Divergent branches of mitochondrial signaling regulate specific genes and the viability of specialized cell types of differentiated yeast colonies.

Mitochondrial retrograde signaling mediates communication from altered mitochondria to the nucleus and is involved in many normal and pathophysiological changes, including cell metabolic reprogramming linked to cancer development and progression in mammals. The major mitochondrial retrograde pathway described in yeast includes three activators, Rtg1p, Rtg2p and Rtg3p, and repressors, Mks1p and Bmh1p/Bmh2p. Using differentiated yeast colonies, we show that Mks1p-Rtg pathway regulation is complex and includes three branches that divergently regulate the properties and fate of three specifically localized cell subpopulations via signals from differently altered mitochondria. The newly identified RTG pathway-regulated genes ATO1/ATO2 are expressed in colonial upper (U) cells, the cells with active TORC1 that metabolically resemble tumor cells, while CIT2 is a typical target induced in one subpopulation of starving lower (L) cells. The viability of the second L cell subpopulation is strictly dependent on RTG signaling. Additional co-activators of Rtg1p-Rtg3p specific to particular gene targets of each branch are required to regulate cell differentiation.

SUN family proteins Sun4p, Uth1p and Sim1p are secreted from Saccharomyces cerevisiae and produced dependently on oxygen level.

The SUN family is comprised of proteins that are conserved among various yeasts and fungi, but that are absent in mammals and plants. Although the function(s) of these proteins are mostly unknown, they have been linked to various, often unrelated cellular processes such as those connected to mitochondrial and cell wall functions. Here we show that three of the four Saccharomyces cerevisiae SUN family proteins, Uth1p, Sim1p and Sun4p, are efficiently secreted out of the cells in different growth phases and their production is affected by the level of oxygen. The Uth1p, Sim1p, Sun4p and Nca3p are mostly synthesized during the growth phase of both yeast liquid cultures and colonies. Culture transition to slow-growing or stationary phases is linked with a decreased cellular concentration of Sim1p and Sun4p and with their efficient release from the cells. In contrast, Uth1p is released mainly from growing cells. The synthesis of Uth1p and Sim1p, but not of Sun4p, is repressed by anoxia. All four proteins confer cell sensitivity to zymolyase. In addition, Uth1p affects cell sensitivity to compounds influencing cell wall composition and integrity (such as Calcofluor white and Congo red) differently when growing on fermentative versus respiratory carbon sources. In contrast, Uth1p is essential for cell resistance to boric acids irrespective of carbon source. In summary, our novel findings support the hypothesis that SUN family proteins are involved in the remodeling of the yeast cell wall during the various phases of yeast culture development and under various environmental conditions. The finding that Uth1p is involved in cell sensitivity to boric acid, i.e. to a compound that is commonly used as an important antifungal in mycoses, opens up new possibilities of investigating the mechanisms of boric acid's action.

The transport of carboxylic acids and important role of the Jen1p transporter during the development of yeast colonies.

On solid substrates, yeast colonies pass through distinct developmental phases characterized by the changes in pH of their surroundings from acidic to nearly alkaline and vice versa. At the beginning of the alkali phase colonies start to produce ammonia, which functions as a quorum-sensing molecule inducing the reprogramming of cell metabolism. Such reprogramming includes, among others, the activation of several plasma membrane transporters and is connected with colony differentiation. In the present study, we show that colony cells can use two transport mechanisms to import lactic acid: a 'saturable' component of the transport, which requires the presence of a functional Jen1p transporter, and a 'non-saturable' component (diffusion) that is independent of Jen1p. During colony development, the efficiency of both transport components changes similarly in central and outer colonial cells. Although the lactate uptake capacity of central cells gradually decreases during colony development, the lactate uptake capacity of outer cells peaks during the alkali phase and is also kept relatively high in the second acidic phase. This lactate uptake profile correlates with the localization of the Jen1p transporter to the plasma membrane of colony cells. Both lactic acid uptake mechanisms are diminished in sok2 colonies where JEN1 expression is decreased. The Sok2p transcription factor may therefore be involved in the regulation of non-saturable lactic acid uptake in yeast colonies.

Ato protein interactions in yeast plasma membrane revealed by fluorescence lifetime imaging (FLIM).

