Biogenesis of mitochondria: XXV. Studies on the mitochondrial genomes of petite mutants of yeast using ethidium bromide as a probe

This paper describes investigations into the effects of ethidium bromide on the mitochondrial genomes of a number of different petite mutants derived from one respiratory competent strain of Saccharomyces cerevisiae. It is shown that the mutagenic effects of ethidium bromide on petite mutants occur by a similar mechanism to that previously reported for the action of this dye on grande cells. The consequences of ethidium bromide action in both cases are inhibition of the replication of mitochondrial DNA, fragmentation of pre-existing mitochondrial DNA, and the induction, often in high frequency, of cells devoid of mitochondrial genetic information (ρ ° cells).The susceptibility of the mitochondrial genomes to these effects of ethidium bromide varies in the different clones studied. The inhibition of mitochondrial DNA replication requires higher concentrations of ethidium bromide in petite cells than in the parent grande strain. Furthermore, the susceptibility of mitochondrial DNA replication to inhibition by ethidium bromide varies in different petite clones.It is found that during ethidium bromide treatment of the suppressive petite clones, the over-all suppressiveness of the cultures is reduced in parallel with the reduction in the over-all cellular levels of mitochondrial DNA. Furthermore, ethidium bromide treatment of petite clones carrying mitochondrial erythromycin resistance genes (ρ^?ER^r) leads to the elimination of these genes from the cultures. The rates of elimination of these genes are different in two ρ^?ER^r clones, and in both the gene elimination rate is slower than in the parent ρ⁺ ER^r strain. It is proposed that the rate of elimination of erythromycin resistance genes by ethidium bromide is related to the absolute number of copies of these genes in different cell types. In general, the more copies of the gene in the starting cells, the slower is the rate of elimination by ethidium bromide. These concepts lead us to suggest that petite mutants provide a system for the biological purification of particular regions of yeast mitochondrial DNA and of particular relevance is the possible purification of erythromycin resistance genes.     

Biogenesis of mitochondria

Summary The action of ethidium bromide and berenil on the mitochondrial genome of Saccharomyces cerevisiae has been compared in three types of study: (i) early kinetics (up to 4 h) of petite induction by the drugs in the presence or absence of sodium dodecyl sulphate; (ii) genetic consequences of long-term (8 cell generations) exposure to the drugs; (iii) inhibition of mitochondrial DNA replication, both in whole cells and in isolated mitochondria.The results have been interpreted as follows. Firstly, the early events in petite induction differ markedly for the two drugs, as indicated by differences in the short-term kinetics. After some stage a common pathway is apparently followed because the composition of the population of petite cells induced after long-term exposure are very similar for both ethidium bromide and berenil. Secondly, both drugs probably act at the same site to inhibit mitochondrial DNA replication, in view of the fact that a petite strain known to be resistant to ethidium bromide inhibition of mitochondrial DNA replication was found to have simultaneously acquired resistance to berenil. From consideration of the drug concentrations needed to inhibit mitochondrial DNA replication in vivo and in vitro it is suggested that in vivo permeability barriers impede the access of ethidium bromide to the site of inhibition of mitochondrial DNA replication, whilst access of berenil to this site is facilitated. The site at which the drugs act to inhibit mitochondrial DNA replication may be different from the site(s) involved in early petite induction. Binding of the drugs at the latter site(s) is considered to initiate a series of events leading to the fragmentation of yeast mitochondrial DNA and petite induction.     

GC clusters and the stability of mitochondrial genomes of<Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> and related yeasts

The occurrence of GC clusters inSaccharomyces spp. and related yeasts was examined to clarify their association with the stability of intact mitochondrial genome. Abundance of nonspecific or specific GC clusters in these species decreases with phylogenetic distance fromS. cerevisiae. Their number but not the number of replication origins correlates with the ability to form respiration-deficient mutants induced by ethidium bromide. This effect is not associated with the nuclear background since the cybrids having identical nuclei and mitochondria from different species gave similar results. In contrast to grand genomes, the presence of GC clusters in ρ^- mutants does not play any role in ethidium bromide induced mtDNA loss. The most plausible explanation for mitotically lost petite mtDNA seems to be dilution during the distribution.     

