Respiration Of Yeast Research Articles

Effects of glucose on the cellular respiration in fission yeast expressing human GSK3B gene

Effects of glucose on the cellular respiration in fission yeast expressing human GSK3B gene

Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast

Control of protein stoichiometry is essential for cell function. Mitochondrial oxidative phosphorylation (OXPHOS) presents a complex stoichiometric challenge as the ratio of the electron transport chain (ETC) and ATP synthase must be tightly controlled, and assembly requires coordinated integration of proteins encoded in the nuclear and mitochondrial genome. How correct OXPHOS stoichiometry is achieved is unknown. We identify the Mitochondrial Regulatory hub for respiratory Assembly (MiRA) platform, which synchronizes ETC and ATP synthase biogenesis in yeast. Molecularly, this is achieved by a stop-and-go mechanism: the uncharacterized protein Mra1 stalls complex IV assembly. Two "Go" signals are required for assembly progression: binding of the complex IV assembly factor Rcf2 and Mra1 interaction with an Atp9-translating mitoribosome induce Mra1 degradation, allowing synchronized maturation of complex IV and the ATP synthase. Failure of the stop-and-go mechanism results in cell death. MiRA controls OXPHOS assembly, ensuring correct stoichiometry of protein machineries encoded by two different genomes.

Detection of L-lysine in food supplement based on amperometric biosensors

L-lysine is an essential amino acid not synthesized by the body and is used as a nutritional supplement, and is considered an index of the nutritional quality of foodstuffs. The level of L-lysine consumption depends on age, where an imbalance in L-lysine levels can cause certain disease conditions. This study identified the effects of L-lysine contained in food supplements using the yeast-based amperometric biosensor Saccharomyces cerevisiae, which measures dissolved oxygen (DO) levels due to cellular respiration of yeast with an analyte assay sample. The measurements were made by calibrating pure L-lysine at 100, 200 and 300 mM concentrations. The results show that the higher the concentration of L-lysine, the smaller the level of DO remaining detected, where the percentage range of DO is 13.47% - 26.02%. The dietary supplement sample test, namely Curcuma Plus, has an error of 1.01% which states that the biosensor used can detect L-lysine levels in samples with high sensitivity and selectivity and can be applied to the food and health industries. The measurement results are clustered using Principal Component Analysis (PCA) to see the resulting clusters and data patterns.

Divergence of cytokinesis and dimorphism control by myosin II regulatory light chain in fission yeasts

Non-muscle myosin II activation by regulatory light chain (Rlc1Sp) phosphorylation at Ser35 is crucial for cytokinesis during respiration in the fission yeast Schizosaccharomyces pombe. We show that in the early divergent and dimorphic fission yeast S.japonicus non-phosphorylated Rlc1Sj regulates the activity of Myo2Sj and Myp2Sj heavy chains during cytokinesis. Intriguingly, Rlc1Sj-Myo2Sj nodes delay yeast to hyphae onset but are essential for mycelial development. Structure-function analysis revealed that phosphorylation-induced folding of Rlc1Sp α1 helix into an open conformation allows precise regulation of Myo2Sp during cytokinesis. Consistently, inclusion of bulky tryptophan residues in the adjacent α5 helix triggered Rlc1Sp shift and supported cytokinesis in absence of Ser35 phosphorylation. Remarkably, unphosphorylated Rlc1Sj lacking the α1 helix was competent to regulate S.pombe cytokinesis during respiration. Hence, early diversification resulted in two efficient phosphorylation-independent and -dependent modes of Rlc1 regulation of myosin II activity in fission yeasts, the latter being conserved through evolution.

Inactivation of HAP4 Accelerates RTG-Dependent Osmoadaptation in Saccharomyces cerevisiae.

Mitochondrial RTG (an acronym for ReTroGrade) signaling plays a cytoprotective role under various intracellular or environmental stresses. We have previously shown its contribution to osmoadaptation and capacity to sustain mitochondrial respiration in yeast. Here, we studied the interplay between RTG2, the main positive regulator of the RTG pathway, and HAP4, encoding the catalytic subunit of the Hap2-5 complex required for the expression of many mitochondrial proteins that function in the tricarboxylic acid (TCA) cycle and electron transport, upon osmotic stress. Cell growth features, mitochondrial respiratory competence, retrograde signaling activation, and TCA cycle gene expression were comparatively evaluated in wild type and mutant cells in the presence and in the absence of salt stress. We showed that the inactivation of HAP4 improved the kinetics of osmoadaptation by eliciting both the activation of retrograde signaling and the upregulation of three TCA cycle genes: citrate synthase 1 (CIT1), aconitase 1 (ACO1), and isocitrate dehydrogenase 1 (IDH1). Interestingly, their increased expression was mostly dependent on RTG2. Impaired respiratory competence in the HAP4 mutant does not affect its faster adaptive response to stress. These findings indicate that the involvement of the RTG pathway in osmostress is fostered in a cellular context of constitutively reduced respiratory capacity. Moreover, it is evident that the RTG pathway mediates peroxisomes-mitochondria communication by modulating the metabolic function of mitochondria in osmoadaptation.

