Mitochondrial DNA and suppressiveness of petite mutants in Saccharomyces cerevisiae

Mitochondrial depolarization in yeast zygotes inhibits clonal expansion of selfish mtDNA

Non-identical copies of mitochondrial DNA (mtDNA) compete with each other within a cell and the ultimate variant of mtDNA present depends on their relative replication rates. Using yeast Saccharomyces cerevisiae cells as a model, we studied the effects of mitochondrial inhibitors on the competition between wild-type mtDNA and mutant selfish mtDNA in heteroplasmic zygotes. We found that decreasing mitochondrial transmembrane potential by adding uncouplers or valinomycin changes the competition outcomes in favor of the wild-type mtDNA. This effect was significantly lower in cells with disrupted mitochondria fission or repression of the autophagy-related genes ATG8, ATG32 or ATG33, implying that heteroplasmic zygotes activate mitochondrial degradation in response to the depolarization. Moreover, the rate of mitochondrially targeted GFP turnover was higher in zygotes treated with uncoupler than in haploid cells or untreated zygotes. Finally, we showed that vacuoles of zygotes with uncoupler-activated autophagy contained DNA. Taken together, our data demonstrate that mitochondrial depolarization inhibits clonal expansion of selfish mtDNA and this effect depends on mitochondrial fission and autophagy. These observations suggest an activation of mitochondria quality control mechanisms in heteroplasmic yeast zygotes.

The [KIL-d] cytoplasmic genetic element of yeast results in epigenetic regulation of viral M double-stranded RNA gene expression

[KIL-d] is a cytoplasmically inherited genetic trait that causes killer virus-infected cells of Saccharomyces cerevisiae to express the normal killer phenotypes in a/alpha cells, but to show variegated defective killer phenotypes in a or alpha type cells. Mating of [KIL-d] haploids results in "healing" of their phenotypic defects, while meiosis of the resulting diploids results in "resetting" of the variegated, but mitotically stable, defects. We show that [KIL-d] does not reside on the double-stranded RNA genome of killer virus. Thus, the [KIL-d] effect on viral gene expression is epigenetic in nature. Resetting requires nuclear events of meiosis, since [KIL-d] can be cytoplasmically transmitted during cytoduction without causing defects in killer virus expression. Subsequently, mating of these cytoductants followed by meiosis generates spore clones expressing variegated defective phenotypes. Cytoduction of wild-type cytoplasm into a phenotypically defective [KIL-d] haploid fails to heal, nor does simultaneous or sequential expression of both MAT alleles cause healing. Thus, healing is not triggered by the appearance of heterozygosity at the MAT locus, but rather requires the nuclear fusion events which occur during mating. Therefore, [KIL-d] appears to interact with the nucleus in order to exert its effects on gene expression by the killer virus RNA genome.

Replicator regions of the yeast mitochondrial DNA responsible for suppressiveness

Hypersuppressiveness is a heritable property of some rho- mutants (called HS) that, in crosses to rho+, give rise to about 100% rho- cells. The mtDNAs of all HS rho- mutants reveal a common organization: they all share a homologous region of about 300 base pairs (called rep) and the fragments retained are always short (ca. 1% of the wild-type genome) and tandemly repeated. Using one HS rho- mutant as an example, we show that, after crosses with rho+ strains, the mitochondrial genome of the progeny is indistinguishable from that of the HS parent. This suggests that HS mtDNA molecules have a decisive selective advantage for replication during the transient heteroplasmic stage that follows zygote formation, the rep regions playing a role in the control of replication initiation of the mtDNA molecules. The complete nucleotide sequence of one HS rho- mutant and its localization in the oli1-rib3 segment of the rho+ mitochondrial genome are presented. Comparison of the nucleotide sequences of the rep regions of two different HS rho- mutants reveals that several rep sequences must exist in the wild-type genome, probably as a result of duplications of an originally unique ancestor.

Fine structure of the 21S ribosomal RNA region on yeast mitochondrial DNA. II. The organization of sequences in petite mitochondrial DNAs carrying genetic markers from the 21S region

