Etudes Sur La SuppressivitE Des Mutants a Deficience Respiratoire De La Levure. II. Etapes De La Mutation Grande En Petite Provoquee Par Le Facteur Suppressif

Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis

Reorganization of cellular proteins into subcellular compartments, such as the concentration of RNA-binding proteins into cytoplasmic stress granules and P-bodies, is a well-recognized, widely studied physiological process currently under intense investigation. One example of this is the induction of the yeast Nab3 transcription termination factor to rearrange from its pan-nucleoplasmic distribution to a granule at the nuclear periphery in response to nutrient limitation. Recent work in many cell types has shown that protein condensation in the nucleus is functionally important for transcription initiation, RNA processing, and termination. However, little is known about how subnuclear compartments form. Here, we have quantitatively analyzed this dynamic process in living yeast using a high-throughput computational tool and fluorescence microscopy. This analysis revealed that Nab3 granule accumulation varies in penetrance across yeast strains. A concentrated single granule is formed from at least a quarter of the nuclear Nab3 drawn from the rest of the nucleus. Levels of granule accumulation were inversely correlated with a growth defect in the absence of glucose. Importantly, the basis for some of the variation in penetrance was attributable to a defect in mitochondrial function. This publicly available computational tool provides a rigorous, reproducible, and unbiased examination of Nab3 granule accumulation that should be widely applicable to a variety of fluorescent images. Thousands of live cells can be readily examined enabling rigorous statistical verification of significance. With it, we describe a new feature of inducible subnuclear compartment formation for RNA-binding transcription factors and an important determinant of granule biogenesis.

Prevention of mitochondrial genomic instability in yeast by the mitochondrial recombinase Mhr1

Mitochondrial (mt) DNA encodes factors essential for cellular respiration, therefore its level and integrity are crucial. ABF2 encodes a mitochondrial DNA-binding protein and its null mutation (Δabf2) induces mtDNA instability in Saccharomyces cerevisiae. Mhr1 is a mitochondrial recombinase that mediates the predominant form of mtDNA replication and acts in mtDNA segregation and the repair of mtDNA double-stranded breaks (DSBs). However, the involvement of Mhr1 in prevention of mtDNA deletion mutagenesis is unknown. In this study we used Δabf2 mhr1-1 double-mutant cells, which lose mitochondrial function in media containing fermentable carbon sources, to investigate whether Mhr1 is a suppressor of mtDNA deletion mutagenesis. We used a suppresivity assay and Southern blot analysis to reveal that the Δabf2 mutation causes mtDNA deletions rather than an mtDNA-lacking (ρ⁰) phenotype, and observed that mtDNA deletions are exacerbated by an additional mhr1-1 mutation. Loss of respiratory function due to mtDNA fragmentation occurred in ∆mhr1 and ∆abf2 mhr1-1 cells. However, exogenous introduction of Mhr1 into Δabf2 mhr1-1 cells significantly rescued respiratory growth, suggesting that Mhr1-driven homologous mtDNA recombination prevents mtDNA instability.

Mitochondrial DNA: an advance in eukaryotic cell biology in the 1960s

Between 1950 and 1960 mitochondria were recognized as well-characterized organelles of animal and fungal cells. They shared more functional autonomy than other cellular structures. The transmission of some mitochondrial characteristics did not obey Mendelian rules and followed cytoplasmic inheritance patterns. Was this situation a consequence of still unknown complexities? We present a personal account on how approaches were set up to test very different hypotheses. In the end, it was shown that mitochondria had their own DNA, mitochondrial DNA, and that this molecule carried information specific to these organelles.

The petite mutation in yeasts: 50 years on

Fifty years ago it was reported that baker's yeast, Saccharomyces cerevisiae, can form "petite colonie" mutants when treated with the DNA-targeting drug acriflavin. To mark the jubilee of studies on cytoplasmic inheritance, a review of the early work will be presented together with some observations on current developments. The primary emphasis is to address the questions of how loss of mtDNA leads to lethality (rho 0-lethality) in petite-negative yeasts and how S. cerevisiae tolerates elimination of mtDNA. Recent investigation have revealed that rho 0-lethality can be suppressed by specific mutations in the alpha, beta, and gamma subunits of the mitochondrial F1-ATPase of the petite-negative yeast Kluyveromyces lactis and by the nuclear ptp alleles in Schizosaccharomyces pombe. In contrast, inactivation of genes coding for F1-ATPase alpha and beta subunits and disruption of AAC2, PGS1/PEL1, and YME1 genes in S. cerevisiae convert this petite-positive yeast into a petite-negative form. Studies on nuclear genes affecting dependence on mtDNA have provided important insight into the functions provided by the mitochondrial genome and the maintenance of structural and functional integrity of the mitochondrial inner membrane.