Dissecting the lipidic determinants of inner mitochondrial membrane structure.

The inner mitochondrial membrane (IMM) is the primary site of ATP synthesis within eukaryotic cells. The IMM possesses unique, highly curved morphologies defined by cristae membranes (CM), whose large surface area functions to optimize respiration. While a plethora of studies have demonstrated the role of cristae-shaping proteins in generating characteristic CM morphologies, analysis of the roles mitochondrial phospholipids play in shaping CM structure is distinctly lacking. Here we combine lipidomic analysis with multi-scale modelling to demonstrate how multiple components of CMs shape IMM morphology and respiration in yeast. Tuning of phospholipid saturation in engineered strains revealed a surprising breakpoint in CM structure and respiration which phenocopied losses of CM-shaping proteins. Reaction-diffusion simulations on tomogram-derived mitochondrial morphologies showed that lower curvature CM structures can directly contribute to a loss of ATP synthesis. Molecular dynamics (MD) simulations of mitochondrial lipidomes revealed changes in membrane mechanical properties controlled by lipid saturation. We modelled CM tubule formation using continuum mechanics, which revealed that CM formation is defined by a snap-through instability, controlled by the mitochondrial lipidome. Our model also predicted a cooperative interaction between lipid saturation and cardiolipin (CL), which both contribute to curvature. While loss of CL has a minimal phenotype in aerobically-grown yeast, we found that it becomes essential in conditions of increased saturation, induced either genetically or by growth in microaerobic conditions. These results demonstrate how the formation of a highly curved CM is dependent on the mechanical contributions of multiple lipid species, which then dictate mitochondrial function.

Development of a Yeast Inhibitive Assay for Anionic Heavy Metals Using the 1-(4,5-Dimethylthiazol-2-Yl)-3,5-Diphenyltetrazolium Bromide (MTT) Assay

Currently, heavy metals pollution is significantly becoming a global concern as it causes severe toxicity towards human health and the environmental condition. Intensive efforts to develop a highly sensitive, rapid, and simple toxicity assay to assess the toxic effects of heavy metals in aquatic bodies have been done. An emerging tool to solve this matter is by using microorganisms and one of them is yeast. In this study, a rapid, simple, and cost-efficient toxicity assay by using the Baker’s yeast (Saccharomyces cerevisiae) respiration assay with a tetrazolium dye (MTT) is developed as potential environmental biomonitoring tool. To achieve high sensitivity, optimization using one-factor-at-a-time (OFAT) was first carried out. The best conditions giving optimum response occurred at pH 5.8 and 30 min contact time. Molybdate and chromate exhibited exponential decay type inhibition curves with calculated half maximal inhibitory concentration, IC50 of 1.137 mg/L for molybdate and 1.247 mg/L for chromate. The Limits of detection (LOD) were 0.313 mg/L and 1.247 mg/L for molybdate and chromate, respectively. The newly developed assay can help in monitoring heavy metals pollution in rivers and agricultural areas.

Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation.

Hypusine is a post-translational modification on eukaryotic translation initiation factor 5A (eIF5A). The last step of hypusine biosynthesis, deoxyhypusine hydroxylation, is an oxygen-dependent reaction. Here we show that deletion of the deoxyhypusine hydroxylase Lia1 compromises yeast respiration through translation downregulation of selected proteins in the respiration pathway. The translation suppression, because of the lack of deoxyhypusine hydroxylation, mainly affects translation of the N termini of the proteins, independent of the presence of proline residues but likely dependent on the interaction between the N-terminal nascent peptide and the ribosomal peptide exit tunnel. Proteomics and biochemical studies reveal that Lia1 deletion decreases N-terminal translation of proteins involved in mitochondrial respiration, oxidative stress response, and protein folding. Our work uncovers functions of the hypusine modification by considering the substrate requirement of the post-translational modification, highlights the unique challenges of translating the N termini of proteins, and reveals an oxygen-sensing mechanism in eukaryotic cells.

