1.692 g/cm3 (minor component). The major component is nuclear and the minor component is of cytoplasmic origin. The latter contains mitochondrial DNA as well as an extramitochondrial DNA fraction. Reiterated sequences make up approximately 14% of the total and are mainly cytoplasmic. They are characterized by three families of nucleotide sequences. The mitochondrial DNA exhibits a complex renaturation pattern. The fast renaturing component has a calculated complexity of 4.107 daltons. The slower renaturing component has a kinetic complexity tentatively estimated as 1.1010 daltons. The melting profile of mitochondrial DNA suggests heterogeneity in base composition.

Circular mitochondrial DNA from the avian malarial parasite Plasmodium lophurae

The avian malarial parasite, Plasmodium lophurae, was liberated from duck erythrocytes with antiduck erythrocyte serum and freed from host cell nuclei by differential centrifugation followed by treatment with trypsin and DNAase. Total as well as mitochondrial DNA isolated from such a preparation of free parasites showed overlapping densities of 1.679 g/ml in CsCl density gradients. To retain the structural integrity of mitochondrial DNA, the treatment of liberated parasites with trypsin and DNAase was eliminated and all steps of isolation of the mitochondrial fraction was performed at ice bath temperature. Under these conditions, mtDNA liberated by osmotic lysis appeared as super coiled molecules. After isolation of DNA from mitochondrial pellets prepared under the above conditions, only a single DNA band was apparent in ethidium bromide/CsCl gradients and open circular molecules with a mean contour length of 10.3 mum were observed.

Size, conformation and purity of chloroplast DNA of some higher plants

1. Chloroplast DNA of Antirrhinum majus, Oenothera hookeri, Beta vulgaris and Spinacia oleracea band at the same buoyant density of 1.697 g-cm-3 in neutral CsCl equilibrium gradients. The corresponding nuclear DNAs band at 1.691, 1.703, 1.695 and 1.695 g-cm-3, respectively. The purity of chloroplast and nuclear DNA can be assessed objectively only in the cases of Antirrhinum and Oenothera. 2. Electron microscopic analysis of chloroplast DNA, purified in CsCl or CsCl/ethidium bromide gradients, revealed up to 80% circular molecules. Of these about 15% were of supertwisted conformation. Best yields of circular molecules were recovered when populations of unbroken chloroplasts were subjected to DNAase and phosphodiesterase treatment, and when the DNA was purified from viscous lysates by centrifugation into a CsCl cushion. Treatment of plastids with DNAase alone did not guarantee complete degradation of nuclear DNA. 3. The average contour length of the open circular chloroplast DNA molecules was basically similar for all four plants. They were 45.9 plus or minus 2.1 mum for Antirrhinum, 45.7 plus or minus 1.9 mum for Spinacia, 44.9 plus or minus 1.7 mum for Beta and 45.2 mum for Oenothera. This is comparable to the size derived for the coding capacity of chloroplast DNA from reassociation experiments. As much as 15% of the total population of circles in chloroplast DNA of Spinacia were circular dimers.

Isolation and characterization of mitochondrial deoxyribonucleic acid of Acanthamoeba castellanii

DNA was prepared from isolated mitochondria of Acanthamoeba castellanii and was shown to behave as a single component in density gradients, on ;melting' and on renaturation. From measurements of renaturation kinetics, sedimentation coefficient and electron micrographs the genome size of the mitochondrial DNA was calculated to be about 3.4x10(7) daltons. A small proportion of the preparations could be isolated as relaxed circular molecules of mean contour length 16.2mum.