Inorganic Phosphate and Sulfate Transport in S. cerevisiae

Fungal commensalism modulated by a dual-action phosphate transceptor

Successful host colonization by fungi in fluctuating niches requires response and adaptation to multiple environmental stresses. However, our understanding about how fungal species thrive in the gastrointestinal (GI) ecosystem by combing multifaceted nutritional stress with respect to homeostatic host-commensal interactions is still in its infancy. Here, we discover that depletion of the phosphate transceptor Pho84 across multiple fungal species encountered a substantial cost in gastrointestinal colonization. Mechanistically, Pho84 enhances the gastrointestinal commensalism via a dual-action activity, coordinating both phosphate uptake and TOR activation by induction of the transcriptional regulator Try4 and downstream commensalism-related transcription. As such, Pho84 promotes Candida albicans commensalism, but this does not translate into enhanced pathogenicity. Thus, our study uncovers a specific nutrient-dependent dual-action regulatory pathway for Pho84 on fungal commensalism.

Low phosphate mitigates cadmium-induced oxidative stress in Saccharomyces cerevisiae by enhancing endogenous antioxidant defence system

Cadmium is a highly toxic heavy metal that causes many harmful effects on human health and ecosystems. Metal chelation-based techniques have become a common approach for the treatment of metal poisoning and also for the remediation of metal contamination. Phosphate, an essential nutrient required for key cellular functions, has been supposed to be effective in reducing cadmium bioavailability, possibly through its chelating potential. In this study, we explored the effects of phosphate on cadmium toxicity and cellular response to cadmium stress in the eukaryotic model Saccharomyces cerevisiae. Our results reveal that cadmium toxicity is unexpectedly enhanced during phosphate repletion and optimal phosphate levels for yeast growth under cadmium stress conditions decline with increasing cadmium concentrations. The profound cadmium toxicity during phosphate repletion is unlikely to result from either elevated cadmium accumulation or dysregulated homeostasis of essential metals, but rather due to increased production of intracellular reactive oxygen species. We show that, under phosphate-depleted conditions, the activities of antioxidant enzymes, especially Mn-superoxide dismutase and catalase, are significantly promoted through transcriptional upregulation. Our findings highlight the important role of cellular response to phosphate limitation in mitigating cadmium toxicity and endogenous oxidative stress through the enhancement of antioxidant enzyme activity.

Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium

Although the strategies used by bacteria to adapt to specific environmental conditions are widely reported, fewer studies have addressed how microbes with a cosmopolitan distribution can survive in diverse ecosystems. Exiguobacterium is a versatile genus whose members are commonly found in various habitats. To better understand the mechanisms underlying the universality of Exiguobacterium, we collected 105 strains from diverse environments and performed large-scale metabolic and adaptive ability tests. We found that most Exiguobacterium members have the capacity to survive under wide ranges of temperature, salinity, and pH. According to phylogenetic and average nucleotide identity analyses, we identified 27 putative species and classified two genetic groups: groups I and II. Comparative genomic analysis revealed that the Exiguobacterium members utilize a variety of complex polysaccharides and proteins to support survival in diverse environments and also employ a number of chaperonins and transporters for this purpose. We observed that the group I species can be found in more diverse terrestrial environments and have a larger genome size than the group II species. Our analyses revealed that the expansion of transporter families drove genomic expansion in group I strains, and we identified 25 transporter families, many of which are involved in the transport of important substrates and resistance to environmental stresses and are enriched in group I strains. This study provides important insights into both the overall general genetic basis for the cosmopolitan distribution of a bacterial genus and the evolutionary and adaptive strategies of Exiguobacterium.

IMPORTANCE The wide distribution characteristics of Exiguobacterium make it a valuable model for studying the adaptive strategies of bacteria that can survive in multiple habitats. In this study, we reveal that members of the Exiguobacterium genus have a cosmopolitan distribution and share an extensive adaptability that enables them to survive in various environments. The capacities shared by Exiguobacterium members, such as their diverse means of polysaccharide utilization and environmental-stress resistance, provide an important basis for their cosmopolitan distribution. Furthermore, the selective expansion of transporter families has been a main driving force for genomic evolution in Exiguobacterium. Our findings improve our understanding of the adaptive and evolutionary mechanisms of cosmopolitan bacteria and the vital genomic traits that can facilitate niche adaptation.

