Yeast Saccharomyces Cerevisiae Research Articles

Impact of Encapsulated Saccharomyces cerevisiae Yeasts on the Chemical and Sensory Profiles of Sparkling Cider Produced by the Champenoise Method

The cider market has been significantly expanding and gaining momentum in Eastern Europe. As such, the aim of this study was to obtain sparkling cider via the Champenoise method using two Romanian apple varieties (Topaz and Red Topaz) alongside the employment of two fermentations. Four yeast strains were used in the first fermentation, while encapsulated Saccharomyces cerevisiae was used in the second fermentation. The resulting cider was subjected to a comprehensive investigation to quantitatively determine the carbohydrates, organic acids, volatile and phenolic compounds, and amino acids from all the cider samples. A trained panel evaluated the sensory profile of the samples, and a chemometric analysis was used to interpret the data. Secondary fermentation increased the accumulation of malic acid and lactic acid, as well as the volatile profile complexity. The total polyphenol content in the sparkling cider samples increased by almost 20% in the S. cerevisiae sample and over 217% in the P. kluyveri + S. cerevisiae sample compared to the base cider. Additionally, studying the production and consumption trends of sparkling cider offers valuable insights for both producers and consumers. By understanding consumer preferences and refining production techniques, the industry can deliver higher-quality products that better align with market demands.

Reduction of Ferric Chloride in Yeast Growth Media, by Sugars and Aluminum

Iron compounds can be used in antimicrobial applications by exploiting the toxicity of divalent iron to living organisms due to the Fenton reaction. In this study, the growth inhibitory effects of ferrous sulfate FeSO4·7H2O and ferric chloride FeCl3·6H2O were observed on Metschnikowia clade and Saccharomyces cerevisiae yeast cells. The relatively high amount of reduced Fe3+ to Fe2+ in the growth medium determined by Mössbauer spectroscopy may contribute to the antimicrobial activity of ferric chloride. In order to test the reducing ability of sugars in the growth media of yeasts, the reaction of ferric chloride FeCl3·6H2O with sugars was investigated. In mixtures of FeCl3·6H2O and fructose, approximately two thirds of Fe3+ can be reduced to Fe2+. When the mixture of FeCl3·6H2O and fructose is placed on the surface of aluminum foil, an iron film is formed on the surface of the aluminum due to the reduction by both fructose and aluminum. The relative amount of Fe3+ which was reduced to Fe0 reached 68%.

Targeted Formation of Biofilms on the Surface of Graphite Electrodes as an Effective Approach to the Development of Biosensors for Early Warning Systems

Biofilms based on bacteria Pseudomonas veronii (Ps. veronii) and Escherichia coli (E. coli) and yeast Saccharomyces cerevisiae (S. cerevisiae) were used for novel biosensor creation for rapid biochemical oxygen demand (BOD) monitoring. Based on the electrochemical measurement results, it was shown that the endogenous mediator in the matrix of E. coli and Ps. veronii biofilms and ferrocene form a two-mediator system that improves electron transport in the system. Biofilms based on Ps. veronii and E. coli had a high biotechnological potential for BOD assessment; bioreceptors based on such biofilms had high sensitivity (the lower limits of detectable BOD5 concentrations were 0.61 (Ps. veronii) and 0.87 (E. coli) mg/dm3) and high efficiency of analysis (a measurement time 5–10 min). The maximum biosensor response based on bacterial biofilms has been observed in the pH range of 6.6–7.2. The greatest protective effect was found for biofilms based on E. coli, which has high long-term stability (151 days for Ps. veronii and 163 days for E. coli). The results of the BOD5 analysis of water samples obtained using the developed biosensors had a high correlation with the results of the standard 5-day method (R2 = 0.9820, number of tested samples is 10 for Ps. veronii, and R2 = 0.9862, number of tested samples is 10 for E. coli). Thus, biosensors based on Ps. veronii biofilms and E. coli biofilms could be a novel analytical system to give early warnings of pollution.

