Ca(2+) homeostasis in the budding yeast Saccharomyces cerevisiae: Impact of ER/Golgi Ca(2+) storage

Shedding Light on Calcium Dynamics in the Budding Yeast: A Review on Calcium Monitoring with Recombinant Aequorin

Recombinant aequorin has been extensively used in mammalian and plant systems as a powerful tool for calcium monitoring. While aequorin has also been widely applied in yeast research, a notable gap exists in the literature regarding comprehensive reviews of these applications. This review aims to address that gap by providing an overview of how aequorin has been used to explore calcium homeostasis, signaling pathways, and responses to stressors, heavy metals, and toxic compounds in Saccharomyces cerevisiae. We also discuss strategies for further developing the aequorin system in yeast, with particular emphasis on its use as a model for human calcium signaling studies, such as the reproduction of the mitochondrial calcium uniporter. By highlighting previous research and pinpointing potential future applications, we discuss the untapped potential of aequorin in yeast for drug screening, environmental toxicity testing, and disease-related studies.

The yeast Gdt1 protein mediates the exchange of H+ for Ca2+ and Mn2+ influencing the Golgi pH

The GDT1 family is broadly spread and highly conserved among living organisms. GDT1 members have functions in key processes like glycosylation in humans and yeasts, and photosynthesis in plants. These functions are mediated by their ability to transport ions. While transport of Ca²⁺ or Mn²⁺ is well established for several GDT1 members, their transport mechanism is poorly understood. Here, we demonstrate that H⁺ ions are transported in exchange for Ca²⁺ and Mn²⁺ cations by the Golgi-localized yeast Gdt1 protein. We performed direct transport measurement across a biological membrane by expressing Gdt1p in Lactococcus lactis bacterial cells and by recording either the extracellular pH or the intracellular pH during the application of Ca²⁺, Mn²⁺ or H⁺ gradients. Besides, in vivo cytosolic and Golgi pH measurements were performed in Saccharomyces cerevisiae with genetically encoded pH probes targeted to those subcellular compartments. These data point out that the flow of H⁺ ions carried by Gdt1p could be reversed according to the physiological conditions. Together, our experiments unravel the influence of the relative concentration gradients for Gdt1p-mediated H⁺ transport and pave the way to decipher the regulatory mechanisms driving the activity of GDT1 orthologs in various biological contexts.

Ca2+ administration prevents α-synuclein proteotoxicity by stimulating calcineurin-dependent lysosomal proteolysis

The capacity of a cell to maintain proteostasis progressively declines during aging. Virtually all age-associated neurodegenerative disorders associated with aggregation of neurotoxic proteins are linked to defects in the cellular proteostasis network, including insufficient lysosomal hydrolysis. Here, we report that proteotoxicity in yeast and Drosophila models for Parkinson's disease can be prevented by increasing the bioavailability of Ca2+, which adjusts intracellular Ca2+ handling and boosts lysosomal proteolysis. Heterologous expression of human α-synuclein (αSyn), a protein critically linked to Parkinson's disease, selectively increases total cellular Ca2+ content, while the levels of manganese and iron remain unchanged. Disrupted Ca2+ homeostasis results in inhibition of the lysosomal protease cathepsin D and triggers premature cellular and organismal death. External administration of Ca2+ reduces αSyn oligomerization, stimulates cathepsin D activity and in consequence restores survival, which critically depends on the Ca2+/calmodulin-dependent phosphatase calcineurin. In flies, increasing the availability of Ca2+ discloses a neuroprotective role of αSyn upon manganese overload. In sum, we establish a molecular interplay between cathepsin D and calcineurin that can be activated by Ca2+ administration to counteract αSyn proteotoxicity.

Coordinated glucose-induced Ca2+ and pH responses in yeast Saccharomyces cerevisiae