Phosphate efflux as a test of plasma membrane leakage in Saccharomyces cerevisiae cells

Plasma membrane integrity is a key to cell viability. Currently, the main approach to assessing plasma membrane integrity is the detection of penetration of special dyes, such as trypan blue and propidium iodide, into the cells. However, this method needs expensive equipment: a fluorescent microscope or a flow cytometer. Besides, staining with propidium iodide occasionally gives false-positive results. Here, we suggest the phosphate (Pi) leakage assay as an approach to assess the increase in permeability of the plasma membrane of yeast cells. We studied the dependence of phosphate efflux and uptake into Saccharomyces cerevisiae cells on the composition of the incubation medium, time, and ambient pH. The difference in optimal conditions for these processes suggests that Pi efflux is not conducted by the Pi uptake system. The Pi efflux in water correlated with the proportion of cells stained with propidium iodide. This indicated that Pi efflux is associated with cytoplasmic membrane disruption in a portion of the yeast cell population. The assay of Pi efflux was used to evaluate membrane disruption in S. cerevisiae cells treated with some heavy metal ions and detergents.

Nitrate and Phosphate Transporters Rescue Fluoride Toxicity in Yeast

Organisms are exposed to fluoride in the air, water, and soil. Yeast and other microbes utilize fluoride channels as a method to prevent intracellular fluoride accumulation and mediate fluoride toxicity. Consequently, deletion of fluoride exporter genes (FEX) in S. cerevisiae resulted in over 1000-fold increased fluoride sensitivity. We used this FEX knockout strain to identify genes, that when overexpressed, are able to partially relieve the toxicity of fluoride exposure. Overexpression of five genes, SSU1, YHB1, IPP1, PHO87, and PHO90, increase fluoride tolerance by 2- to 10-fold. Overexpression of these genes did not provide improved fluoride resistance in wild-type yeast, suggesting that the mechanism is specific to low fluoride toxicity in yeast. Ssu1p and Yhb1p both function in nitrosative stress response, which is induced upon fluoride exposure along with metal influx. Ipp1p, Pho87p, and Pho90p increase intracellular orthophosphate. Consistent with this observation, fluoride toxicity is also partially mitigated by the addition of high levels of phosphate to the growth media. Fluoride inhibits phosphate import upon stress induction and causes nutrient starvation and organelle disruption, as supported by gene induction monitored through RNA-Seq. The combination of observations suggests that transmembrane nutrient transporters are among the most sensitized proteins during fluoride-instigated stress.

Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways

Systems biology approaches provide means to study the interplay between biological processes leading to the mechanistic understanding of the properties of complex biological systems. Here, we developed a vector format rule-based Boolean logic model of the yeast S. cerevisiae cAMP-PKA, Snf1, and the Snf3-Rgt2 pathway to better understand the role of crosstalk on network robustness and function. We identified that phosphatases are the common unknown components of the network and that crosstalk from the cAMP-PKA pathway to other pathways plays a critical role in nutrient sensing events. The model was simulated with known crosstalk combinations and subsequent analysis led to the identification of characteristics and impact of pathway interconnections. Our results revealed that the interconnections between the Snf1 and Snf3-Rgt2 pathway led to increased robustness in these signaling pathways. Overall, our approach contributes to the understanding of the function and importance of crosstalk in nutrient signaling.

Dissection of differential vanadate sensitivity in two Ogataea species links protein glycosylation and phosphate transport regulation

The closely related yeasts Ogataea polymorpha and O. parapolymorpha differ drastically from each other by sensitivity to the toxic phosphate analog vanadate. Search for genes underlying this difference revealed two genes, one designated as ABV1 (Alcian Blue staining, Vanadate resistance), which encodes a homologue of Saccharomyces cerevisiae Mnn4 responsible for attachment of mannosylphosphate to glycoside chains of secretory proteins, and the other designated as its S. cerevisiae homologue PHO87, encoding the plasma membrane low affinity phosphate sensor/transporter. The effect of Pho87 on vanadate resistance was bidirectional, since it decreased the resistance on phosphate-depleted medium, but was required for pronounced protection against vanadate by external phosphate. This highlights the dual function of this protein as a low affinity phosphate transporter and an external phosphate sensor. Involvement of Pho87 in phosphate sensing was confirmed by its effects on regulation of the promoter of the PHO84 gene, encoding a high affinity phosphate transporter. The effect of Abv1 was also complex, since it influenced Pho87 level and enhanced repression of the PHO84 promoter via a Pho87-independent pathway. Role of the identified genes in the difference in vanadate resistance between O. polymorpha and O. parapolymorpha is discussed.