Population-level heterogeneity as a reflection of mixed strategy: A computational perspective on the Crabtree effect

Is population-level heterogeneity a reflection of distinct subpopulations, exhibiting different metabolic functions, or dynamic metabolism of individuals within the population? This fascinating question has remained a subject of great interest in studying metabolic specialization in microorganisms. The Crabtree effect – i.e., the ability of some microorganisms to switch from respiration to fermentation in the presence of oxygen - is an appropriate case study to address the aforementioned question. Game-theoretical approaches have been routinely used to examine and explain the way a microorganism, such as yeast, would switch between the two ATP-producing pathways, i.e., respiration and fermentation. Here we attempt to explain the switch between respiration and fermentation in yeast by constructing a simple metabolic switch. We then utilize an individual-based model, in which each individual is equipped with all the relevant chemical reactions, to see how cells equipped with such metabolic switch would behave in different conditions. We further investigate our proposed metabolic switch using the game-theoretical approach. Based on this model, we postulate that the population-level metabolic heterogeneity in microorganisms can simply arise from individuals utilizing a mixed strategy.

Why is Yeast Such a Widely Used Eukaryotic Model Organism? A Literature Review

Introduction: The use of yeasts in various fields dates back to thousands of years ago, but their biological significance has only recently been discovered. Genomes of many members of this relatively small group have been sequenced, and the consequent studies on them and on various cell processes have revealed similarities between yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe, and other eukaryotes, suggesting that they may be used as eukaryotic model organisms. Methods: A literature search was conducted investigating general yeast characteristics, genetics and physiology, as well as modern applications in biomedical research as model organisms. Results: Yeasts have many traits that make them especially favorable in research: they can easily be cultivated in laboratory conditions where their metabolism may be altered by tweaking the growth medium properties. Additionally, analyzing the yeast and human genome sequences has revealed astonishing similarities, with many successfully mapped homologous genes. Discussion: By varying environmental conditions of a S. cerevisiae culture, it was found that such treatments could affect respiration in yeast. Proving useful in research of antifungal drugs and interactions between fungal pathogens and hosts, yeast was also used as a model for studying prion related diseases, Alzheimer’s disease and cancer, amongst others. Conclusion: With all the yeast characteristics—their simple requirements for growth, their genome and metabolism similar to other eukaryotes, and their use in studying varying disease conditions—it is understandable and clear why yeasts are such widely used model organisms. Considering recent advancements, their application in biomedical research will inevitably increase over time.

Choline restores respiration in Psd1-deficient yeast by replenishing mitochondrial phosphatidylethanolamine

Phosphatidylethanolamine (PE) is essential for mitochondrial respiration in yeast, Saccharomyces cerevisiae, whereas the most abundant mitochondrial phospholipid, phosphatidylcholine (PC), is largely dispensable. Surprisingly, choline (Cho), which is a biosynthetic precursor of PC, has been shown to rescue the respiratory growth of mitochondrial PE-deficient yeast; however, the mechanism underlying this rescue has remained unknown. Using a combination of yeast genetics, lipid biochemistry, and cell biological approaches, we uncover the mechanism by showing that Cho rescues mitochondrial respiration by partially replenishing mitochondrial PE levels in yeast cells lacking the mitochondrial PE-biosynthetic enzyme Psd1. This rescue is dependent on the conversion of Cho to PC via the Kennedy pathway as well as on Psd2, an enzyme catalyzing PE biosynthesis in the endosome. Metabolic labeling experiments reveal that in the absence of exogenously supplied Cho, PE biosynthesized via Psd2 is mostly directed to the methylation pathway for PC biosynthesis and is unavailable for replenishing mitochondrial PE in Psd1-deleted cells. In this setting, stimulating the Kennedy pathway for PC biosynthesis by Cho spares Psd2-synthesized PE from the methylation pathway and redirects it to the mitochondria. Cho-mediated elevation in mitochondrial PE is dependent on Vps39, which has been recently implicated in PE trafficking to the mitochondria. Accordingly, epistasis experiments placed Vps39 downstream of Psd2 in Cho-based rescue. Our work, thus, provides a mechanism of Cho-based rescue of mitochondrial PE deficiency and uncovers an intricate interorganelle phospholipid regulatory network that maintains mitochondrial PE homeostasis.

Repairing Creep-Resistant and Kinetically Inert Hydrogels via Yeast Activity-Regulated Energy Dissipation.

Energy dissipation, a ubiquitous process in biological systems, has been intensively studied and widely used to guide the transient assembly of natural or synthetic molecules, but very few examples of material transient healability controlled by this important process have been reported. Herein, we realize the healing of creep-resistant and kinetically inert polymer hydrogels that is driven by the respiration of baker's yeast (Saccharomyces cerevisiae) and spontaneous energy dissipation. The entire healing process can be simply controlled by a single variable: sucrose concentration. Due to the high activity and stability of yeast in the hydrogels, multiple local healing events become possible and healing of damaged hydrogels is also efficient after a long waiting time. All these results indicate that our yeast-containing polymer hydrogels are kinetically stable materials, which can be readily healable on demand.