Ca²⁺ and pH homeostasis are closely intertwined and this interrelationship is crucial in the cells' ability to adapt to varying environmental conditions. To further understand this Ca²⁺-pH link, cytosolic Ca²⁺ was monitored using the aequorin-based bioluminescent assay in parallel with fluorescence reporter-based assays to monitor plasma membrane potentials and intracellular (cytosolic and vacuolar) pH in yeast Saccharomyces cerevisiae. At external pH 5, starved yeast cells displayed depolarized membrane potentials and responded to glucose re-addition with small Ca²⁺ transients accompanied by cytosolic alkalinization and profound vacuolar acidification. In contrast, starved cells at external pH 7 were hyperpolarized and glucose re-addition induced large Ca²⁺ transients and vacuolar alkalinization. In external Ca²⁺-free medium, glucose-induced pH responses were not affected but Ca²⁺ transients were abolished, indicating that the intracellular [Ca²⁺] increase was not prerequisite for activation of the two primary proton pumps, being Pma1 at the plasma membrane and the vacuolar and Golgi localized V-ATPases. A reduction in Pma1 expression resulted in membrane depolarization and reduced Ca²⁺ transients, indicating that the membrane hyperpolarization generated by Pma1 activation governed the Ca²⁺ influx that is associated with glucose-induced Ca²⁺ transients. Loss of V-ATPase activity through concanamycin A inhibition did not alter glucose-induced cytosolic pH responses but affected vacuolar pH changes and Ca²⁺ transients, indicating that the V-ATPase established vacuolar proton gradient is substantial for organelle H⁺/Ca²⁺ exchange. Finally, a systematic analysis of yeast deletion strains allowed us to reveal an essential role for both the vacuolar H⁺/Ca²⁺ exchanger Vcx1 and the Golgi exchanger Gdt1 in the dissipation of intracellular Ca²⁺.

Investigating the Antifungal Mechanism of Action of Polygodial by Phenotypic Screening in Saccharomyces cerevisiae

Polygodial is a "hot" peppery-tasting sesquiterpenoid that was first described for its anti-feedant activity against African armyworms. Using the haploid deletion mutant library of Saccharomyces cerevisiae, a genome-wide mutant screen was performed to shed more light on polygodial's antifungal mechanism of action. We identified 66 deletion strains that were hypersensitive and 47 that were highly resistant to polygodial treatment. Among the hypersensitive strains, an enrichment was found for genes required for vacuolar acidification, amino acid biosynthesis, nucleosome mobilization, the transcription mediator complex, autophagy and vesicular trafficking, while the resistant strains were enriched for genes encoding cytoskeleton-binding proteins, ribosomal proteins, mitochondrial matrix proteins, components of the heme activator protein (HAP) complex, and known regulators of the target of rapamycin complex 1 (TORC1) signaling. WE confirm that polygodial triggers a dose-dependent vacuolar alkalinization and that it increases Ca²⁺ influx and inhibits glucose-induced Ca²⁺ signaling. Moreover, we provide evidence suggesting that TORC1 signaling and its protective agent ubiquitin play a central role in polygodial resistance, suggesting that they can be targeted by polygodial either directly or via altered Ca²⁺ homeostasis.

Aequorin as a Useful Calcium-Sensing Reporter in Candida albicans

In Candida albicans, calcium ions (Ca²⁺) regulate the activity of several signaling pathways, especially the calcineurin signaling pathway. Ca²⁺ homeostasis is also important for cell polarization, hyphal extension, and plays a role in contact sensing. It is therefore important to obtain accurate tools with which Ca²⁺ homeostasis can be addressed in this fungal pathogen. Aequorin from Aequorea victoria has been used in eukaryotic cells for detecting intracellular Ca²⁺. A codon-adapted aequorin Ca²⁺-sensing expression system was therefore designed for probing cytosolic Ca²⁺ flux in C. albicans. The availability of a novel water-soluble formulation of coelenterazine, which is required as a co-factor, made it possible to measure bioluminescence as a readout of intracellular Ca²⁺ levels in C. albicans. Alkaline stress resulted in an immediate influx of Ca²⁺ from the extracellular medium. This increase was exacerbated in a mutant lacking the vacuolar Ca²⁺ transporter VCX1, thus confirming its role in Ca²⁺ homeostasis. Using mutants in components of a principal Ca²⁺ channel (MID1, CCH1), the alkaline-dependent Ca²⁺ spike was greatly reduced, thus highlighting the crucial role of this channel complex in Ca²⁺ uptake and homeostasis. Exposure to the antiarrhythmic drug amiodarone, known to perturb Ca²⁺ trafficking, resulted in increased cytoplasmic Ca²⁺ within seconds that was abrogated by the chelation of Ca²⁺ in the external medium. Ca²⁺ import was also dependent on the Cch1/Mid1 Ca²⁺ channel in amiodarone-exposed cells. In conclusion, the aequorin Ca²⁺ sensing reporter developed here is an adequate tool with which Ca²⁺ homeostasis can be investigated in C. albicans.