Role of phosphate sensing in bone and mineral metabolism

Inorganic phosphate (P_i) is essential for signal transduction and cell metabolism, and is also an essential structural component of the extracellular matrix of the skeleton. P_i is sensed in bacteria and yeast at the plasma membrane, which activates intracellular signal transduction to control the expression of P_i transporters and other genes that control intracellular P_i levels. In multicellular organisms, P_i homeostasis must be maintained in the organism and at the cellular level, requiring an endocrine and metabolic P_i-sensing mechanism, about which little is currently known. This Review will discuss the metabolic effects of P_i, which are mediated by P_i transporters, inositol pyrophosphates and SYG1-Pho81-XPR1 (SPX)-domain proteins to maintain cellular phosphate homeostasis in the musculoskeletal system. In addition, we will discuss how P_i is sensed by the human body to regulate the production of fibroblast growth factor 23 (FGF23), parathyroid hormone and calcitriol to maintain serum levels of P_i in a narrow range. New findings on the crosstalk between iron and P_i homeostasis in the regulation of FGF23 expression will also be outlined. Mutations in components of these metabolic and endocrine phosphate sensors result in genetic disorders of phosphate homeostasis, cardiomyopathy and familial basal ganglial calcifications, highlighting the importance of this newly emerging area of research.

Transcriptional profile of a bioethanol production contaminant Candida tropicalis

The fermentation process is widely used in the industry for bioethanol production. Even though it is widely used, microbial contamination is unpredictable and difficult to control. The problem of reduced productivity is directly linked to competition for nutrients during contamination. Yeasts representing the Candida species are frequently isolated contaminants. Elucidating the behavior of a contaminant during the fermentation cycle is essential for combatting the contamination. Consequently, the aim of the current study was to better understand the functional and transcriptional behavior of a contaminating yeast Candida tropicalis. We used a global RNA sequencing approach (RNA-seq/MiSeq) to analyze gene expression. Genes with significantly repressed or induced expression, and related to the fermentations process, such as sugar transport, pyruvate decarboxylase, amino acid metabolism, membrane, tolerance to high concentrations of ethanol and temperatures, nutrient suppression), and transcription-linked processes, were identified. The expression pattern suggested that the functional and transcriptional behavior of the contaminating yeast during fermentation for bioethanol production is similar to that of the standard yeast Saccharomyces cerevisiae. In addition, the analysis confirmed that C. tropicalis is an important contaminant of the alcoholic fermentation process, generating bioethanol and viability through its tolerance to all the adversities of a fermentation process essential for the production of bioethanol. According on the gene expression profile, many of these mechanisms are similar to those of S. cerevisiae strains currently used for bioethanol production. These mechanisms can inform studies on antimicrobials, to combat yeast contamination during industrial bioethanol production.

Evolutionary conservation of a core fungal phosphate homeostasis pathway coupled to development in Blastocladiella emersonii

The model yeast Saccharomyces cerevisiae elicits a transcriptional response to phosphate (P_i) depletion. To determine the origins of the phosphate response (PHO) system, we bioinformatically identified putative PHO components in the predicted proteomes of diverse fungi. Our results suggest that the PHO system is ancient; however, components have been expanded or lost in different fungal lineages. To show that a similar physiological response is present in deeply-diverging fungi we examined the transcriptional and physiological response of PHO genes to P_i depletion in the blastocladiomycete Blastocladiella emersonii. Our physiological experiments indicate that B. emersonii relies solely on high-affinity Na⁺-independent Pho84-like transporters. In response to P_i depletion, BePho84 paralogues were 4-8-fold transcriptionally upregulated, whereas several other PHO homologues like phosphatases and vacuolar transporter chaperone (VTC) complex components show 2-3-fold transcriptional upregulation. Since P_i has been shown to be important during the development of B. emersonii, we sought to determine if PHO genes are differentially regulated at different lifecycle stages. We demonstrate that a similar set of PHO transporters and phosphatases are upregulated at key points during B. emersonii development. Surprisingly, some genes upregulated during P_i depletion, including VTC components, are repressed at these key stages of development indicating that PHO genes are regulated by different pathways in different developmental and environmental situations. Overall, our findings indicate that a complex PHO network existed in the ancient branches of the fungi, persists in diverse extant fungi, and that this ancient network is likely to be involved in development and cell cycle regulation.