Assessment of the distribution of nucleic acid intercalators in yeast cells by pseudospectral image analysis

The intracellular location of nucleic acid intercalators (NAI) in native (not fixed) Saccharomyces cerevisiae cells has been studied using fluorescence microscopy combined with computer pseudospectral image analysis. Three NAI: anthracycline anticancer drug doxorubicin and nucleic acid dyes ethidium bromide and 4′,6-diamidino-2-phenylindole (DAPI) were used. All three NAI were shown to be localized in nuclei and mitochondria. In contrast to DAPI, which interacted only with DNA, a large fraction of doxorubicin and ethidium bromide apparently bound to mitochondrial membranes. Upon combined application, competition between these intercalators for binding sites in the nuclear and mitochondrial DNA occurred. It was concluded that this approach may be used in designing new DNA-targeted drugs and in preliminary studies of their interaction with eukaryotic cells.     

Mechanism of Mitochondrial Mutation in Yeast

THE yeast Saccharomyces cerevisiae can mutate to the respiratory-incompetent petite colony form. The mutation is probably caused by damage to, or loss of, the yeast's mitochondrial DNA, for petite mutants often lack mitochondrial DNA, possess it in abnormal amounts or with abnormal buoyant density¹. Some of the agents, such as acrifiavine or ethidium bromide, which induce the petite mutation interfere with mitochondrial DNA synthesis^2,3 whereas ethidium bromide also causes or permits degradation of Saccharomyces cerevisiae mitochondrial DNA^2,3. We have observed that nalidixate (50 µg/ml.), an inhibitor of DNA synthesis, can prevent or delay petite mutation induced by ethidium bromide⁴. A similar effect has been observed by Hollenberg and Borst using a higher nalidixate concentration⁵. We have investigated the mechanism of this effect. A diploid prototrophic strain of Saccharomyces cerevisiae (NCYC 239) was used throughout.     

Comparative studies of the effects of acridines and other petite inducing drugs on the mitochondrial genome of Saccharomyces cerevisiae.

Summary The effects of the acridines euflavine and proflavine on mitochondrial DNA (mtDNA) replication and mutation inSaccharomyces cerevisiae have been compared. In contrast to previous results we found that under our conditions proflavine can indeed induce high levels (>80%) of petite mutants, although six times less efficiently than euflavine. The parameters measured for mutagenesis of the mitochondrial genome and inhibition of mtDNA replication in whole cells suggest that the modes of action of euflavine and proflavine are very similar. After extended (18h) treatment of growing cells with each drug the percentage loss of mtDNA or genetic loci was almost coincidental with the extent of petite induction.It was found that proflavine is equally as effective as euflavine in inhibiting mtDNA replication in isolated mitochondria in contrast to the differential between the drugs observed in vivo. However, proflavine and euflavine inhibit cellular growth at almost the same concentrations. It is therefore proposed that there is some intracellular permeability barrier which impedes proflavine access to the mitochondrial DNA replicating system.The petites induced by euflavine (and proflavine) are characterized by there being a preferential induction ofrho ⁰ petites lacking mtDNA as opposed torho ^- petites retaining mtDNA. This is in contrast to the relative proportions of such petites induced by ethidium bromide or berenil. A scheme for the production of petites by euflavine is presented, in which euflavine inhibits the replication of mtDNA, but does not cause direct fragmentation of mtDNA (unlike ethidium bromide and berenil). The proposed scheme explains the production of the high frequency ofrho ^o cells, as well as therho ^- cells induced by euflavine. The scheme also accounts for previous observations that euflavine only mutants growing cultures, and that the buds, but not mother cells, become petite.     