Screening and In Silico Analyses of the Yeast Saccharomyces cerevisiae Σ1278b Bank Mutants Using Citral as a Natural Antimicrobial

The antimicrobial function of citral, one of the main compounds of the essential oils (EO) of the Citrus genus, and widely used by the food industry toward spoilage yeast, was previously proven. In this study, the possible mode of action of citral against yeast cells was evaluated by using a global deletome approach. Firstly, the suitability of Saccharomyces cerevisiae Σ1278b to serve as model yeast was assessed by determining its sensitivity to citral (MIC = 0.5 μL/mL). Subsequently, the complete library of Σ1278b haploid mutants deleted in 4019 non-essential genes was screened to identify potential molecular targets of citral. Finally, the deleted genes in the 590 mutants showing increased citral resistance was analyzed with an in-silico approach (Gene Ontology). The significantly enriched GO Terms were “cytoplasm”, “vacuole”, and “mitochondrion” (cellular components); “catalytic activity” (molecular function); “pseudohyphal growth” (biological process). For molecular function, resistant mutants were grouped into thiosulfate sulfur transferase activity, transferase activity, and oxidoreductase activity; for cellular components, resistant mutants were grouped as: cytoplasm, intracellular organelle, membrane-bounded organelle, mitochondrion, organelle membrane, and vacuole; and finally, with regard to biological process, deleted genes were grouped as: pseudohyphal growth, mitochondrion organization, lipid metabolic process, DNA recombination and repair, and proteolysis. Interestingly, many identified genes were associated with the cellular response to oxidative stress and ROS scavenging. These findings have important implications for the development of citral-based antimicrobials and the elucidation of its mechanism of action.

Large enrichments in fatty acid 2H/1H ratios distinguish respiration from aerobic fermentation in yeast Saccharomyces cerevisiae

Shifts in the hydrogen stable isotopic composition (2H/1H ratio) of lipids relative to water (lipid/water 2H-fractionation) at natural abundances reflect different sources of the central cellular reductant, NADPH, in bacteria. Here, we demonstrate that lipid/water 2H-fractionation (2εfattyacid/water) can also constrain the relative importance of key NADPH pathways in eukaryotes. We used the metabolically flexible yeast Saccharomyces cerevisiae, a microbial model for respiratory and fermentative metabolism in industry and medicine, to investigate 2εfattyacid/water. In chemostats, fatty acids from glycerol-respiring cells were >550‰ 2H-enriched compared to those from cells aerobically fermenting sugars via overflow metabolism, a hallmark feature in cancer. Faster growth decreased 2H/1H ratios, particularly in glycerol-respiring cells by 200‰. Variations in the activities and kinetic isotope effects among NADP+-reducing enzymes indicate cytosolic NADPH supply as the primary control on 2εfattyacid/water. Contributions of cytosolic isocitrate dehydrogenase (cIDH) to NAPDH production drive large 2H-enrichments with substrate metabolism (cIDH is absent during fermentation but contributes up to 20 percent NAPDH during respiration) and slower growth on glycerol (11 percent more NADPH from cIDH). Shifts in NADPH demand associated with cellular lipid abundance explain smaller 2εfattyacid/water variations (<30‰) with growth rate during fermentation. Consistent with these results, tests of murine liver cells had 2H-enriched lipids from slower-growing, healthy respiring cells relative to fast-growing, fermenting hepatocellular carcinoma. Our findings point to the broad potential of lipid 2H/1H ratios as a passive natural tracker of eukaryotic metabolism with applications to distinguish health and disease, complementing studies that rely on complex isotope-tracer addition methods.