Yeast mitochondrial genomes consisting of only A.T base pairs replicate and exhibit suppressiveness

Mutants, called p-, that result from extensive deletions of the 75-kilobase Saccharomyces cerevisiae mitochondrial genome arise at high frequency. The remaining mitochondrial DNA is amplified in the p- cells, often as head-to-tail multimers, producing a cell with the normal amount of mitochondrial DNA. In matings, some of these p- mutants exhibit zygotic hypersuppressiveness, excluding the wild-type mitochondrial genome (p+) from all the diploids that are produced. From a hypersuppressive p- strain, we isolated two mutants with reduced suppressiveness. These mutants, one moderately suppressive and one nonsuppressive, retain only 89 and 70 base pairs, respectively, of the wild-type mitochondrial genome. Their sequences consist of 100% A . T base pairs. Replication of DNA in the mitochondrion, formation and amplification of new deletion genomes, and exhibition of suppressiveness do not require a single G . C base pair.

Volume-related mitochondrial deoxyribonucleic acid synthesis in zygotes and vegetative cells of Saccharomyces cerevisiae

The synthesis of mitochondrial deoxyribonucleic acid (DNA) in Saccharomyces cerevisiae cells has been examined during conjugation, in preconjugal conditions, and in control cultures that were not exposed to obverse diffusible sex factors. The ratios of mitochondrial to nuclear DNA varied from about 0.1 in control cells, to about 0.3 in alpha cells exposed for 180 min to cell-free culture medium from a cells, and to about 0.4 in conjugating cells 150 min after mixing. The enhanced levels of mitochondrial DNA during preconjugal and conjugal conditions seem correlated with enhanced cell volumes. Likewise, amounts of mitochondrial DNA in vegetative cells were found to be correlated with cytoplasmic volumes.

Genetic analysis of petite mutants of Saccharomyces cerevisiae: transmissional types

We have studied a number of petite [rho-] mutants of Saccharomyces cerevisiae induced in a wild-type strain of mitochondrial genotype [ome- CHL(R) ERY(S) OLI(S) (1, 2, 3) PAR(S)] by Berenil and ethidium bromide, all of which have retained two mitochondrial genetic markers, [CHL(R)] and [ERY(S)], but have lost all other known markers. Though stable in their ability to retain these markers in their genome, these mutants vary widely among themselves in suppressiveness and in the extent to which the markers are transmitted on crossing to a common wild-type tested strain. In appropriate crosses all of the strains examined in this study demonstrate mitochondrial polarity, and thus have also retained the [ome-] locus in a functional form; however, five different transmissional types were obtained, several of them quite unusual, particularly among the strains originally induced by Berenil. One of the most interesting types is the one that appears to reverse the parental genotypes with [CHL(R) ERY(S)] predominating over [CHL(S) ERY(R)] in the diploid [rho+] progeny, rather than the reverse, which is characteristic of analogous crosses with [rho+] or other petites. Mutants in this class also exhibited low or no suppressiveness. Since all of the petites reported here are derived from the same wild-type parent, and so have the same nuclear background, we have interpreted the transmissional differences as being due to different intramolecular arrangements of largely common retained sequences.

Zygote heterogeneity and uniparental inheritance of mitochondrial genes in yeast

A number of different crosses between strains of Saccharomyces cerevisiae differing in mitochondrial genotype are analyzed with respect to the extent to which individual zygotes transmit mitochondrial genes from one parent or the other. Many crosses produce two or more distinct classes of zygotes in this respect. Some crosses produce a high frequency of uniparental zygotes, which transmit mitochondrial genes exclusively or nearly so from one parent. Such zygotes cannot be accounted for in terms of an unequal input of mitochondrial DNA molecules from the two parents; they indicate that mitochondrial DNA from one parent is selectively replicated, or mitochondrial DNA from the other parent is selectively destroyed, in the zygote. Multiple zygote classes, and uniparental zygotes, are seen in studies of mitochondrial and chloroplast inheritance in other organisms, and may have a common explanation.

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.

"Killer" character does not influence the transmission of mitochondrial genes in Saccharomyces cerevisiae

Three cytoplasmic genetic elements have been shown to be separate from mitochondrial deoxyribonucleic acid (DNA), [rho], in Saccharomyces cerevisiae: the killer character [k], omicron-DNA, and psi [psi]. Griffiths has suggested genetic interactions between [VENR] and [TETR] mutants possibly located on omicron-DNA and mitochondrial genetic markers, but possible interactions between the best characterized of the three, the killer character, and mitochondrial DNA have not been investigated. To test this we isolated cycloheximide-induced nonkiller segregants (NKS) of killer cells with suitable genetic markers and mated them in [k] x [k], [k] x [k], and (NKS) x (NKS) combinations. No differences in quantitative mitochondrial marker transmission between these groups were found in crosses illustrating the mitochondrial phenomena of bias, polarity, and suppressiveness. Our studies show that no intercellular interactions between [k] and (NKS) cells influence mitochondrial transmission genetics. Intracellular interactions between the smaller double-stranded ribonucleic acid of [k] and mitochondrial DNA also were not detected.

