Membrane potentials in respiring and respiration-deficient yeasts monitored by a fluorescent dye

Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

Background

In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD.

Results

Heterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9.

Conclusions

Activity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure–function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40694-021-00117-4.

A high-throughput assay for mitochondrial membrane potential in permeabilized yeast cells

A fluorometric assay for mitochondrial membrane potential in permeabilized yeast cells has been developed. This method involves permeabilizing the plasma membrane and measuring the distribution of a mitochondrial membrane potential sensitive probe 3,3'-dipropylthiadicarbocyanine iodide (DiSC(3)(5); DiSC(3)). In permeabilized cells, DiSC(3) fluorescence decreased when introduced into energized mitochondria and increased three- to sixfold when the mitochondrial membrane potential was dissipated by the chemical uncoupler carbonylcyanide m-chlorophenyl hydrazone. Plasma membrane potential was abolished by permeabilization, as shown by a lack of polarization of the plasma membrane induced by K(+) and glucose. Uncoupling protein 1 (UCP1), a mitochondrial H(+) transporter, was used as a model for method validation. The fluorescence intensity responded vigorously to specific modulators in UCP1-expressing cells. This method has been adapted as a high-throughput assay to screen for modulators of mitochondrial membrane potential.

Factors and processes involved in membrane potential build-up in yeast: diS-C3(3) assay

No methods are currently available for fully reliable monitoring of membrane potential changes in suspensions of walled cells such as yeast. Our method using the Nernstian cyanine probe diS-C3(3) monitors even relatively fast changes in membrane potential delta psi by recording the shifts of probe fluorescence maximum lambda max consequent on delta psi-dependent probe uptake into, or exit from, the cells. Both increased [K+]out and decreased pHout, but not external NaCl or choline chloride depolarise the membrane. The major ion species contributing to the diS-C3(3)-reported membrane potential in S. cerevisiae are thus K+ and H+, whereas Na+ and Cl- do not perceptibly contribute to measured delta psi. The strongly pHout-dependent depolarisation caused by the protonophores CCCP and FCCP, lack of effect of the respiratory chain inhibitors rotenone and HQNO on the delta psi, as well as results obtained with a respiration-deficient rho- mutant show that the major component of the diS-C3(3)-reported membrane potential is the delta psi formed on the plasma membrane while mitochondrial potential forms a minor part of the delta psi. Its role may be reflected in the slight depolarisation caused by the F1F0-ATPase inhibitor azide in both rho- mutant and wildtype cells. Blocking the plasma membrane H(+)-ATPase with the DMM-11 inhibitor showed that the enzyme participates in delta psi build-up both in the absence and in the presence of added glucose. Pore-forming agents such as nystatin cause a fast probe entry into the cells signifying membrane damage and extensive binding of the probe to cell constituents reflecting obviously disruption of ionic balance in permeabilised cells. In damaged cells the probe therefore no longer reports on membrane potential but on loss of membrane integrity. The delta psi-independent probe entry signalling membrane damage can be distinguished from the potential-dependent diS-C3(3) uptake into intact cells by being insensitive to the depolarising action of CCCP.

The plasma membrane electrical gradient (membrane potential) in Leishmania donovani promastigotes and amastigotes

The equilibrium distribution of tetraphenylphosphonium bromide was used to measure the membrane potential in Leishmania donovani amastigotes and promastigotes and to investigate mechanisms underlying the maintenance of membrane potential. At pH 7.0, membrane potential ranges between -90 and -113 mV. Increasing the external concentrations of hydrogen or potassium ions decreased membrane potential as did treatments with carbonylcyanide chlorophenylhydrazone or valinomycin. These observations are consistent with a membrane potential set by hydrogen and potassium ion diffusion gradients. Anaerobiosis lowered membrane potential, suggesting the involvement of ATPase(s) in maintaining membrane potential. Membrane potential was insensitive to treatment with ouabain, demonstrating the absence of a Na+/K(+)-ATPase. Treatment with dicyclohexylcarbodiimide caused a temporary hyperpolarization of the membrane suggesting the participation of a proton ATPase in the maintenance of membrane potential. Determination of the membrane potential makes it possible to quantitate the total proton motive force which is the force for active transport across the parasite membrane.

Growth defects in intramitochondrial energy depleted cells: role of mitochondrial biogenesis

Simultaneous inhibition of oxidative phosphorylation by rho- mutation and adenine nucleotide exchange by op1 mutation or bongkrekic acid results in intramitochondrial energy depletion and cessation of growth in yeast. Effect of energy depletion of mitochondria on mitochondrial biogenesis was studied in intact yeast cells. Immunoblot analysis revealed an overall decrease in cellular content of two mitochondrial proteins - ADP/ATP translocase and beta subunit of mitochondrial ATPase - together with their lower ability to reach the proper intramitochondrial compartment. Both effects indicate disturbed biogenesis of energy depleted mitochondria. Quantitative differences in growth abilities and mitochondrial damage observed in two studied systems - op1 rho- double mutants and rho- cells treated with bongkrekic acid - can be explained by different degree of intramitochondrial energy depletion due to leakiness of op1 mutation in op1 rho- cells.