Anaerobic and Aerobic Respiration in Yeast: Small-Scale Variations on a Classic Laboratory Activity

This activity describes a mini- to microscale setup that offers an affordable, reproducible, and accurate method to compare the aerobic and anaerobic respiration of Saccharomyces boulardii, a strai...

Synthesis of Biomass-Derived Carbon Induced by Cellular Respiration in Yeast for Supercapacitor Applications.

Because activated carbon is extensively used in supercapacitors, optimization of its precursors and synthetic strategies are crucial. Inspired by the rich sugar content of banana peel waste, which can be transformed through the respiration of yeast into alcohol with the release of CO2 , we developed an environmentally benign and highly efficient process for the production of renewable heteroatom-doped hierarchical porous carbon materials (yeast-treated banana-peel-based carbon, denoted as YBP) without any additional templates or activation agents. The resulting biologically activated carbon was characterized by near-edge X-ray absorption fine-structure spectroscopy, X-ray photoelectron spectroscopy, and other physical methods. The biologically activated carbon achieved a maximum gravimetric specific capacitance of 476 F g-1 in 1 m H2 SO4 electrolyte. Remarkably, with a moderate specific surface area of 1084 m2 g-1 , the as-obtained activated carbon was found to have a high packing density. With enriched pseudocapacitance sites, the YBP symmetric supercapacitor has a high volumetric specific capacitance and energy density (maximum values of 264 F cm-3 and 23.5 Wh L-1 , respectively). The supercapacitor showed superior cyclic stability, with 94 % capacitance retention for voltage values up to 1.6 V after 10 000 cycles, which confirmed the promising application of this supercapacitor in miniature electronic devices.

Small molecules that target group II introns are potent antifungal agents.

Specific RNA structures control numerous metabolic processes that impact human health, and yet efforts to target RNA structures de-novo have been limited. In eukaryotes, the self-splicing group II intron is a mitochondrial RNA tertiary structure that is absent in vertebrates but essential for respiration in plants, fungi and yeast. Here we show that this RNA can be targeted through a process of high-throughput in vitro screening, SAR and lead optimization, resulting in high affinity compounds that specifically inhibit group IIB intron splicing in vitro and in vivo and lack toxicity in human cells. The compounds are potent growth inhibitors of the pathogen Candida parapsilosis, displaying antifungal activity comparable with Amphotericin B. These studies demonstrate that RNA tertiary structures can be successfully targeted de-novo, resulting in pharmacologically valuable compounds.

An Eco-friendly Microorganism Method To Activate Biomass for Cathode Materials for High-Performance Lithium–Sulfur Batteries

Biomass-based carbon has attracted considerable attention as a host material of active sulfur in lithium–sulfur batteries, while chemical activators of H3PO4, KOH, or ZnCl2 are essential to construct the porous structure of the materials. Inspired by traditional Chinese steamed buns, herein a unique porous microcellular carbon composed of cross-linked nanopores has been synthesized by an eco-friendly biological fermentation using banana peel as a carbon precursor. The specially hierarchical carbon framework obtained under the aerobic respiration and anaerobic breathing of biological yeast during fermenting, and simultaneously the inherent doping of N (3.28 at. %), produce a promising carbon host material to stabilize the structure of electrodes and restrict the dissolution of polysulfides during charging and discharging. The amount of biological yeast has an important influence on the microstructure of the biomass carbons and the correlated electrochemical properties of carbon/sulfur electrodes. The optimal amount of biological yeast is 3.0 wt %, where the carbon/sulfur composite electrode possesses a sulfur loading of 74.34 wt % and achieves a large initial reversible capacity of 1174 mAh g–1 at 0.1 C and a high capacity hold of 58.35% after 100 cycles. Our study provides a novel eco-friendly strategy to fabricate the interconnected hierarchical porous carbon framework from living wastes for various energy storage and conversion applications, including lithium–ion battery, supercapacitor, etc.

