RNA synthesis in yeast mitochondria: a derepressible activity

Mitochondrial transcription is regulated via an ATP "sensing" mechanism that couples RNA abundance to respiration

The information encoded in both the nuclear and mitochondrial genomes must be coordinately regulated to respond to changes in cellular growth and energy states. Despite identification of the mitochondrial RNA polymerase (mtRNAP) from several organisms, little is known about mitochondrial transcriptional regulation. Studying the shift from fermentation to respiration in Saccharomyces cerevisiae, we have demonstrated a direct correlation between in vivo changes in mitochondrial transcript abundance and in vitro sensitivity of mitochondrial promoters to ATP concentration (K(m)ATP). Consistent with the idea that the mtRNAP itself senses in vivo ATP levels, we found that transcript abundance correlates with respiration, but only when coupled to mitochondrial ATP synthesis. In addition, we characterized mutations in the mitochondrial promoter and the mtRNAP accessory factor Mtf1 that alter both in vitro K(m)ATP and in vivo transcription in response to respiratory changes. We propose that shifting cellular pools of ATP coordinately control nuclear and mitochondrial transcription.

Petite and sectored induction in Saccharomyces cerevisiae by propidium iodide: synergistic effect of sodium dodecyl sulfate

Sodium dodecyl sulfate (SDS) was examined for its effect on petite and sectored colony induction in Saccharomyces cerevisiae by propidium iodide (PI) and ethidium bromide (EB). 4-h cultivation with 100 microM PI and 100 micrograms/ml SDS resulted in virtually all plated cells growing as sectored colonies with no decrease in viability. Sectored colonies are mixed colonies comprised of respiratory deficient and competent cells believed to be derived from an unstable respiratory deficient cell. Further cultivation with PI and SDS prior to plating led to induction of complete petite colonies with a rapid decrease in viable cells. PI alone at this concentration exhibited weak induction of sectored colonies (maximum 12.3% at 8 h) and petite colonies (maximum 10.8% at 12 h), but SDS alone caused induction of neither. 50 microM PI had almost the same activity as 100 microM except for a delay in the induction of sectored colonies in the initial stage, and a decreased rate of petite colony induction. The effects of 20 microM PI and SDS were much lower than that by 50 microM and no inhibition of growth was observed. 10 microM PI was quite inactive even in the presence of SDS. Under resting conditions, 10 approximately 100 microM PI and 100 micrograms/ml SDS induced about 60% sectored colonies at 12 h incubation and more than 60% petite colonies at 24 h. After 6 h incubation, decrease in survival was also observed.

Studies on the biosynthesis of bacterio-opsin. Demonstration of the existence of protein species structurally related to bacterio-opsin

1. The kinetics of processing newly synthesized bacterio-opsin from the non-crystalline state within the brown membrane to the crystalline state within the purple membrane was followed by pulse-chase experiments. 2. Biosynthesis of bacterio-opsin was found to be highly resistant to RNA-synthesis inhibitors like rifampicin and ethidium bromide. In the presence of ethidium bromide, only five protein species continue to be synthesized in halobacteria, one of them being bacterio-opsin. 3. In spheroplasts, synthesis of bacterio-opsin is found to be selectively disturbed. The purple membrane isolated from spheroplasts contains new, additional protein species with apparent molecular weights of 19 000, 23 000 and 29 000. These proteins share common amino acid sequences with bacterio-opsin. 4. In the halobacterial cell membrane, two membrane proteins with apparent molecular weights of 30 000 and 36 000 were detected which are structurally related to bacterio-opsin. 5. Bacterio-opsin as well as the 30 000 Mr and 36 000-Mr proteins contain covalently bound sulphate.

The isolation and properties of a DNA-directed RNA polymerase from yeast mitochondria

A method is described for the rapid isolation of yeast mitochondrial DNA-directed RNA polymerase. The enzyme obtained had a specific activity of 1.56 nmol UMP incorporated per mg protein in 20 min at 37 degrees C, and is some 95% pure. This purified enzyme upon polyacrylamide gel elctrophoresis consists of a single polypeptide of 68 000 mol. wt. However, the enzyme forms aggregates easily which are affected by ionic strength, an increase decreasing the apparent molecular weight of the aggregates. This property also explains the presence of two peaks of activity upon DEAE-cellulose chromatography. The purified enzyme is still sensitive to rifamycin and to a number of rifamycin derivatives. The enzyme's sensitivity to rifamycin and rifamycin derivatives was compared with Escherichia coli and yeast nuclear RNA polymerases.