Effects of Mango Pectin Concentration on the Calcium Pectate Bead Properties and on the Cell Leakage of Yeast (Saccharomyces cerevisiae) Immobilized by Entrapment Technique

Immobilized yeast cells have advantages for use in industries due to their stability, viability, and productivity. As a support material, pectin is suitable because of its stability, strong mechanical attributes, and favorable absorption properties. In this study, the influence of mango pectin concentration on the CP bead characteristics and the leakage of immobilized yeast cells were determined. Results have indicated that yeast cells can be immobilized using low-methoxyl pectin (LMP) from mango peels via entrapment technique. Pectin concentration did not affect the size (3.0323 to 3.4315 mm) of the CP beads. Only 5% and 7% (w/v) pectin concentrations produced spherical beads (SF&lt;0.05). Increasing the pectin concentration from 3% to 7% (w/v) resulted in a 36.21% decrease in swelling ratio for CP beads with yeast. The pectin concentration significantly affects the cell leakage (p-value&lt;0.05). The results further indicate the feasibility of using locally available materials as a matrix for immobilization.

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein coexpression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship.

Mitochondrial citrate transporters Ctp1-Yhm2 and respiratory chain: A coordinated functional connection in Saccharomyces cerevisiae metabolism

The mitochondrial inner membrane contains some hydrophobic proteins that mediate the exchange of metabolites between the mitochondrial matrix and the cytosol. Ctp1 and Yhm2 are two carrier proteins in the yeast Saccharomyces cerevisiae responsible for the transport of citrate, a tricarboxylate involved in several metabolic pathways.Since these proteins also contribute to respiratory metabolism, in this study we investigated for the first time whether changes in citrate transport can affect the structural organization and functional properties of respiratory complexes.Through experiments in yeast mutant cells in which the gene encoding Ctp1 or Yhm2 was deleted, we found that in the absence of either mitochondrial citrate transporter, mitochondrial respiration was impaired. Structural analysis of the respiratory complexes III and IV revealed different expression levels of the catalytic and supernumerary subunits in the Δctp1 and Δyhm2 strains. In addition, Δyhm2 mitochondria appeared to be more sensitive than Δctp1 to the oxidative damage.Our results provide the first evidence for a coordinated modulation of mitochondrial citrate transport and respiratory chain activity in S. cerevisiae metabolism.

Optimization of Fermented White Glutinous Rice Tape for Ethanol Content Using the Gas Chromatography Method

One of the traditional foods that have health-preserving properties is tape which can prevent an increase in cholesterol and prevent a shortage of red blood cells. Tape products are the result of the fermentation of processed raw materials that contain starch, that is, these food ingredients become simple forms such as sugar with the addition of microbes such as yeast or yeast (Saccharomyces cerevisiae) which work to break down carbohydrate foods into alcohol and carbon dioxide by settling to form compounds. namely ethanol. The test was carried out to determine the fermentation time of the ethanol content in white sticky rice tape. The test used the gas chromatography method. The location of the testing carried out at the Pharmacy and Food Analysis Campus was obtained. The results obtained for the system suitability test analysis consisted of precision, column efficiency, and accompanying factors that met the requirements. Meanwhile, the ethanol content in samples carried out continuously for five days on days I, II, III, IV, and V respectively was 2.94%; 3.03%; 3.12%; 3.14%, and 3.28%. The greatest ethanol content obtained on day V was 3.28%, and the smallest content on day I was 2.94%. So it can be concluded that the ethanol content resulting from fermentation in white sticky rice tape increases every day and the quality of the tape decreases

Production of liquid organic fertilizer using residual yeast (Saccharomycescerevisiae) from the brewing process

The goal of the researchwas to re-evaluate the yeast (Saccharomyces cerevisiae) from the brewing process to obtain liquid organic fertilizer. The experiment was conductedin two stages: in the field by collecting raw material; and,in the laboratory by determining the moisture percentage and the microbiological, physicochemical, and agronomic analyses. A complete randomized design (CRD) with a 4x4 factorial arrangement withthree replications wasperformed. The yeast characterization was pH: 6.52, EC: 3.60 dS/m;relative RH: 84.94%;and,organic matter in solution: 66.64%; while, the liquid organic fertilizer characterization was pH: 3.96;EC: 21.40 dS/m;total solids: 183.30 g/L;and,organic matter in solution: 146.40 g/L.Lactic acid fermentation carried out by lactic acid bacteria of the microbial consortium (B-lac) is an option for producing liquid organic fertilizer using residual yeast from the brewing process. Through yeast characterization, it was shownthat the concentration of organic matter, macronutrient and micronutrient content of the residual yeast is high in certain elements, such as nitrogen (9681 mg/L), phosphorus (2203.70 mg/L), and potassium (3850 mg/L), resulting in a product of agronomic quality.