K+-specific importers Trk1 and Trk2 play different roles in Ca2+ homeostasis and signalling in Saccharomyces cerevisiae cells

The maintenance of K+ and Ca2+ homeostasis is crucial for many cellular functions. Potassium is accumulated in cells at high concentrations, while the cytosolic level of calcium, to ensure its signalling function, is kept at low levels and transiently increases in response to stresses. We examined Ca2+ homeostasis and Ca2+ signalling in Saccharomyces cerevisiae strains lacking plasma-membrane K+ influx (Trk1 and Trk2) or efflux (Tok1, Nha1 and Ena1-5) systems. The lack of K+ exporters slightly increased the cytosolic Ca2+, but did not alter the Ca2+ tolerance or Ca2+-stress response. In contrast, the K+-importers Trk1 and Trk2 play important and distinct roles in the maintenance of Ca2+ homeostasis. The presence of Trk1 was vital mainly for the growth of cells in the presence of high extracellular Ca2+, whilst the lack of Trk2 doubled steady-state intracellular Ca2+ levels. The absence of both K+ importers highly increased the Ca2+ response to osmotic or CaCl2 stresses and altered the balance between Ca2+ flux from external media and intracellular compartments. In addition, we found Trk2 to be important for the tolerance to high KCl and hygromycin B in cells growing on minimal media. All the data describe new interconnections between potassium and calcium homeostasis in S. cerevisiae.

The V-ATPase regulates localization of the TRP Ca2+ channel Yvc1 in response to oxidative stress in Candida albicans

The vacuolar-type H⁺-ATPase (V-ATPase) is a highly conserved protein complex among the eukaryotic cells. We previously revealed that both the V-ATPase and the transient receptor potential (TRP) channel Yvc1 are involved in oxidative stress response (OSR). However, the relationship between V-ATPase and Yvc1 during OSR remains unknown. In this study, disruption of the V-ATPase-encoding genes VPH2 and TFP1, similar with disruption of YVC1, caused H₂O₂ hypersensitivity and enhancement of vacuolar membrane permeability (VMP) under oxidative stress. Further investigations showed that unlike the wild type strain with vacuole membrane-localized Yvc1, both vph2Δ/Δ and tfp1Δ/Δ had Yvc1 localization in the vacuole cavity, indicating that disruption of VPH2 or TFP1 impaired normal vacuolar membrane-localization of Yvc1. Interestingly, addition of CaCl₂ alleviated the growth defect of vph2Δ/Δ and tfp1Δ/Δ under oxidative stress, leading to prevention of VMP, decrease in ROS levels and activation of OSR. In contrast, addition of the Ca²⁺ chelating agent glycol-bis-(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) aggravated H₂O₂ hypersensitivity of the mutants. These results showed that the V-ATPase plays an important role in maintenance of normal Yvc1 localization, which contributes to Ca²⁺ transport from the vacuoles to the cytosol for activation of OSR. This work sheds a novel light on the interaction between V-ATPase and Ca²⁺ transport for regulation of OSR in C. albicans.

Decreased Vacuolar Ca2+ Storage and Disrupted Vesicle Trafficking Underlie Alpha-Synuclein-Induced Ca2+ Dysregulation in S. cerevisiae

The yeast Saccharomyces cerevisiae is a powerful model to study the molecular mechanisms underlying α-synuclein (α-syn) cytotoxicity. This is due to the high degree of conservation of cellular processes with higher eukaryotes and the fact that yeast does not endogenously express α-synuclein. In this work, we focused specifically on the interplay between α-syn and intracellular Ca²⁺ homeostasis. Using temperature-sensitive SEC4 mutants and deletion strains for the vacuolar Ca²⁺ transporters Pmc1 and Vcx1, together with aequorin-based Ca²⁺ recordings, we show that overexpression of α-syn shifts the predominant temporal pattern of organellar Ca²⁺ release from a biphasic to a quasi-monophasic response. Fragmentation and vesiculation of vacuolar membranes in α-syn expressing cells can account for the faster release of vacuolar Ca²⁺. α-Syn further significantly reduced Ca²⁺ storage resulting in increased resting cytosolic Ca²⁺ levels. Overexpression of the vacuolar Ca²⁺ ATPase Pmc1 in wild-type cells prevented the α-syn-induced increase in resting Ca²⁺ and was able to restore growth. We propose that α-syn-induced disruptions in Ca²⁺ signaling might be an important step in initiating cell death.