We have investigated the organization of sequences in ten rho- petite mtDNAs by restriction enzyme analysis and electron microscopy. From the comparison of the physical maps of the petite mtDNAs with the physical map of the mtDNA of the parental rho+ strain we conclude that there are at least three different classes of petite mtDNAs: I. Head-to-tail repeats of an (almost) continuous segment of the rho+ mtDNA. II. Head-to-tail repeats of an (almost) continuous segment of the rho+ mtDNA with a terminal inverted duplication. III. Mixed repeats of an (almost) continuous rho+ mtDNA segment. In out petite mtDNAs of the second type, the inverted duplications do not cover the entire conserved rho+ mtDNA segment. We have found that the petite mtDNAs of the third type contain a local inverted duplication at the site where repeating units can insert in two orientations. At least in one case this local inverted duplication must have arisen by mutation. The rearrangements that we have found in the petite mtDNAs do not cluster at specific sites on the rho+ mtDNA map. Large rearrangements or deletions within the conserved rho+ mtDNA segment seem to contribute to the suppressiveness of a petite strain. There is also a positive correlation between the retention of certain segments of the rho+ mtDNA and the suppressiveness of a petite strain. We found no correlation between the suppressiveness of a petite strain and its genetic complexity. The relevance of these findings for the mechanism of petite induction and the usefulness of petite strains for the physical mapping of mitochondrial genetic markers and for DNA sequence analysis are discussed.

Pet18: a chromosomal gene required for cell growth and for the maintenance of mitochondrial DNA and the killer plasmid of yeast

Mutations in the pet18 gene of Saccharomyces cerevisiae (formerly denoted pets) confer three phenotypes on mutant strains: (i) inability to respire (petite), (ii) inability to maintain the double-stranded RNA killer plasmid (sensitive), and (iii) temperature sensitivity for growth. We find that pet18 mutants lack mitochondrial DNA. However, despite their inability to maintain the killer RNA plasmid and mitochondrial DNA, pet18 mutants still can carry the other yeast plasmids, [URE3--1], [PSI], and 2-micron DNA. The temperature sensitivity of the pet18 mutants is not expressed as a selective defect in total DNA, RNA, or protein synthesis.

Detection of specific DNA sequences in yeast by colony hybridization

A procedure is described for the detection of specific DNA sequences in Saccharomyces cerevisiae. This method allows a rapid screening of a large number of yeast colonies. The yeast cells of each colony, grown on nitrocellulose filters, are converted, in situ, to protoplasts by snail enzyme, and are then lysed and their DNAs are denatured and fixed on the filter. The presence of the specific DNA sequence is detected directly on the filter by hybridization with a radioactive cRNA. We have used successfully this technique to detect the presence or the absence of specific mt DNA sequences in p+, p- and p0 strains, and to detect the presence or the absence of the 2 mum DNA sequences in different strains.

Mapping of the two mitochondrial antimycin A resistance loci in Saccharomyces cerevisiae

Retention or loss of the two new mitochondrial antimycin A resistance loci AI and AII has been analyzed in a large number of stable cytoplasmic petite mutants. Using these deletion mutants it was possible to localize the two antimycin A resistance loci in the OI--OII region of mitochondrial DNA. The genetic loci are mapped in the following order: OII--AI--AII--cobl--OI. The mapping relationship of mutants resistant to antimycin A or funiculosin to various cob mutants is described.

Effect of genetic and physiological manipulations onthe kinetic and binding parameters of the adenine nucleotide translocator in Saccharomyces cervisiae and Candida utilis

1. Ghe kinetic and binding parameters of adenine-nucleotide transport have been studied in mitochondria isolated from yeast cells in which the mitochondrial protein-synthetizing system had been inhibited by growth in the presence of erythromycin. These parameters have also been studied in promitochondria isolated from yeast grown in anaerobiosis aesence of ethidium bromide results in a loss of cytochromes b, alpha and alpha 3, but it does not affect the rate constant of ADP transport in isolated mitochondria, nor the number of binding sites for atractyloside, bongkrekic acid and ADP. 3. Promitochondria from S. cerevisiae grown in anaerobiosis, mitochondria from a qo mutant (qo mitochondria) and mitochondria from S. cerevisiae grown in the presence of erythromycin (ERY-mitochondria) are able to transport ADP by the same exchange-diffusion mechanism, sensitive to carboxy-atractyloside, and with the same rate constant as the wild type mitochondria. Promitochondria, qo mitochondria and ERY-mitochondria bind atractyloside, bongkrekic acid and ADP with the same high affinity as the wild type mitochondria. They only differ from the wild type mitochondria by a lower number of binding sites for ADP and for specific inhibitors of ADP transport. 4. Mitochondria isolated from the nuclear mutant p9 of S. cerevisae, called also op1, are characterized by a much lower affinity for bongkrekic acid than mitochondria from the wild type (20 times less). 5. Manipulation of the fatty acid composition of the mitochondrial membranes in the desaturase auxotroph mutant KD115 does not modify the number of sites, no their affinity of bongkrekic acid. 6. The above results are interpreted to mean that the structure and function of the mitochondrial adN translocator are not affected by any change in the mitochondrial protein synthetizing system.