Mitochondrial DNA replication in petite mutants of yeast: Resistance to inhibition by ethidium bromide, berenil and euflavine

Summary Mitochondrial DNA (mtDNA) replication in petite mutants ofSaccharomyces cerevisiae is generally less sensitive to inhibition by ethidium bromide than in grande (respiratory competent) cells. In every petite that we have examined, which retain a range of different grande mtDNA sequences, this general phenomenon has been demonstrated by measurements of the loss of mtDNA from cultures grown in the presence of the drug. The resistance is also demonstrable by direct analysis of drug inhibition of mtDNA replication in isolated mitochondria. Furthermore, the resistance to ethidium bromide is accompanied, in every case tested, by cross-resistance to berenil and euflavine, although variations in the levels of resistance are observed.In one petite the level of in vivo resistance to the three drugs was very similar (4-fold over the grande parent) whilst another petite was mildly resistant to ethidium bromide and berenil (each 1.6-fold over the parent) and strongly resistant (nearly 8-fold) to inhibition of mtDNA replication by euflavine. The level of resistance to ethidium bromide in several other petite clones tested was found to vary markedly. Using genetic techniques it is possible to identify those petites which display an enhanced resistance to ethidium bromide inhibition of mtDNA replication.It is considered that the general resistance of petites arises because a product of mitochondrial protein synthesis is normally involved in facilitating the inhibitory action of these drugs on mtDNA synthesis in grande cells. The various levels of resistance in petites may be modulated by the particular mtDNA sequences retained in each petite.     

Effects of netropsin on yeast mitochondria

Netropsin binds tightly to AT rich regions of DNA and correspondingly is an efficient inhibitor of mitochondrial DNA replication in $\text{Saccharomyces}\text{cerevisiae}$. Netropsin treatment does not cause formation of large populations of petite cells. However, a large portion of cells grown in cultures with ethanol as carbon source are killed by 1 μg/ml netropsin. When petite induction by berenil or ethidium bromide is carried out in the presence of netropsin, the petite cells are killed. This appears to be an effect of netropsin action on the cells during the process of petite formation.     

The role of the HCR system in the repair of lethal lesions ofBacillus subtilis phages and their transfecting DNA damaged by radiation and alkylating agents

The role of the HCR system in the repair of prelethal lesions induced by UV-light, γ-rays and alkylating agents was studied in theBacillus subtilis SPP1 phage, its thermosensitive mutants (N3, N73 endts ₁) and corresponding infectious DNA. The survival of phages and their transfecting DNA after treatment with UV light is substantially higher inhcr ⁺ cells than inhcr cells, the differences being more striking in intact phages than in their transfecting DNA’s. Repair inhibitors reduce the survival inhcr ⁺ cells: caffeine lowers the survival of UV-irradiated phage SPP1 in exponentially growinghcr ⁺ cells but has no effect on its survival in competenthcr ⁺ cells; acriflavin and ethidium bromide decrease the survival of UV-irradiated SPP1 phage in both exponentially growing and competenthcr ⁺ cells to the level of survival observed inhcr cells; moreover, ethidium bromide lowers the number of infective centres inhcr ⁺ cells of UV-irradiated DNA of the SPP1 phage. Repair inhibitors do not lower the survival of UV-irradiated phages or their DNA inhcr cells. The repair mechanism under study repairs effectively also lesions induced by polyfunctional alkylating agents in transfecting DNA’s ofB. subtilis phages but is not functional with lesions induced by these agents in free phages and lesions caused in phages and their DNA by ethyl methanesulphonate or γ-rays.     

