Mitochondrial DNA synthesis in permeable cells

Isolation of yeast DNA replication mutants in permeabilized cells

A random population of temperature-sensitive mutants was screened by assaying for defects in DNA synthesis in a permeabilized yeast DNA replication system. Twenty mutants defective in in vitro DNA synthesis have been isolated. In this paper we describe eight of these mutants. Seven of them fall into three complementation groups--cdc2, cdc8, and cdc16--involved in the control of the cell-division cycle. Because synthesis in vitro represents propagation of replication forks active in vivo at the time of permeabilization, our finding that cdc2 and cdc16 mutants can incorporate dTMP into DNA in such permeabilized cells at 23 degrees C but not at 37 degrees C supports the conclusion that these two mutations directly affect DNA synthesis at replication forks. Such an involvement was previously suggested by in vivo analysis for CDC2 but was less clear for CDC16. Finally, the usefulness of our screening procedure is demonstrated by the isolation of replication mutants in previously undescribed complementation groups. One strain shows a serious defect in in vivo DNA synthesis but normal RNA synthesis.

Purification of the cdc8 protein of Saccharomyces cerevisiae by complementation in an aphidicolin-sensitive in vitro DNA replication system

DNA synthesis in vitro in Brij-treated Saccharomyces cerevisiae requires the product of the CDC8 gene (Hereford, L. M. & Hartwell, L. H. (1971) Nature (London) New Biol. 234, 171-172). Extracts of wild-type A364a yeast restore DNA synthesis in Brij-treated cdc8, a mutant containing a thermolabile cdc8 gene product. This constitutes a complementation assay by which the cdc8 gene product can be monitored during purification. A heat-stable protein responsible for this complementation has been partially purified from both wild-type A364a cells and from a cdc8 temperature-sensitive mutant. The complementation activity from the mutant is thermolabile when compared to the wild-type activity, indicating that CDC8 is the structural gene for the protein.

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.

Repair of double-strand breaks and lethal damage in DNA of Ustilago maydis

The size of nuclear DNA from wild-typeUstilago maydiswas determined to be approximately 6·09 ± 0·3 × 108daltons from neutral sucrose gradient sedimentation analysis. Following exposure to ionizing radiation the nuclear DNA size was reduced due to the production of double-strand breaks in the DNA. These breaks were repaired when the irradiated cells were incubated in medium for at least one hour after irradiation. The repair was seen as a shift in the DNA profile from a low molecular weight region where the control DNA sedimented. Inhibition of protein synthesis by cycloheximide prevented this type of repair. Blocking protein synthesis also decreased the survival of irradiated wild-type cells but not radiation-sensitive mutants. Protein synthesis was necessary within the first one and a half hours after irradiation for the survival of wild-type cells to be unaffected. The results provide additional evidence for an inducible repair process inU. maydis.

Deoxyribonucleic acid synthesis in Saccharomyces cerevisiae cells permeabilized with ether

Cells of Saccharomyces cerevisiae permeabilized by treatment with ether take up and incorporate exogenous deoxynucleoside triphosphate into deoxyribonucleic acid (DNA). With rho(+) strains, more than 95% of the product was mitochondrial DNA (mtDNA). This report characterizes ether-permeabilized yeast cells and describes studies on the mechanism of mtDNA synthesis with this system. The initial rate of in vitro mtDNA synthesis with one strain (X2180-1Brho(+)) was close to the rate of mtDNA replication in vivo. The extent of synthesis after 45 min was sufficient for the duplication of about 25% of the total mtDNA in the cells. The incorporated radioactivity resulting from in vitro DNA synthesis appeared in fragments that were an average of 30% mitochondrial genome size. Density-labeling experiments showed that continuous strands of at least 7 kilobases after denaturation, and up to 25 kilobase pairs before denaturation, were synthesized by this system. Pulse-chase experiments demonstrated that a large proportion of DNA product after short labeling times appeared in 0.25-kilobase fragments (after denaturation), which served as precursors of high-molecular-weight DNA. It is not yet clear whether the short pieces participate in a mechanism of discontinuous replication similar to that of bacterial and animal cell chromosomal DNA or whether they are related to the rapidly turning over, short initiation sequence of animal cell mtDNA. In rho(0) strains, which lack mtDNA, the initial rate of nuclear DNA synthesis in vitro was 1 to 2% of the average in vivo rate. With temperature-sensitive DNA replication mutants (cdc8), the synthesis of nuclear DNA was temperature sensitive in vitro as well, and in vitro DNA synthesis was blocked in an initiation mutant (cdc7) that was shifted to the restrictive temperature before the ether treatment.

Synthesis of chloroplast ribonucleic acid in Chlamydomonas reinhardtii toluene-treated cells

Chlamydomonas reinhardtii cells treated with toluene at 0 degrees C and 25 degrees C incorporate ribonucleoside triphosphates (NTPs) into chloroplast RNA at 25 degrees C and also at 35 degrees C. The incorporation requires all four NTPs and Mg2+, and is completely inhibited by DNase, RNase, actinomycin D (40 microgram/ml) and rifampicin (350 microgram/ml). However, the incorporation is almost totally insensitive to both alpha-amanitin and streptolydigin at 200 microgram/ml.