Each of the three plasma membrane Ato proteins is involved in ammonium signalling and the development of yeast colonies. This suggests that although these proteins are homologous, they do not functionally substitute for each other, but may form a functional complex. Here, we present a detailed combined FRET, FLIM and photobleaching study, which enabled us to detect interactions between Ato proteins found in distinct compartments of yeast cells. We thus show that the proteins Ato1p and Ato2p interact and can form complexes when present in the plasma membrane. No interaction was detected between Ato1p and Ato3p or Ato2p and Ato3p. In addition, using specially prepared strains, we were able to detect an interaction between molecules of the same Ato protein, namely Ato1p-Ato1p and Ato3p-Ato3p, but not Ato2p-Ato2p.

Synchronous plasma membrane electrochemical potential oscillations during yeast colony development and aging.

Microorganisms that survive in natural environments form organized multicellular communities, biofilms and colonies with specific properties. During stress and nutrient limitation, slow growing and senescent cells in such communities retain vital processes by maintaining plasma membrane integrity and retaining the ability to generate transmembrane electrochemical gradients. We report the use of a Saccharomyces cerevisiae colonial model to show that population growth in a multicellular community depends on nutrient diffusion and that resting cells start to accumulate from the beginning of the second acidic phase of colony development. Despite differentiation of colony members, synchronous transmembrane potential oscillation was detected in the organized colony. The electrochemical membrane potential periodically oscillated at frequencies between those for circadian to infradian rhythms during colony aging and transiently decreased at time points previously linked with rebuilding of yeast metabolism. Despite extensive decreases in the intracellular ATP concentration and in the amount and activity of the plasma membrane proton pump during nutrient limited growth and colony aging, the transmembrane electrochemical potential appeared to be maintained above a level critical for population survival.

Putative role for ABC multidrug exporters in yeast quorum sensing.

Pleiotropic drug resistance (PDR) transporters play essential roles in cell resistance to various toxic compounds in various organisms including bacteria, mammals and yeasts. A large group of PDR transporters have been described in yeasts so far, including those that are controlled by transcription factor Pdr1p. Here, we show that besides their role in removing extracellularly added toxic compounds, the Pdr5p and Snq2p transporters play important physiological roles and significantly influence the developmental phases and physiology of yeast populations growing in a liquid culture. They appear to be involved in population quorum sensing, which consequently influences transcription factor Pdr1p level via feedback regulation.

Metabolic diversification of cells during the development of yeast colonies.

Microorganisms in nature form organized multicellular structures (colonies, biofilms) possessing properties absent in individual cells. These are often related to the better ability of communities to survive long-lasting starvation and stress and include mechanisms of adaptation and cell specialization. Thus, yeast colonies pass through distinct developmental phases characterized by changes in pH and the production of ammonia-signalling molecules. Here, we show that Saccharomyces cerevisiae colony transition between major developmental phases (first acidic, alkali, second acidic) is accompanied by striking transcription changes, while the development within each particular phase is guided mostly at the post-transcriptional level. First- and second-acidic-phase colonies markedly differ. Second-acidic-phase colonies maintain the adaptive metabolism activated in the ammonia-producing period, supplemented by additional changes, which begin after colonies enter the second acidic phase. Cells with particular properties are not homogenously dispersed throughout the colony population, but localize to specific colony regions. Thus, cells located at the colony margin are able to export higher amounts of ammonium than central cells and to activate an adaptive metabolism. In contrast, central chronologically aged cells are unable to undergo these changes but they maintain higher levels of various stress-defence enzymes. These divergent properties of both cell types determine their consequent dissimilar fate.

Influence of aggregation on interaction of lipophilic, water-insoluble azaphthalocyanines with DOPC vesicles.