Virtually identical does not mean exactly identical: Discrepancy in energy metabolism between glucose and fructose fermentation influences the reproductive potential of yeast cells

The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signaling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands. Using Saccharomyces cerevisiae yeast cells and potentially similar fermentable carbon sources i.e. glucose and fructose we analyzed the parameters concerning the metabolic status of the cells and connected with them alteration in cell reproductive potential. Those parameters were related to the specific metabolic network: the hexose uptake - glycolysis and activity of the cAMP/PKA pathway - pentose phosphate pathway and biosynthetic capacities - the oxidative respiration and energy generation. The results showed that yeast cells growing in a fructose medium slightly increased metabolism redirection toward respiratory activity, which decreased pentose phosphate pathway activity and cellular biosynthetic capabilities. These differences between the fermentative metabolism of glucose and fructose, lead to long-term effects, manifested by changes in the maximum reproductive potential of cells.

Grain by-products and Saccharomyces cerevisiae application in paper packaging material: impact on physical–mechanical and barrier properties

AbstractRenewable materials and material circularity are key priorities for the coming decades. While paper is the most utilized material in the packaging sector, its applications in food packaging are limited due to low barrier properties. Coating it with petroleum-based polymer barrier coatings renders it unrecyclable both mechanically and biologically. Bio-coated paper packaging, made from agricultural waste or by-products, presents environmentally favorable solutions that can benefit the biological cycle of the circular economy. The main objective of this study is to assess the applicability of grain and beer production by-products in wood pulp food packaging materials. It examines the effects of different grain by-products (industrial wheat grain processing residues and wheat bran) particles and concentrations (15 wt% and 40 wt%), as well as the impact of brewer’s yeast (Saccharomyces cerevisiae) at a concentration of 10 wt%, on the physical–mechanical and barrier properties of Northern bleached softwood kraft (NBSK) and chemithermomechanical (CTMP) pulps. Material composites were fabricated using a standard sheet forming method. Physical–mechanical properties were analyzed through tensile strength, strain at break, tear resistance, and bending stiffness tests. Barrier-related properties were analyzed through roughness, air permeance, and water contact angle tests. Results revealed that the vast majority of physical–mechanical properties decreased with the increase of both types of grain production fillers. Industrial wheat grain processing residues had a lower impact on physical–mechanical properties than wheat bran filler. A higher percentage of property decrease was absorbed in NBSK pulp than in CTMP. Roughness of CTMP can be improved by adding both industrial wheat grain processing residues and wheat bran. Wheat bran particles can increase hydrophobicity. CTMP pulp strength properties can be increased with the addition of yeast; however, the yeast additive’s effect on air permeance demonstrated a negative impact. In the case of NBSK pulp, which has higher primary strength properties, the addition of yeast does not make any significant changes. The conducted experiments demonstrated that, overall, the addition of these fillers resulted in a decline in physical–mechanical properties such as tensile strength, strain at break, tear resistance, and bending stiffness. This decline was more pronounced with higher concentrations of fillers. In the case of CTMP pulp, both types of fillers exhibited similar trends in affecting properties, whereas for NBSK pulp, wheat bran had a more significant impact compared to wheat grain processing residues. The addition of yeast generally led to a reduction in physical–mechanical properties, particularly in tensile strength and tear resistance. However, samples containing yeast displayed increased flexibility compared to controls. The influence on barrier properties varied: while yeast increased air permeability, it also enhanced surface hydrophobicity, thereby reducing the paper’s receptivity to liquids.

