Genetic modification of energy-conserving systems in yeast mitochondria

Activation of the pleiotropic drug resistance pathway can promote mitochondrial DNA retention by fusion-defective mitochondria in Saccharomyces cerevisiae

Genetic and microscopic approaches using Saccharomyces cerevisiae have identified many proteins that play a role in mitochondrial dynamics, but it is possible that other proteins and pathways that play a role in mitochondrial division and fusion remain to be discovered. Mutants lacking mitochondrial fusion are characterized by rapid loss of mitochondrial DNA. We took advantage of a petite-negative mutant that is unable to survive mitochondrial DNA loss to select for mutations that allow cells with fusion-deficient mitochondria to maintain the mitochondrial genome on fermentable medium. Next-generation sequencing revealed that all identified suppressor mutations not associated with known mitochondrial division components were localized to PDR1 or PDR3, which encode transcription factors promoting drug resistance. Further studies revealed that at least one, if not all, of these suppressor mutations dominantly increases resistance to known substrates of the pleiotropic drug resistance pathway. Interestingly, hyperactivation of this pathway did not significantly affect mitochondrial shape, suggesting that mitochondrial division was not greatly affected. Our results reveal an intriguing genetic connection between pleiotropic drug resistance and mitochondrial dynamics.

Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside

ATP, the principal energy currency of the cell, fuels most biosynthetic reactions in the cytoplasm by its hydrolysis into ADP and inorganic phosphate. Because resynthesis of ATP occurs in the mitochondrial matrix, ATP is exported into the cytoplasm while ADP is imported into the matrix. The exchange is accomplished by a single protein, the ADP/ATP carrier. Here we have solved the bovine carrier structure at a resolution of 2.2 A by X-ray crystallography in complex with an inhibitor, carboxyatractyloside. Six alpha-helices form a compact transmembrane domain, which, at the surface towards the space between inner and outer mitochondrial membranes, reveals a deep depression. At its bottom, a hexapeptide carrying the signature of nucleotide carriers (RRRMMM) is located. Our structure, together with earlier biochemical results, suggests that transport substrates bind to the bottom of the cavity and that translocation results from a transient transition from a 'pit' to a 'channel' conformation.

A comprehensive compilation of 1001 nucleotide sequences coding for proteins from the yeast Saccharomyces cerevisiae (= ListA2)

The amount of nucleotide sequence data is increasing exponentially. We therefore continued our effort to make a comprehensive database for the yeast Saccharomyces cerevisiae. In this database (ListA2) we have compiled 1001 protein coding sequences from this organism. Each sequence has been attributed a single genetic name and in the case of allelic duplicated sequences, synonyms are given, if necessary. For the nomenclature we have introduced a standard principle for naming gene sequences based on priority rules. We have also applied a simple method to distinguish duplicated sequences of one and the same gene from non-allelic sequences of duplicated genes. By using these principles we have sorted out a lot of confusion in the literature and databanks. Along with the genetic name, the mnemonic from the EMBL databank, the codon bias, reference of the publication of the sequence and the EMBL accession numbers are included for each entry. The database is available on request.

CBP1 function is required for stability of a hybrid cob-oli1 transcript in yeast mitochondria

The nuclear gene product CBP1 stabilizes cytochrome b transcripts in yeast mitochondria. In cbp1 mutant strains, cytochrome b gene (cob) transcripts are not detectable by Northern blot analysis. The results of previous studies led to the hypothesis that CBP1 interacts with the 5'-untranslated sequence of the cob mRNA, or pre-mRNA, to stabilize the message. To determine what portion of the cob leader is sufficient for interaction with CBP1, we have investigated the stability of transcripts from a novel hybrid gene, cob-oli1, in which the 5'-terminal third of the cob leader sequence was fused to the coding sequence of the gene for ATP synthase subunit 9, oli1. The hybrid cob-oli1 transcript was stable in a strain wild-type at the CBP1 locus, but was undetectable in the cbp1 mutant background. That the cob-oli1 transcript was translated to produce ATP synthase subunit 9 in CBP1 strains containing the cob-oli1 gene was verified by 35S-methionine labeling of mitochondrial proteins. We conclude that the 5'-terminal portion of the cob message is sufficient for CBP1 function and discuss the hypothesis that CBP1 interacts directly with this region of the transcript to promote cob mRNA stability.