Calcium signaling pathway is involved in non-CYP51 azole resistance in Aspergillus fumigatus

The opportunistic fungal pathogen Aspergillus fumigatus, which is one of the primary airborne ascomycete pathogens and allergens worldwide, causes invasive fungal infections, which have high morbidity and mortality rates among immunosuppressed patients. The abuse of azole antifungals results in serious drug resistance in clinical therapy. Thus, a thorough understanding of the azole drug resistance mechanism and screening of antifungal agents with a novel mode of action and new drug targets are required to fight against drug resistance. Current studies suggest that there are three major azole resistance mechanisms in fungal pathogens, including changes of the drug target Cyp51, activation of drug efflux pumps and induction of cellular stress responses. Fungi must adapt to a variety of external environmental stressors to survive. These obstacles include stress to the plasma membrane after azole antifungal treatments, high temperature, pH variation, and oxidative stress. As a filamentous fungus, A. fumigatus has evolved numerous signal-transduction systems to sense and respond to azole stresses to survive and proliferate in harsh environmental conditions. Among these signal-transduction systems, the Ca2+ signaling pathway is one of the most important response systems, which has been verified to be involved in stress adaptation. In this review, we have summarized how the components of the calcium-signaling pathway and their interaction network are involved in azole stress response in A. fumigatus.

A Noisy Analog-to-Digital Converter Connects Cytosolic Calcium Bursts to Transcription Factor Nuclear Localization Pulses in Yeast

Several examples of transcription factors that show stochastic, unsynchronized pulses of nuclear localization have been described. Here we show that under constant calcium stress, nuclear localization pulses of the transcription factor Crz1 follow stochastic variations in cytosolic calcium concentration. We find that the size of the stochastic calcium bursts is positively correlated with the number of subsequent Crz1 pulses. Based on our observations, we propose a simple stochastic model of how the signaling pathway converts a constant external calcium concentration into a digital number of Crz1 pulses in the nucleus, due to the time delay from nuclear transport and the stochastic decoherence of individual Crz1 molecule dynamics. We find support for several additional predictions of the model and suggest that stochastic input to nuclear transport may produce noisy digital responses to analog signals in other signaling systems.

Redox regulation of the yeast voltage-gated calcium channel homolog, Cch1p, by glutathionylation of specific cysteines

CCH1, the yeast homolog of the pore-forming subunit α1 of the mammalian Voltage-gated calcium channel (VGCC) located on the plasma membrane mediates the redox-dependent influx of calcium. Cch1p is known to undergo both rapid activation (oxidative stress, high pH) and slow activation (ER stress, mating pheromone activation), but the mechanism of activation is not known. We demonstrate here that the fast activation, as well as the slow activation (tunicamycin or α-factor) is mediated through a common redox-dependant manner. Further, through mutational analysis of all 18 exposed cysteines in the Cch1p protein, we show that four of these mutants, C587A, C606A, C636A and C642A, which are clustered together in a common cytoplasmic loop region were functionally defective during both fast and slow activations and also showed reduced glutathionylation. These four cysteines are also conserved across phyla suggesting a conserved mechanism of activation. Investigations into the enzymes involved in the activation reveal that the yeast glutathione-s-transferase, Gtt1p is involved in the glutathionylation of Cch1p, while the thioredoxin, Trx2p plays a role in the Cch1p deglutathionylation.

Overexpression of Sly41 suppresses COPII vesicle-tethering deficiencies by elevating intracellular calcium levels

SLY41 is a multicopy suppressor of mutations in the essential Ypt1 GTPase. Overexpression of Sly41 elevates cytosolic Ca²⁺ concentration, which stimulates SNARE-dependent fusion of COPII vesicles with Golgi membranes and suppresses deficiencies in Ypt1-dependent vesicle tethering. Thus Ca²⁺ positively regulates vesicle fusion with Golgi membranes.

SLY41 was identified as a multicopy suppressor of loss of Ypt1, a Rab GTPase essential for COPII vesicle tethering at the Golgi complex. SLY41 encodes a polytopic membrane protein with homology to a class of solute transporter proteins, but how overexpression suppresses vesicle-tethering deficiencies is not known. Here we show that Sly41 is efficiently packaged into COPII vesicles and actively cycles between the ER and Golgi compartments. SLY41 displays synthetic negative genetic interactions with PMR1, which encodes the major Golgi-localized Ca²⁺/Mn²⁺ transporter and suggests that Sly41 influences cellular Ca²⁺ and Mn²⁺ homeostasis. Experiments using the calcium probe aequorin to measure intracellular Ca²⁺ concentrations in live cells reveal that Sly41 overexpression significantly increases cytosolic calcium levels. Although specific substrates of the Sly41 transporter were not identified, our findings indicate that localized overexpression of Sly41 to the early secretory pathway elevates cytosolic calcium levels to suppress vesicle-tethering mutants. In vitro SNARE cross-linking assays were used to directly monitor the influence of Ca²⁺ on tethering and fusion of COPII vesicles with Golgi membranes. Strikingly, calcium at suppressive concentrations stimulated SNARE-dependent membrane fusion when vesicle-tethering activity was reduced. These results show that calcium positively regulates the SNARE-dependent fusion stage of ER–Golgi transport.