Transient hyperpolarization of yeast by glucose and ethanol

At pH 7, addition of glucose under anaerobic conditions to a suspension of the yeast Saccharomyces cerevisiae causes both a transient hyperpolarization and a transient net efflux of K+ from the cells. Hyperpolarization shows a peak at about 3 min and a net K+ efflux at 4-5 min. An additional transient hyperpolarization and net K+ efflux are found after 60-80 and 100 min, respectively. Addition of 2-deoxyglucose instead of glucose does not lead to hyperpolarization of the cells or K+ efflux. At low pH, neither transient hyperpolarization nor a transient K+ efflux are found. With ethanol as substrate and applying aerobic conditions, both a transient hyperpolarization and a transient K+ efflux are found at pH 7. The fluorescent probe 2-(dimethylaminostyryl)-1-ethylpyridinium appears to be useful for probing changes in the membrane potential of S. cerevisiae. It is hypothesized that the hyperpolarization of the cells is due to opening of K+ channels in the plasma membrane. Accordingly, the hyperpolarization of the cells at pH 7 is almost completely abolished by 1.25 mM K+, whereas the same amount of Na+ does not reduce the hyperpolarization.

A method for determining the intracellular distribution of enzymes in yeast provides no evidence for the association of hexokinase with mitochondria

A simple procedure based upon the principle discovered by Dürr et al. (Arch. Microbiol. (1975) 105, 319-327) was used to measure the intracellular distribution of enzymes in S. cerevisiae grown under both glucose repression and derepression. No substantial hexokinase activity was found to be associated with cellular organelles. The result does not support the hypotheses that reversible binding of hexokinase to mitochondria is important in regulation of glycolysis and cell growth.

The putative electrogenic nitrate-proton symport of the yeast Candida utilis. Comparison with the systems absorbing glucose or lactate

Strain N.C.Y.C. 193 of Candida utilis was grown aerobically at 30 degrees C with nitrate as limiting nutrient in a chemostat. The washed yeast cells depleted of ATP absorbed up to 5 nmol of nitrate/mg dry wt. of yeast. At pH 4-6, extra protons and nitrate entered the yeast cells together, in a ratio of about 2:1. Charge balance was maintained by an outflow of about 1 equiv. of K+. Nitrate stimulated the uptake of about 1 proton equivalent during glycolysis or aerobic energy metabolism. Studies with 3,3'-dipropylthiadicarbocyanine indicated that the proton-linked absorption of nitrate, amino acids or glucose depolarized the yeast cells. Proton uptake along with lactate led neither to net expulsion of K+ nor to membrane depolarization.

All-or-none interactions of inhibitors of the plasma membrane ATPase with Saccharomyces cerevisiae

The inhibitors of the yeast plasma membrane ATPase, Dio-9, miconazole, suloctidil, N,N'-dicyclohexycarbodiimide, triphenyltin and diethylstilbestrol provoke an all-or-none K+ loss from the cells. Some of the K+-depleted cells also show an increased permeability for the dye, Bromophenol blue, indicating that the barrier properties of these cells are drastically changed. Apart from this all-or-none process, a graded loss of K+ is also observed. These observations warn against the use of the inhibitors in studies aimed at evaluating the role of the ATPase in the energy transduction of membrane transport processes of yeasts.

Ionophores and intact cells. I. Valinomycin and nigericin act preferentially on mitochondria and not on the plasma membrane of Saccharomyces cerevisiae

Valinomycin and nigericin prevented growth of 13 strains of the yeast Saccharomyces cerevisiae on non-fermentable substrate glycerol without affecting much fermentative growth on glucose. The two antibiotics did not induce swelling and lysis of yeast protoplasts in potassium acetate and did not modify uptake and release of Rb+ by the yeast cells. Both antibiotics were taken up by yeast cells at a relatively low rate. Nigericin accelerated the glucose-induced changes of fluorescence of a cyanine dye absorbed by yeast cells, which had been previously ascribed to a depolarization-repolarization cycle of the mitochondrial membrane. The data suggest that valinomycin and nigericin act as ionophores in the inner mitochondrial membrane and not in the plasma membrane of intact yeast cells.

The energetics of D-fucose transport in Saccharomyces fragilis. The influence of the protonmotive force on sugar accumulation

The protonmotive force in Saccharomyces fragilis has been estimated under various experimental conditions. The transmembrane potential has been monitored with tetraphenylphosphonium and 3,3'-dipropylthiadicarbocyanine. The distribution ratio of these cations between intracellular and extracellular water appeared to be governed by the electrical potential difference across the membrane of this yeast strain. The transmembrane pH difference was deduced from dimethyloxazolidinedione uptake experiments and from direct measurements of intracellular pH after freezing and boiling of the cells. Both methods yielded similar results. D-Fucose is transported by S. fragilis via H+ symport, with a H+/fucose stoichiometry of approximately 1. Accumulation of this sugar appeared to be closely correlated with the protonmotive force.

Requirement of a membrane potential for the posttranslational transfer of proteins into mitochondria

Posttranslational transfer of most precursor proteins into mitochondria is dependent on energization of the mitochondria. Experiments were carried out to determine whether the membrane potential or the intramitochondrial ATP is the immediate energy source. Transfer in vitro of precursors to the ADP/ATP carrier and to ATPase subunit 9 into isolated Neurospora mitochondria was investigated. Under conditions where the level of intramitochondrial ATP was high and the membrane potential was dissipated, import and processing of these precursor proteins did not take place. On the other hand, precursors were taken up and processed when the intramitochondrial ATP level was low, but the membrane potential was not dissipated. We conclude that a membrane potential is involved in the import of those mitochondrial precursor proteins which require energy for intracellular translocation.