PET genes of Saccharomyces cerevisiae

We describe a collection of nuclear respiratory-defective mutants (pet mutants) of Saccharomyces cerevisiae consisting of 215 complementation groups. This set of mutants probably represents a substantial fraction of the total genetic information of the nucleus required for the maintenance of functional mitochondria in S. cerevisiae. The biochemical lesions of mutants in approximately 50 complementation groups have been related to single enzymes or biosynthetic pathways, and the corresponding wild-type genes have been cloned and their structures have been determined. The genes defined by an additional 20 complementation groups were identified by allelism tests with mutants characterized in other laboratories. Mutants representative of the remaining complementation groups have been assigned to one of the following five phenotypic classes: (i) deficiency in cytochrome oxidase, (ii) deficiency in coenzyme QH2-cytochrome c reductase, (iii) deficiency in mitochondrial ATPase, (iv) absence of mitochondrial protein synthesis, and (v) normal composition of respiratory-chain complexes and of oligomycin-sensitive ATPase. In addition to the genes identified through biochemical and genetic analyses of the pet mutants, we have cataloged PET genes not matched to complementation groups in the mutant collection and other genes whose products function in the mitochondria but are not necessary for respiration. Together, this information provides an up-to-date list of the known genes coding for mitochondrial constituents and for proteins whose expression is vital for the respiratory competence of S. cerevisiae.

A minimum structured adenine nucleotide for ADP/ATP transport in mitochondria

An ADP analogue, i.e. 3H- or 14C-labeled 5'-diphosphate of 6-(beta-D-ribofuranosyl-methyl)-4-pyrimidinamine, was synthesized, the structure of which was deduced from structure-activity studies on the substrate specificity of the nucleotide-binding center of the inner mitochondrial membrane integrated ADP/ATP carrier protein. Bearing only the minimal but substrate-essential recognition structures, minimum structured ADP (msADP) is bound to the cytosol-facing active center and transported by the highly specific carrier system across the inner mitochondrial membrane.

Rapid method for isolation and screening of cytochrome c oxidase-deficient mutants of Saccharomyces cerevisiae

We describe here a new method for the specific isolation of cytochrome c oxidase-deficient mutants of Saccharomyces cerevisiae. One unique feature of the method is the use of tetramethyl-p-phenylenediamine as a cytochrome c oxidase activity stain for yeast colonies. The staining of yeast colonies by tetramethyl-p-phenylenediamine is dependent upon a functional cytochrome c oxidase and is unaffected by other lesions in respiration. Since the tetramethyl-p-phenylenediamine colony staining reaction is rapid and simple, it greatly facilitates both the identification and characterization of cytochrome c oxidase-deficient mutants. Another feature of the method, which is made possible by the tetramethyl-p-phenylenediamine colony stain, is the use of an op1 parent strain for the isolation of nuclear pet or mitochondrial mit mutants in specific protein-coding genes. A parent strain that carries this marker selects against rho0 or rho- classes of pleiotropic respiratory-deficient mutants, since these are lethal in op1 strains. We have used this method to isolate 123 independently derived cytochrome c oxidase-deficient pet mutants and 300 independently derived mit mutants.

Petite-negative mutants of Saccharomyces cerevisiae

A series of yeast mutants has been isolated with the inability to grow on fermentable carbon sources whilst growing normally on ethanol media. One of the mutants, namely MC16/206 lacks pyruvate decarboxylase activity and does not grow on glucose at 37 degrees C but grows on both ethanol and glucose at 27 degrees C. In this strain rho- petites are non-viable.

Influence of specific growth limitation and dilution rate on the phosphorylation efficiency and cytochrome content of mitochondria of Candida utilis NCYC 321

With Candida utilis cells that had been removed directly from a 61 chemostat culture, in steady state, well-coupled mitochondria generally could be isolated. This requires a modified snail-gut enzyme procedure that allowed the total processing time to be decreased to 3 h, or less. Examination of these mitochondria in an oxygraph showed the presence of 3 sites of energy conservation when the cells were grown at various dilution rates between 0.1 and 0.45 h-1 in environments that were, successively, glucose-, ammonia-, magnesium-, phosphate- and sulphate-limited. Potassium-limited cells also apparently possessed 3 sites of oxidative phosphorylation when growing at dilution rates greater than 0.2 h-1, but only 2 sites when growing at lower dilution rates. Analysis of cytochrome spectra obtained with these intact mitochondria revealed large quantitative (but not qualitative) differences, depending on the environmental conditions under which the yeast had been cultured. In particular, comparison of the ratio of cytochrome b to cytochrome a showed a pattern of change with dilution rate in mitochondria from potassium-limited cells that was distinctly different from those evident in mitochondria from cells that had been limited in their growth by the availability of other nutrients.