Mitochondrial DNA synthesis during fungal spore germination

Summary Germinating spores of the fungus Botryodiplodia theobromae incorporated guanine-8-C¹⁴ into both the nuclear DNA and mitochondrial DNA fractions. Ethidium bromide inhibited the synthesis of mitochondrial DNA without having a significant effect on nuclear DNA synthesis or on the rate and extent of spore germination. Rates of leucine and uracil incorporation and of oxygen uptake were not significantly affected by ethidium bromide until germination was nearly completed. Mitochondrial DNA synthesis is apparently not required for germination of the spores of B. theobromae but is probably essential to continued vegetative growth.Abbreviations DNA deoxyribonucleic acid - mit-DNA mitochondrial DNA - nuc-DNA nuclear DNA - RNA ribonucleic acid - EB ethidium bromide - Tris tris (hydroxymethyl)aminomethane Published with the approval of the Director as Paper No. 3331, Journal Series, Nebraska Agricultural Experiment Station. Research reported was conducted under Project No. 21-17. Paper No. 7877, Scientific Journal Series, Minnesota Agricultural Experiment Station.     

The reversibility of the ethidium bromide-induced alterations of mitochondrial structure and function in the cellular slime mold,Dictyostelium discoideum

Addition of ethidium bromide to ameboid cultures of the slime mold,Dictyostelium discoideum, caused a cessation of cell division after 1 or 2 generations. The replication of mitochondrial DNA was immediately blocked as indicated by the 50% decrease in the DNA content of purified mitochondria from ethidium-bromide-treated cultures. The activity of the respiratory chain was also inhibited, resulting in a 75% decrease in cyanide-sensitive whole cell respiration. Spectral analysis at low temperature indicated that the amount of cytochromec ₁ was decreased 80% and that of cytochromec increased 100% in mitochondria from treated cells. Two cytochromesb absorbing at 556 and 561 nm were observed in mitochondria from both control and ethidium-bromide-treated cultures. The content of cytochromeb ₅₆₁ appeared to decline more than didb ₅₅₆, but it is hard to quantitate the decrease. The effects of ethidium bromide were fully reversible. When the drug was removed, the cells resumed a normal growth rate without any discernible lag. The activity of oligomycin-sensitive ATPase, cytochrome oxidase, and succinate-cytochrome-c reductase as well as the cytochrome content began to increase after 1 day returning to control levels within 5 days. Electron micrographs of whole cells treated with ethidium bromide revealed that mitochondrial profiles were elongated and had greatly reduced cristae. Numerous membrane whorls were apparent, as was a profound loss of rough endoplasmic reticulum. Three days after removal of ethidium bromide, mitochondria were again ovoid in shape and contained well-developed cristae. In all of the cells during recovery, there was a single large vacuole that appeared to enclose a large portion of the cell volume, forming a new cellular compartment that may simplify the breakdown of previously damaged organelles.This work is in partial fulfillment of the requirements for the Doctor of Philosophy degree at the City University of New York.     

Mitochondrial membranes and mutagenesis by ethidium bromide

The conversion of wild type (ρ⁺) to cytoplasmic petites (ρ^?) in Saccharomyces cerevisiae, à mutation in mitochondrial DNA, can be brought about with high efficiency by low concentrations of ethidium bromide (EB). The rate and extent of mutagenesis and its expression can be influenced, and even reversed, by a number of genetic lesions, agents or treatments affecting mitochondrial structure and metabolism. Among them are incubation at 45°, exposure to Antimycin A, growth on different carbon sources and the presence or absence of 2 different gene products previously implicated in the repair of UV induced lesions in mitochondrial DNA. Based on these observations a model for EB mutagenesis is advanced which postulates a complex between mitochondrial DNA and the inner membrane as the target susceptible to modification by EB. This model predicts that altered membranes should lead to changes in the susceptibility of cells to the mutagenic action of EB. This prediction has been verified by comparing cells that contain one of 2 structurally quite distinct monounsaturated C₁₈ fatty acids in their mitochondrial phospholipids: greater resistance to mutagenesis and ease of thermal protection is exhibited when cells – and mitochondria – contain oleic (Δ⁹cis, m.p. < 5°) rather than petroselinic (Δ⁶cis, m.p. 28°) acid in their phospholipids. As a corollary, studies on EB mutagenesis and mitochondrial DNA may be used as probes for the mitochondrial inner membrane to reveal some perhaps novel functions.     