Investigation of metabolic processes of alcohol yeast during the fermentation of buckwheat-corn wort

To expand the range of competitive alcoholic beverages with original organoleptic properties, it is promising to study the use of new types of plant raw materials in grain distillate technologies. The purpose of this work was to establish the influence of the characteristics of the composition of grain wort prepared with the joint use of an alternative raw material source — buck- wheat and corn, which is widely used in alcohol production, on the metabolic processes of the yeast Saccharomyces cerevisiae 985-T and alcoholic fermentation. The objects of the study were buckwheat and corn; enzyme preparations — sources of amylases, xylanases, β-glucanases and proteases; samples of grain wort, mash and mash distillates. The prospects of introducing mixed grain media prepared using non-traditional buckwheat raw materials into the technology of original alcoholic bever- ages are substantiated. It was shown that the use of buckwheat as a source of biocomplete protein, essential amino acids and minerals together with corn containing a high level of starch and a low level of non-starch polysaccharides contributed both to an increase in the yield of alcohol and a change in the quantitative content of secondary metabolites in the composition of volatile impurities. It was found that an increase in the concentration of soluble carbohydrates in the wort and a decrease in its viscosity by 15.5–40.3% occurred due to the inclusion of corn in the composition of the grain mixture, and the enrichment of the wort with nitrogen assimilated by yeast by 19.0–41.8% — as a result adding buckwheat. The optimal ratio of corn and buckwheat in the composition of the grain mixture (7:3) was selected, which made it possible to improve the biochemical and technological parameters of grain must, increase the efficiency of the vital processes of yeast and alcoholic fermentation, ensure an increase in the yield of alcohol by 1.8%, reduce the formation of side metabolites, especially higher alcohols, and change their composition in the direction of increasing the proportion of aldehydes and esters, which can have a positive effect on the organoleptic characteristics of the distillate.

Glutathionylation of a glycolytic enzyme promotes cell death and vigor loss during aging of elm seeds.

Seed deterioration during storage is a major problem in agricultural and forestry production and for germplasm conservation. Our previous studies have shown that a mitochondrial outer membrane protein VOLTAGE-DEPENDENT ANION CHANNEL (VDAC) is involved in programmed cell death (PCD)-like viability loss during the controlled deterioration treatment (CDT) of elm (Ulmus pumila L.) seeds, but its underlying mechanism remains unclear. In this study, we demonstrate that the oxidative modification of GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH) is functioned in the gate regulation of VDAC during the CDT of elm seeds. Through biochemical and cytological methods and observations of transgenic material [Arabidopsis (Arabidopsis thaliana), Nicotiana benthamiana, and yeast (Saccharomyces cerevisiae)], we demonstrate that cysteine S-glutathionylated UpGAPDH1 interacts with UpVDAC3 during seed aging, which leads to a mitochondrial permeability transition and aggravation of cell death, as indicated by the leakage of the mitochondrial pro-apoptotic factor cytochrome c and the emergence of apoptotic nucleus. Physiological assays and inductively coupled plasma mass spectrometry (ICP-MS) analysis revealed that GAPDH glutathionylation is mediated by increased glutathione, which might be caused by increases in the concentrations of free metals, especially Zn. Introduction of the Zn-specific chelator TPEN [(N, N, N', N'-Tetrakis (2-pyridylmethyl)ethylenediamine)] significantly delayed seed aging. We conclude that glutathionylated UpGAPDH1 interacts with UpVDAC3 and serves as a pro-apoptotic protein for VDAC-gating regulation and cell death initiation during seed aging.

How does active yeast supplementation reduce the deleterious effects of aflatoxins in Wistar rats? A radiolabeled assay and histopathological study