The molecular events involved in the induction of petite yeast mutants by fluorinated pyrimidines

The fluorinated pyrimidines 5-fluorouracil (5FU) and 5-fluorocytosine (5FC) induce the cytoplasmic petite mutation in the yeast Saccharomyces cerevisiae with high efficiency. It was found that in order to induce the mutation, 5FC must first be deaminated to 5FU. However, mutagenesis does not depend on the further conversion of 5FU to its deoxyriboside (5FUDR) and subsequent blockade of intracellular thymidine synthesis, since 5FUDR itself was found not to be mutagenic, and 5FU-induced mutagenesis was not antagonised by supplying thymidine monophosphate (dTMP) to a dTMP permeable strain. In any case, observations of the molecular changes accompanying petite induction in log phase cells ruled out the possibility that mutagenesis resulted simply from the dilution out of replication blocked mitDNA molecules, since the appearance of mutants coincided with the synthesis of altered mitDNA molecules. In different strains, the resulting defective molecules were either maintained, giving rise to suppressive rho- petites, or completely degraded, to give pure clones of neutral rho0 mutants. It is suggested that this degradative process was a conseuqence of the incorporation of 5FU into RNA.

Cytoplasmic inheritance of antimycin A resistance in Saccharomyces cerevisiae

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 pO 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 indicates 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.

Genetic analysis of mitochondrial biogenesis and function in Saccharomyces cerevisiae

Different mitochondrial mutants have been isolated that affect mitochondrial ribosome function. These mutants were used to establish most of the known methods and principles of mitochondrial genetics in yeast. Another class of mitochondrial mutants have been shown to affect mitochondrial ATPase and, more specifically, the "membrane factor" of mitochondrial ATPase. These mutants might be very useful in studying the energy-conserving function, and the interaction between the hydrophobic and hydrophylic parts, of the ATPase complex. New types of mitochondrial point mutations, concerning cytochrome a-a3 or b, will soon open up new fields of investigation. The biochemical and genetic analysis of numerous mutants belonging to that category and recently obtained [31] is being currently pursued in Tzagoloff's and Slonimski's laboratories.

Factors affecting petite induction and the recovery of respiratory competence in yeast cells exposed to ethidium bromide

When growing cultures of S. cerevisiae are treated with high concentrations of ethidium bromide (greater than 50 mug/ml), three phases of petite induction may be observed: I. the majority of cells are rapidly converted to petite, II. subsequently a large proportion of cells recover the ability to form respiratory competent clones, and III. slow, irreversible conversion of all cells to petite. The extent of recovery of respiratory competence observed is dependent on the strain of S. cerevisiae employed and the temperature and the carbon source used in the growth medium. The effects of 100 mug/ml ethidium bromide are also produced by 10 mug/ml ethidium bromide in the presence of the detergent, sodium dodecyl sulphate, and recovery is also observed when cells are treated with 10 mug/ml ethidium bromide under starvation conditions. Genetic analysis of strain differences indicates that a number of nuclear genes influence petite induction by ethidium bromide. In one strain, S288C, petite induction by 100 mug/ml ethidium bromide is extremely slow under certain conditions. Mitochondria isolated from from S288C lack the ethidium bromide stimulated nuclease activity found in D243-4A, a strain which shows triphasic kinetics of petite formation. This enzyme may, therefore, be responsible for the initial phase of rapid petite formation.

Molecular and genetic events accompanying petite induction and recovery of respiratory competence induced by ethidium bromide

The treatment of yeast cells with high levels of ethidium bromide causes a rapid induction of respiratory deficient mutants followed by a period of recovery to respiratory competence in 60 to 70% of the cells. Prolonged exposure then results in a final irreversible phase of petite formation. Sucrose gradient sedimentation analysis of 3H-adenine labelled mtDNA indicates that limited fragmentation (to about 16-18S) occurs during the initial phase of petite induction followed by a reassembly of the fragments during the period corresponding to the recovery of respiratory competence. The reassembly is associated with an ethidium bromide insensitive incorporation of 3H-adenine into mtDNA at a level consistent with repair synthesis. Genetic analyses, based on the transmission of five markers carried on the mtDNA of "repaired rho+" clones, suggests that reassembly occurs with a high degree of fidelity, though in two of a total of twenty five clones differences in marker transmission frequency were observed which could possibly reflect an altered gene order. In addition, a description is given of the marked changes in the suppressive nature of the treated cells and the temporary reduction in the capacity for marker transmission seen to accompany the transitory fragmentation of the mtDNA. The final phase of petite induction is an energy dependent degradation of the mtDNA to produce a rho degrees culture.