Cytoplasmic inheritance of antimycin A resistance in Saccharomyces cerevisiae

Summary Three antimycin resistant mutants of Saccharomyces cerevisiae are characterized genetically. The mutations have been shown to be cytoplasmically inherited by four criteria. The phenotype persists in diploids formed by a cross with a ⁰ strain of yeast of the opposite mating type. Diploids heterozygous for the antimycin marker, however, show segregation of the resistance and sensitivity during mitosis. Tetrad analysis indicated a non-Mendelian segregation (4:0 and 0:4) of the mutations. The antimycin marker can be eliminated by ethidium bromide treatment under conditions that should have deleted all of the mitochondrial DNA.     

Studies on the induction of petite mutants in yeast by analogues of berenil

Summary Compound Hoe 15 030 is an analogue of berenil which is as effective as berenil in inducing petite mutants in Saccharomyces cerevisiae. Hoe 15 030 has greater stability than berenil in aqueous solution, and is less toxic to yeast at high drug concentrations. Mutants of S. cerevisia strain J69-1B have been isolated which are resistant to the petite inducing effects of Hoe 15 030. Three mutant strains (HR7, HR8 and HR10) were characterized and each was shown to carry a recessive nuclear mutation determining resistance to Hoe 15 030. The degree of resistance to Hoe 15 030 is different for each mutant, and each was found to be co-ordinately cross-resistant both to berenil and to another analogue of berenil, Hoe 13 548. However, the three mutants show no cross-resistance to other unrelated petite inducing drugs, including ethidium bromide, euflavine and 1-methyl phenyl neutral red.Further studies on the mutants revealed that each strain exhibits characteristic new properties indicative of changes in mitochondrial membrane functions concerned with the replication (and probably also repair) of mitochondrial DNA. Thus, mutant HR7 is hypersensitive to petite induction by the detergent sodium dodecyl sulphate under conditions where the parent J69-1B is unaffected by this agent. Mutant HR8 is even more sensitive to sodium dodecyl sulphate than is HR7, and additionally shows a markedly elevated spontaneous petite frequency. Isolated mitochondria from strains HR8 and HR10 (but not HR7) show resistance to the inhibitory effects of Hoe 15 030 on the replication of mitochondrial DNA in vitro.     

Janus green resistance in Saccharomyces cerevisiae: interaction of nuclear and cytoplasmic factors.

Summary Janus green B was found to be a specific inhibitor of mitochondrial function in yeast. This is consistent with the Janus green specificity in supravital staining of mitochondria.A mutant of S. cerevisiae resistant to Janus green B was isolated. It shows cross resistance to oligomycin, ethidium bromide and a weak resistance to chloramphenicol. The mutant was found to be sensitive to cycloheximide and erythromycin.Genetic analysis of this mutant showed that mitochondrial genes are not involved in the determination of Janus green resistance. Tetrad analysis suggested that two or more nuclear genes are concerned, but many unusual genetic features suggestive of the involvement of a cytoplasmic element remain to be explained.     

Excision sequences in the mitochondrial genome of yeast

We report an analysis of the sequences used in the excision of the mitochondrial genomes of 22 spontaneous and ten ethidium bromide (EtBr)-induced Saccharomyces cerevisiae petite mutants. In all cases, excision sequences were found to be perfect direct repeats, often flanked on one or both sides by regions of patchy homology. Sequences used in the excision of the genomes of spontaneous petites were always located in the AT spacers and GC clusters of intergenic regions of the genome; the GC clusters corresponded to ori and ori^s sequences, namely to canonical and surrogate origins of DNA replication, respectively. In the case of the ethidium bromide-induced petites, excision sequences were found not only in intergenic sequences, but also in the introns and exons of mitochondrial genes.     