The aim of this study was to investigate the mechanisms by which yeasts (Saccharomyces cerevisiae) control the toxic effects of aflatoxins, which are not yet fully understood. Radiolabeled aflatoxin B1 (AFB13H) was administered by gavage to Wistar rats fed with aflatoxin (AflDiet) and aflatoxin supplemented with active dehydrated yeast Y904 (AflDiet + Yeast). The distribution of AFB13H and its metabolites were analyzed at 24, 48 and 72 h by tracking back of the radioactivity. No significant differences were observed between the AflDiet and AflDiet + Yeast groups in terms of the distribution of labeled aflatoxin. At 72 h, for the AflDiet group the radiolabeled aflatoxin was distributed as following: feces (79.5%), carcass (10.5%), urine (1.7%), and intestine (7.4%); in the AflDiet + Yeast the following distribution was observed: feces (76%), carcass (15%), urine (2.9%), and intestine (4.9%). These values were below 1% in other organs. These findings indicate that even after 72 h considerable amounts of aflatoxins remains in the intestines, which may play a significant role in the distribution and metabolism of aflatoxins and its metabolites over time. The presence of yeast may not significantly affect this process. Furthermore, histopathological examination of hepatic tissues showed that the presence of active yeast reduced the severity of liver damage caused by aflatoxins, indicating that yeasts control aflatoxin damage through biochemical mechanisms. These findings contribute to a better understanding of the mechanisms underlying the protective effects of yeasts against aflatoxin toxicity.Graphical abstract

Acetic Fermentation of Cagaita Pulp: Technological and Chemical Characteristics

The Brazilian Cerrado region has a rich plant diversity, with fruits that have peculiar and unique sensory characteristics. For these reasons, using these fruits for biotechnological production is a promising alternative, mainly to protect this biome from deforestation and degradation. The production of fermented acetic acid is an option to add value to native fruits and offer the market beverages with better nutritional quality and bioactive compounds. This work aimed to characterize fruits and to develop cagaita (Eugenia dysenterica DC.) acetic fermented beverage. The fruits were subjected to physical-chemical analyses in the first part. Subsequently, different treatments for fermentation were tested using two types of enzymes (amylase and pectinase), two subspecies of Saccharomyces cerevisiae yeast (UFLA CA11 and thermoresistant LNF Angel), and the chaptalization of the must with sucrose (16 °Brix). Alcoholic fermentation was carried out in an incubator with temperature control at 34 ± 1 °C. The pH, total soluble solids, titratable acidity, alcohol content, and density of the fermented products were monitored daily. The chaptalized must with amylase addition and thermoresistant yeast had the best performance during alcoholic fermentation, demonstrating that thermoresistant yeast is an economically advantageous and efficient alternative for the cagaita juice fermentation process. Subsequently, acetic fermentation was carried out using the slow method. Heat-resistant yeast without added enzymes was used to produce cagaita acetic fermented beverages within the parameters of the Brazilian legislation. Furthermore, phenolic compounds and antioxidant activity in the final product were observed. The work demonstrated the possibility of using cagaita fruits in biotechnological processes to produce new food products.

Unraveling the Anti-Aging Properties of Phycocyanin from the Cyanobacterium Spirulina (Arthrospira platensis).

In recent years, marine natural products have become one of the most important resources of novel lead compounds for critical diseases associated with age. Spirulina, a dietary supplement made from blue-green algae (cyanobacteria: scientific name Arthrospira platensis), is particularly rich in phycocyanin, a phycobiliprotein, which accounts for up to 20% of this cyanobacterium's dry weight and is considered responsible for its anti-cancer, anti-inflammatory and antioxidant activities. Although the anti-aging activity of phycocyanin has been investigated, how exactly this compound works against aging remains elusive. The aim of our research is to use the yeast Saccharomyces cerevisiae as a model organism to investigate the anti-aging properties of phycocyanin from A. platensis. Our results show that phycocyanin has a powerful anti-aging effect, greatly extending the chronological life span of yeast cells in a dose-dependent way, as the effect was also pronounced when cells were grown in SD medium under calorie restriction conditions (0.2% glucose). Both ROS and accumulation of dead cells were followed by staining chronologically aged cells with dihydrorhodamine 123 (DHR123) and propidium iodide (PI). Interestingly, we found that most of the aged phycocyanin-treated cells, which were unable to form colonies, were actually ROS+/PI-. Finally, we show that the moment in which phycocyanin is added to the culture does not substantially influence its effectiveness in counteracting chronological aging.