The segregation of mitochondrial genes in yeast. I. Analysis of zygote pedigrees of petite X grande crosses

A large number of spontaneous, cytoplasmic petite mutants from six grande strains of Saccharomyces cerevisiae were crossed to a pair of isogenic tester strains. Suppressivity values were obtained by randomly sampling the diploid progeny from these crosses, and this basis, crosses were broadly categorized as having high, intermediate, or low suppressivity. For each cross, individual zygotes were obtained also. All successive first-generation buds were isolated from the zygotes, and analyzed for the presence of petite genotypes. We found that, though early buds may be mixed, all zygotes eventually produce a succession of buds which have the same genotype--either all petite or all grande. Many more zygotes from crosses in all categories of suppressivity purified to petite than expected from the population values for suppressivity. Reconstruction experiments indicate that most petite mutants may actually generate over 90% petite progeny in a petite X grande cross.

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.

Glucose-induced crypticity toward succinate metabolism in Saccharomyces lactis

Saccharomyces lactis grown on glucose adapted very slowly to growth on succinate. This initial inability of glucose-grown cells to grow on succinate was paralleled by their inability to oxidize succinate. The possibility that repression by glucose of respiratory chain components was responsible for these observations was examined. Glucose-grown cells were able to respire glucose, ethyl alcohol, and lactate and were able to initiate growth on ethyl alcohol as rapidly as succinate-grown cells. Respiratory enzyme levels were essentially the same in cells grown on succinate or on glucose. Spectroscopic analysis revealed that glucose-grown cells possessed a full complement of cytochrome bands. Since by these criteria glucose-grown S. lactis appears to possess a competent respiratory system, the penetration of succinate-2,3-(14)C into succinate- and glucose-grown cells was examined directly. Glucose-grown cells exhibited a strong permeability barrier to succinate. Comparison of glucose oxidation by S. lactis and by S. cerevisiae suggests that the crypticity to succinate does not depend upon a strong Crabtree effect in S. lactis.

Reversion of spontaneously arising respiratory deficiency in Saccharomyces cerevisiae

Reversion of naturally-arising cytoplasmically-inherited respiratory deficiency in Saccharomyces cerevisiae was indicated by the occurrence of colonies with a respiratory sufficient apex arising from a respiratory deficient base. The basal respiratory deficient cells were shown to contain the suppressive factor. It was suggested that genetic information for the suppressive factor resided in abnormal mitochondrial DNA and that mosaic colonies arose from a heteroplasmic cell containing both normal and abnormal mitochondrial DNA.

Cytoplasmic DNA from petite colonies of Saccharomyces cerevisiae: a hypothesis on the nature of the mutation

The density of the cytoplasmic DNA of two strains of "petite" mutants of yeast, obtained by treatment with acriflavin and with ultraviolet light, was examined in cesium chloride density-gradient centrifugation and in all cases appeared to be less than that of the wild type. A cytoplasmic respiratory-deficient strain, treated with additional acriflavin, can show a further shift of the position of the satellite band, always in the direction of reduction of density. Also, from the p(+) x p(-) cross, p(-) strains can be recovered in which the density of the satellite DNA is different from the density of the parent p(-) strain. This finding suggests the existence of recombination in cytoplasmic DNA moleciules.

Fine-structure analysis of intercellular and intracellular mitochondrial diversity in Saccharomyces cerevisiae

Crosses were made between haploid wild-type and suppressive petite strains of bakers' yeast to obtain zygotes for analysis of mitochondrial heterogeneity. Wild-type x petite zygotes contained about 40% noncristate mitochondria when immediate mating mixtures were examined. The frequency of defective mitochondria had decreased to an average of 9.2% in 1-week-old zygote isolate cultures, and to 4.4% in slant cultures 1.5 years after initial zygote isolation. The latter value was not significantly different from values obtained with wild x wild zygotes of either age. The noncristate mitochondria were of two types: one lacking inner membrane invaginations or elaborations and the other containing concentrically arranged loops of inner membrane. The significance of these two types of respiration-deficient mitochondria is unknown. The gradual decrease in frequency of noncristate mitochondria, perhaps due to selection pressures in mixed chondriomes, was discussed as a further indication of the semiautonomous nature of the yeast organelle.

Heterogeneous length distribution of circular DNA filaments from yeast mitochondria

Images