Dioleoylphosphatidylcholine unilamellar vesicles made by extrusion technique (LUVETs) were studied as the delivery system for lipophilic water-insoluble potential photosensitizers for photodynamic therapy (PDT). Two azaphthalocyanines (AzaPcs) with hydrophobic substituents only and two also possessing two charged amino groups were introduced into the study. All compounds are insoluble in water and form aggregates in PBS with tetrahydrofuran as cosolvent. The size of these aggregates depends on the concentration of AzaPc in solution. AzaPcs with tert-butyl substituents were found to be incorporated into the lipid bilayer of vesicles in the monomeric form even at high concentrations. The stability of LUVETs with incorporated AzaPc was excellent for at least 4 weeks. Therefore, they are suitable for use as a delivery system for these water-insoluble photosensitizers. Very low amount of AzaPc with n-octyl substituents incorporated into LUVETs due to its stronger self-aggregation. Values of binding constants determined for all AzaPcs showed inverse order than expected from their lipophilicities. However, the binding constants followed the order of the strength of aggregation forces. Aggregation of AzaPcs in water medium plays a very important role in the interaction of AzaPcs with LUVETs.

Association of putative ammonium exporters Ato with detergent-resistant compartments of plasma membrane during yeast colony development: pH affects Ato1p localisation in patches.

It was proposed that Ato1p, Ato2p and Ato3p have a role in ammonia production by Saccharomyces cerevisiae colonies (Palkova et al., Mol Biol Cell 13: 3901-3914, 2002). In this study, we show that all three Ato proteins localise to the plasma membrane and their appearance correlates with the beginning of ammonia release. The expression of ATO genes is controlled by ammonia. All three Ato-GFP proteins associate with detergent-resistant membranes; two of them, Ato1p-GFP and Ato3p-GFP, localise to patches visible under the fluorescence microscope. In contrast with Ato3p-GFP which forms stable patches, the formation of those of Ato1p-GFP is pH dependent. Ato1p-GFP patches form at pH above 6 and they disappear at pH 5 or lower. Both changes, Ato1p-GFP clustering and patches spreading are reversible. The Ato1p-GFP spreading at low pH is independent on endocytosis. These data suggest that besides the ammonia induction of Ato protein synthesis, pH may rapidly regulate Ato1p function.

Sok2p transcription factor is involved in adaptive program relevant for long term survival of Saccharomyces cerevisiae colonies.

Volatile ammonia functions as a long range alarm signal important for the transition of yeast colonies to their adaptive alkali developmental phase and for their consequent long term survival. Cells of aged Saccharomyces cerevisiae sok2 colonies deleted in the gene for Sok2p transcription factor are not able to release a sufficient amount of ammonia out of the cells, they are more fragile than cells of wild type colonies, and they exhibit a survival defect. Genome-wide analysis on gene expression differences between sok2 and WT colonies revealed that sok2 colonies are not able to switch on the genes of adaptive metabolisms effectively and display unbalanced expression and activity of various enzymes involved in cell protection against oxidative damage. Impaired amino acid metabolism and insufficient activation of genes for putative ammonium exporters Ato and of those for some other membrane transporters may be responsible for observed defects in ammonia production. Thus, Sok2p appears to be an important regulator of S. cerevisiae colony development. Gene expression differences caused by its absence in colonies differ from those described previously in liquid cultures, which suggests a pleiotropic effect of Sok2p under different conditions.

External factors involved in the regulation of synthesis of an extracellular proteinase in Bacillus megaterium: effect of temperature.

We studied the effect of temperature on the production of an extracellular neutral metalloproteinase of Bacillus megaterium in a laboratory fermentor under constant aeration and pH. The optimal temperature for growth (35-38° C) was higher than that for the synthesis of proteinase during exponential growth (below 31° C). The critical biomass concentration at which the exponential growth terminated decreased with increase in cultivation temperature. The specific rate of proteinase synthesis decreased when the critical biomass concentration was achieved. The observed decrease in proteinase synthesis was related to the cultivation temperature. The temperature also influenced the level of mRNA coding for proteinase. We formulated a mathematical model of cultivation describing the dependence of growth and proteinase synthesis on dissolved oxygen and temperature. The parameters of the model were identified for temperature intervals from 21 to 41° C using a computer. The optimum temperature for the enzyme production was 21° C. The productivity (enzyme activity/time) was maximal at 24-28° C. When optimizing the temperature profile of cultivation, we designed a suboptimal solution represented by a linear temperature profile. We have found that under conditions of continuous decrease in temperature, the maximal production of the proteinase was achieved at a broad range of temperature (26-34° C) when the rate of temperature decrease was 0.2-0.8° C/h. The initial optimal temperature for the enzyme productivity was in the range of 32-34° C. The optimum temperature decrease was 0.8° C/h.