Regulation of translation in response to iron deficiency in human cells

Protein synthesis is a highly energy-consuming process that is downregulated in response to many environmental stresses or adverse conditions. Studies in the yeast Saccharomyces cerevisiae have shown that bulk translation is inhibited during adaptation to iron deficiency, which is consistent with its requirement for ribosome biogenesis and recycling. Although iron deficiency anemia is the most common human nutritional disorder, how iron modulates translation in mammals is poorly understood. Studies during erythropoiesis have shown that iron bioavailability is coordinated with globin synthesis via bulk translation regulation. However, little is known about the control of translation during iron limitation in other tissues. Here, we investigated how iron depletion affects protein synthesis in human osteosarcoma U-2 OS cells. By adding an extracellular iron chelator, we observed that iron deficiency limits cell proliferation, induces autophagy, and decreases the global rate of protein synthesis. Analysis of specific molecular markers indicates that the inhibition of bulk translation upon iron limitation occurs through the eukaryotic initiation factor eIF2α and mechanistic target of rapamycin (mTOR) pathways. In contrast to other environmental and nutritional stresses, iron depletion does not trigger the assembly of messenger ribonucleoprotein stress granules, which typically form upon polysome disassembly.

Analyzing the heterogeneous structure of the genes interaction network through the random matrix theory

There have been massive efforts devoted to understanding the collective behavior of genes. In this regard, a wide range of studies has focused on pairwise interactions. Understanding collective performance beyond pairwise interactions is a great goal in this field of research. In this work, we aim to analyze the structure of genes’ interaction networks through the random matrix theory. We focus on the Pearson Correlation Coefficient network of about 6000 genes of the yeast Saccharomyces cerevisiae. By comparing the spectrum of the eigenvalues of the interaction networks itself with the spectrum of the shuffled ones, we observe clear evidence that unveils the existence of the structure beyond pairwise interactions in the network of genes. Such difference preserves even when the hubs are excluded. In the global network, we identify 140 eigenvectors that have unnormal large eigenvalues. We then derive the spectrum of genes based on the node participation ratio (NPR) index. We again observe noticeable deviation from a random structure. We indicate about 500 genes that have high values of NPR. Compared with the records of the shuffled network, we present clear pieces of evidence that these high values of NPR are a consequence of the structures of the network.

Ykt6 functionally overlaps with vacuolar and exocytic R-SNAREs in the yeast Saccharomyces cerevisiae

The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex forms a 4-helix coiled-coil bundle consisting of 16 layers of interacting side chains upon membrane fusion. The central layer (layer 0) is highly conserved and comprises three glutamines (Q) and one arginine (R), and thus SNAREs are classified into Qa-, Qb-, Qc-, and R-SNAREs. Homotypic vacuolar fusion in Saccharomyces cerevisiae requires the SNAREs Vam3 (Qa), Vti1 (Qb), Vam7 (Qc), and Nyv1 (R). However, the yeast strain lacking NYV1 (nyv1Δ) shows no vacuole fragmentation, whereas the vam3Δ and vam7Δ strains display fragmented vacuoles. Here, we provide genetic evidence that the R-SNAREs Ykt6 and Nyv1 are functionally redundant in vacuole homotypic fusion in vivo using a newly isolated ykt6 mutant. We observed the ykt6-104 mutant showed no defect in vacuole morphology, but the ykt6-104 nyv1Δ double mutant had highly fragmented vacuoles. Furthermore, we show the defect in homotypic vacuole fusion caused by the vam7-Q284R mutation was compensated by the nyv1-R192Q or ykt6-R165Q mutations, which maintained the 3Q:1R ratio in the layer 0 of the SNARE complex, indicating that Nyv1 is exchangeable with Ykt6 in the vacuole SNARE complex. Unexpectedly, we found Ykt6 assembled with exocytic Q-SNAREs when the intrinsic exocytic R-SNAREs Snc1 and its paralog Snc2 lose their ability to assemble into the exocytic SNARE complex. These results suggest that Ykt6 may serve as a backup when other R-SNAREs become dysfunctional and that this flexible assembly of SNARE complexes may help cells maintain the robustness of the vesicular transport network.