Environmentally induced changes in mitochondria and endoplasmic reticulum of Saccharomyces carlsbergensis yeast

The effects of culture environment on the volume density and surface density of mitochondria and endoplasmic reticulum in a facultative yeast were studied. When compared with cells grown aerobically on a nonrepressive substrate, cells grown in the absence of oxygen showed a sharp reduction in both volume density of mitochondria and surface density of the inner mitochondrial membrane (imm) in the remaining mitochondrial profiles. Use of fermentable (repressive) substrates under aerobic conditions restricted the volume density of mitochondria to a much greater extent than the surface density of imm. The range of mitochondrial volume densities in these experiments was 4-11%. Surface density of endoplasmic reticulum (ER) was sensitive to growth rate and in particular to changes in oxygen tension, showing large fluctuations during both anaerobic and aerobic adaptation. These fluctuations in ER are discussed in relation to the known role of this organelle in lipid metabolism.

Nucleo-cytoplasmic interaction between oligomycin-resistant mutations in Saccharomyces cerevisiae

1.A single-gene nuclear mutant of Saccharomyces cerevisiae, isolated as oligomycin-resistant, exhibits in vivo cross-resistance to venturicidin and collateral sensitivity to Synthalin. All three compounds are inhibitors of mitochondrial oxidative phosphorylation. Oligomycin resistance and Synthalin sensitivity are recessive, while venturicidin resistance is dominant. 2. Acytoplasmic mutant, also isolated as oligomycin-resistant, shows collateral sensitivity to both Synthalin and venturicidin. All three traits undergo mitotic segregation in diploids formed by crossing mutant and normal halpoids. 3. A novel nucleocytoplasmic interaction is observed in diploids formed by crossing haploid strains containing the nuclear and the cytoplasmic mutations, respectively. The dominant venturicidin resistance determined by the nuclear gene undergoes mitotic segregation, which results from a suppression of the nuclear phenotype by the cytoplasmic mutation. When a diploid mitotic segregant contains primarily mutant-type mitochondria, venturicidin resistance is completely suppressed. In haploids containing both the nuclear and cytoplasmic mutations, suppression is only partial. 4. Oxidative phosphorylation and ATPase in mitochondrial fractions isolated fromcytoplasmic mutant cells are less sensitive to inhibition by oligomycin than normal, but in vitro sensitivity to venturicidin is not significantly changed. In similar mitochondrial fractions isolated from normal and nuclear mutant cells, no significant differences in sensitivity to either inhibitor are detected. 5. The molecular basis for the nucleocytoplasmic suppression of venturicidin resistance may involve participation of mitochondrial membrane, plasma membrane or both. Either mitochondria can undergo changes in venturicidin sensitivity upon isolation, or the molecular entity which controls access of venturicidin to the mitochondria resides outside of the organelles. 6. Our data establish that aspects of the response in vivo of both venturicidin and Snythalin are controlled by the mitochondrial genome. 7. The nucleocytoplasmic interaction described here is the first example in which a specific restricted mitochondrial mutation modifies the phenotypic expression of a nuclear gene.

Segregational respiratory-deficient mutants of a "petite negative" yeast Schizosaccharomyces pombe 972h-

No viable respiratory-deficient mutants of Schizosaccharomyces pombe 972h(-) could be obtained by acriflavine and ethidium bromide treatments. These mutagens induce 15 to 70% of microcolonies which, after a growth-lag of a few days, further develop into normal, respiratory-competent colonies. These results suggest that unstable petites were induced. Segregational respiratory-deficient mutants resistant to cobalt sulfate inhibition were isolated. Some of these strains are deficient in cytochrome a + a(3) and respire at low rates. The morphology of their mitochondrial membranes is modified: either the cristae are absent or they show aberrant concentric or tubular structures. Segregational mutants resistant to the respiratory inhibitors, 2,4-dinitrophenol or decamethylene diguanidine, were obtained. Neither mitochondrial structure nor function seems to be modified in these mutants. A segregational mutant resistant to benzimidazole inhibition does not grow on glycerol, although neither growth on glucose nor respiration appear to be affected.

Mutants of yeast with altered oxidative energy metabolism: selection and genetic characterization

Isolation of a series of mutants, characterized by decreased ability to utilize nonfermentable carbon sources for growth and presence of all cytochromes, is reported. A total of 161 mutants, showing deficient growth on glycerol but able to reduce 2,3,5-triphenyltetrazolium chloride, were isolated, purified, and characterized by ability to grow on various carbon sources. Mutants showing decreased growth were examined by low-temperature spectroscopy, and the 35 strains shown to possess all cytochromes were retained for further studies. These strains were characterized by growth on various nonfermentable carbon sources, relative yield on glucose medium, and respiration (Q(O2)) of glucose and ethyl alcohol. Genetic studies revealed that at least 19 of the 35 mutants are the result of mutation in single nuclear genes. Furthermore, at least 11 complementation groups are represented among these 19 mutants. Mutants within two complementation groups were shown to be very similar in various properties. These studies demonstrate that a large number of nuclear genes control oxidative energy metabolism and that the characteristics of mutants of the general class are extremely diverse.