Calcium and reactive oxygen species in regulation of the mitochondrial permeability transition and of programmed cell death in yeast

Mitochondria-dependent programmed cell death (PCD) in yeast shares many features with the intrinsic apoptotic pathway of mammals. With many stimuli, increased cytosolic [Ca(2+)] and ROS generation are the triggering signals that lead to mitochondrial permeabilization and release of proapoptotic factors, which initiates yeast PCD. While in mammals the permeability transition pore (PTP), a high-conductance inner membrane channel activated by increased matrix Ca(2+) and oxidative stress, is recognized as part of this signaling cascade, whether a similar process occurs in yeast is still debated. The potential role of the PTP in yeast PCD has generally been overlooked because yeast mitochondria lack the Ca(2+) uniporter, which in mammals allows rapid equilibration of cytosolic Ca(2+) with the matrix. In this short review we discuss the nature of the yeast permeability transition and reevaluate its potential role in the effector phase of yeast PCD triggered by Ca(2+) and oxidative stress.

Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan

Chitosan is a natural polymer with antimicrobial activity. Chitosan causes plasma membrane permeabilization and induction of intracellular reactive oxygen species (ROS) in Neurospora crassa. We have determined the transcriptional profile of N. crassa to chitosan and identified the main gene targets involved in the cellular response to this compound. Global network analyses showed membrane, transport and oxidoreductase activity as key nodes affected by chitosan. Activation of oxidative metabolism indicates the importance of ROS and cell energy together with plasma membrane homeostasis in N. crassa response to chitosan. Deletion strain analysis of chitosan susceptibility pointed NCU03639 encoding a class 3 lipase, involved in plasma membrane repair by lipid replacement, and NCU04537 a MFS monosaccharide transporter related to assimilation of simple sugars, as main gene targets of chitosan. NCU10521, a glutathione S-transferase-4 involved in the generation of reducing power for scavenging intracellular ROS is also a determinant chitosan gene target. Ca(2+) increased tolerance to chitosan in N. crassa. Growth of NCU10610 (fig 1 domain) and SYT1 (a synaptotagmin) deletion strains was significantly increased by Ca(2+) in the presence of chitosan. Both genes play a determinant role in N. crassa membrane homeostasis. Our results are of paramount importance for developing chitosan as an antifungal.

The Cch1-Mid1 High-Affinity Calcium Channel Contributes to the Virulence of Cryptococcus neoformans by Mitigating Oxidative Stress

Pathogenic fungi have developed mechanisms to cope with stresses imposed by hosts. For Cryptococcus spp., this implies active defense mechanisms that attenuate and ultimately overcome the onslaught of oxidative stresses in macrophages. Among cellular pathways within Cryptococcus neoformans' arsenal is the plasma membrane high-affinity Cch1-Mid1 calcium (Ca(2+)) channel (CMC). Here we show that CMC has an unexpectedly complex and disparate role in mitigating oxidative stress. Upon inhibiting the Ccp1-mediated oxidative response pathway with antimycin, strains of C. neoformans expressing only Mid1 displayed enhanced growth, but this was significantly attenuated upon H2O2 exposure in the absence of Mid1, suggesting a regulatory role for Mid1 acting through the Ccp1-mediated oxidative stress response. This notion is further supported by the interaction detected between Mid1 and Ccp1 (cytochrome c peroxidase). In contrast, Cch1 appears to have a more general role in promoting cryptococci survival during oxidative stress. A strain lacking Cch1 displayed a growth defect in the presence of H2O2 without BAPTA [(1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid, cesium salt] or additional stressors such as antimycin. Consistent with a greater contribution of Cch1 to oxidative stress tolerance, an intracellular growth defect was observed for the cch1Δ strain in the macrophage cell line J774A.1. Interestingly, while the absence of either Mid1 or Cch1 significantly compromises the ability of C. neoformans to tolerate oxidative stress, the absence of both Mid1 and Cch1 has a negligible effect on C. neoformans growth during H2O2 stress, suggesting the existence of a compensatory mechanism that becomes active in the absence of CMC.