Derepression in Saccharomyces cerevisiae can be dissociated from cellular proliferation and deoxyribonucleic acid synthesis

A method has been developed that permits precise control of release from catabolite repression in Saccharomyces cerevisiae. It consists of transferring cells growing exponentially on 5% glucose to derepression medium at high cell density. Derepression then proceeds with reproducible kinetics and is complete within 6 to 7.5 h for various intra- and extramitochondrial markers, in the absence of any substantial increase in cellular dry weight or protein. Nuclear (and mitochondrial) deoxyribonucleic acid synthesis can be interrupted in certain thermosensitive (cdc) mutants at the nonpermissive temperature; a shift to this temperature before the onset of derepression has no effect on its outcome.

Autonomy of mitochondria in Saccharomyces cerevisiae in their production of messenger RNA

In ts(-)136, a temperature-sensitive mutant of Saccharomyces cerevisiae, nuclear and mitochondrial RNA production can be inhibited selectively by exposure to 36 degrees and ethidium bromide, respectively. Using the programming of mitochondrial polysomes, as measured by their ability to form nascent polypeptide chains, as an assay for functional messenger RNA, we have determined its response to temperature shifts and ethidium bromide. Only ethidium bromide produced a measurable effect; in contrast the cell-sap system responded exclusively to temperature shifts. We conclude that transcription of mitochondrial DNA is sufficient and that import of messenger RNA transcribed from nuclear chromosomes makes no measurable contribution to intramitochondrial protein synthesis.

Characterization of insoluble protein fractions of mitochondria from Saccharomyces cerevisiae

Saccharomyces cerevisiae was grown in a chemostat in the presence of excess oxygen. Cells harvested from fully derepressed and strongly repressed steady states show typical promitochondria-like structures under conditions of strong repression. Insoluble membrane proteins were extracted from highly purified mitochondria and submitted to isoelectric focusing in 6% polyacrylamide gels. Some 20 protein bands were obtained from derepressed cells. The pattern was clearly different (quantitatively and possibly qualitatively) from repressed mitochondria. In contrast to ribosomal proteins, insoluble membrane protein fractions were found in the acid section (pH 4 to 6.8) of the ampholyte gels. It can be concluded that glucose repression plays a prominent role in the synthesis of the functional mitochondrial membranes.

A paracrystalline inclusion in Neurospora crassa. Induction by ethidium and acridine, isolation, and characterization

A paracrystal indistinguishable from the one which occurs in the mitochondrial mutant abnormal-1 can be induced in wild-type Neurospora crassa after growth in either ethidium or euflavine. This paracrystal has been isolated and partially characterized. It appears to be composed of a single polypeptide (mol wt 68,000) which can be reversibly crystallized and dissociated by changes in the pH and ionic strength. When aggregated, the polypeptide forms oligomers which are arranged end-to-end into fibers. During the characterization of the polypeptide, it was found that the polypeptide's electrophoretic and immunological properties could be used as assays. Using these methods it was found that the polypeptide normally accumulates in a soluble form in the cytoplasm of wild-type Neurospora at the end of the log-phase of growth.

Isolation and biochemical characterization of nuclei from chick embryo liver

A procedure is described for the isolation of enzymatically active nuclei from chick embryo liver. It consists of the homogenization of the pooled tissue in 0.32 M sucrose-3 mM MgCl(2) followed by a slow centrifugation. The resulting nuclear pellet is then purified further in a discontinuous density gradient composed of sucrose solutions containing Mg(2+) ions, the lower portion of the gradient being 2.2 M sucrose-1 mM MgCl(2). Based on DNA recovery, the nuclear fraction isolated by the procedure described contained an average of 62% of the nuclei in the original filtered homogenate. Light and electron microscope examinations showed that 90% of the isolated nuclei were derived from hepatocytes. They appeared intact with well preserved nucleoplasmic and nucleolar components, nuclear envelope, and pores. The isolated nuclei were quite pure, having a very low level of cytoplasmic contamination as indicated by cytoplasmic enzyme marker activities and electron microscope studies. The nuclear fraction consisted of 19.9% DNA, 6.2% RNA, 74% protein, the average RNA/DNA ratio being 0.32. Biosynthetic activities of the two nuclear enzymes NAD-pyrophosphorylase and DNA-dependent RNA polymerase were preserved. The specific activities of these enzymes were: NAD-pyrophosphorylase, 0.049 micromoles nicotinamide adenine dinucleotide (NAD) synthesized/min per mg protein; Mg(2+) activated RNA polymerase, 4.3 micromicromoles UMP-2-C(14) incorporated into RNA/microg DNA per 10 min; and Mn(2+)-(NH(4))(2)SO(4) activated RNA-polymerase, 136 micromicromoles UMP-2-C(14) incorporated into RNA/microg DNA per 45 min.