Inhibition of Respiration in Yeast by 2-Phenylethylamine

Background: 2-phenylethylamine (2-PEA) is an organic neurotransmitter which belongs to a class of biogenic amines that are essential for regulation of cellular development, differentiation and homeostasis. This class of compounds have been reported to cause oxidative stress to neuronal cells in the brain, which have a high oxygen consumption rate, elevated iron content and low antioxidant concentration. 2-phenylethylamine can metabolise into hydroxyl radicals which have been found to be a direct cause of oxidative stress within cells. Methods: This study has examined the toxicity of 2-phenylethylamine in the yeasts, Saccharomyces cerevisiae and Candida glabrata by examining growth with glucose or ethanol as sources, in the presence of 2-phenylethylamine. Results: 2-phenylethylamine was found to be inhibitory to all strains of yeast where respiratory function was necessary, while growth where glucose was the carbon source was unaffected. Almost all growth inhibition could be reversed by antioxidants ascorbate and glutathione, indicating oxidative stress was the likely cause of toxicity through 2-PEA or one of its metabolites. Conclusion: Yeast studies show that the biogenic amine, 2-phenylethylamine, targets respiratory function and that the inhibition can be reversed alleviated by the addition of glutathione or ascorbate. Keywords: 2-phenylethylamine, ascorbic acid, glutathione, mitochondrial respiratory function, reactive oxygen, yeast.

Studying anti-oxidative properties of inclusion complexes of α-lipoic acid with γ-cyclodextrin in single living fission yeast by confocal Raman microspectroscopy

α-lipoic acid (ALA) is an essential cofactor for many enzyme complexes in aerobic metabolism, especially in mitochondria of eukaryotic cells where respiration takes place. It also has excellent anti-oxidative properties. The acid has two stereo-isomers, R- and S- lipoic acid (R-LA and S-LA), but only the R-LA has biological significance and is exclusively produced in our body. A mutant strain of fission yeast, Δdps1, cannot synthesize coenzyme Q10, which is essential during yeast respiration, leading to oxidative stress. Therefore, it shows growth delay in the minimal medium. We studied anti-oxidant properties of ALA in its free form and their inclusion complexes with γ-cyclodextrin using this mutant yeast model. Both free forms R- and S-LA as well as 1:1 inclusion complexes with γ-cyclodextrin recovered growth of Δdps1 depending on the concentration and form. However, it has no effect on the growth of wild type fission yeast strain at all. Raman microspectroscopy was employed to understand the anti-oxidant property at the molecular level. A sensitive Raman band at 1602cm−1 was monitored with and without addition of ALAs. It was found that 0.5mM and 1.0mM concentrations of ALAs had similar effect in both free and inclusion forms. At 2.5mM ALAs, free forms inhibited the growth while inclusion complexes helped in recovered. 5.0mM ALA showed inhibitory effect irrespective of form. Our results suggest that the Raman band at 1602cm−1 is a good measure of oxidative stress in fission yeast.

Melatonin improves survival and respiratory activity of yeast cells challenged by alpha-synuclein and menadione.

One of the hallmarks of Parkinson disease is α-synuclein aggregate deposition that leads to endoplasmic reticulum stress, Golgi fragmentation and impaired energy metabolism with consequent redox imbalance. In the last decade, many studies have used Saccharomyces cerevisiae as a model in order to explore the intracellular consequences of α-synuclein overexpression. In this study we propose to evaluate the respiratory outcome of yeast cells expressing α-synuclein. Cell viability or growth on selective media for respiratory activity was mainly affected in the α-synuclein-expressing cells if they were also treated with menadione, which stimulates reactive oxygen species production. We also tested whether melatonin, a natural antioxidant, would counteract the deleterious effects of α-synuclein and menadione. In fact, melatonin addition improved the respiratory growth of α-synuclein/menadione-challenged cells, presented a general improvement in the enzymatic activity of the respiratory complexes and finally elevated the rate of mitophagy, an important cellular process necessary for the clearance of damaged mitochondria. Altogether, our data confirms that α-synuclein impairs respiration in yeast, which can be rescued by melatonin addition.

Switched Latent Force Models for Reverse-Engineering Transcriptional Regulation in Gene Expression Data.

To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult task to measure experimentally TF behaviors, and the challenges to capture their quick-time dynamics, different types of models based on differential equations have been proposed. However, those approaches usually incur in costly procedures, and they present problems to describe sudden changes in TF regulators. In this paper, we present a switched dynamical latent force model for reverse-engineering transcriptional regulation in gene expression data which allows the exact inference over latent TF activities driving some observed gene expressions through a linear differential equation. To deal with discontinuities in the dynamics, we introduce an approach that switches between different TF activities and different dynamical systems. This creates a versatile representation of transcription networks that can capture discrete changes and non-linearities. We evaluate our model on both simulated data and real data (e.g., microaerobic shift in E. coli, yeast respiration), concluding that our framework allows for the fitting of the expression data while being able to infer continuous-time TF profiles.