H+ and Pi Byproducts of Glycosylation Affect Ca2+ Homeostasis and Are Retrieved from the Golgi Complex by Homologs of TMEM165 and XPR1

Glycosylation reactions in the Golgi complex and the endoplasmic reticulum utilize nucleotide sugars as donors and produce inorganic phosphate (Pi) and acid (H⁺) as byproducts. Here we show that homologs of mammalian XPR1 and TMEM165 (termed Erd1 and Gdt1) recycle luminal Pi and exchange luminal H⁺ for cytoplasmic Ca²⁺, respectively, thereby promoting growth of yeast cells in low Pi and low Ca²⁺ environments. As expected for reversible H⁺/Ca²⁺ exchangers, Gdt1 also promoted growth in high Ca²⁺ environments when the Golgi-localized V-ATPase was operational but had the opposite effect when the V-ATPase was eliminated. Gdt1 activities were negatively regulated by calcineurin signaling and by Erd1, which recycled the Pi byproduct of glycosylation reactions and prevented the loss of this nutrient to the environment via exocytosis. Thus, Erd1 transports Pi in the opposite direction from XPR1 and other EXS family proteins and facilitates byproduct removal from the Golgi complex together with Gdt1.

Key Residues and Phosphate Release Routes in the Saccharomyces cerevisiae Pho84 Transceptor: THE ROLE OF TYR179 IN FUNCTIONAL REGULATION

Pho84, a major facilitator superfamily (MFS) protein, is the main high-affinity P_i transceptor in Saccharomyces cerevisiae Although transport mechanisms have been suggested for other MFS members, the key residues and molecular events driving transport by P_i:H⁺ symporters are unclear. The current Pho84 transport model is based on the inward-facing occluded crystal structure of the Pho84 homologue PiPT in the fungus Piriformospora indica However, this model is limited by the lack of experimental data on the regulatory residues for each stage of the transport cycle. In this study, an open, inward-facing conformation of Pho84 was used to study the release of P_i A comparison of this conformation with the model for P_i release in PiPT revealed that Tyr¹⁷⁹ in Pho84 (Tyr¹⁵⁰ in PiPT) is not part of the P_i binding site. This difference may be due to a lack of detailed information on the P_i release step in PiPT. Molecular dynamics simulations of Pho84 in which a residue adjacent to Tyr¹⁷⁹, Asp¹⁷⁸, is protonated revealed a conformational change in Pho84 from an open, inward-facing state to an occluded state. Tyr¹⁷⁹ then became part of the binding site as was observed in the PiPT crystal structure. The importance of Tyr¹⁷⁹ in regulating P_i release was supported by site-directed mutagenesis and transport assays. Using trehalase activity measurements, we demonstrated that the release of P_i is a critical step for transceptor signaling. Our results add to previous studies on PiPT, creating a more complete picture of the proton-coupled P_i transport cycle of a transceptor.

The yeast Aft2 transcription factor determines selenite toxicity by controlling the low affinity phosphate transport system

The yeast Saccharomyces cerevisiae is employed as a model to study the cellular mechanisms of toxicity and defense against selenite, the most frequent environmental selenium form. We show that yeast cells lacking Aft2, a transcription factor that together with Aft1 regulates iron homeostasis, are highly sensitive to selenite but, in contrast to aft1 mutants, this is not rescued by iron supplementation. The absence of Aft2 strongly potentiates the transcriptional responses to selenite, particularly for DNA damage- and oxidative stress-responsive genes, and results in intracellular hyperaccumulation of selenium. Overexpression of PHO4, the transcriptional activator of the PHO regulon under low phosphate conditions, partially reverses sensitivity and hyperaccumulation of selenite in a way that requires the presence of Spl2, a Pho4-controlled protein responsible for post-transcriptional downregulation of the low-affinity phosphate transporters Pho87 and Pho90. SPL2 expression is strongly downregulated in aft2 cells, especially upon selenite treatment. Selenite hypersensitivity of aft2 cells is fully rescued by deletion of PHO90, suggesting a major role for Pho90 in selenite uptake. We propose that the absence of Aft2 leads to enhanced Pho90 function, involving both Spl2-dependent and independent events and resulting in selenite hyperaccumulation and toxicity.