Synthesis of DNA in permeabilized cells of Kluyveromyces lactis

Kluyveromyces lactis cells permeabilized with nystatin, though no longer viable, were able to incorporate 3H-dATP into DNA. Maximum rate of synthesis was obtained when all four deoxyribonucleoside triphosphates were present. For prolonged incorporation of 3H-dATP into DNA rATP or phosphoenolpyruvate were of absolute requirement. DNA synthesis was inhibited by p-chloromercuribenzoate, N-ethylmaleimide, nalidixate, ethidium bromide and distamycin A. The density of DNA synthesized in permeabilized cells grown on non-fermentable and fermentable carbon sources was analyzed on CsCl gradients in the presence or absence of distamycin A. The DNA synthesized by permeabilized cells previously grown on glycerol was essentially mitochondrial DNA; nuclear DNA (30% of total) was also synthesized by cells previously grown on glucose.

Deoxyribonucleic acid synthesis in permeabilized spheroplasts of Saccharomyces cerevisiae

Osmotically shocked spheroplasts from Saccharomyces cerevisiae incorporated deoxynucleoside triphosphates specifically into double-stranded nuclear and mitochondrial deoxyribonucleic acid (DNA). Results with this in vitro system for cells with and without mitochondrial DNA were compared. Strains lacking mitochondrial DNA were used to study nuclear DNA replication. With a temperature-sensitive mutant defective in DNA replication in vivo, DNA synthesis in vitro was temperature sensitive as well. The product of synthesis with all strains after very short labeling times consisted principally of short fragments that sedimented at approximately 4S in alkali; with longer pulse times or a chase with unlabeled nucleotides, they grew to a more heterogenous size, with an average of 6 to 8S and a maximum of 15S. There was little, if any, integration of these DNA fragments into the high-molecular-weight nuclear DNA. Analysis by CsCl density gradient centrifugation after incorporation of bromodeoxyuridine triphosphate showed that most of the product consisted of chains containing both preexisting and newly synthesized material, but there was also a small fraction (ca. 20%) in which the strands were fully synthesized in vitro. (32)P-label transfer ("nearest-neighbor") experiments demonstrated that at least a part of the material synthesized in vitro contained ribonucleic acid-DNA junctions. DNA pulse-labeled in vivo in a mutant capable of taking up thymidine 5'-monophosphate, sedimented in alkali at 4S, as in the case of the in vitro experiments.

Replicative deoxyribonucleic acid synthesis in isolated mitochondria from Saccharomyces cerevisiae

The characteristics of a system for the in vitro synthesis of mitochondrial deoxyribonucleic acid (mtDNA) in mitochondria isolated from Saccharomyces cerevisiae are described. In this system the exclusive product of the reaction is mtDNA. Under optimal conditions the initial rate of synthesis is close to the calculated in vivo rate; the rate is approximately linear for 20 min but then decreases gradually with time. DNA synthesis proceeds for at least 60 min and the de novo synthesis of an amount of mtDNA equivalent to 15% of the mtDNA initially present is achieved. The rate and extent of synthesis observed with mitochondria isolated from grande and petite (rho(-)) strains were similar. The mode of DNA synthesis is semiconservative; after density labeling with 5-bromodeoxyuridine triphosphate, in vitro, the majority of labeled DNA fragments of duplex molecular weight, 6 x 10(6), are of a density close to that calculated for hybrid yeast mtDNA. The density label is incorporated into one strand of the duplex molecules. These properties indicate that the synthesis resembles replicative rather than repair synthesis. This system therefore provides a convenient method for the study of mtDNA synthesis in S. cerevisiae. The observation that mtDNA synthesis is semiconservative in vitro suggests that the dispersive mode of synthesis observed in S. cerevisiae in vivo labeling studies is the result of some other process, possibly a high recombination rate.

Differential chromosomal and mitochondrial DNA synthesis in temperature-sensitive mutants of Ustilago maydis

The amount and type of residual DNA synthesis was determined in eight temperature-sensitive mutants of the smut fungus Ustilago maydis after incubation at the restrictive temperature (32 degrees C) for eight hours. Mutants ts-220, ts-207, ts-432 and ts-346 were found to have an overall reduction in the synthesis of both nuclear and mitochondrial DNA comparison to the wild-type. In mutants ts-20, tsd 1-1, ts-84 and pol 1-1 nuclear DNA synthesis was depressed relative to mitochondrial synthesis. The DNA-polymerase mutant pol 1-1 had persistent nuclear synthesis at about 50% of the rate of synthesis of mitochondrial DNA and similar behavior was observed in a diploid homozygous strain. Mutant ts-84 had an initial burst of DNA synthesis which was reduced for nuclear but not mitochondrial synthesis after three hours preincubation at 32 degrees C. tsd 1-1 and ts-20 had nuclear residual synthesis amounting to about 25% of the relative rate of mitochondrial synthesis which correlates to increasing UV sensitivity of these strains on incubation at 32 degrees C. A pol 1-1 ts-84 double mutant had an additive loss of nuclear DNA synthesis which indicates that the steps of replication involved may be sequential.

DNA polymerase of Ustilago maydis: partial characterization of the enzyme and a pol 1 mutation

The major DNA polymerase activity of wild-type U. maydis has been extensively purified. It possesses a molecular weight of about 150,000 daltons and appears to require a DNA primer with a 3'-hydroxyl terminus as well as a template. The polymerase activity has also been purified from the pol 1-1 strain, which is temperature sensitive fro growth and DNA synthesis, and which at the restrictive temperature contains only 10-25% levels of the DNA polymerase activity obtained from wild-type strains. It was similar in all properties studied, except that the activity was thermolabile at 40 degrees C compared to that from the wild-type strain. Physiological studies on the mutant showed that it was only slightly sensitive to UV, ionising radiation and nitrosoguanidine at the permissive temperature, and was proficient in genetic recombination. The results suggest that the pol 1-1 gene product does not play an important role in repair and recombination processes within the cell, and that its primary function lies in replication.