Alterations in mitochondrial DNA of yeast which accompany genetically and environmentally controlled changes in rho- mutability

Alterations in the physical characteristics of mitochondrial DNA accompanied increased spontaneous mutability to cytoplasmic respiratory-deficiency in yeast. Two systems were used to modify mutation rates, one physiological, the other genetic. Cells in log phase were shown to be more mutable than cells in stationary phase, and glucose-repressed cells were shown to be more mutable than unrepressed cells. A nuclear gene which acts as a mitochondrial mutator was found to increase spontaneous mutation rate by a factor of ten. An increase in endogenous formation of G+G-rich fragments of mt-DNA accompanied a physiological state conducive to higher mutability, and it is proposed that increased in vivo digestion of A+T-rich regions is involved in these alterations. Greater nuclease(s) activity accompanied the presence of the mutator gene, and it is proposed that this gene is concerned with the regulation of nuclease activity or with repair mechanisms.

The induction of mutation in yeast by hydrogen peroxide

The inactivation and mutation to respiratory deficiency of yeast cells by H2O2 are shown to vary progressively with the phase of cell growth, with a sharp transition occurring as the cells complete logarithmic growth. Respiratory deficient mutants isolated from the wild-type population are of two types, one of which is much more sensitive to H2O2 but forms only a small fraction of the mutant sub-population. Based upon the response of the more resistant type, mutation frequency increases appear to result from selection of pre-existing mutants in log phase populations, while induction occurs in stationary phase cells. The induced mutation frequency fits a (dose)2 relationship, but the frequency is depressed when the dose is high (or number of cells treated is low). All the induced mutants are extranuclear and of the resistant type, and show a wide range of suppressiveness in crosses to respiratory competent cells. This may indicate mitochondrial DNA is altered to different extents by H2O2; by the same criterion, the spontaneously occurring H2O2 -sensitive mutants retain a large amount of mitochondrial DNA information, in agreement with their colonial morphology. A small increase in forward mutation of nuclear genes was also found after H2O2 treatment. Parallels are drawn between the response of yeast cells to ionising radiation and to H2O2, and it is suggested that radical action may be involved in inactivation and mitochondrial genome mutation induced by both agents.

Biogenesis of mitochondria. 43. A comparative study of petite induction and inhibition of mitochondrial DNA replication in yeast by ethidium bromide and berenil

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.

Cytoplasmic inheritance in Saccharomyces cerevisiae: comparison of first zygotic budsite to mitochondrial inheritance patterns

Zygotic first budsite in Saccharomyces cerevisiae was studied in relation to defined mitochondrial inheritance systems: both petite and drug resistance. It was hypothesized that a highly asymmetric inheritance pattern would be correlated to a high frequency of first budsites on the petite or drug resistant end of the zygote (i.e., that portion of the zygote which was originally the drug resistant or petite haploid before zygote formation). The data collected did not support the hypothesis. For drug resistance, the budsite pattern is identical for a highly biased and a moderately biased inheritance pattern. In a grande by grande cross there is a high probability of the first bud appearing on the conjugation bridge, with lower but equal probabilities of the first bud appearing on one end or the other of the zygote. A grande by petite cross changes this pattern to a high probability of the first bud appearing on the grade end of the zygote, with a lesser probability of the first bud appearing on the conjugation bridge and virtually no budding of the petite end. This phenomenon is independent of degree of neutrality or suppressiveness of the petite strain used, however. The difference between a grande and a grande by petite pattern may be due to the relative functional ability of the mitochondria in each end of the zygote. Tests using antimitochondrial drugs suggest that selection of first budsite on a zygote is a complex phenomenon, not simply dependent upon mitochondrial phenotype. In conclusion, selection of the first zygotic budsite appears to be independent of mitochondrial inheritance patterns.

Saccharomyces cerevisiae petite mitochondrial DNA of suppressive and neutral haploids and of [rho-] diploids obtained from crossing [rho+] to a neutral petite

An unusual property of GR25a [rho+] was the production of 20 to 30 percent [rho-] zygote colonies when crossed to a tester strain lacking mitochondrial DNA. Spontaneous [rho-] isolates of GR25a [rho+] were observed to be highly suppressive and to contain mitochondrial DNA of a parental buoyant density (1.685 g/cm3). Three ethidium bromide induced neutral petites of GR25 a [rho+] did not have detectable mitochondrial DNA and were neutral in crosses to [rho+] strains. Seven [rho-] zygote colony isolates obtained from crossing GR25a [rho+] to a neutral peptite were shown to contain abnormal mitochondrial DNA. Six zygote colony isolates had mitochondrial DNA of a buoyant density less than, or equal to, GR25a (1.682 - 1.685 g/cm3), whereas one isolate had a buoyant density greater than GR25a (1.688 g/cm3). It was suggested that abnormal mitochondrial DNA is generated during the mating reaction.