Induction of respiration deficient mutants in Saccharomyces cerevisiae by Berenil

Summary Some characteristic details of mutagenesis by Berenil, a non-intercalating trypanocidal dye, that govern the change from wild type (⁺) to vegetative petite (^–) in Saccharomyces cerevisiae are presented and contrasted with the intercalating mutagens ethidium bromide and euflavine.The extent and rate of mutagenesis by Berenil is affected by a variety of parameters controlling the cellular and mitochondrial phenotype: among them are exposure to 45°; competition with EB but not euflavine; a requirement for an energy source during and subsequent to exposure to the mutagen; exposure to caffeine; and the presence of genetic blocks in various steps of the mitochondrial repair system for uv-induced lesions. It is, however, insensitive to exposure to Antimycin A. Except for the first of these observations, qualitative differences have emerged between the responses induced by Berenil and the other mutagens, especially ethidium bromide.Using these observations we have postulated a stepwise sequence of events that can account for the mutagenic action of Berenil.Publication No. 2122.     

Evidence for plasmid-associated lactose metabolism inLactobacillus casei subsp.casei

Lac variants ofLactobacillus casei subsp.casei DR1002 (formerly 64H) have been produced using acriflavin, ethidium bromide, mitomycin C, or combinations of these agents. Two successive transfers in the presence of acriflavin and mitomycin C or ethidium bromide and mitomycin C resulted in nearly a 100% loss of lactose fermentation. Cesium chloride-ethidium bromide isopycnic gradient ultracentrifugal analysis of purified lysates demonstrated that the 23-mdal plasmid (pDR101) found inL. casei DR1002 was consistently absent in Lac⁻ clones. We concluded that, as in lactic streptococci, lactose metablism is a plasmid-mediated train inL. casei DR1002.     

Effects of Ethidium Bromide and Several Acridine Dyes on the Kinetoplast DNA of Leishmania tropica*†

Whole cell DNA from Leishmania tropica has 2 peaks when banded by CsCl equilibrium density centrifugation. The main band has a buoyant density of 1.721 and the satellite band a buoyant density of 1.705, with Clostridium perfringens DNA (ρ= 1.6915) used as a reference. The satellite band has been identified as the kinetoplast DNA by purifying DNA from isolated kinetoplasts. L. tropica has the highest G + C content of both nuclear and kinetoplastic DNA thus far reported for trypanosomatids. The effects of ethidium bromide, acriflavin, proflavin, and 5-aminoacridine on the kinetoplast of L. tropica have been compared. Ethidium bromide and acriflavin, but not proflavin or 5-aminoacridine, induce dyskinetoplasty. L. tropica is one of the most sensitive trypanosomatids to ethidium bromide and acriflavin. Examination of the DNA from drug-treated cells in CsCl gradients revealed a loss of the satellite band after ethidium bromide or acriflavin treatment, but not after proflavin or 5-aminoacridine treatment. Cell division was required to produce these effects on the kinetoplast.     

Ethidium bromide-induced loss of mitochondrial DNA from primary chicken embryo fibroblasts.

Chicken embryo fibroblasts in uridine-containing medium are inherently resistant to the growth-inhibitory effect of ethidium bromide. The drug was found to inhibit the incorporation of [3H]thymidine into mitochondrial DNA circular molecules. Mitochondrial DNA was quantitated by DNA-DNA reassociation kinetics with a probe of chicken liver mitochondrial DNA. A mean number of 604 copies of mitochondrial DNA per cell was found. This number decreased progressively in cells exposed to ethidium bromide, and by day 13 ca. one copy of mitochondrial DNA was detected per cell. When the cells were then transferred to drug-free medium, the number of copies increased very slowly as a function of time. On the other hand, analyses of DNA extracted from cell populations exposed to ethidium bromide for 20 or more days, with or without subsequent transfer to drug-free medium, revealed very little or no mitochondrial DNA by reassociation kinetics or by Southern blot hybridization of AvaI- or HindIII-digested total cellular DNA. As a result of the elimination of mitochondrial DNA molecules, the establishment of cell populations with a respiration-deficient phenotype was confirmed by measuring cytochrome c oxidase activity as a function of the number of cell generations and the absorption spectrum of mitochondrial cytochromes.