Isolation and properties of a thymidylate-less mutant in Saccharomyces cerevisiae

A mutant, tmp3, has been isolated in Saccharomyces cerevisiae. Genetic and physiological analysis show that a single mendelian gene controls the multiple requirements for thymidylate, methionine, adenine and histidine and a neutral cytoplasmic petite character. Crude extracts of this mutant present a 60% decrease of serine transhydroxymethylase specific activity as compared to a wild-type strain.

Manganese mutagenesis in yeast. II. Conditions of induction and characteristics of mitochondrial respiratory deficient Saccharomyces cerevisiae mutants induced with manganese and cobalt

Manganese and cobalt are capable of inducing ρ−mutations* in non-growing cells ofSaccharomyces cerevisiae, but their mutagenic action is much stronger in growing cells. At a given concentration cobalt and manganese can be either strongly mutagenic or non-mutagenic, depending on the cell density.

Most of the ρ−mutants induced with manganese and a considerable proportion of those induced with cobalt are suppressive and/or transmit drug resistance markers, so they must still carry mitochondrial DNA. Cobalt can decrease suppressiveness with low efficiency and eliminate drug resistance markers from established ρ−clones.

Mitochondrial genetics in Bakers' yeast: a molecular mechanism for recombinational polarity and suppressiveness

Recombinational polarity and suppressiveness are two well-known but puzzling cytoplasmic genetic phenomena in bakers' yeast, Saccharomyces cerevisiae. Little progress has been made in characterizing the underlying molecular mechanisms of these phenomena. In this paper we describe a molecular model for recombinational polarity that is compatible with the available genetic evidence. The model stresses the role of small deletions and excision/repair processes in otherwise canonical recombinational events. According to the model, both phenomena require recombination and may share mechanistic elements.

Mitochondrial genetics, circular DNA and the mechanism of the petite mutation in yeast

We propose a general hypothesis involving properties of circular DNA which can explain such phenomena as thepetitemutation, suppressiveness, and the polarity observed in mitochondrial recombination in the yeastSaccharomyces cerevisiae. This hypothesis involves excision and insertion events between circular DNA molecules as well as structural rearrangements in the DNA generated by these events. The special properties of circular DNA have been considered in analysing recombination, and a number of results are obtained which are not intuitively apparent.

This hypothesis can be applied to any situation involving circular DNA such as bacterial plasmids and cytoplasmic circular DNAs, where the opportunity exists for recombination and rearrangement events.

Germination of yeast spores lacking mitochondrial deoxyribonucleic acid

A population of petite ascospores (mitochondrial deoxyribonucleic acid [mtDNA]-less), produced by brief ethidium bromide (EthBr) mutagenesis prior to transfer to sporulation medium, was used to examine the role of the mitochondrial genetic system on germination and outgrowth in Saccharomyces cerevisiae. Petite ascospores, which are morphologically indistinguishable by phase-contrast microscopy from wild-type spores, germinate and proceed through outgrowth at a rate and extent only slightly less than that of wild-type spores. Both developmental processes occurred in the absence of mtDNA synthesis and measurable cytochrome oxidase activity. These results indicate that neither respiration nor a functional mitochondrial genome are required for germination and outgrowth. The properties of the petite clones were typical of petites formed during vegetative growth. Individual sporal clones differed markedly from each other in suppressiveness. Petite sporal clones which exhibited a high degree of supressiveness also contained a reduced but detectable amount of mtDNA of altered buoyant density. One clone contained a unique mtDNA with a buoyant density higher than that of wild-type mtDNA.

Evidence for an extrakaryotic mutation affecting the maintenance of the rho factor in yeast

A newly isolated, temperature-sensitive mutant of a haploid strain of Saccharomyces cerevisiae is described. Its shift to nonpermissive temperature (35 C) resulted in an irreversible change to rho(-), causing, within four to six generations, more than 90% of the cells to form petite colonies. Genetic analysis revealed extrakaryotic inheritance of this temperature-sensitive mutation. Data presented indicate mutation of a gene in the mitochondrial deoxyribonucleic acid affecting the maintenance of the rho factor.